Regina wrote:So which of the rocks is designed? You are the expert, after all.
Btw, it's "Hintern".

Coroama wrote:

Regina wrote:So which of the rocks is designed? You are the expert, after all.
Btw, it's "Hintern".

Oh yes. H like this H

Coroama wrote:It doesnt take much brainpower to understand, that is designed....

Coroama wrote:

Rumraket wrote:
Point out the designed rock using your brilliant, design-detecting intuition.

Of course, i can design a rock, that looks exactly the same as normal rocks.... your argument is superfluous.

Romans 1.21

LucidFlight wrote:

Coroama wrote:It doesnt take much brainpower to understand, that is designed....

I think that's part of the problem.

Coroama wrote:

LucidFlight wrote:

Coroama wrote:It doesnt take much brainpower to understand, that is designed....

I think that's part of the problem.

Amazing how we understand each other.....

continuing from the same webpage :

Of course such incredibly sophisticated bio-technology screams “Design”, but does God get the glory in the scientific literature describing these amazing machines and processes? No, ‘nature’ does:

http://michigantoday.umich.edu/04/Fall0 ... ?molecular

“It is impressive how nature (emphasis mine) manages to combine all of these functions in one molecule. In this respect it is still far superior to all the efforts of modern nanotechnology and serves as a great example to us all.”

but lets look a littlebit further in the linked page :

The ATP Synthase motor has the classic stator and rotor structure familiar in man-made motors. It spans a cellular membrane which admits protons (H+) one at a time. For each proton, the motor turns once, adding a phosphate to adenosine di-phosphate and converting it to adenosine tri-phosphate, the universal fuel source of cells.

Its famaliar to man-made motors, but its all due to natural selection.... aham.....

Rumraket wrote:

Oh my god it's so complex, see how complex that is? That is so complex, holy fuck is it complex. Irreducibly complex, Oh my oh my, so complex it is. Allakhazam - therefore god.

Also, "machines", "information", "storage capacity", "algorithmic programming", "code and language system", "memory in DNA", "error correction" and "double helix". Omg omg, so complex, sooooo so so compelx, also btw... "shannon uncertainty" - Woooo, whoa, wow! Fancy lights, gasping audience. Allakhazam - therefore god.

LucidFlight wrote:But, design doesn't necessarily need to be complex, it can be artistic, like a snowflake.

scientists and engineers at the University of Michigan are looking at these self-assembled, ultra-efficient, incredibly small, natural motors that exist all around us and within us. The blueprints and operating instructions for them are contained within DNA.

"These things are machines!" says Michael Mayer, an assistant professor of chemical and biomedical engineering. "It would be amazing to figure out how to make them

Coroama wrote:

Rumraket wrote:

Oh my god it's so complex, see how complex that is? That is so complex, holy fuck is it complex. Irreducibly complex, Oh my oh my, so complex it is. Allakhazam - therefore god.

Also, "machines", "information", "storage capacity", "algorithmic programming", "code and language system", "memory in DNA", "error correction" and "double helix". Omg omg, so complex, sooooo so so compelx, also btw... "shannon uncertainty" - Woooo, whoa, wow! Fancy lights, gasping audience. Allakhazam - therefore god.

YESSSS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! exactly. You got it. THAT is intelligent reasoning.

why did you not grasp this earlier ??!!

Coroama wrote:

Calilasseia wrote:Oh dear, he's brought up the "I know it's designed because it looks designed" canard.

Canard mein hintern.

Coroama wrote:[http://creation.com/incredible-kinesin

A typical kinesin has two ‘arms’ on one end (that hold onto the cargo) and two ‘legs’ on the other end that walk along the microtubule, pulling the cargo toward its final destination. In a sense they are like the ‘postman’ delivering mail inside cells.

Abdel-Ghany et al, 2005 wrote:Kinesin-like calmodulin-binding protein (KCBP), a member of the Kinesin-14 family, is a C-terminal microtubule motor with three unique domains including a myosin tail homology region 4 (MyTH4), a talin-like domain, and a calmodulin-binding domain (CBD). The MyTH4 and talin-like domains (found in some myosins) are not found in other reported kinesins. A calmodulin-binding kinesin called kinesin-C (SpKinC) isolated from sea urchin (Strongylocentrotus purpuratus) is the only reported kinesin with a CBD. Analysis of the completed genomes of Homo sapiens, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and a red alga (Cyanidioschyzon merolae 10D) did not reveal the presence of a KCBP. This prompted us to look at the origin of KCBP and its relationship to SpKinC. To address this, we isolated KCBP from a gymnosperm, Picea abies, and a green alga, Stichococcus bacillaris. In addition, database searches resulted in identification of KCBP in another green alga, Chlamydomonas reinhardtii, and several flowering plants. Gene tree analysis revealed that the motor domain of KCBPs belongs to a clade within the Kinesin-14 (C-terminal motors) family. Only land plants and green algae have a kinesin with the MyTH4 and talin-like domains of KCBP. Further, our analysis indicates that KCBP is highly conserved in green algae and land plants. SpKinC from sea urchin, which has the motor domain similar to KCBP and contains a CBD, lacks the MyTH4 and talin-like regions. Our analysis indicates that the KCBPs, SpKinC, and a subset of the kinesin-like proteins are all more closely related to one another than they are to any other kinesins, but that either KCBP gained the MyTH4 and talin-like domains or SpKinC lost them.

Abdel-Ghany et al, 2005 wrote:Members of the kinesin superfamily of microtubule (MT) motor proteins have been identified in many taxa ranging from protists to plants and animals (Reddy and Day, 2001; Vale, 2003). The members of the kinesin superfamily have a highly conserved motor domain with ATP- and MT-binding sites. In addition, most kinesins have a less conserved coiled-coil region that is important for dimerization and a nonconserved tail domain that is thought to interact with specific cargo (see Fig. 1). Kinesins bind MTs and a variety of cargoes and perform force-generating tasks such as transport of vesicles and organelles, spindle formation and elongation, chromosome segregation, and MT organization (Leopold et al., 1992; Sawin et al., 1992; Barton and Goldstein, 1996; Moore and Endow, 1996; Wein et al., 1996; Raich et al., 1998; Goldstein and Philip, 1999; Manning and Snyder, 1999; Reddy, 2001). Analysis of completed genome sequences of eukaryotes has resulted in identification of a large number of kinesins (Reddy and Day, 2001; Vale, 2003). Recently, all known kinesins have been grouped into 14 families that were designated as Kinesin-1 to Kinesin-14 (Lawrence et al., 2004). One of these families (Kinesin-14) possesses a C-terminal motor domain with minus-end motility, and the rest of the subfamilies have either an N-terminal or an internal motor domain (Fig. 1) and move toward the plus-end of MTs (Reddy and Day, 2001; Vale, 2003; Lawrence et al., 2004).

Plant kinesins were first identified in tobacco (Nicotiana tabacum) pollen tubes (pollen kinesin homolog) and tobacco phragmoplasts (tobacco kinesin related protein 125; Asada et al., 1991; Tiezzi et al., 1992; Cai et al., 1993). Since then, many kinesins have been identified in plants (Mitsui et al., 1993, 1994; Liu et al., 1996; Reddy et al., 1996a; Asada et al., 1997; Tamura et al., 1999; Barroso et al., 2000; Nishihama et al., 2002; Reddy, 2003; Tanaka et al., 2004). In Arabidopsis (Arabidopsis thaliana) alone there are at least 61 kinesins (Reddy and Day, 2001). Using genetic and cell biological approaches, functions of some plant kinesins have been reported (Reddy, 2003; Lee and Liu, 2004). Functional studies with a few kinesins have shown their involvement in mitosis and meiosis (Liu et al., 1996; Bowser and Reddy, 1997; Lee and Liu, 2000; Lee et al., 2001; Chen et al., 2002; Nishihama et al., 2002; Strompen et al., 2002; Yang et al., 2003; Pan et al., 2004; Ambrose et al., 2005), morphogenesis (Oppenheimer et al., 1997; Lu et al., 2005), and oriented deposition of cellulose myofibrils (Zhong et al., 2002). A kinesin that interacts with a geminivirus replication protein has also been reported in Arabidopsis (Kong and Hanley-Bowdoin, 2002). Predicted mitochondrial targeting sequences in two Arabidopsis kinesins mined from the database were shown to direct a green fluorescent protein fusion protein to mitochondria, suggesting that these kinesins are likely to function in these organelles (Itoh et al., 2001). A kinesin containing a calponin homology domain has been shown to interact with actin microfilaments, suggesting the involvement of some kinesins in coordinating actin and MT cytoskeleton (Preuss et al., 2004). The motility properties of only a few of these kinesins have been reported (Asada and Shibaoka, 1994; Song et al., 1997; Marcus et al., 2002).

A calmodulin-binding kinesin (kinesin-like calmodulin-binding protein [KCBP]) has been characterized from several flowering plants (Reddy et al., 1996a, 1996b; Wang et al., 1996; Abdel-Ghany and Reddy, 2000; Preuss et al., 2003). KCBP, like other kinesins, has a motor domain, a stalk, and a tail domain. In addition, it has some unique domains. These include: (1) a calmodulin-binding domain (CBD) at the C terminus that is responsible for Ca2+/calmodulin regulation of its ATPase activity, interaction with MTs, and motor activity (Narasimhulu et al., 1997; Song et al., 1997; Deavours et al., 1998; Narasimhulu and Reddy, 1998), and (2) the myosin tail homology region 4 (MyTH4) and the talin-like region found in some myosins (Reddy and Reddy, 1999). We have shown that the MyTH4 and talin-like region has an MT-binding site (Narasimhulu and Reddy, 1998). Recently, a similar region in animal myosins has also been found to bind MTs (Weber et al., 2004). Biochemical studies together with the crystal structure of the KCBP motor domain with the CBD indicate that calcium/calmodulin negatively regulates KCBP activity by blocking the MT binding sites on the motor (Reddy and Reddy, 2002; Vinogradova et al., 2004).

Immunolocalization studies and antibody injection using antibodies specific to KCBP indicate that KCBP has a role in cell division (Bowser and Reddy, 1997; Smirnova et al., 1998; Vos et al., 2000). Consistent with its role in cell division, the level of KCBP is cell cycle regulated with a high amount in the mitotic phase (Bowser and Reddy, 1997). KCBP is localized to the plant-specific preprophase band, phragmoplast, and to the spindle apparatus in dividing cells (Bowser and Reddy, 1997; Smirnova et al., 1998; Preuss et al., 2003). KCBP is capable of bundling MTs, suggesting the involvement of KCBP in establishing mitotic MT arrays during different stages of cell division (Kao et al., 2000). Genetic studies have shown that KCBP is essential for trichome morphogenesis, and KCBP mutants (zwichel, zwi) have abnormal trichomes with a shorter stalk and a reduced number of branches (Oppenheimer et al., 1997; Reddy and Day, 2000). In cotton (Gossypium hirsutum) fibers, KCBP was shown to associate with cortical MTs as well as with mitotic MT arrays (Preuss et al., 2003). In addition to calmodulin, KCBP interacts with three other proteins (KCBP interacting Ca2+ binding protein, ANGUSTIFOLIA, and KCBP-interacting protein kinase), and two of these are also involved in trichome morphogenesis (Day et al., 2000; Folkers et al., 2002; Reddy et al., 2004).

Searches of the National Center for Biotechnology Information (NCBI) and species-specific sequence databases have not identified a homolog of KCBP in the completely sequenced genomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Cyanidioschyzon merolae, or Mus musculus (Miki et al., 2001; Schoch et al., 2003; Matsuzaki et al., 2004). However, a calmodulin-binding kinesin called kinesin-C (hereafter called SpKinC), a member of the C-terminal family, has been cloned from the sea urchin (Strongylocentrotus purpuratus; Rogers et al., 1999). The amino acid sequence of CBD of SpKinC shares 35% identity with KCBP. Since SpKinC lacks the MyTH4 and talin-like regions found in plant KCBPs, it is not classified as a KCBP.

The presence of KCBP in flowering plants but not in fungal or animal genomes raises two questions. Is KCBP found in photosynthesizing organisms but not other eukaryote lineages, and what is the level of conservation of KCBP among phylogenetically divergent eukaryotes? To answer these questions, we have cloned and characterized KCBPs from a gymnosperm (Picea abies) and a green alga (Stichococcus bacillaris). In addition, we searched NCBI sequence databases and other databases of phylogenetically divergent photosynthetic and nonphotosynthetic eukaryotes for KCBP (See ‘‘Materials and Methods’’). Gene tree analysis suggests that the KCBP-like motor domain originated prior to the divergence of plants and animals. However, the addition of the MyTH4 and talin-like domains appears to be limited to the plant lineage. Our data suggest that KCBP is highly conserved in land plants and green algae.

Abdel-Ghany et al, 2005 wrote:RESULTS AND DISCUSSION

Cloning, Characterization, and Identification of KCBPs

KCBP has been cloned from representative members of monocots and dicots and is highly conserved among angiosperms. In order to examine the presence and the level of conservation of unique domains in KCBP outside the angiosperms, we used PCR and library screening to clone KCBP from a gymnosperm (P. abies) and an alga (S. bacillaris). Primers corresponding to the conserved ATP-binding site of kinesins and the CBD of KCBP were used in PCR with P. abies cDNA library or S. bacillaris genomic DNA. PCR products from each species with sequences highly similar to KCBP from angiosperms were used as probes to screen the P. abies cDNA library and S. bacillaris library. Clones from the screens were isolated and sequenced. The predicted amino acid sequence (PaKCBP) of the longest isolated P. abies cDNA showed from 75% to 80.5% sequence identity to the motor domains of KCBPs from angiosperms. This clone contained the coding region for the motor domain and CBD. An S. bacillaris genomic clone was isolated that coded for a KCBP (SbKCBP, Fig. 2) with the unique KCBP domains (CBD, MyTH4, and talin-like region).

Using both the full-length and motor domain sequences of Arabidopsis KCBP (AtKCBP), we searched databases at NCBI, The Institute for Genomic Research (TIGR), and the Joint Genome Institute (JGI) including individual databases of species whose genomes are either completely sequenced or are being completed (see ‘‘Materials and Methods’’ for list of genomes searched), as well as expressed sequence tag (EST) databases, for the presence of KCBP homologs. KCBP sequences were identified only in land plants and green algae genomes (Table I). Using BLAST searches, full-length KCBPs were found in rice (Oryza sativa) and Chlamydomonas reinhardtii at NCBI and JGI, respectively. The rice amino acid sequence (OsKCBP) shows 90% similarity to Zea mays KCBP (ZmKCBP). The C. reinhardtii amino acid sequence (CrKCBP, Fig. 2) has the conserved-motor domain, CBD, coiled coil, MyTH4 region, and talin-like region found in other KCBPs. The sequence was originally generated from an unannotated scaffold (scaffold_633) DNA sequence using a splice site prediction program, two EST sequences, and comparison to the KCBP sequence. JGI has now annotated this sequence, and their annotation is in agreement with our generated sequence except that our sequence contains an additional sequence of about 100 amino acids at the N terminus, which is similar to other KCBPs. A scaffold sequence for a KCBP, which included the MyTH4, talin, coiled coil, motor, and CBD domains, was also identified for Populus trichocarpa. Its sequence was closest to cotton KCBP. A KCBP-like sequence was found at http://moss.nibb.ac.jp/ for the moss Physcomitrella patens.

Fungi genomes including yeasts and plasmodium do not have a KCBP. It has been previously reported that KCBP is not present in the human, Drosophila, or C. elegans genomes (Miki et al., 2001; Reddy and Day, 2001; Siddiqui, 2002). Searches of other animal genomes (mouse, rat, dog, etc.) at http://www.ncbi.nih.gov/Genomes/index.html did not identify aKCBP in these species. Searches of the genomes at JGI resulted in identification of scaffold sequences with similarity to the KCBP motor domain (but did not contain the domains unique to KCBP) in the water molds Phytophthora sojae and Phytophthora ramoru and the diatom Thalassiora pseudonana. A scaffold sequence from Ciona intestinalis showed closest similarity to sea urchin SpKINC. The predicted Giardia lamblia amino acid sequence (G. lamblia kinesin-like protein [GlKLP]; Fig. 2) encodes a region of coiled coil followed by a kinesin motor domain that in BLAST searches showed the most similarity to KCBP motor domain from angiosperms. However, it does not contain the MyTH4, talin-like region, or CBD domain. A partial kinesin sequence in the protozoan Tetrahymena thermophila in TIGR also showed similarity to KCBP motor domain but lacked the CBD. Proteins were named KCBP if they were placed in the KCBP clade in our gene tree analysis (see below) and contained MyTH4, talin-like region, and CBD. Proteins that have motor domains most similar to KCBPs, but (1) lack MyTH4 and talin-like regions and (2) are not nested within the KCBP clade are not considered to be KCBPs.

A region that defines kinesin class specificity is the neck region, an approximately 45-amino acid-long segment that emerges from the catalytic core of the motor domain (Vale and Fletterick, 1997). Carboxyterminal kinesins as a group share a short conserved sequence (ELKGNI) in their neck region. The sequence of the neck region has been shown to be critical for directionality of motor movement (Endow and Waligora, 1998). The neck in KCBPs contains a conserved sequence (EDMKGIRV) that diverges slightly from other Kinesin-14 proteins (Fig. 3A). With the exception of SbKCBP (EDL) and GlKLP (EEM), all of the KCBPs and kinesins with a KCBP-like motor have an initial EDM sequence, whereas it is not conserved in other Kinesin-14 proteins.

A comparison of the sequence following the motor domain of known KCBPs and the KCBP-like proteins reported here is shown in Figure 3B. All reported KCBPs have a conserved CBD (70%–87% similar to AtKCBP) in this region. PaKCBP and CrKCBP show a high level of similarity to angiosperm CBDs (65% and 61%, respectively), while the SbKCBP sequence is more diverged (48%). A bacterially produced protein encompassing the CBD and motor domain of PaKCBP was shown to bind 35S calmodulin in the presence of Ca2+ but not in the presence of EGTA (data not shown). The sequence for the moss (P. patens) KCBPlike protein (PpKLP) shows 58% similarity to the CBD of AtKCBP. The sea urchin kinesin (SpKinC) showing similarity to the KCBP motor domain also contains a CBD, but the sequence is less conserved than the CBDs of angiosperm KCBPs (30% identical to AtKCBP). However, the bacterially expressed SpKinC has been shown to bind calmodulin (Rogers et al., 1999). A kinesin from C. intestinalis (CiKLP) also has a CBD that is 30% identical to AtKCBP and is similar to SpKinC (Fig. 3B). Although the binding of CiKLP to calmodulin has not been shown, it is likely that it also binds to calmodulin. The sequences following the motor domain in the T. thermophila and G. lamblia kinesin sequences have little similarity to the CBD of angiosperm KCBPs (9% and 13% identity to AtKCBP).

Gene Tree Analysis of KCBP-Like Proteins

Supplemental data, consisting of the DIALIGN alignment, the data matrices, and the complete Bayesian and parsimony trees, are available online (Supplemental Figs. 1–5). The grouping of Arabidopsis kinesins in the complete trees is consistent with the earlier tree presented by Reddy and Day (2001). Both the Bayesian and parsimony analyses support all KCBPs as more closely related to one another than they are to any other kinesin family. The unrooted Bayesian tree for the kinesin superfamily, based on their motor domains, is presented in Figure 4. All families other than Kinesin-14 (C terminal) are represented as single branches in the abbreviated tree. The members of each group are provided in the supplemental figures. Consistent with the inferred phylogeny of plants (Melkonian and Surek, 1995; Lewis and McCourt, 2004) the KCBPs of the two chlorophyte algae are resolved as a clade, sister to KCBPs from the seed plants, and all angiosperm KCBPs are resolved as a clade sister to the P. abies KCBP. TtKLP is resolved as the sister group to the plant KCBPs, but it is poorly supported as such in both the parsimony and Bayesian analyses; no conclusion can be made about its inclusion or exclusion from the KCBP lineage. Sequences from the water molds (PrKLP and PsKLP), the sea squirt (CiKLP), sea urchin (SpKinC), and cyanophora (CpKLP) and the diatom (TpKLP) are resolved as closely related to the KCBP group. Based on the inferred phylogeny of the eukaryotes (Baldauf, 2003), the resolution of GlKLP as the sister group of the remaining KCBP-like proteins suggests that the KCBP like motor was present in the ancestral eukaryotic lineage prior to the diversification of the major extant groups of eukaryotes.

Evolution of KCBP

Kull et al. (1998) used several criteria to evaluate the evolutionary relationships between motor proteins and concluded that the motor domain of kinesins and myosins may have evolved from an ancestral protomotor by divergent evolution. A hypothetical ancestor was proposed that was possibly shared with G proteins. The three proteins are proposed to have diverged from a common core nucleotide-binding motif (Kull et al., 1998). Distinct families of kinesins are thought to have evolved from the protokinesin. Using G. lamblia as a representative of the early derived extant eukaryotes, Iwabe and Miyata (2002) addressed the question of whether the subfamilies might have arisen early in eukaryotic evolution. They cloned 13 G. lamblia kinesins and four kinesins from four different metazoan species and analyzed them along with the motor domain of 142 kinesins in the databases. They concluded that most gene duplications that gave rise to different kinesin subfamilies had been completed before the earliest divergence of extant eukaryotes (Iwabe and Miyata, 2002). Based on their study of the kinesins in filamentous ascomycetes, Schoch et al. (2003) concluded that the founding members of most kinesin subfamilies were present before fungi, metazoans, and plants diverged. Gene tree analysis of the uncoordinated-104 family suggested that the divergence of the members of the kinesin family by gene duplications seems to have occurred intermittently. Iwabe and Miyata (2002) suggest three active periods: before the separation of G. lamblia, after the separation from fungi and plants but before the parazoan-eumetazoan split, and early in the evolution of vertebrates before the cyclostomegnathostome split. A study of the kinesins in the Arabidopsis genome suggests duplication events in the kinesin families in plants after their separation from animals (Reddy and Day, 2001).

KCBP orthologs with the MyTH4, talin-like region, and CBD have been isolated from phylogenetically divergent land plants and green algae including Arabidopsis, tobacco, Solanum tuberosum, Z. mays, cotton (Reddy et al., 1996a, 1996b; Wang et al., 1996; Abdel-Ghany and Reddy, 2000; Preuss et al., 2003) and S. bacillaris (a cholorophyte alga). Sequences retrieved from databases for the alga C. reinhardtii and rice also contain these domains. The genome for the red alga C. merolae has been sequenced and five kinesins were reported (Matsuzaki et al., 2004; http://merolae.biol.s.u-tokyo.ac.jp/). However, none of them contain domains unique to KCBP. ESTs for several partial sequences from flowering plants and from the moss P. patens contain the motor domain and CBD that is similar to KCBP. However, kinesins from Tetrahymena and G. lamblia that showed the closest similarity to KCBP motor domain did not have a conserved CBD.

The only reported KCBP-like motor domain outside photosynthetic organisms is SpKinC isolated from sea urchin (Rogers et al., 1999). Searches of the genomes of fungi, invertebrates, and vertebrates have not identified a KCBP ortholog (Miki et al., 2001; Iwabe and Miyata, 2002; Schoch et al., 2003). However, our database searches revealed the presence of a kinesin with a KCBP-like motor domain in two protozoans, T. thermophila and G. lamblia. The G. lamblia kinesin was not included in the study by Iwabe and Miyata (2002). Gene tree analysis using the motor domain sequence resolved the sea urchin, Ciona intesnialis, P. ramorum, P. sojae, and G. lamblia proteins as members of the KCBP subfamily of the C-terminal kinesins (Fig. 4). While the motor domains of SpKinC, GlKLP, PrKLP, and PsKLP show a close relationship, the proteins do not contain the conserved N-terminal MyTH4 and talin-like regions found in KCBPs. The sequences for CiKLP, TpKLP, and TtKLP are not full length so the presence of these domains cannot be determined.

Our results show that complete KCBP with the N-terminal MyTH4 and talin-like regions, C-terminal motor, and CBD is found only in land plants and green algae. These results are consistent with the phylogeny of the eukaryotes, with the land plants and the green algae supported as a monophyletic group. (Baldauf, 2003; Philippe et al., 2004). In a review of kinesins functioning in intracellular transport, Vale (2003) suggested that kinesin motors expanded in higher eukaryotes through gene duplication, alternative splicing, and the addition of associated subunits. KCBP appears to be an example of a kinesin motor to which the MyTH4 and talin-like domains were added after the divergence of the green algae. These observations suggest that KCBP, with its characteristic domains, may have evolved early in the plant lineage from a single common ancestor to perform plant-specific functions.

Abdel-Ghany et al, 2005 wrote:Relationship between KCBP and SpKinC

All reported KCBPs from land plants and green algae and SpKinC from sea urchin have a CBD at the C terminus that is responsible for regulating the interaction of the motor domain with MTs in a Ca2+-dependent manner (Song et al., 1997; Deavours et al., 1998; Narasimhulu and Reddy, 1998; Rogers et al., 1999; Kao et al., 2000). Over 250 KLPs have been characterized from various eukaryotes. However, kinesin-heavy chains other than KCBP and SpKinC are not known to bind calmodulin (Matthies et al., 1993; Reddy et al., 1996b; Rogers et al., 1999). In the kinesin gene tree (Fig. 4), SpKinC is resolved as nested within the clade of KCBP-like proteins. Outside the motor domain, there is no sequence similarity between KCBPs and SpKinC, whereas, as stated above, the KCBP tail is highly conserved among land plants and green algal KCBPs. Two evolutionary propositions may explain the relationship between KCBPs and SpKinC. First, KCBP and SpKinC are not closely related and the CBD was added to both of them independently (convergent evolution) during the course of evolution (e.g. as a result of gene transfer [Smith et al., 1992] or domain swaps [Doolittle and Bork, 1993]) to confer Ca2+/calmodulin regulation. The arguments in support of this proposition include the fact that the conserved MyTH4 and talin-like regions present in the N-terminal region of all characterized KCBPs are not present in SpKinC (Fig. 1). A second argument in support of this proposition is that KCBP orthologs are not found in the completely sequenced genomes of C. elegans, D. melanogaster, and S. cerevisiae, or in the draft human genome. Also, fusion of the CBD from Arabidopsis to the motor domain of C-terminal or N-terminal kinesin of Drosophila confers calmodulin-binding property to these motifs (Reddy and Reddy, 2002).

The second proposition is that the common ancestor of KCBPs and SpKinC with a CBD existed before the divergence of plants and animals, which is believed to have occurred about 1.5 billion years ago (Wang et al., 1999). The differences in domain organization between KCBP and SpKinC could have occurred through domain insertion or deletion at the amino-terminal region of the motor in order to carry specific cargoes or to confer plant-specific functions. One argument in support of this notion is that the motor domain of SpKinC is resolved in a well-supported clade that includes the KCBPs in both the Bayesian and parsimony analyses (Fig. 4). In addition, the class-specific coiled-coil linker, a short motif that links the catalytic core of the motor domain to the coiled-coil region, is mostly identical in SpKinC and KCBPs and is diverged from other C-terminal KLPs (Fig. 2A). The class specific cluster of residues in the kinesin motor domain is found in the neck linker and not within the catalytic core (Case et al., 2000). However, based on the inferred phylogeny of the metazoa (Halanych and Passamaneck, 2001) this proposition would require at least three independent losses (one in the S. cerevisiae lineage, a second in the Ecdysozoa prior to the divergence of the arthropods and nematodes, and a third in the chordates [and perhaps fourth in the oomycetes]). Although, we cannot exclude either of these propositions based on our results, we favor the second proposition based on the resolution in our gene tree and the presence of a CBD in both KCBPs and SpKinC.

Lawrence et al, 2004 wrote:In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered.

Lawrence et al, 2004 wrote:Kinesins constitute a superfamily of microtubule-based motor proteins that perform diverse functions, including the transport of vesicles, organelles, chromosomes, protein complexes, and RNPs; they also help to regulate microtubule dynamics (for review see Hirokawa, 1998). Individually identified kinesins are often named on the basis of their functional characteristics (McDonald et al., 1990). Systematically identified kinesins have different names (Stewart et al., 1991; Aizawa et al., 1992; Vernos et al., 1993). Kinesins also have been named by other criteria, including the position of the motor core within the protein (Vale and Fletterick, 1997), and their evolutionary relatedness to other kinesins (for reviews see Goodson et al., 1994; Sekine et al., 1994; Hirokawa, 1998; Kirchner et al., 1999). Early in the process of kinesin discovery, it was relatively simple to be familiar with the names and potential functional relationships of all known kinesins (Goodson et al., 1994). Today, however, there are literally hundreds of kinesins being named by diverse criteria, and inconsistencies are emerging that cause genuine confusion (for specific examples, see “Problems with Previous Nomenclature” at http://www.proweb.org/kinesin/Nomenclature_Details.html).

Lawrence et al, 2004 wrote:Criteria for kinesin classification

Finally, for publication there should be an accepted protocol for identifying the family to which an unclassified kinesin sequence belongs. How this determination was made should be explicitly stated in the manuscript within the methods section. Our suggestion is to first do a BLAST search (Altschul et al., 1990) using the full-length protein sequence for the kinesin of interest as the query. If all top hits are members of a single kinesin family, the kinesin of interest is probably also a member of that family. To confirm the BLAST results and also to classify sequences where BLAST results do not clearly indicate assignment to a particular family, we recommend that the researcher download a published kinesin motor core alignment such as one of the Lawrence et al. (2002) alignments or the alignment available through the kinesin home page (http://www.proweb.org/kinesin/KinesinAlign.html), and add their own kinesin’s motor core to that alignment (by hand or using an alignment tool such as Clustal; Higgins et al., 1996). (Lawrence et al., 2002 alignments ALIGN_000356, ALIGN_000357, and ALIGN_000358 are available online from EMBL at ftp://ftp.ebi.ac.uk/pub/databases/embl/align.) Next, use a simple method for building a phylogenetic tree (such as neighbor joining; Saitou and Nei, 1987) to find the family most closely related to the kinesin of interest. We also recommend that bootstrap resampling (easily performed by phylogenetic analysis programs such as Clustal) be used to determine whether a kinesin should be assigned to a particular family or remain an ungrouped “orphan kinesin.” These alignment and treebuilding methods are available together on a webserver at http://www.ebi.ac.uk/clustalw. Analysis of nonmotor regions can help to confirm family assignments (Dagenbach and Endow 2004), and as previously noted by Hirokawa (1998) and Vale (2003), specific domains or motifs should be used as secondary criteria for classification. For instance, many Kinesin-3 family members can be identified by the presence of both a fork head homology (FHA) domain COOH-terminal to the motor and a conserved insertion present within the third loop (Vale, 2003). Although the relatedness of families to one another varies among published phylogenies, the members of each family are relatively consistent among published trees, making it possible to use any published phylogeny as a guide to classification.

Kull et al, 1998 wrote:Summary

Recent studies have shown surprising structural and functional similarities between the motor domains of kinesin and myosin. Common features have also been described for motor proteins and G proteins. Despite these similarities, the evolutionary relationships between these proteins, even among the motor proteins, has not been obvious, since the topological connectivities of the core overlapping structural elements in these transducing proteins are not identical to one another. Using secondary structure topology, comparison of functional domains and active site chemistry as criteria for relatedness, we propose a set of rules for determining potential evolutionary relationships between proteins showing little or no sequence identity. These rules were used to explore the evolutionary relationship between kinesin and myosin, as well as between motor proteins and other phosphate-loop (P-loop) containing nucleotide-binding proteins. We demonstrate that kinesin and myosin show significant chemical conservations within and outside of the active site, and present an evolutionary scheme that produces their respective topologies from a hypothetical ancestral protein. We also show that, when compared with various other P-loop-containing proteins, the cytoskeletal motors are most similar to G proteins with respect to topology and active site chemistry. We conclude that kinesin and myosin, and possibly G proteins, are probably directly related via divergent evolution from a common core nucleotide-binding motif, and describe the likely topology of this ancestor. These proteins use similar chemical and physical mechanisms to both sense the state of the nucleotide bound in the active site, and then transmit these changes to protein partners. The different topologies can be accounted for by unique genetic insertions that add to the edge of a progenitor protein structure and do not disrupt the hydrophobic core.

This is a complex coordinated effort, as something must first access the creature’s DNA library, unzip it at the exact location needed for the specific information required (for whatever part is to be manufactured), create a duplicate of the information for the part and deliver it to the factory. (See animation, below left.)

Then another organelle in the cell (called the Golgi apparatus) packages the needed part by wrapping it in a bag (called a vesicle) and imprints the ‘address’ where the part is to be delivered in the cell onto the outside of the vesicle ‘parcel’.

Then a kinesin is summoned. It picks up the parcel and ‘walks’ along microtubule roadways in the cell and delivers the parcel where it is needed. (Many different types of kinesin [and kinesin-related proteins] with different specifications and functions have been discovered in various organisms from yeast to humans. The above example was simply an example of a ‘common’ task.)

Coroama wrote:It doesnt take much brainpower to understand assume, that is designed....

Coroama wrote:actually , it inspires awe, its simply amazing what we discover in the cells.

Coroama wrote:Only blinded wishful thinking naturalists supernaturalists which do not want to acknoledge assert blindly about a God at any cost are unable to grasp this.......

Coroama wrote:

Rumraket wrote:Point out the designed rock using your brilliant, design-detecting intuition.

Of course, i can design a rock, that looks exactly the same as normal rocks....

Coroama wrote:your argument is superfluous.

Coroama wrote:Romans 1.21

campermon wrote:

Coroama wrote:http://www.evolutionnews.org/2013/09/mechanical_gear076801.html



How do we know these gears evolved, as opposed to having been designed? Because we know that everything in biology evolved. And how do we know that everything evolved? Because we know that nothing was designed. Right. But how do we know that nothing was designed? Because we know everything evolved.

Ah, got it now. Everyone clear?

Those cogs don't look like they're designed. Each tooth has slight variations to it - a sure sign of an evolved system, If it had been designed, surely each cog would be identical to ensure maximum power transmission?

Darwinsbulldog wrote:I am just amazed that creationists have never attacked cell theory. I guess it is because they know fuck all about it, but that is also true of their knowledge about evolution, genetics, development.................etc..........etc...........etc

One should not confuse a design specification issue with a manufacturing quality control issue.

Darwinsbulldog wrote:Coroama wrote:

One should not confuse a design specification issue with a manufacturing quality control issue.

I don't see how this helps your case John.

The universe began ~ about 14 billion years ago from the big-bang and inflation. God not only creates the Earth [after a 10 billion year delay] but trillions of stars in billions of galaxies. He bombards the Earth for 300+ million years during the Hadean era, then creates bacteria [more formally prokaryotes] a further wait of about 2 billion years before "human-grade" cells appear [eukaryotes], then after fucking about for a further half billion years decides to make god's favourite ape. Not content with that, he creates haemoroids, cancer, pathogens of imaginable evil, a fucked birthing process that almost kills the mothers off, and shoddy design as often as brilliant design.
No wonder the smarter theolgians are now praising Darwin, for he was the get out of free-card for the eternal [and unsolvable] theological "problem of evil"!!

Calilasseia wrote:Origin And Evolution Of Kinesin-Like Calmodulin-Binding Protein by Salah E. Abdel-Ghany, Irene S. Day, Mark P. Simmons, Paul Kugrens, and Anireddy S.N. Reddy, Plant Physiology, 138: 1711-1722 (July 2005) [Full paper downloadable from here].

Coroama wrote:
What for me is obvious evidence of a powerful of a incredibly intelligent designer, of course you hand wish away as result of unguided forces. Feel free to do so.

Such a explanation would not satisfy my intellect and my intelligence.

Fortunately, i am a happy admirer and believer in the God of the bible, which i honor also as creator of all this amazing technology, that is far more superior than anything human brains were ever capable of inventing.

John Platko wrote:

Darwinsbulldog wrote:Coroama wrote:

One should not confuse a design specification issue with a manufacturing quality control issue.

I don't see how this helps your case John.

The universe began ~ about 14 billion years ago from the big-bang and inflation. God not only creates the Earth [after a 10 billion year delay] but trillions of stars in billions of galaxies. He bombards the Earth for 300+ million years during the Hadean era, then creates bacteria [more formally prokaryotes] a further wait of about 2 billion years before "human-grade" cells appear [eukaryotes], then after fucking about for a further half billion years decides to make god's favourite ape. Not content with that, he creates haemoroids, cancer, pathogens of imaginable evil, a fucked birthing process that almost kills the mothers off, and shoddy design as often as brilliant design.
No wonder the smarter theolgians are now praising Darwin, for he was the get out of free-card for the eternal [and unsolvable] theological "problem of evil"!!

My case? I was simply pointing out that one can't infer from actual gear variance that it was a design error. Although it could be a design error, a poor tolerance specification for example, it could also be a manufacturing quality control problem.

As for the creation vs evolution choice, I'm betting the farm on evolution.