posted 14. September 2003 21:09                   

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And, FWIW, I think that Front-Loading-Evolution is about the least likely, least efficient, least-likely-to-succeed design method I've heard of yet. Assuming that the designer has a goal in mind and wants to use evolution (they've got millions/billions of years to kill), the way to reach it is via controlling selection, not the starting materials.

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posted 14. September 2003 23:00                   

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ID theorists focus, perhaps obsessively, on living things in their search for "fingerprints" or other hints of design. yersinia's statement in essence asks the question "why there?". Why not look elsewhere for the clues of intelligent intervention? For example, why not ask if particular series of environmental events might be so improbable as to satisfy Dembski's criteria? Perhaps environmental "information" is the issue here, and not the underpinnings of life itself.

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posted 14. September 2003 23:33                   

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Perhaps it's not surprising that critics see my book as depending crucially on the NFL theorems (given my title it might seem the theorems have to be right and applicable across all of biology for my conclusions to hold). But in fact, my key point concerns displacement (the shifting of specified complexity from one place to another -- in the case of evolutionary theorists like Tom Schneider usually unwittingly), and the NFL theorems simply exemplify one instance (not the general case). Indeed, the core idea of chapter 4 of NFL was in my head before I had even heard of the NFL theorems.

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I went back and reviewed chapter 4. Every section except for section 4.10 is either introducing “blind search” or using the NFL theorems to claim that evolutionary processes (in essence) are no better than blind search. The “displacement problem” is in there in several places, not just 4.7. But it is based on the NFL theorems concept. Dr. Dembski may have had the ideas of chapter 4 before learning about NFL theorems, but he based the chapter on the ideas of the NFL theorem. The “displacement problem” is still based on claims that “displacement” is required because we are to believe that blind search insufficient. Of course 4.1 through 4.4 are devoted to debunking any misconception that Dawkins’ “Methinks it is like a weasel” program is a true representation of an evolutionary algorithm. Since it is only a teaching example of a goal seeking system that uses evolutionary steps, and that goal is obviously unlike any fitness landscape of real evolution and clearly designed outcome. It has no relevance, but using 4 sections to show that the oversimplified program is indeed oversimplified can have a confusing influence on those who don’t understand its real purpose.

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Essentially, Dembski's point is that natural laws are ontologically incapable of producing specified complexity. His reasoning behind this claim includes both 1. an inductive argument that all known specified complexity to date is associated with an intelligence (most often human intelligence) and 2. a displacement problem argument deduced from the proven NFL theorems.

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First off, let us be clear about that the No Free Lunch theorems that underwrite the displacement problem apply with perfect generality NFL applies to any information that might supplement a blind search, and not just to fitness functions.

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But NFL theorems can just as well be formulated for informational contexts that do not comprise fitness functions. The challenge facing biological evolution, then, is to avoid the force of NFL when evolutionary algorithms also have access to information other than fitness functions.

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posted 15. September 2003 06:50                   

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A classification of four possible routes of Darwinian evolution is presented. These are: serial direct evolution, parallel direct evolution, elimination of functional redundancy, and adoption from a different function.

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posted 15. September 2003 09:00                    

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I think that Front-Loading-Evolution is about the least likely, least efficient, least-likely-to-succeed design method I've heard of yet.

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posted 15. September 2003 09:59                   

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The last sentence, of course, identifies the so-called "displacement" issue: to the extent that living things display CSI (or SC) they have in some way transcribed it from the environment; "information" in biological systems is derivative.

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posted 15. September 2003 14:31                   

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Of course, it would be not be easy to measure something like a cooption frequency. Lots of things in biology come with similar difficulties. But you did say we “can take almost anything and sooner or later, if you trace it back far enough, you will end up at a change-in-function "event". It would thus seem some type of measurement is possible, eh?

You also appear to take the position that cooption is essentially inevitable. But this, in turn, seems to be a function of how you choose to define it (where changing beak morphology becomes cooption), as you appear to be defining things such that cooption shares an identity relationship with Darwinian evolution. Yet as I have mentioned, there are many examples of Darwinian evolution where cooption was not involved.

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In fact, in their paper, A classification of possible routes of Darwinian evolution , Thornhill and Ussery define four routes, where cooption is only one of four possible routes:

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A classification of four possible routes of Darwinian evolution is presented. These are: serial direct evolution, parallel direct evolution, elimination of functional redundancy, and adoption from a different function.
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Perhaps you can begin to see why simply asserting that cooption is “ubiquitous” is not good enough.

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Given the way you have demanded precise definitions of ID and IC, I find it quite ironic that you are satisfied with leaving cooption in the realm of fuzzy thinking.

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We can play these types of rhetorical games all day. The fact remains that for some time I have explained my design logic about cooption (it is even addressed in my web page essay about IC that I wrote a long time ago and you read). As for skepticism, it still remains. I simply don’t invoke cooption in an ad hoc manner, regardless of the evidence. I invoke it when the data calls for it. And this will get us back on topic.

If cooption really is common, then we have even less reason to suspect ID in the first place, because it is even easier to explain the complex structures that were your original ID-flags.

Not really. Both examples of IC are not sufficiently supported with evidence of cooption. Of course, if you define things such that “cooption is ubiquitous,” I suppose things like evidence cease to be a concern. Consider the topic of the OP. Recall that you predicted that “all major structurual components of IFT complexes, that are well-conserved between cilia IFT complexes, will have identifiable homologs in noncilial tubulin-based transport systems.” Well, as I discuss in the OP, as it appears this cooption prediction has failed.

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And, FWIW, I think that Front-Loading-Evolution is about the least likely, least efficient, least-likely-to-succeed design method I've heard of yet. Assuming that the designer has a goal in mind and wants to use evolution (they've got millions/billions of years to kill), the way to reach it is via controlling selection, not the starting materials. Selection is what can give direction to evolution.

And how do you propose that selection be controlled?

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Your front-loaded critters are more likely to scrabble off and get busy evolving ever more pointy spines in a predator-prey arms race as they are to do whatever it is you were hoping they would do.

And there are many aspects of biology that suggest it’s just not that bad. For example, when Simon Conway-Morris’ new book about convergence comes out, perhaps we should return to this in another context.

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In the meantime, I would simply point out that your assertion is not rooted in experimental analysis. You are appealing to the results of experiments not done. Clearly, we can see yet another way FLE splits apart from DE, as the only the former would lead to such experimentation.

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Nature 422, 741 - 745 (17 April 2003); doi:10.1038/nature01598

The cytoskeleton, cellular motility and the reductionist agenda

THOMAS D. POLLARD

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven

Eukaryotic cells depend on cytoskeletal polymers and molecular motors to establish their asymmetrical shapes, to transport intracellular constituents and to drive their motility. Cell biologists are using diverse experimental approaches to understand the molecular basis of cellular movements and to explain why defects in the component proteins cause disease. Much of the molecular machinery for motility evolved in early eukaryotes, so a limited set of general principles can explain the motility of most cells.

Three cytoskeletal polymers — actin filaments, microtubules and intermediate filaments (Table 1) — cooperate to maintain the physical integrity of eukaryotic cells and, together with molecular motors, allow cells to move themselves and their intracellular components. Although cellular motility has fascinated small groups of biologists for 300 years, interest in these processes has now spread to biologists more generally. The field has expanded as a result of insights gleaned about molecular mechanisms and the participation of cytoskeletal and motility molecules in many aspects of cellular function, including embryology, learning and memory, spread of cancer and microbial pathogenesis. The carefully regulated assembly of the cytoskeletal polymers and action of the associated motors is largely responsible for establishing cellular architecture and thus tissue structure.

This collection of reviews will bring readers up to date on several active areas of research. Howard and Hyman (page 753) explain how assembly and disassembly of microtubules produce forces to transport some intracellular molecules, chromosomes and organelles. Cellular locomotion powered by the assembly and disassembly of actin filaments1 has many parallels with these microtubular mechanisms. Schliwa and Woehlke (page 759) cover the molecular motors that interact with actin filaments and microtubules to generate tension in the cytoskeleton as well as to move cargo as large as nuclei and as small as RNA molecules. Nelson (page 766) reviews how cells use cytoskeletal polymers and motors to generate asymmetry. Gruenheid and Finlay (page 775) cover the many ways that infectious organisms can hijack the motility system for their own purposes, while Scholey et al. (page 746) describe what we know about the segregation of chromosomes during mitosis and pinching daughter cells in two during cytokinesis.

These are spectacular examples of events where the cytoskeletal polymers and motors transiently assemble complex machines to carry out vital processes with high fidelity. The machines used for cellular locomotion, intracellular transport, mitosis and cytokinesis consist of millions of protein molecules held together by relatively weak, non-covalent bonds, which allows these machines to disassemble when their jobs are done, recycling their protein components for use at a later time.

[...]

Genes for actin and tubulin arose in prokaryotes5. Although the primary structures diverged extensively, crystal structures of prokaryotic actin-like and tubulin-like proteins are remarkably similar to their eukaryotic counterparts. Bacterial FtsZ binds GTP just like tubulin but polymerizes into long ribbons that participate in cytokinesis. Eukaryotic tubulin is a heterodimer of similar - and -subunits that assemble into cylindrical polymers (Table 1). The GTP bound to tubulin is hydrolysed and the -phosphate dissociates soon after incorporation of each tubulin molecule in a polymer. Dissociation of the -phosphate puts tubulin into a strained conformation that favours disassembly of the microtubules (see review by Howard and Hyman, page 753). Bacterial MreB binds ATP and forms actin-like filaments5 that are required for the elongated shape of rod-like bacteria. Some bacterial actins also help to partition DNA during mitosis6. (The assembly properties of actin are considered below.) In a fascinating role reversal early in eukaryotic evolution, actin filaments took over cytokinesis and microtubules assumed the partitioning of the genome.

Although actin filaments and microtubules differ in origin and structure, their shared features (Table 1) shows that evolution favoured extensive convergence of function. Moreover, nematodes evolved completely different cytoskeletal polymers for their amoeboid sperm. Polymers of 'major sperm protein' lack any molecular similarity to actin, but carry out a cycle of assembly and disassembly that mimics that of actin in motile cells7.

Intermediate filaments arose during eukaryotic evolution rather than in prokaryotes and share little with the other cytoskeletal polymers. The rod-shaped protein subunits of intermediate filaments consist of a coiled-coil of -helices and do not bind nucleotides. Owing to the symmetry of the subunits, the polymers are not polar like actin filaments and microtubules. Duplication and divergence of the genes for intermediate filament proteins produced a family of related genes in vertebrates. The protein products are expressed selectively in specialized cell types where they act as intracellular tendons that resist deformation of cells and tissues.

[...]

The molecular motors that move along microtubules and actin filaments had two origins. Dyneins are part of the family of AAA ATPases9 that also contribute to protein folding (Hsp100 chaperones), membrane traffic (N-ethylmaleimide-sensitive factor or NSF) and DNA synthesis (clamp loader proteins). The kinesin and myosin families of ATPase motors share a common core structure and may have the same common ancestor as the GTPases involved in signalling and protein synthesis10. Although GTPases are present in prokaryotes, compelling evidence for prokaryotic motors is still lacking.

The reductionist approach
Our understanding of the cytoskeleton and cellular motility is a triumph of the reductionist strategy, the approach that now dominates research in cell biology. Sophisticated methods drive rapid progress, but we should aware of the limitations of these methods and the unfulfilled items on the reductionist agenda. The reductionist tasks include an inventory of the relevant molecules, determination of molecular structures, identification of molecular partners, measurement of rate and equilibrium constants for each reaction, localization of the molecules in live cells, physiological tests for participation in cellular processes and formulation of mathematical models to understand the system's behaviour. Each review in this Insight section emphasizes parts of this agenda.

Reductionism starts with a list of the components. Most of the cytoskeletal proteins were discovered the 'old-fashioned' way, using purification by biochemical fractionation. Complete genome sequences and expressed sequence tag collections have expanded the inventory of cytoskeletal and motor proteins, particularly the diversity of isoforms of many of the proteins found in higher organisms. In a few cases experts have completed the annotation of selected genomes and defined the size of certain gene families such as myosins, which consists of more than 40 genes in humans11. Similar work remains to be done for many other cytoskeletal gene families. Far less is known about the diversity of products generated by alternative splicing of pre-messenger RNAs.

Genetic screens and yeast two-hybrid assays have accelerated detection of protein partners, but traditional biochemical assays and affinity chromatography remain useful, particularly when empowered by sensitive analytical methods such as mass spectrometry. When scaled up to sample entire genomes or proteomes, these assays produce impressive interaction maps12, 13. Such efforts have saved an immense amount of work and laid out a broad research agenda that is required to understand each interaction. These maps are, of course, a beginning rather than an end, as simple knowledge of an interaction will not explain how anything actually works.

Structure determines function, so the field eagerly awaits each new structure. Recent crystal structures include tubulin bound to a small regulator protein Op18/stathmin (see review in this issue by Howard and Hyman, page 753), bacterial actin and tubulin homologues5, and Arp2/3 complex (a seven-subunit nucleator of actin filaments14). Lacking crystals, three alternative approaches have yielded valuable structural information. First, Wiskott–Aldrich syndrome protein (WASP), a multi-domain protein that activates Arp2/3 complex, has been studied one domain at a time by nuclear magnetic resonance15, 16. Second, homology modelling based on other AAA ATPases was used to construct a preliminary model of dynein9. And third, technical advances in processing electron micrographs yielded an 8-Å structure of the microtubule17. Electron microscopy of single dynein molecules has recently led to a proposal for the mechanism of their ATP-driven power stroke18. Much work remains to complete a reference set of structures of cytoskeletal proteins.

Tracking the suspects
Light microscopy of live cells containing proteins tagged with fluorescent markers has revolutionized much of cell biology and replaced fluorescent antibody methods for many purposes. Expression of proteins fused to green fluorescent protein (GFP; and related proteins with different spectral properties) has made it possible to localize and study the dynamics of virtually any protein inside a living cell (and even in tissues of live organisms; see review by Howard and Hyman, page 753, for examples). Investigators have embraced these methods with justifiable enthusiasm, but caution is required, as some fusion proteins cannot take the place of their wild-type counterparts in gene replacement experiments. Genetic manipulations make such controls routine in yeast laboratories, but they are rarely done in experiments on animal or plant cells.

Speckle microscopy has increased the power of fluorescent protein methods19. Expression of a low level of a GFP fusion protein or microinjection a low concentration of purified protein labelled with a fluorescent dye leads to stochastic incorporation of labelled protein into microtubules, actin filaments or other cellular structures. The resulting speckles of fluorescence serve as fiduciary marks for orientation as the labelled structures move or turn over in live cells (see, for example, ref. 20).

Single-particle assays continue to make valuable contributions to understanding motility. One example is provided by the surprising solution to decades of controversy surrounding the mechanism of slow axonal transport. In this process, proteins such as the subunits of intermediate filaments move slowly (only 1–100 nm per second) from their site of synthesis in a neuronal cell body to the end of an axon or dendrite. Different experimental approaches gave apparently conflicting results regarding the movement of the molecules, whereas observation of single intermediate filaments revealed that they actually move rapidly but infrequently21. Propelled by motors, they move in fits and starts (but mostly stops) along microtubules.

Another example is bacteria that usurp the cytoplasmic actin system for propulsion through the cytoplasm of host cells. Observations of single bacteria and particles coated with bacterial proteins (or other activators) have defined the physics of the process22 and allowed reconstitution of the machinery from pure proteins23. Similarly, much has been learned about the behaviour of microtubules24 and actin filaments25 by real-time observations of single polymers.

[...]

Unmet challenges
Although we now have in hand a broad outline of the strategies that evolution has provided cells to produce motility and asymmetry, actual understanding of the physical mechanisms will require completion of the reductionist agenda. We still have gaps in our parts list and especially in biochemical mechanisms. [...]

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Nature 422, 746 - 752 (17 April 2003); doi:10.1038/nature01599

Cell division

JONATHAN M. SCHOLEY, INGRID BRUST-MASCHER & ALEX MOGILNER

Laboratory of Cell and Computational Biology, Center for Genetics and Development, University of California, Davis, California 95616, USA

In creating the mitotic spindle and the contractile ring, natural selection has engineered fascinating precision machines whose movements depend upon forces generated by ensembles of cytoskeletal proteins. These machines segregate chromosomes and divide the cell with high fidelity. Current research on the mechanisms and regulation of spindle morphogenesis, chromosome motility and cytokinesis emphasizes how ensembles of dynamic cytoskeletal polymers and multiple motors cooperate to generate the forces that guide the cell through mitosis and cytokinesis.

[...]

Cells use a significant fraction of their proteins to divide — functional proteomics12 indicates that Caenorhabditis elegans uses 6% of its open reading frames to encode proteins required for cell division and an important subset of these proteins comprise actin filaments, MTs, motor proteins and accessory proteins13, 14. MTs and actin filaments are linear, polar, multistranded polymers, built from 13 strands of -tubulin heterodimers and 2 strands of G-actin monomers, respectively. These polymers can generate pushing and pulling forces as they grow and shrink by addition and loss of subunits from their ends, and they also serve as tracks for motor proteins that use ATP hydrolysis to generate force and motility7 (Box 1). At the single-molecule level, cytoskeletal proteins generate piconewton-scale forces and nanometre-scale movements7, 13, 14, but during cell division they function as ensembles that are capable of generating forces in the range of nanonewtons and serve to accurately move intracellular components and rearrange areas of the cell surface over distances of tens of microns7, 13-17. How do these cytoskeletal force generators cooperate to drive the motility events underlying the mechanics and regulation of cell division?

Spindle morphogenesis and elongation

The purpose of mitosis is to segregate sister chromatids by moving them to opposite poles. To this end, spindle MTs become oriented into a bipolar array whose dyad axis divides the structure into two half spindles (Fig. 1c). Within each half-spindle, the MTs lie on trajectories that point their minus-ends towards a focus at the poles, allowing spindle forces to accomplish their goal by translocating chromatids along these trajectories (Fig. 1d). Bipolar spindles can form by two pathways, the centrosome-directed assembly pathway4, in which MT assembly is nucleated by centrosomes, or the chromosome-directed pathway5, 6, in which chromosomes induce MT assembly (Fig. 2a). The relationship between these pathways is unresolved, as is the question of why some cells (such as Drosophila embryos) use the centrosome-directed pathway whereas others (for example, Drosophila female oocytes) lack centrosomes and use the alternate chromosome-directed pathway.

Centrosomes consist of a pair of cylindrical centrioles surrounded by pericentriolar material that contains the MT-nucleating -tubulin ring complex (-TuRC). Electron microscopy suggests that the -TuRC acts as a helical template for new MTs which grow by subunit addition at their plus ends18-21. Recent work suggests that a MT-associated protein (MAP) called XMAP215 is important for MT nucleation at centrosomes22. Perhaps the -TuRC and XMAP215 play complementary roles, stabilizing lateral and longitudinal bonds between subunits, respectively22.

In the chromosomal pathway, the guanine nucleotide-exchange factor of the small GTPase, Ran, generates a spatial gradient of active Ran–GTP around chromosomes23. Ran–GTP promotes the release of factors that induce MT assembly from a pool that is sequestered in an inactive form by importin-, thereby activating spindle assembly around chromosomes24. Spindles that lack conventional centrosomes may contain 'pseudo-centrosomes' consisting of various MAPs that are important for spindle pole formation and stability25. One of these MAPs is XMAP215, which may be transported to the poles by a minus-end-directed C-terminal kinesin, where it could nucleate MT assembly as in the centrosome-directed pathway25.

MT motors have subtly different roles in the centrosome- and chromosome-directed assembly pathways4-6. In the latter case, MTs randomly organized around chromosomes become crosslinked into antiparallel bundles by bipolar kinesins, then plus-end-directed chromokinesins reorganize these MTs to position their minus ends distal to chromosomes, and finally minus-end-directed motors (dynein or Ncd) crosslink the MT minus ends into focused poles26. In the former case, duplicated centrosomes are moved apart by shifts in a balance of outward and inward forces generated by the cooperative action of dynamic MTs, cortical dynein and multiple MT sliding motors localized to interpolar MT (ipMT) bundles4, 27. Bipolar (plus-end-directed) and C-terminal (minus-end-directed) kinesins acting on ipMTs are candidates for generating some of the antagonistic outward and inward forces that position spindle poles4. Recent computer simulations have suggested that bipolar and C-terminal kinesins could generate outward and inward forces on the poles, as expected, but various mixtures of these motors were unable to produce a robust isometric spacing of two spindle poles unless the two kinesins were organized into co-polymers28.

[...]

The separation of the spindle poles that accompanies the morphogenesis and elongation of the spindle is an example of mitotic motility that reveals some of the basic principles by which cytoskeletal force generators drive the motility events underlying spindle mechanics (Box 1). Ostergren36 proposed that shifts in a balance of antagonistic forces serve to move and position structures in the spindle, and evidence has accumulated showing that forces generated by growing and shrinking MTs and by antagonistic mitotic motors provide a molecular explanation for such a balance2, 4, 6, 27, 28. Indeed a quantitative model (Box 1) can explain how a balance of opposing forces generated by ensembles of dynamic MTs and mitotic motors drives spindle pole motility4, 27, 37, and similar models are likely to be relevant to other forms of motility (for example, chromosome motility).

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Nature. 2003 Apr 17;422(6933):759-65.

Molecular motors.

Schliwa M, Woehlke G.
[...]

Molecular motors are amazing biological machines that are responsible for most forms of movement we encounter in the cellular world. Three types of cytoplasmic motors are known: myosins, which move on actin filaments, and dyneins and kinesins, which use microtubules as tracks. The mechanism they use to convert chemical energy into mechanical work is both simple and ingenious. In all three motor classes, ATP hydrolysis causes a small conformational change in a globular motor domain that is amplified and translated into movement with the aid of accessory structural motifs. Additional domains outside the motor unit are responsible for dimerization, regulation and interactions with other molecules (Fig. 1).

This modular design of motors has given rise to considerable complexity so that each of the three motors comprises a superfamily whose members may vary appreciably in makeup and function. Today, we can distinguish at least 18 different classes of myosins, 10 different families of kinesins, and 2 groups of dyneins, each with up to several dozen members. The complement of motors varies widely between different organisms. Yeast, for example, gets by with 6 kinesins, 5 myosins and 1 dynein, whereas mammals have genes for over 40 kinesins, 40 myosins and more than a dozen dyneins. These numbers may easily be tripled as a result of post-translational modifications or varied combinations of associated proteins. Many motors are not yet characterized, and clear functions are assigned to only a small subset. Nevertheless, remarkable insights into motor mechanochemistry and function have been gained. This introductory overview highlights recent developments; for a compilation of comprehensive reviews, see ref. 1.

[...]

Motor mechanochemistry
Conformational changes Our understanding of the molecular mechanisms that convert chemical energy into movement is most advanced for representatives of the myosin and kinesin families. High-resolution crystal structures of the motor domain uncovered an unexpected relationship between these two classes of motors: the region surrounding the ATP-binding pocket is virtually identical in structure, although sequence homology is restricted to only a few key residues. The architecture of the active site further revealed a relationship to the G proteins, suggesting that these three classes of molecules are of common evolutionary origin2. This notion recently received support from molecular dynamics simulations suggesting that G proteins — usually mediators in signalling pathways — may be able to generate force3.

Among the various families of kinesins and myosins we find motors that work as monomers, dimers, trimers or tetramers, move to the plus end or the minus end of their track, and take just one or many steps before dissociating. Despite this wide spectrum of behaviours, in all motors the initial events in the generation of movement are similar and can be explained by stepwise amplification (Fig. 2a, b).

[...]

Mechanistic analysis of the dynein motor is severely hampered by the lack of a high-resolution structure. It is clear though that, based on sequence features, the molecular design of dyneins is fundamentally different from myosins and kinesins. The motor domain of dynein comprises a ring of six AAA-ATPase modules, members of a widespread and highly diverse superfamily of proteins. ATP-dependent conformational changes in the ring of AAA-modules are believed to be transmitted to a stalk that carries the microtubule-binding site at its tip14. A swing in the position of this stalk leads to a 15-nm displacement of the tip (Fig. 2c)15. Although superficially resembling a swinging lever-arm movement, the structural and molecular basis of this force-generating 'power stroke' differs markedly from the conformational changes in myosins and kinesins.

Stepping The conversion of these conformational changes into a step (or series of steps) leads us to the next level of complexity. Two fundamentally different behaviours of motors can be distinguished. In one, a single motor molecule can move along the track for long distances without detaching, a behaviour referred to as processivity. In the second, motors lose contact to the track usually after one cycle and therefore are non-processive. These modes of operation are physiological adaptations to different cellular functions. Processive motors are individualists, whereas non-processive motors often work as a team; the former hold on to the track for as long as possible, whereas the latter are optimized for brief, fast interactions.

[note that IFT would be an example using processive motors, and cilial motion using processive motors]

Cellular functions

The initial belief that the three types of motors are associated with clearly separate functions (that is, myosin with contraction and movement, dynein with ciliary beating, and kinesin with organelle transport) could not be upheld for long. Now we are aware of, for example, myosins involved in organelle transport, dyneins implicated in vesicle and cell movement, and kinesins required for ciliary function. In addition, we count among their tasks unexpected functions such as signalling, RNA localization and sensory transduction; we are beginning to appreciate their implications in cellular architecture, basic developmental processes and a growing number of diseases; and we know that all three are important in cell division (see review in this issue by Scholey, page 746). This already is an impressive list, but because many motors have not yet been characterized, the full spectrum of cellular roles has yet to be appreciated.

Membrane association and regulation

Members of all three types of cytoskeletal motors are involved in organelle and vesicle transport (for reviews, see ref. 1). To understand these functions, it is essential to determine how motors link up to their cargoes and how transport is regulated. In both processes, non-motor domains and associated proteins have a key role, and a wide spectrum of attachment mechanisms is observed (Fig. 3).

Perhaps the most direct (but seemingly least specific) mechanism of membrane association is linkage to the phospholipid bilayer. Thus, acidic phospholipids are the binding partner for monomeric myosins41 possessing a basic tail region, whereas a member of the Unc104/KIF1 family of kinesins binds to lipids via a pleckstrin homology domain42. This association depends on the presence of phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), which promotes clustering of the motor in PtdIns(4,5)P2-containing rafts. Clustering, in turn, may trigger the onset of transport.

In certain cell types, motors such as conventional kinesin and cytoplasmic dynein can latch onto their cargo via integral membrane proteins. In neurons, the kinesin light chains bind amyloid precursor protein (APP), a transmembrane protein of certain axonally transported vesicles43. This link is of potential medical significance as APP has gained fame as the precursor of a proteolytic fragment that gives rise to amyloid plaques in patients with Alzheimer's disease. Impaired APP transport may well contribute to the development of the disease. In photoreceptor cells, cytoplasmic dynein, which normally requires the dynactin complex for attachment (see below), binds directly to rhodopsin, an integral membrane protein, with its Tctex-1 light chain44. This link, too, is significant as certain rhodopsin mutations inhibit this interaction, leading to retinitis pigmentosa.

The most widespread mode of association with integral membrane proteins occurs via linker proteins, often in the form of large assemblies. Work over the past few years has advanced various attachment modes for all three motor types. For example, conventional kinesin, again via its light chains, interacts with Jun kinase-interacting proteins (JIPs), a class of scaffolding proteins that bind components of the JNK signalling pathway45, 46. JIPs, in turn, bind a transmembrane receptor of the low-density lipoprotein receptor family. Certain other kinesin-like proteins likewise use large linker complexes47.

Among the myosins, the machinery that links myosin V to cargo is characterized best. In pigment cells, the small GTPase Rab27a and a recently identified Rab-binding protein, melanophilin48, attach myosin V to melanosomes. The GTPase binds to membranes first and recruits melanophilin, which then binds myosin V. Melanophilin binding is GTP dependent, thus offering a convenient means of regulating motor–cargo association. This Rab-dependent machinery may well be paradigmatic for myosin–cargo association in other systems. Recent discoveries link Rabs and Rab-like effectors not only to several other myosin motors, but also to kinesins and dynein49, thus opening the possibility of a significant functional interdependence of GTPases, motors and membrane traffic.

Finally, a large protein assembly seems to be involved in linking dynein to membranes (Fig. 4). Through its intermediate chains, dynein interacts with a unique activator complex, dynactin, which has the protein p150glued and a short filament of the actin-related protein Arp1 as its most prominent components50. Precisely how the dynein–dynactin complex associates with vesicular cargoes is not understood, although in certain circumstances it binds to membrane-associated spectrin51, making this the most complex linkage machinery known.

These examples, which represent the proverbial tip of the iceberg, indicate a wide spectrum of attachment mechanisms. Direct association with lipids or transmembrane proteins, linkage via an adaptor, or association mediated by complex protein assemblies all have been found. Given that one motor can interact with several different cargoes, there may well be dozens of specific membrane attachment mechanisms matching the dozens of potential cargoes in a cell.

Motors in novel contexts

Organelle transport and ciliary movement or contraction are paradigmatic tasks of cytoskeletal motors, but there is more to motors than meets the microscopist's eye. Some motors are implicated in the transport of messenger RNA or macromolecular complexes. Others are unable to move and yet are indispensable for certain cellular activities (see review in this issue by Howard and Hyman, page 753). Some deletions or mutations of motors can be lethal for multicellular organisms, indicating that these motors are essential for crucial steps in development. In other circumstances, the loss of certain motors leads to debilitating diseases. Finally, motors may participate in cellular homeostasis and cell architecture in ways that extend beyond functions in transport. These are exciting research fields unforeseen only a few years ago.

[...]

A final issue concerns an involvement of motors in cell architecture and cytoskeletal remodelling (Fig. 5). We have seen that some motors can be part of large macromolecular complexes and, through their associated proteins, can interact with a wide spectrum of cytoplasmic constituents. A paradigm is the dynein/dynactin machinery, which has been shown to be important not only in organelle transport, but also in cytoskeletal architecture. Dynein associates with adherens junctions of epithelial cells through an interaction with -catenin and a novel protein, PLAC-24, that binds the dynein intermediate chain73. This protein complex may help to tether microtubule ends at sites of cell–cell contact. Additional interactions of cortical cytoplasmic dynein with microtubule plus ends affect spindle orientation, nuclear movement, centrosome positioning and cell polarity74. Thus, cortical dynein can profoundly influence the spatial organization of the entire microtubule apparatus, which in turn provides a framework for the organization of cellular membrane systems. In addition, dynein as well as conventional kinesin are required for the assembly and dynamics of the vimentin intermediate filament system75 and neurofilament transport76, supporting the long-standing notion of a close spatial relationship between these two cytoskeletal systems. Both motors, or their interacting proteins, can also be part of the microtubule plus-end complex, a large assemblage of proteins associated with growing microtubule ends77, 78.

Outlook
Extrapolating into the future is always challenging and often wrong. Using current work as a guide, four main areas of future research on molecular motors can be identified. First, even though we seem to have a general idea of motor chemomechanics, important details still need to be worked out. Atomic resolution structures will be the guide. In combination with single-molecule techniques of improved spatiotemporal resolution and sensitivity and the rational design of motor mutants, common principles of motor physiology will emerge. Second, many motors are known only by sequence, particularly in plants, so this is a fertile playground for the cell biological hunter-gatherer. Functional characterization will help answer questions of motor targeting and motor regulation: how does a motor find its cargo, what directs it to the correct target site, and how is its activity regulated in the process? Only partial answers are available at present. Third, the implication of motors in disease and developmental defects will attract increasing attention. The questions, and the answers they demand, will undoubtedly be complex, as motor defects will frequently be just one of many factors that contribute to the manifestation of a disease. Fourth, motors are believed to hold promise for use in nanobiotechnological devices, although marketable applications have yet to be achieved.

"Our progress is narrow; it takes a vast world unchallenged and for granted," writes J. Robert Oppenheimer87. "This is why we will have to accept the fact that no one of us really will ever know very much. This is why we shall have to find comfort in the fact that, taken together, we know more and more." The field of molecular motors is no exception.

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posted 17. September 2003 12:12                   

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Nic,

You note that “things boil down to improving function or changing function.” I agree. And it is at this point where we can see that cooption is not ubiquitous. According to Websters, ubiquitous means “existing or being everywhere at the same time : constantly encountered.” But change in function is not everywhere and constantly encountered.

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In spite of the ubiquitous beggars, gypsies and `naked urchins', Skopje was an attractive town in the early part of the century.
--Anne Sebba, Mother Teresa: Beyond the Image

Airborne gambling, shopping and videoconferencing may all be ubiquitous in the future.
--Peter H. Lewis, "The Cybercompanion," New York Times, February 7, 1999

Adding to my perplexity, this lack of clarity even appeared evident among the best and brightest sociologists, historians, literary scholars, art historians, those working in cultural studies, American Studies, and journalism; the problem looked to be ubiquitous.
--Michael Kammen, American Culture, American Tastes: Social Change and the 20th Century

Before Tarzan, nobody understood just how big, how ubiquitous, how marketable a star could be.
--John Taliaferro, Tarzan Forever: The Life of Edgar Rice Burroughs, Creator of Tarzan

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What we typically see is a change in function followed by a long history of refinement. Thus, for any change in function, there is a tremendously higher incidence of the refinement of that function that follows. And this gets back to my original point. Evolutionary events that merely “improve function” are not cooption events. But then neither would we call this evolution non-Darwinian. Otherwise, we’re in the odd position of taking one of the leading examples of Darwinian evolution, the Peppered Moth, and having to relabel it non-Darwinian.

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Thus, we can have Darwinian evolution without cooption. Meaning that Darwinian evolution does not entail the existence of cooption. And that makes sense, as there is nothing inherent in the principles of neo-Darwinism (variation and selection) that entails cooption simply because you can have variation and selection without cooption. If cooption occurs, it is because of factors other than mere variation and selection.

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Again, I will draw attention to the emphases of our respective positions about evolutionary mechanisms. My perspective of FLE creates a huge impetus to look more closely at the evolutionary mechanisms, cooption being one. It’s part of the brainstorming spirit that is supposed to predominate on this forum. Thus, one place to start is to ponder the frequency of cooption, as this could turn out to be a very useful measure in these debates (from several different angles). Your non-teleological perspective, on the other hand, rejects such an effort as ridiculous and as a “distracting detour,” as you would rather we simply accept cooption as a ubiquitous brute given. As it stands, while you can point to many examples of cooption, such appeals are largely anecdotal. Example here and example there help to illustrate evolution as tinkerer. But why not look more closely?

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posted 17. September 2003 22:01                   

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Function just is fuzzy, that's life. It is a useful term of description, but cannot legitimately be rarified in the way you are demanding before you will accept that cooption is ubiquitous.

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To describe biological functions we need a vocabulary that contains concepts such as amplification, adaptation, robustness, insulation, error correction and coincidence detection.

Hartwell, L. H., et .al. 1999 From molecular Biology to modular cell biology Nature Suppl. 402:C47

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However you define it, though, cooption is ubiquitous. Just thinking of random human body parts: Jaws: gill arches. Hands: feet, then fins. Earbones: jawbones. There are a zillion examples in the molecular world, too: Dynein is a modified AAA ATPase, etc.

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Well, because the proponents of IC switch definitions regularly in order to avoid falsification, this is perfectly reasonable.

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Yes, critters converge...on things like producing ever-more pointy spines. The Cambrian is easily interpreted as one big armor vs. teeth predator-prey arms race. Convergence is due to similar selective pressures, something I'm sure that Conway Morris would agree with. Which gets us back to my point that evolution is only predictable from the selection end of things.

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There remains a paradox, however, inasmuch as although molecular biology is to be thanked for largely revitalizing our views of metazoan phylogeny, when it comes to developmental biology, it may transpire that the real evolutionary action is in the realm of functional morphlogy and ecology, and particularly the realm of neurology and behavioral sophistication. When combined with new insights from epigenesis, the study of evolution seems poised to break free from a steady and increasingly arid reductionism. And those all powerful genes? Perhaps their importance is better pursued if we view them as a necessary tool kit, to be used as and when required, than as some sort of master template upon which evolution is meant both to act and unfold.

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I presume that assembly of the spindle involves dynein-associated cargo complexes, like cilial assembly and other forms of intracellular cargo transport, but I don't think that anyone has characterized these components yet....

3. In particular, it appears that the cargo-attachment complexes used during the assembly of the spindle and centrosome remain uncharacterized. This is key because on Cavalier-Smith's scenario, the cilium is basically another extension of the spindle.

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posted 19. September 2003 23:36                   

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In particular, it appears that the cargo-attachment complexes used during the assembly of the spindle and centrosome remain uncharacterized. This is key because on Cavalier-Smith's scenario, the cilium is basically another extension of the spindle.

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