Saturday, January 7, 2012

Michael Behe versus N.J. Matzke: Hví eg enn haldi mína undirtøku av Michael Behe verða rætta

Áhaldandi í kjakinum millum menningarlæruna og tilhengarir av ID rørðsluni verður kjakast um upprunan av bakteriu flagelluni (bacteria flagellum). 
Framstandi ID forsprákarin Michael Behe er ivaleyst tann sum serstakliga befinnur seg í andglettinum. Áhaldandi verður pástaði, at Behe framleggur ein pástand sum als ikki vísir seg berandi í tí vísindaliga høpinum. Hesi pástanda ikki bara, at Behe er afturvístur, men harvið eisini at vísindafólk hava framlagt eitt betri alternativ.
Eg eri ikki vísindamaður og havi tí ikki førleikan at verja Behe, men haldi meg kortini kunna lugta tørvandi samanhengin í hesi viðgerðini av Behe.

Behe pástendur at upprunin av flagelluni byggir uppá nakað sum er alt ov komplisera fyri nátturliga menning, óansæð hvussu ótilvildarlig tilgongdin var. Ein kann sjálvandi dedusera út frá slíkum pástandi, at orsøkin var skapandi hondin, kraftin ella viljin hjá einum skapara gudi, men í veruleikanum sigur hetta ikki meira enn at orsøkin var intelligensur; onkur vildi kanska verið við at ein yvirklók rúmdarvera var orsøkin aftanfyri.

Í hesum innlegginum er tað ikki í mínum áhuga at verja Behe ella ID, men at vísa á greinina hjá N.J. Matzke (2003). 


Matzke leggur upp til at bakteriuflagellan er av evolutiónsuppruna, men kortini lýsir hann alternativi mótvegis Behe sum bæði tunt og líti undirbygt; eg haldi hetta verða djarvt og erligt av manninum. 
Ein dagføring av greinini sum var framløgd í 2006, er eisini at lesa á síðuni og vísir, at alternativi verður pástaði at standa eitt sindur sterkari trý ár seinni (tað vil siga í 2006).

So óvísindaligur sum eg eri, so síggi eg kortini ikki hví royndin at undirkasta bakteriuflagelluna menningarlæruna stendur so nógv sterkari enn pástandurin hjá Behe.

Hví?


Í greinini, lýsir Matzke í veruleikanum, ikki støðuna størst øðrvísi enn Behe gerð í bókini ‘Darwin’s Black Box’, har okkum er fortalt at menningarlæran stendur á nokso berum í samband við bakteriuflagelluna.

Hetta er sjálvsagt ein døpur mynd um ein er kensluliga bundin til menningarlæruna.

Fleiri mær vitandi, hava kritisera mannin fyri hansara óvitan um tað gransking sum vísindafólk hava gjørt áðrenn bókin ‘Darwin’s Black Box’ útkom. Ein av hesum var Duve sum breyt ígjøgnum við sínari kanning í 1995, men sum Matzke sigur um, mistók seg. 


Spurningurin er tí um Behe fer skeivur tá hann skrivar:

Yet here again, the evolutionary literature is totally missing. Even though we are told that all biology must be seen through the lens of evolution, no scientist has ever published a model to account for the gradual evolution of this extraordinary molecular machine (Darwin’s Black Box, síða 72)

Men Behe nevnir og viðgerð fleiri av hesum í bókini, eisini Cavalier-Smith, hvørs verk Matzke viðger út frá einum miseydnaðum gjøgnumbrotið í 2000 (fýra ár eftir at Darwin’s Black Box útkom). Behe sipar tó til skriving hansara um evnið í 1978 og Matzke sigur at vitanin um flagelluna um hesa tíð var lítil, sum eisini var høvuðs orsøkin til at royndin hjá Cavalier-Smith ikki eydnaðist.

Víðari dylur Behe ongastaðni at nógv er skriva um evnið:

‘The general professional literature on the bacterial flagellum is about as rich as the literature on the cilium, with thousands of papers published on the subject over the years’.

Við øðrum orðum, vísindafólk arbeiddu við hesum áðrenn Behe skrivaði bókina. Tó má leggjast aftrat, at tey heilt stóru gjøgnumbrotini vóru ikki útkomin tá bókin hjá Behe, ‘Darwin’s Black Box’ útkom í 1996.

Eisini má sigast, at tá ein so lesur Matzke, so hava granskarir innan menningarlæruna roynt við hópum av modellum og hypotesum at greiða frá flagelluni mótvegis ID pástandinum. Her hevur Behe møguliga ikki lisið hópin av greinunum, men í 2003 lýsir Matzke ikki støðuna so nógv øðrvísi enn Behe lýsir hana, og í hesum samanhengi haldi eg at viðgerðin hjá Behe kann nøkulunda undirbyggjast.

Nøkur slík dømir í greinini hjá Matzke staðfesta tildømis at:

1) Viðraking av bakteriu flagellum hevur skapt mikið postýr í tí vísindaliga heiminum:

‘The bacterial flagellum is one of the most striking organelles found in biology.  In Escherichia coli the flagellum is about 10 μm long, but the helical filament is only 20 nm wide and the basal body about 45 nm wide.  The flagellum is made up of approximately 20 major protein parts with another 20-30 proteins with roles in construction and taxis (Berg, 2003; Macnab, 2003).  Many but not all of these proteins are required for assembly and function, with modest variation between species.  Over several decades, thousands of papers have gradually elucidated the structure, construction, and detailed workings of the flagellum.  The conclusions have often been surprising.  Berg and Anderson (1973) made the first convincing case that the flagellar filament was powered by a rotary motor. This hypothesis was dramatically confirmed when flagellar filaments were attached to coverslips and the rotation of cells was directly observed (Silverman and Simon, 1974).  The energy source for the motor is proton motive force rather than ATP (Manson et al., 1977)’.

2) Víðari tykist tað, sum um Matzke pástendur, at vit hava ómetaliga gott innlit inn propelluna:

   ‘The bacterial flagellum is now one of the best understood molecular complexes’

Men hetta skal kortini ikki skiljast, sum um at vísindafólk hava framlagt eitt grundleggjandi kritiskt argument móti Behe, tí víðari skrivar hann:

although numerous detailed questions remain concerning the function of various protein components and the exact mechanism of torque generation.  However, the origins of this remarkable system have hardly been examined.  This article will propose a detailed model for the evolutionary origin of the bacterial flagellum, along with an assessment of the available evidence and proposal of further tests.  That the time is ripe for a serious consideration of this question is discussed below.


Við øðrum orðum, nógvir háfloygdir spurningar eru framvegis ósvaraðir, eisini í samband við mekanismuna sjálva. Somuleiðis í samband við upprunan av flagelluni, sum Matzke sigur um, nóg illa hevði verið vísindaliga kannað tá hann skrivar í 2003.


3) Harífrá uppstendur enn ein faktorur sum ID tilhengarir ivaleyst hanga seg í, tí Matzke lýsir støðuna soleiðis:


Biologists find it almost inescapable to compare the bacterial flagellum to human designs: DeRosier remarks, “More so than other structures, the bacterial flagellum resembles a human machine” (DeRosier, 1998).  The impression is heightened by electron micrograph images (Figure 1) reminiscent of a engine turbine (e.g., Whitesides, 2001), and the scientific literature on the flagellum is filled with analogies to human-designed motors.  There is no shortage of authorities willing to express mystification on the question of the evolutionary origin of flagella.  




In a 1978 review, Macnab concluded,
As a final comment, one can only marvel at the intricacy, in a simple bacterium, of the total motor and sensory system which has been the subject of this review and remark that our concept of evolution by selective advantage must surely be an oversimplification. What advantage could derive, for example, from a “preflagellum” (meaning a subset of its components), and yet what is the probability of “simultaneous” development of the organelle at a level where it becomes advantageous?” (Macnab, 1978). 
The basic puzzle is that the flagellum is made up of dozens of protein components, and deletion experiments show that the flagellum will not assemble and/or function if any one of these components is removed (with some exceptions).  How, then, could this system emerge in a gradual evolutionary fashion, if function is only achieved when all of the required parts are available? 
Her uppstanda jú fleiri punktir:

  • Vísindafólk vóru nærum tikin av bólið, tá hugsa verður um hvussu flagellan líkist einari maskinu sum uppstaðin er av mannahond.
  • Menning ljóðar sum ein yvireinfalding.
  • Spurningurin er hvussu maskinan var samla saman og hvussu hon kundi virka á einum sub-støði?
Men hetta er jú ikki so langt av leið skoti frá tí pástandinum, sum Behe hevur framlagt í bókini ‘Darwin’s Black Box’.

Um pástendurin mótvegis Behe í veruleikanum stendur so berður, hvussu forklára menningarfólkini so upprunan til og tilgongdina av menningini av flagelluni?

Her er at siga sum greinin hjá Matzke eisini leggur upp til, at sum tað grundleggjandi útgangstøði byggir pástandurin uppá menningarlæruna generelt sæð:

In order to explain the origin of a specific system such as the flagellum, the general theory discussed above must be combined with the available evidence in order to produce a detailed, testable model. 

Í mínum oyrum, ljóðar hetta sum reina spekulatión og var tað ikki spekulatión, var tað neyvan neyðugt hjá serfrøðingum at leggja á negativa holdningin, at hetta er “unwarranted speculation”.

 Detail in evolutionary scenarios makes them more testable, not less: Cavalier-Smith argues that “Specifying transitional stages in considerable detail is not unwarranted speculation, but a way of making the ideas sufficiently explicit to be more easily tested and rigorously evaluated” 

Víðari skrivar Matzke:

Furthermore, an evolutionary model might have testable implications for other fields: for example, if a biological system is hypothesized to be derived from a homologous system, similarities in mechanism between the two systems would be suspected.  The fact that we do not have all of the data that we would like, and that uncertainty is high, are not problems unique to evolutionary models; rather, these problems are commonplace in any advancing science.  For example, many contradictory models have been published for the mechanism of motor action in the flagellum, and most (or all) of them must be wrong, but this has not stopped anyone from proposing new models (Schmitt, 2003).  Science is advanced by proposing and testing hypotheses, not by declaring questions unsolvable.

Nú pástandi eg ongastaðni, at eg eri serfrøðingurin við teimum neyðugu førleikunum at afturvísa granskingini, men tað sum eg bíti meg í, er at granskarir ikki hava alt tað innlit (data) sum teir vildu var til taks og at óvissan er stór, somuleiðis at talið av mótstríðandi modellum er stórt, har í flestu ella allar, mugu (sum Matzke sigur tað) verða skeivar og hareftir, at nýggj modellir framvegis verða samansmíða.
Matzke endar paragraffuna við at siga, at í slíkum torførum dømum, mennir vísindin seg við framleggja og royna hypotesur heldur enn at geva upp. Eg eri samdur, men eg dugi bara ikki at síggja hvussu hetta afturvísur niðurstøðuni hjá Michael Behe.

Síðani framleggur Matzke tríggjar royndir at forklára bakteriuflagelluna við øðrum alternativum. 


Tann fyrsti er Duve:

A slightly more detailed attempt at explaining the origin of the bacterial flagellum was made by de Duve (1995), who apparently got the bacterial flagellum confused with the completely different eukaryotic cilium (also known as the eukaryotic flagellum or undulipodium in an interminable terminological dispute; see Corliss, 1980; Margulis, 1980; Cavalier-Smith, 1982).

Nágreiniliga royndin hjá Duve í 1995 royndist tí ikki so vísindaliga nøktandi.

Ein annar var Cavalier-Smith, sum seinni, eisini mátti bíta bitra veruleikan í seg. Hann náddi heldur ikki nógv longuri við sínari gransking í ár 2000 og mátti ásannað og viðganga at menningin av flagelluni mátti verða nógv meiri komplisera enn hann sjálvur grunaði:

Cavalier-Smith was hampered by the relatively primitive state of knowledge at the time, and he conceded that the actual evolutionary process must have been much more complicated than his suggestions. 

Triði veitarin var Rizzotti. Matzke skrivar at líka til 2003 var ískoti hjá Rizzotti tann einasta stóra royndin at forklára flagellu upprunan (hetta eru heili sjey ár eftir at bóki hjá Behe var útkomin):

The only major recent attempt at explaining the origin of the flagellum is that of Rizzotti (2000), which, like Goodenough, proposes that the flagellum was derived from the F1F0 ATP synthetase.  The initial appeal of this hypothesis derives from the spate of recent comparisons between the flagellum and ATP synthetase as proton-driven, rotary motors (Block, 1997; Boyer, 1997; Khan, 1997; Sabbert and Junge, 1997; Berg, 1998; Oplatka, 1998a, 1998b; Berry, 2000; Walz and Caplan, 2002), sometimes leading to the suggestion of homology (Oster and Wang, 2003). 

Men modelli hjá Rizzotto er heldur ikki uttan trupuleikar (uttan at fara út í detaljur her, eftirsum mær tørvar neyðuga innlitið, so latið eg bara tekstin hjá Matzke tala fyri seg sjálvan):

Additional difficulties with Rizzotti’s model exist.  While it is unrealistic to expect sequence similarity to give evidence for the ancestry of every component of the 3+ billion year old flagellum, considering the time lapse and large nature of some of the changes that must be postulated on any scenario, a scenario certainly should not contradict those homologies that have been identified.

If type III virulence systems are derived from flagella, what is the basis for hypothesizing a type III secretion system ancestral to flagella?  The question would be resolved if nonflagellar homologs of the type III export apparatus were to be discovered in other bacterial phyla, performing functions that would be useful in a pre-eukaryote world.

Matzke í dagføringini av greinini í 2006, sigur at ‘nonflagellar homologs’ eru funnin aðrastaðni:

 As I predicted in 2003, sequence studies have now confirmed homology between FliH/YscL and F0-b (and its equivalents in other ATPases). They also strongly indicate that F1-delta is homologous to the C-terminal domain of FliH; I did not predict this, but it does further confirm my more general prediction of “a strong possibility, previously unrecognized, of further homologies between the type III export apparatus and F1F0-ATP synthetase.”

Hetta sum hann sigur, veitir kortini ikki naka prógv, men styrkir tó (sum hann sigur) møguleikan fyri alternativinum. 


Ein annar trupuleikið er sum hann víðari skrivar:

However, I would retract some of my more speculative suggestions for ATPase homology to FliJ, FliO, and FliP (FliJ and FliO are apparently not even universally required in flagella). I am still hopeful regarding the suggestions for FliQ and FliR.

Trupuleikin er sum áður sagt, at granskarum tørva innlit og neyðug eygleiðing vantar; fara vit aftur til greinina frá 2003 skrivar Matzke:

That such an observation has not yet been made is a valid point against the present model, but at the same time serves as a prediction: the model will be considerably strengthened if a such a homolog is discovered.  For the moment, it is easy enough to explain the lack of discovery of such a homolog on the basis of lack of data.  Knowledge of microbial diversity is quite poor (Whitman et al., 1998): far less than 1% of bacteria extant in a particular environment are readily culturable (Hayward, 2000).

Her steðga so mínar viðmerkingar til greinina. Hevur onkur áhugan at lesa víðari, so eru linjurnar við reyðum tær sum staðfesta trupuleikar og veika støðið undir alternativinum hjá hesum sum framleggja eina flagellu uppruna orsøk aðra enn tað hjá Michael Behe:

“However, the type III secretion system exports proteins from the cytoplasm in one step.  By exporting a number of individual subunits, a short filament binding to the outer membrane pore can be formed, but its possible length will be severely limited by the decreasing chances of successfully adding monomers to the receding distal tip.  This problem might be overcome in a gradual manner by modifications to the open helix, so that it better corralled the monomers as they exited the secretin.

The flagellar motor is made up of two proteins, MotA and MotB.  MotB binds to the peptidoglycan cell wall, allowing the complex to serve as a stator.  MotB (and perhaps MotA) also forms a proton conducting channel.  Although the exact mechanism of motor function is still mysterious, with many proposed models (Berg, 2003; Schmitt, 2003), energy from the translocation of proteins in the vicinity of MotB is somehow transformed into mechanical energy to move the rotor.  Probably this occurs by conformational change in MotA, which then binds reversibly with the rotor protein FliG, causing rotation. Speaking very metaphorically, FliG appears to act like the teeth of a gear, converting (in one model) the power stroke of MotA into rotary motion.

No nonflagellar homologs of FliG have been discovered (except in type III virulence systems), perhaps not surprisingly given the peculiar function of this protein and the radical change it must have undergone, whatever its ancestral function. 

Once functional motility was even marginally established, however, there would be rapid selection for improvements.  These might have occurred in more or less any order, or concurrently, so they will be discussed topically.

A pre-existing sensory transduction system could be coupled to flagellar rotation in a single step on the hypothesis that a FliN-like protein existed for some nonflagellar cellular response purpose, serving as a receptor for CheC.  The exact function of modern CheC is not known, but it appears to interact with CheA, CheD, and McpB, which form a receptor complex (Kirby et al., 2001).  CheC may also have a FliM-like function via interaction with the C-ring (Szurmant et al., 2003).  The ancestor of FliN might therefore be found among the other proteins that CheC interacts with.

This form of protein subfunctionalization (Force et al., 1999) can probably explain the rest of the axial proteins as well: the hook (FlgE) might well have originated as an adaptor between the proto-rod and proto-filament in the very early flagellum.  As FlgE specialized for the hook role, adaptors for the filament (FlgK) and rod (FlgG) would have been produced from copied hook proteins.  The reason that the flagellum has three proximal rod proteins (FlgBCF) is not clear, but may have something to do with assembly checkpoints and coordinating the addition of the P- and L-rings at the appropriate moment. FlgB is the proximal rod component, interfacing with FliF via FliE (Berg, 2003); the relative order of FlgC and FlgF has not been determined, but perhaps one assembles while the P-ring is being assembled around it, and the other assembles coincident with the L-ring.  These components are highly conserved across all known bacterial flagella, probably because of co-adapted interactions between the components, but their dispensability for building a basic filament appears to be shown by type III virulence systems, where no rod homologs have yet been discovered (Blocker et al., 2003)

At this early stage of investigation this mixed bag should not be surprising.

the model can be falsified by discovery of homologies in unexpected locations: for example, if the proteins of the flagellar basal body are discovered to be homologous to proteins of the junctional pore of gliding motility rather than a primitive type III secretion system, then the entire model would be overthrown and replaced by a model relating these two systems.

The bacterial flagellum (and prokaryote motility systems in general) probably arose in large, coccus-shaped bacteria that were essentially modern in terms of complexity.  It is not necessary to suppose that the flagellum co-evolved with the cell wall and membranes before the last common ancestor of life.  This would be a much more difficult event to study in any case.