Calilasseia wrote:Really?
Let's take a look at some scientific papers shall we?
From The Origin of Species to the Origin of Bacterial Flagella by Mark J. Pallen and Nicholas J. Matzke, Nature Reviews Microbiology Online, DOI 10.1038/nrmicro1493, 5th September 2006
This paper lists the various proteins that are contained in the bacterial flagellum. Are they present in all bacteria with flagella? NO. Here's the list:
FlgA (P ring) - Absent from Gram-Positive bacteria
FlgBCFG (Rod) - universal
FlgD (Hook) - universal
FlgE (Hook) - universal
FlgH (L Ring) - Absent from Gram-Positive bacteria
FlgI (P Ring) - Absent from Gram-Positive bacteria
FlgJ (Rod) - FlgJ Rod N-terminal domain absent from some systems
FlgK (Hook-Filament Junction) - universal
FlgL (Hook-Filament Junction) - universal
FlgM (Cytoplasm & Exterior) - Absent from Caulobacter
FlgN (Cytoplasm) - Undetectable in some systems
FlhA (T3SS apparatus) - universal
FlhB (T3SS apparatus) - universal
FlhDC (Cytoplasm) - Absent from many systems
FlhE (Unknown) - Mutant retains full motility
FliA (Cytoplasm) - Absent from Caulobacter
FliB (Cytoplasm) - Absent from Escherichia coli
FliC (Filament) - universal
FliD (Filament) - Absent from Caulobacter
FliE (Rod/Basal Body) - universal
FliF (T3SS apparatus) - universal
FliG (Peripheral) - universal
FliH (T3SS apparatus) - Mutant retains some motility
FliI (T3SS apparatus) - universal
FliJ (Cytoplasm) - Undetectable in some systems
FliK (Hook/Basal Body) - universal
FliL (Basal body) - Mutant retains full motility
FliM (T3SS apparatus) - universal
FliN (T3SS apparatus) universal
FliO (T3SS apparatus) Undetectable in some systems
FliP (T3SS apparatus) - universal
FliQ (T3SS apparatus) - universal
FliR (T3SS apparatus) - universal
FliS (Cytoplasm) - Absent from Caulobacter
FliT (Cytoplasm) - Absent from many systems
FliZ (Cytoplasm) - Absent from many systems
MotA (Inner membrane) - universal
MotB (Inner membrane) - universal
So, not all bacteria have the full complement of parts. More to the point, some bacteria have parts missing that are found in others, and vice versa.
Plus, given that bacteria possessing mutations in some of the genes coding for the above proteins retain partial or total motility, the notion that the bacterial flagellum is "irreducibly complex" starts to look as if it is based upon less than rigorous foundations.
More to the point, when Nick Matzke published his original paper back in 2001, he hypothesised that various homologies would be found between the proteins of the bacterial flagellum and those of the Type 3 Secretory system. When those homologies were put to the test, his predictions were confirmed by experiment.
This later paper, which covers the known homologies in detail, continues with the following:
Pallen & Matzke, 2006 wrote: wrote:Many paths to motility
Although the evolution by random mutation and natural selection of something as complex as a contemporary bacterial flagellum might, in retrospect, seem highly improbable, it is important to appreciate that probabilities should be assessed by looking forward not back2. For example, from studies on protein design it is clear that creating proteins from scratch that, like flagellin, self-assemble into filaments is not very difficult39,40. Furthermore, it is clear that there are many other filamentous surface structures in bacteria that show no apparent evolutionary relationship to bacterial flagella41,42. In other words, there are plenty of potential starting points for the evolution of a molecular propeller. Evolution of something like the flagellar filament is therefore far less surprising than it might at first seem. In fact, microorganisms have adopted other routes to motility besides the bacterial flagellum43. Most strikingly, although archaeal flagella superficially resemble bacterial flagella, in that they too are rotary structures driven by a proton gradient, they are fundamentally distinct from their bacterial counterparts in terms of protein composition and assembly.
Intermediate forms
What about intermediate forms between bacterial flagella and other biological entities? Darwin encountered a similar argument about gaps in the fossil record, and in response he pointed out how improbable fossilization was, so that little of any extinct biosphere could ever be expected to appear in the fossil record14. Although fossils are of no use in reconstructing flagellar evolution, similar arguments might be made at the molecular level. Despite a decade of bacterial genome sequencing, we have scarcely begun to sample the molecular diversity of the biosphere. Yet even with the scant coverage of genome sequence data to date, several curiosities have already been revealed. For example, there is growing evidence that flagellin and the flagellar filament are homologous to the NF T3SS protein EspA and the EspA filament, respectively35,44–48. The EspA filament therefore provides a model for how the ancestral flagellar filament might have functioned for purposes other than locomotion (adhesion or targeted protein secretion). Furthermore, the EspA protein from E. coli initially seemed to be one of a kind. However, thanks to genome sequencing, related proteins have been identified in several bacteria occupying diverse niches, including: S. typhimurium, Edwardsiella ictaluri, Shewanella baltica, Chromobacterium violaceum, Yersinia frederiksenii, Yersinia bercovieri and Sodalis glossinidius. In addition, proteins that resemble flagellar components but that are encoded in the genomes of bacteria that do not engage in flagellar motility have also been identified. The first example of these potential ‘missing links’ came from the chlamydias[/sup]49[/sup]. More recently, flagellar-related genes have been detected in the genome of the soil bacterium Myxococcus xanthus, which uses gliding rather than flagellar motility35. It seems likely that other examples of potential evolutionary intermediaries will be found as we sequence an increasing proportion of the biosphere.
So we have evidence for the requisite homologies via genome sequencing. So the various workers who have been proposing an evolutionary model for the bacterial flagellum have been basing their work on observable facts as opposed to pure speculation.
The paper continues with:
Pallen & Matzke, 2006 wrote:Towards a plausible evolutionary model
From the above discussions of sequence homologies and modularity, it is clear that designing an evolutionary model to account for the origin of the ancestral flagellum requires no great conceptual leap. Instead, one can envisage the ur-flagellum arising from mergers between several modular subsystems: a secretion system built from proteins accreted around an ancient ATPase, a filament built from variants of two initial proteins, a motor built from an ion channel and a chemotaxis apparatus built from pre-existing regulatory domains (FIG. 1). As we have seen, each of these function in a modular fashion and share ancestry with simpler systems — thereby answering the question ‘what use is half a flagellum?’ Furthermore, it is not hard to envisage how an ancestral crude and inefficient flagellum, if it conferred any motility at all, could function as the starting material for natural selection to fashion today’s slicker flagellar apparatus.
However, one could still question how, from such bricolage, natural selection could lock on to an evolutionary trajectory leading to an organelle of motility in the first place, when none of the components alone confer the organism with a selective advantage relevant to motility. The key missing concept here is that of exaptation, in which the function currently performed by a biological system is different from the function performed while the adaptation evolved under earlier pressures of natural selection50. For example, a bird’s feathers might have originally arisen in the context of selection for, say, heat control, and only later have been used to assist with flight51,52. Under this argument, a number of slight but decisive functional shifts occurred in the evolution of the flagellum, the most recent of which was probably a shift from an organelle of adhesion or targeted secretion, such as the EspA filament, to a curved structure capable of generating a propulsive force.
More to the point, one line of experimentation being considered is the use of molecular phylogenetic analysis to reconstruct possible ancestral flagellar protein genes, and then demonstrate that the resulting ancestral flagellar proteins work. A precedent for this kind of experimentation has already been set by the following papers:
Crystal Structure Of An Ancient Protein: Evolution By Conformational Epistasis by Eric A. Ortlund, Jamie T. Bridgham, Matthew R. Redinbo and Joseph W. Thornton, Science, 317: 1544-1548 (14 September 2007)
Resurrecting Ancient Genes: Experimental Analysis Of Extinct Molecules by Joseph W. Thornton, Nature Reviews: Genetics, 5: 366-375 (5 May 2004)
Resurrection Of DNA Function In Vivo From An Extinct Genome by Andrew J. Pask, Richard R. Behringer and Marilyn B. Renfree, PLoS One, 3(5): e2240 (online version, May 2008)
The Past As The Key To The Present: Resurrection Of Ancient Proteins From Eosinophils by Steven A. Benner, Proc. Natl. Acad. Sci. USA., 99(8): 4760-4761 (16 April 2002)
From the 2008 paper by Pask et al above, we have:
Pask et al, 2008 wrote:There is a burgeoning repository of information available from ancient DNA that can be used to understand how genomes have evolved and to determine the genetic features that defined a particular species. To assess the functional consequences of changes to a genome, a variety of methods are needed to examine extinct DNA function. We isolated a transcriptional enhancer element from the genome of an extinct marsupial, the Tasmanian tiger (Thylacinus cynocephalus or thylacine), obtained from 100 year-old ethanol-fixed tissues from museum collections. We then examined the function of the enhancer in vivo. Using a transgenic approach, it was possible to resurrect DNA function in transgenic mice. The results demonstrate that the thylacine Col2A1 enhancer directed chondrocyte-specific expression in this extinct mammalian species in the same way as its orthologue does in mice. While other studies have examined extinct coding DNA function in vitro, this is the first example of the restoration of extinct non-coding DNA and examination of its function in vivo. Our method using transgenesis can be used to explore the function of regulatory and protein-coding sequences obtained from any extinct species in an in vivo model system, providing important insights into gene evolution and diversity.
So scientists are already resurrecting ancient proteins and testing their functionality in model organisms. Indeed, one of the results in the scientific literature comes courtesy of this paper:
Resurrecting The Ancestral Steroid Receptor: Ancient Origin Of Oestrogen Signalling by J.W. Thornton, E. Need and D. Crews, Science, 301: 1714-1717 (2003)
in which the scientists determined that the modern receptors for steroid hormones in modern organisms are traceable to an ancestral receptor dating back 600 million years, and reconstructed the ancestral steroid receptor in the laboratory to determine that it worked.
Returning to the present day bacterial flagellum, this paper:
The Bacterial Flagellum: From Genetic Network to Complex Architecture by Lucy Shapiro, Cell, 80: 525-527 (24 February 1995)
contains details of the assembly process that bacteria use in order to construct the flagellum. So it's not as if we're lacking in observable facts here.
Additionally, whilst still dealing with the "irreducible complexity" canard, another paper that is apposite is this one:
Axle-less F1-ATPase rotates in the correct direction by Shou Furuike, Mohammad Delawar Hossain, Yasushi Maki, Kengo Adachi, Toshiharu Suzuki, Ayako Kohori, Hiroyasu Itoh, Masasuke Yoshida and Kazuhiko Kinosita, Jr., Science, 319 955-958 (No. 5865, 15 February 2008)
Furuike et al, 2008 wrote:F1–adenosine triphosphatase (ATPase) is an ATP-driven rotary molecular motor in which the central γ subunit rotates inside a cylinder made of three α and three β subunits alternately arranged. The rotor shaft, an antiparallel α-helical coiled coil of the amino and carboxyl termini of the γ subunit, deeply penetrates the central cavity of the stator cylinder. We truncated the shaft step by step until the remaining rotor head would be outside the cavity and simply sat on the concave entrance of the stator orifice. All truncation mutants rotated in the correct direction, implying torque generation, although the average rotary speeds were low and short mutants exhibited moments of irregular motion. Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase.
In other words, the above scientists experimentally dismantled parts of a supposedly "irreducibly complex" rotation system similar to the bacterial flagellum, and found that the resulting partially dismantled entity still functioned.
However, let's put all of this aside for the moment and address a central issue that has never been faced by any ID proponents. Namely that the entire concept of "irreducible complexity" as erected by Behe was a canard right from the start, because he wasn't even the first person to alight upon such systems. The first person to alight upon such systems was the evolutionary biologist Hermann Joseph Müller, who did so way back in 1918. His paper in Genetics where this is first stated is the following paper:
Genetic Variability, Twin Hybrids and Constant Hybrids in a Case of Balanced Lethal Factors by Hermann Joseph Müller, Genetics, 3(5): 422-499 (1918)
The requisite quote can be found starting near the bottom of page 464 of that paper, and moving on to page 465, where it reads as follows:
Hermann Joseph Müller, 1918 wrote:Most present-day animals are the result of a long process of evolution, in which at least thousands of mutations must have taken place. Each new mutant in turn must have derived its survival value from the effect upon which it produced upon the 'reaction system' that had been brought into being by the many previously formed factors in cooperation; thus, a complicated machine was gradually built up whose effective working was dependent upon the interlocking action of very numerous different elementary parts or factors, and many of the characters and factors which, when new, were originally merely an asset finally became necessary because other necessary characters and factors had subsequently become changed so as to be dependent upon the former. It must result, in consequence, that a dropping out of, or even a slight change in any one of these parts is very likely to disturb fatally the whole machinery.
So, Müller alighted upon so-called "irreducibly complex" systems in 1918. He and other evolutionary biologists placed this on a rigorous footing by the 1930s, before Behe was even born. Behe's canard has been KNOWN to be a canard for over six decades. More to the point, Müller alighted upon these structures NOT as a "problem" for evolutionary biology, but as a natural outcome of evolutionary processes. The mechanism by which they arise is known as the Müllerian Two Step, which is described succinctly as follows:
[1] Add a component;
[2] Make it necessary.
Müller and other contemporaries placed this on a rigorous footing by the 1930s. Therefore Behe's "irreducible complexity" nonsense was known to be a canard by actual biologists the moment he aired it in public.
So, it looks as if once again, the hype surrounding ID doesn't withstand critical scrutiny. More to the point, real science is busy answering the assorted questions that are open in this area, as opposed to adopting the stance of "I can't figure out how it was done, therefore evolution couldn't have done it, therefore magic man".
