Flagellum evolution -- how's your German?

You should be able to cut and paste from the PDF into a text file, which you can then feed to an online translation service.

Looks like you can just upload the whole PDF here...
http://translate.google.com

...produces OK translation, better than I thought...

An algorithm for creationist argumentation.

..Enter ObservationA

..While ObservationA = TRUE

....Print Observation A, "proves God designed living creatures."

....If EvidenceSubroutine(ObservationA) = FALSE, then ObservationA = not(ObservationA)

..Wend

For example, spontaneous generation. When it was thought to be true, it was undeniable proof of God's creation. Now that we know it to be false, it is *lack* of spontaneous generation that is undeniable proof of God's creation.

At least this PDF is further proof that creationism isn't just an American lunacy. Takes the pressure off ... a little bit.

Chris Lawson said: For example, spontaneous generation. When it was thought to be true, it was undeniable proof of God's creation. Now that we know it to be false, it is *lack* of spontaneous generation that is undeniable proof of God's creation.

MrG said: At least this PDF is further proof that creationism isn't just an American lunacy. Takes the pressure off ... a little bit.

Chris Lawson said: When it was thought to be true, it was undeniable proof of God's creation. Now that we know it to be false, it is *lack* of spontaneous generation that is undeniable proof of God's creation.

Stanton said: Actually, I look at it more along the lines of metastasis.

John Vanko said: Sort of like interpreting the Bible, and coming up with innumerable denominations based upon diametrically opposed 'inspirations', wouldn't you say?

MrG said:

Stanton said: Actually, I look at it more along the lines of metastasis.

The spread of the disease is of course not welcome, but at least Americans are not uniquely prone to it.

Stanton said: Look at the various science departments at schools in the Middle East.

Similarly, the focus on tradition tends to promote xenophobia and reaction, not an interest in new ideas and ways of doing things. That hidebound mentality is reflected in a commonly-quoted statistic that more foreign literature is translated every year into Spanish than has been translated into Arabic for a millennium. The low quality of Arab schools similarly reflects this narrowness. A study performed by a university in Shanghai ranking the world's 500 best universities included one, repeat one, Arab university. The list included seven Israeli universities.

How conveniently like evolutionary cooption!

Glen Davidson said: Well sure, why do you think it's true that life looks designed?

Sadly, while I took German in high school, most of what I remember involves beer-drinking songs, which doesn’t help me out much here.

Karen S. said: I would think that drinking songs would be very helpful in dealing with this garbage.

The formation of the bacterial rotary motor is Unknown Siegfried Scherer Completing and updating the section IV.9.4 "Development of a molecular machine by evolution?" From "Evolution - a critical textbook" Stand: April 2010 © 2010 Community word study and knowledge e. V. www.evolutionslehrbuch.info In this text, an in-depth discussion of the issue of macro-evolution of molecular machines on the example of the bacterial rotary motor is presented. It supplements Section 9.4 of Junker & Scherer (2006). Reason for this is inter alia a speculative evolutionary scenario (Matzke, 2006) Nicholas Matzke1 that in drafting Section 9.4 was not known. Although this scenario is still not part of the scientific literature, but was published only in discussion forums and private websites, and despite the highly speculative nature, it is interesting for two reasons. First, before Matzke proposes a hypothetical way in which he can imagine the emergence of bacteria engine without all had to be essential parts of an irreducible complex machine simultaneously. This is significant. Second, it is m.W. still the only one on a mechanistic level proposal put to the emergence of a bacterial rotary motor. Junker and Scherer (2006, p. 162 review), that 16 proteins were needed for a bacterial motor, which must also be present. This view should be questioned in view of Matzke's model of evolution critically. If Matzke model the evolution of the bacterial motor model describes the issues raised by critics of evolutionary gaps in the imaginary evolution of the bacterial motor would be significantly reduced. That would be - all set out below, serious problems of Matzke's hypothesis - first of all a positive step evolutionary model regarding the formation irreducible complex biological structures. After a general introduction to the problems noted that the similarity relations a vast variety of bacteria engines casually referred to a descent from one or a few original, but already complex motors can be interpreted. Then, to explain why it is the bacteria Motor undoubtedly one irreducible complex structure, consisting of at least 20, but is probably more different proteins. On the other hand is represented differently from the popular, particularly in the U.S. ID-literature represented position, why this property of a biological structure is in itself a conclusive argument against evolution based on undirected processes of the bacterial motor. In the main part of the amazing multi-functionality of individual substructures of the bacterial motor, and the fact-based model of evolution are critically analyzed by Matzke. In the following analysis focuses on representing a single evolutionary step in the postulated formation of the bacterial motor, namely the co-opt an adhesion protein. This evolutionary step has been chosen because this is one of the easiest steps in Matzke's model. Only a single protein must be in the process of evolution by co-option and variation will be gained. Other steps in the hypothetical scenario Matzke are far more complex. The result of this detailed discussion is that it is unknown if and how co-option and by mutation in the course of the hypothetical formation of the bacterial motor, the gain would have a single adhesion protein may occur. This conclusion and the reasons were in terms of Matzke's model in the spring of 2008 on an interdisciplinary colloquium at the University of Regensburg for the first time presented (Scherer, 2009). Section 10 of the following text is largely from this source. In addition, to explain why the mechanisms of evolutionary channeling and limiting the variability of multiple functions by [p. 3] Occupied biological structures give rise to the presumption that postulated Matzke stages of evolution - even if they should be selektionspositiv itself - not easily represent basic functional states, leading from a primitive type 3 secretion via the smallest of steps towards a bacterial rotary motor. Matzke's model is generally not reliable and convincing hypothesis to evolution of the bacterial motor. Consequently, she was introduced today in the scientific literature not yet discussed. Matzke themselves have chosen not to present his hypothesis in his publication for the bacterial motor, which was published in a refereed scientific journal, (Pallen & Matzke 2006). The detailed discussion of the various changes that for a co-opted an adhesin protein are probably required, there is evidence of specific research projects that might help to solve a postulated evolutionary path of the emergence of bacteria engine are carried out. Whether a decrease based on experimental data and expected future progress of knowledge of existing problems or declaration will increase is not to say at present. The result of this discussion highlighted a gap in knowledge evolutionary research. Elsewhere, it was explained why such gaps are no compelling arguments against the evolution of a bacterial rotary motor, or the existence of a designer are (Scherer, 2009). It is striking how much has been increasing in recent years the use of concepts from the engineering sciences in molecular biology. Mike Gene (2007) has described in detail. Already nearly 10 years, Lowe (2000) follows this fact to the point: "The molecular machinery of nature outperforms anything that mankind currently knows how to construct with conventional manufacturing technology by many orders of magnitude. ... Almost without exception, there exist analogues of conventional functional biomolecular devices, including structural components, wires, motors, drive shafts, pipes, pumps, production lines and programmable control systems. " Regarding the intestinal bacterium Escherichia coli, says Howard Berg (1999): "In addition to rotary engines and propellers, E. coli's standard accessories include particle counters, rate meters, and gear boxes. This microorganism is a nanotechnologist's dream. " The term "molecular machine" has now become so familiar to biological functions of the cell to beschreiben2 that he is indispensable in the literature. These machines are ribosomes Splicosomen, degradosome, protein complexes in DNA replication play a role (eg, helicase and DNA polymerase), the F1/F0-ATPase, the kinesin-machinery and much more (for B. Gene 2007). A look at modern textbook of biochemistry (Berg et al. 2007, Lodish et al. 2007) and Cell Biology (Alberts et al. 2008) is sufficient to be convinced of this fact. The bacterial flagellum is the molecular machine with the greatest name recognition, as it has played in the U.S. in recent years a prominent role in social policy discussions. Their structure and hypotheses for their formation are the occasion of the court processes to intelligent design has been discussed worldwide. A molecular geneticist, who has looked a whole life with this engine researcher put it, already nearly 20 years (Macnab & Parkinson 1991): "We need to think almost in engineering terms about transmission shafts, mounting plates and bushings - unfamiliar grounds for the microbial geneticicst." Today is not such an unusual mode of expression, but the rule. For example, two years ago, a work relating to the motor in bacteria Journal of Bacteriology, entitled "Fine structure of a fine [p. 4] Hazard, an advantage. Many bacteria can move actively in various ways (Jarrell & McBride 2008) and some provide for this purpose on a rotary motor. Each engine requires a controller. These include sensor proteins (which may, for example, nutrient molecules such as sugar seen in the cell environment, is there a certain extent to the "nose" of the bacteria), signaling proteins transport (they received environmental signal to the motor) and control proteins (for direct control of the motor). Bacteria were found in engines of different type of construction. The E. coli motor is tested for genetic and biochemical level best. We now know that it included installation of cellular proteins (which help in the assembly of the engine, see Chevance & Hughes 2008) of about 40 proteins is formed (but see Box 1). The control contained by chemotaxis (overview eg in Wadhams & Armitage 2004) is carried by less than 10 proteins. With the help of molecular biology and electron process could explain the basic structure of the molecular motor (Fig. 1). A bacterial motor function consists of five basic elements: the filament (flagellum) or the "propeller". By rotation of the filament flexible VorMöglicherweise the number of proteins in the synthesis or function of the bacterial motor play a role is underestimated. This is clear from a study by the investigation of a yeast two-hybrid test interactions of known motor proteins with other proteins in Treponema pallidum (the causative agent of syphilis), Campylobacter jejuni and Escherichia coli. Surprisingly, there was evidence of more than 100 proteins that interact with motor proteins. Because such tests can give false-positive results, an experimental analysis of the predicted interactions is necessary. For Escherichia coli, this analysis was performed on a Deletionsmutantenbank and found 159 deletion strains that showed a Motilitätsdefekt. Among the affected genes, there were 43 known Motilitätsproteine. The significance of the remaining 100 genes for the synthesis, structure and function of the engine is often unclear. There may be unknown, in addition to motor proteins, to genes that have an indirect effect on motor function (eg via the formation of energy-proton). Maybe it has to do with the fact that the fumarate reductase in Escherichia coli Respirationsprotein interacts unexpectedly with the control of the bacterial motor. From such data one must conclude that we know about the bacteria engine not much. All speculation about the evolution of such a structure are regarded with skepticism for that reason. This also applies to the statements in this article. machine "provided (Blair 2006) and recently the same group a" coupling "of the bacteria, Gram positive bacteria found in motor (Blair et al. 2008). One can hardly avoid the impression as if the phenomena of life on a biochemical and cell biological level could best be described in terms of engineering and computer science (eg, Nurse 2008). I think it is an open question whether life is at its molecular function relationships without such concepts at all, to adequately determine kann.3 The philosopher of technology Mutschler HD has this problem discussed in detail and pointed (Mutschler, 2002, Mutschler 2003). Bacteria are dependent for their growth, absorb nutrients from their environment. This may prove advantageous if the cell can move in a concentration gradient in the direction of a nutrient source. On the other bacteria are exposed to negative environmental influences, such as toxins. Here, too, is an active movement, away in this case by the [p. 5] operation of the bacterium produces, it is mainly from about 20,000 copies of the protein flagellin built. This protein in turn consists of several hundred amino acids, its amino acid sequence and the corresponding gene sequence is known. This filament is coupled by a bend (link element) to a rotation axis which is of camps in the cytoplasmic membrane and the cell wall of bacteria cell held in place. The genes that code for proteins of the axle and the bearing are largely unknown. The rotation axis and thus the bacterial flagellum is placed on drive proteins into rotation. The engine is driven by the energy that is stored in the proton gradient across the cytoplasmic membrane. This proton gradient generated outside the cytoplasm to a positively charged environment. The potential gradient (= membrane potential) of approximately 0.2 V. Figuratively speaking, the bacterial cell is a "0.2 volt battery, which can drive these" NanoElektromotor. Important reviews on the structure, biosynthesis and function of the bacterial motor comes from eubacterial Macnab (Macnab 2003, 2004, Jarrell 2009). A very brief but informative overview is given in Berg (2008). This work also shows how much of the bacteria engine not yet be Michael Behe has the bacterial rotary motor known as a clear example that one could make the work of an intelligent designer of biological phenomena sense pin down (Behe, 1996): A bacterial motor is irreducible complex and therefore could not result from a natural process of evolution. On the contrary, the existence of such a structure could be the inference to an intelligent designer. Behe has put forward "Darwin's Black Box," a popular science book, which is an important foundation for the aspirations of the Discovery Institute in Seattle was to bring the perspective of Intelligent Design (hereinafter abbreviated as ID) in the curricula of public schools. Thus, the "bacterial outboard" of some bacteria become an unexpected popularity. In the wake of this popularity, a number of biologists contradicted the views of Behe: The bacteria engine is neither irreducible complexity, yet it is unclear how it arose. On the contrary, could the evolution of this biological nanomachine by known evolutionary mechanisms now explained very well and not be questioned more reasonable (eg Musgrave 2006; Miller 2007; Pallen & Gophna 2007). This view was reflected hasty and not very popular in the literature included (eg, Hemminger, 2007, Jones 2008). The most important design publication, which Behe criticized on a scientific level is provided by Matzke (2006), because the model is the only sufficiently specific to a mechanistic, theoretical examination accessible. Pallen & Matzke (2006) also have a readable critique of Behe argued that in much, however, arguments from comparative Figure 1 Schematic drawing of the bacterial motor of Escherichia coli associated with some of the structural proteins (from Junker & Scherer, 2006). [p. 6] Biology is based and discuss any questions mechanisms. Sikorski (2009) took the model of Matzke without any critical debate, in this respect rightly, however, the observations of Junker and Scherer (2006) on the evolution of the bacterial motor in question. Musgrave (2006), Miller (2007) as well as bracing and Gophna (2007) criticize the view that the flagellum irreducible complexity and therefore be understood only by intelligent design, but the above arguments focus on the multifunctionality of the flagellum, as well as on findings from the comparative biology and in the core of Matzke (2006) and Pallen and Matzke (2006) summarized. For this reason, in this paper mainly discusses the latter two works. ID proponents have defended their position on the flagellum, for example, Behe (2004). The work of Smart and Bracht (Smart 2003), but especially the extensive analysis by Mike Gene5 (2003) are scientifically very well over Behes also quite popular text that can be criticized no doubt with good reason. Mike Gene's work is about the size of a 100-page book and sets the standard by which all scientific discussion based on the origin of the bacterial motor needs. While I know of no case, where Mike Gene's been critical, purely scientific explanations of evolution representatives are discussing, but I should have overlooked a text published on the Internet, I am grateful for a hint. (The discussion in Internet forums is confused and hardly manageable, and make many contributions even miss rudimentary skills.) First, it is gratifying that the dispute from both sides now with technical arguments are held. I write "well" because I can not help but talk about the surprise my style of some colleagues to give expression. Not infrequently, speech and argument are a strikingly emotional, polemical, and sometimes even personally insulting, sometimes you even think of having to exercise fanatic traits. That goes for both sides - and, unfortunately, this style is already arrived in Germany. One may explain the fact that basic philosophical issues are under discussion. An apology is not tolerated and certainly not for the failure of editors that such a level of argumentation would never dürfen6. On different occasions I have expressed my wish that the drift of the discussion on an ideological level, at least in Germany might still be prevented. Criteria for what makes an ideological argument, I have called elsewhere (Scherer 2006b). This wish, I can only repeat, together with the regretful conclusion that the counterparty in the U.S. in this respect is not a good role model sind7. From the few, on a scientific level, limiting work to 1st What are the consequences of the barely manageable variability of different bacterial motors for its existence? 2nd Is a specific bacteria engine from a specific bacterial species in general a non-reducible complex structure? 3rd If it would be possible to establish credible for a given biological structure, the non-irreducible complexity: Does it follow necessarily that they can not arise through evolutionary processes? 4th How important is the fact that some proteins of the bacteria Motors similarities to proteins that carry out elsewhere in the cell a different function? 5th What is the significance of multifunctionality of the bacterial motor or its components for hypotheses about its evolution? 6th Can the probability of formation of a bacterial motor can be estimated? 7th Behes critics have a reliable, plausible theory for the evolutionary origin of a bacterial rotary motor proposed? [p. 7] Formation of a bacterial engine results in a series of questions, which are summarized in Text Box 2. These are treated separately to allow maximum clarity. The main objections to these questions will be taken up and discussed briefly. The reader should be familiar with the contents of the chapter "Molecular mechanisms of evolution" (Junker & Scherer, 2006). Pallen & Matzke (Pallen & Matzke 2006) right when they write: "There is no such thing as, the 'bacterial flagellum." We now know - and not just since complete genome sequencing - to the almost unmanageable diversity of different bacteria motors ( Jarrell & McBride 2008). 4.1 Verschiedene engine types in eubacteria Bacterial motor proteins can be extremely diverse with the same basic blueprint of the engine. This goes to the point that some motors are driven by proton gradient and other Natriumionengradienten (Asai et al. 2003). Both engine types are sometimes in a single cell before (Paulick et al. 2009). Na +-driven motors turn with much greater speed than Protonengetriebene engines and can be up to 100,000 rpm quickly. The protein FliL is another example. The exact function of the protein is still unknown, but it is essential for the SchwärmerPhänotyp Salmonella and E. coli (Attmannspacher et al. 2008). First, it is striking that this protein is highly variable. For example, Caulobacter crescentus FliL proteins of Escherichia coli and have only about 25% similarity (Yu & Shapiro 1992). Obviously, the functions of the proteins are different, because E. coli does not result in a knockout of the gene to a significant impairment of locomotion (see above), while a knockout of C. crescentus has FliL in a non-motile (immovable) phenotype (Jenal et al. 1994). Proteus mirabilis has not motile and this one, or otherwise disturbed phenotype when FliL is turned off (Belas & Suvanasuthi 2005). For Caulobacter and Proteus - but not for Escherichia! - Obviously belongs to this protein complex irreducible Kernproteinset of the engine. This points to different versions of the engine type. In the Eubacteria8 a rotary motor has been found in 8 of 19 phyla (tribes). All Enterobacteriaceae (which include, for example, E. coli and Samonella) have a similar type of engine. But beyond the construction of engines Gram negative and Gram positive bacteria is significantly different. The functional necessity of this is immediately obvious because the former have an outer membrane of the latter are not. Still other rotary engines are found in the spirochetes, which their flagellum between cytoplasmic membrane and outer membrane around the cell body wrap "", these allow for a total of rotation and the entire bacterium is similar to a screwdriver, very effectively through the medium winds (Murphy et al. 2006). These bacteria and molecular motors are built quite differently. Table 1 and in bracing Matzke (2006) illustrates this fact very clearly. There is now good evidence that different bacteria, although not in the core proteins of the engine (see below), but differ greatly in "accessory" Motilitätsproteinen (eg Rajagopala et al. 2007). Overall, the variability of bacterial rotary engines to be unmanageable. 4.2 Comparison of homologous motor proteins In principle, all eubacterial flagella share a common basic structure. However, subject to all parts of engines of evolutionary variation. This means that point mutations, deletions, duplications, the exchange of genes with other bacteria through horizontal gene transfer (Ren et al. 2005) and more intended. An introduction to such evolutionary processes is in Junker and Scherer (2006, Chapter 9.1) given. Within a single engine type it is therefore likely to be uncounted millions of variants. Individual motor proteins can change very quickly if they are recognized by the immune system of the host and thus subject to extreme selection pressure. An example is flagellin, the main protein of the filament [p. 8] (Beatson et al. 2006). However, especially some of mechanically not as heavily used, outward-facing domains of Flagellinproteins are so variable. Sometimes even come in a single bacterium in different flagellin (Ely et al. 2000, McQuiston et al. 2008), which can be explained by diversifying selection after gene duplication or horizontal gene transfer (see disruptive selection, Junker & Scherer 2006, p. 70 ). This finding graded similarity applies not only to the flagellin, but for all motor proteins. In fact, it looks as if the homologous sequences of key proteins of the flagellar motor is a continuum of different eubacteria show sequence similarity. This finding can be explained by an evolutionary relationship suggests - more precisely: it is a direct consequence of the evolutionary origins hypothesis. A mechanistic objection, for example, that today would have been flagellins from a common Vorfahrenprotein (which, however, already part of a complex motor), are formed by gradual evolution seems not to lie, at least at hand. Maybe dip the problems only appear when one examines such a question in detail. Whether all of today's engines have eubacterial rotation by known evolutionary processes can develop from a common ancestor, but is not part of the current discussion. This is about where the "first" engine comes in this ancestor. The observed, graded similarity of motor proteins from different species can be interpreted well by evolutionary descent. 4.3 similarity of motor proteins with proteins of other function Another similar argument relates to proteins of the bacterial motor, which are not similar to proteins of another engine, but to other proteins function. Pallen & Matzke (2006) have led a series of examples. is an illustration of this point, singled out one case (see also Chapter 8). Central to the flagellar motor is the implementation of the proton gradient across the cytoplasmic membrane energy stored in a rotational movement of the motor shaft. Therefore, the two motor proteins MotA and MotB are responsible. Several MotAB complexes are arranged in a ring around the motor axis (Fig. 2A). They belong to the stator of the motor and are anchored to the cell wall via MotB. MotAB part of the complex is a proton channel, which converts the energy of the proton in a conformational change of MotA. This is then transferred to the axis of rotation of the engine and put the axle in rotation (Fig. 2B). The sequences of MotA and MotB are known. The comparative search in sequence databases showed that MotAB have a low but detectable sequence similarity with the proteins TolA and TolQ and ExbD / TonB. These proteins are also anchored in the cytoplasmic membrane, have a proton channel and have binding affinities to the outer membrane or the cell wall. TolAQ play a role in cell division, while ExbD / TonB are transport proteins (Cascales et al 2000, Cascales et al. 2001, Gerding et al. 2007, Zhai et al 2003). If one assumes TolAQ or ExbD / TonB than initially, then one could speculate that these proteins have been co-opted for the construction of an engine. Whether such, from similarities of developed process of evolution is mechanistic at all possible, however, was never investigated (see Section 10). Figure 2 Schematic representation of the arrangement of the drive elements MotAB to the hollow motor shaft (A) and sketch to explain how a conformational change is converted into MotAB in a rotational movement of the motor shaft. Secretion injectisome axis of rotation [p. 9] 4.4 Interpretation of similarities After Pallen and Matzke (Pallen & Matzke 2006), the variability of the eubacterial rotary engines as well as these common basic structure have described, they come first to the conclusion that intelligent design have difficulties to explain the presence of different engine types. You ask how many procedures the designer one should assume for now if you wanted to postulate a Schöpfungsereignis11 for each engine type. Or if one does not need to accept based on these data, that all rotary engines have diversified from an ancestor through evolution, because "all show sequence similarity flagellin indicative of common ancestry (homology). Pallen & Matzke question is justified and indicates a serious problem of ID: a concrete, coherent and scientific criteria and interpretation of diverse variable bacterial rotary engines as part of Intelligent Design (or a "creation model") as an alternative to a descent of the day this flagellar motors of one or a few ancestors has not been submitted. The underlying problem is the lack of a "General Theory for Organic Design" and is generally applicable to biological observation of nature. The theme has also Paul Nelson as an important representative of ID: "Easily the biggest design challenge facing the ID community is to develop a full-fledged theory of biological. We do not have such a theory right now, and that's a problem. Without a theory, it's very hard to know where to direct your research focus. Right now, we've got a bag of powerful intuition, and a handful of notions such as 'irreducible complexity' and 'specified complexity' - but, as yet, no general theory of biological design. "(Nelson 2004) Pallen and Matzke (2006) ask further, now that they postulate an on core proteins (see below) reduced Urflagellum: "This reduced flagellum is still a challenge to explain, but if one accepts that all current flagellar systems diverged from their common ancestor last (the ur-flagellum), why stop there?" The first question is justified and will be discussed below. Is there a tangible difference between the biological hypothesis of the origin of today's Flagellenmotorvarianten a Urflagellum and the emergence of a Urflagellums from unknown precursor structures? Michael Behe has proposed that it is the bacteria engine is a non-reducible complex structure. He defined a non-reducible complex system, first as follows: "... a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. "(Behe 1996) In other words, all belonging to a non-reducible complex structural parts necessary for its function, other functions of sub-structures of irreducible complexity are therefore not excluded. 1.5 Arguments for the irreducible Complexity of the bacterial motor of the experimental molecular genetics The experimental proof that a specific biological structure is indeed irreducible complexity, and above all to answer the question of how complex it actually is quite expensive. In a simple structure based on a targeted mutation approach is then successful if (a) of the genetic blueprint of the structure sufficiently precisely known and (b) of the organism genetic engineering is available. When bacterial motor of enterobacteria, Escherichia coli and Salmonella which are, in principle, both conditions are met. That means you can turn off individual genes coding for the engine, by targeted mutagenesis in several ways. Such mutants also called "knockout mutants. When the engine no longer works ("non-motile phenotype"), was the gene for the motor function is essential. [p. 10] Sometimes a deliberately turned off Motorgen not lead to loss of motility. Either it really was not essential. But it could have been replaced by another protein of the cell. The simplest explanation for the latter would be that the relevant gene or segment of the chromosome is duplicated and the duplicate in a knockout mutant may take over the function. We have recently found the pathogen Yersinia enterocolitica that there are duplications of genes and knock out mutants of Flagellenoperons individual genes do not always function. The importance of such duplications, which are also found in some strains of E. coli, but hardly studied. On the other hand it could be that the function of motor proteins selectively turned off by such proteins in the cell, so to speak "over makeshift" that have a remotely similar function. Paul et al. (2008) constructed a five-knockout mutant, which three ATPase / secretory fliHIJ lack of the flagellum, but it also contained two ATPase-related protein type 3 secretion systems (INVC and Sansandi). The mutant was slightly Schwärmassay Motil, but far less than the wild type. If these three motor proteins that are not essential for motor function? Galan (2008) discusses this issue and advises caution, because it could be that other ATP hydrolyzing proteins from the cell coupled to the secretion apparatus and cause a partial complementation of protein. In Beau's meaning could be the exciting findings of Minamino et al. suggest that in the Zweifachmutante DfliHI found a partial Suppressormutation, which turned out to be a point mutation at the protein FlhB. This protein is part of the "lock" of the secretion injectisome, bind to the FliH and FliI may. A mutation in this protein might bind the imperfect one unknown, complementing protein to improve the secretion apparatus and thus lead to "partial repair" the secretion of motor proteins. Additional mutations would probably lead to further optimization (the principle is in Junker and Scherer 2006, p. 143ff) explains at the end could be a successful co-option of an existing protein. However, this scenario is highly speculative and the Declaration of Suppressormutation could also be quite different, even to remain in the comparison of the phenotypes of the different mutants constructed some questions unanswered. These and similar processes (one could cite many other examples) are often referred to by evolutionary biologists with the rather negative-sounding term "patchwork". One can formulate the findings also positive and understood as an expression of a widely interconnected and highly robust system that has a high degree of built-in potential variability, providing maximum security, so that the cell survival even under adverse conditions still kann.10 The Most of the genes encoding the bacterial motor, were in this way, but initially found by chance. It has been collected previously immovable mutants and to investigate in which genes they were mutated. This engine had to be genes. Today it is partially targeted before, identifies possible engine genes by sequence similarity and then turn them out in order to investigate its effect on the motor structure and motor function. In most cases it is found that has the engine off of an immovable phenotype result in genes. Set an example Chaban et al. (2007). The authors work with the Methanococcus maripaludis Archaebakterium9. Because the genome sequence of a suspected Flagellenoperon was identified. The authors targeted the genes switched FlaB1, flaB2, flac, FlAF, flag, and FLAI flah directed by deletion (loss) and found that all mutants were motionless and showed under the electron microscope no hostages. The genes were therefore essential for motor function. A similar experiment reported (Allan et al. 2000) for the pathogen Helicobacter pylori, the genes Flife, Flis, flhB, fliQ, FliG and FliI also proved to be essential. A comprehensive such experiment conducted (Rajagopala et al. 2007 through), they found in Escherichia coli more than 100 genes that influence the motility (see text box 1). Overall, through such experiments that many genes of a specific bacteria are essential engine, but there are definitely exceptions. (Yokoseki et al. 1995) show, for example, surprised that were motile after knockout mutants of genes flis engine and flit as before, although there is agreement about the fact that these genes are part of the bacterial motor. This can have two causes: either these genes are not [p. 11] essential. Then they do not belong to the potentially non-reducible complex structure, it would thus be built was easier than expected, perhaps. But it could also be that the rejected genes are replaced by other genes of the bacterial cell, in other words, the cell is about the function of such genes redundant. Then no safe conclusion would be possible if the protein is essentially turned off or not (see Box 3). Of particular interest are mutants in which the mobility is not turned off, but is reduced. An example of this type Attmannspacher et al. (2008) for Salmonella enterica. These authors have eliminated the protein FliL, which is localized in the flagellum basal body (shown graphically in Figure 8 of Attmannspacher et al. 2008). They report that the mutants have only a limited ability to swim in liquid medium, it can no longer swarm (in schools refers to the flagella caused by movement on viscous agar surfaces). Undoubtedly fliL not an essential gene of the engine, although it is the first gene in a central Motoroperon. Presumably, it contributes to the mechanical stability of the engine at under high-viscosity conditions. Another example is the gene flaB3 the above aforementioned Methanococcus maripaludis (Chaban et al. 2007). A deletion of this gene led to the movement in circles, the targeted nature of the movement was so disturbed. The electron microscopic analysis showed that flagella were trained, who lacked the "hook" structure (the elbow). The Geißelfilament was with these mutants have been grown directly on the axis of rotation, which has not resulted in a completely inoperative engine. In evolutionary terms this is a very interesting finding. flaB3 is therefore not essential for a rotation of the engine. Does this engine, which only leads to a stochastic motion of the cell, perhaps a selection advantage over the mutant cells isogenischen result, the engine can no longer be made? If you could clarify this experimentally, and if the answer was positive, one could imagine the irreducible complex Motorstrukt ur simply a gene. In most cases, including in the case of a specific bacteria Motors, can probably be said only ensures that a biological structure with regard to a given function contains a non-reducible complex core. The term "irreducible core" is by Dembski, who developed the definition of Behe on, but again a very popular level (Dembski 2007). Joshua Smart has applied this definition clearly detailed on a bacterial engine (Smart 2003). Mike Gene has brought the argument to be a subject-specific level (Gene 2003). This enhancement of the Beheschen argument was in a case known to me also recognized by evolutionary biologists (Musgrave 2004). How many genes includes such a core, in the case of a specific bacteria could be estimated experimentally accurate engine, but only at high costs (Box 4). Overall, one can first say that the assertion, a concrete biological structure is non-reducible complex in principle be experimentally tested by knockoutMutanten. If one second, the feature "irreducible complexity" by Behe (above) defines and applies to bacteria engines, then contain an irreducible complex core structure of several essential components, because many proteins that form a given bacterial motor, can not be eliminated definitively, without the motor function is completely destroyed (see below for other functions). How many essential proteins could contain a given bacterial motor, is discussed in the next section. 5.2Argumente the irreducible complexity of the bacterial motor from comparative biology through comparisons of different structures with similar functions ("similarity search") you can get important information about the necessary ingredients for a real function. Pallen & Matzke write: "Despite this diversity, it is clear that all (bacterial) flagella share a conserved core set of proteins. Of the forty or so proteins in the flagellum of S. typhimurium standard strain LT2 or E. coli K-12, only about half universally seem to be necessary. "(Pallen & Matzke, 2006) [p. 12] Mike Gene (2003) three years earlier a similar analysis is undertaken and concludes that 21 proteins may have belonged to a core set hypothetical original flagellum. He calls this the flagellum "UR-IC-flagellum," which set in about the "core" of non-reducible complex structure of all eubacterial bacteria could reflect motors. Liu & Ochman (2007b) come in a recent study found that the core set consists of 24 genes. Liu & Ochman (2007b) show in the supplementary material of their PNAS article (see below more on this article) a table with the analysis of 41 fully sequenced bacterial genomes, which contain flagellar genes. I have plotted the number of flagellar against the total number of genes in the respective chromosomes (Fig. 3). It is clear that no correlation between genome size and number of flagellar exists. Given the well-founded assumption that small genomes reductive evolution is likely, which avoids non-essential genes by deletion, and this result suggests that the complexity of today's (!) Bacterial rotary motor can not fall below a certain threshold. Analyses must take into account, however, that are found by homology search, not all the genes necessary for motor function, so that the number of genes essential engine may be underestimated. The small group of genomes with about twice the number of motor genes indicates cases in which motor genes were duplicated, or where two different engines available per cell. The fact that both can occur has been demonstrated experimentally. Liu and Ochman have recently been presented to a vergleichendbiologische analysis showing that there has been duplication of the flagellum genes after a much different, line-specific evolutionary disintegration of these genes (Liu & Ochman 2007a). Such comparisons are fraught with some methodological problems to which there can not be discussed in more detail, but at least they allow some basic insights. One can state that there is an extraordinarily large number of quite different bacteria eubacterial engines, and that these contain a common set of proteins. Probably has the number so obtained merely indicates a lower limit of the complexity of today's bacteria engines. The methodology requires only the proteins associated with a core set, which occur in all investigated engines. This comparative method (can not decide a) whether the other form, for each engine belonging to different proteins and essential components that are designed differently for different motors. You can (2) decide not even decide whether in the given case, all 20 proteins of a Core sets are really essential. These questions can only be clarified through a research program carried out separately for each engine type (see text box 4). Of the combination with the knockout experiments discussed in Section 5.1 for the construction of functionless mutants it would not be surprising if 20 proteins are essential for a given motor are bacteria. It does not matter at first whether the Filamentkonstruktion or protein secretion or other important function of the motor is affected by the mutation. Today, existing bacteria motors contain a non-reducible complex core of about 20 essential proteins, as defined by Mike Behe. It is not easy to determine the exact number of essential proteins, and it could be different for different types of bacteria. Figure 3 Number of bacterial genes in motor function of the genome size of different bacteria. Data from Liu & Ochman (2007) [p. 13:00] The transported popular core argument of ID is a direct conclusion about the existence of a non-reducible complex system to its non-Evolvable. Mike Behe wrote: "An irreducibly complex system can not be produced directly by numerous, successive, slight modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition non-functional. .... Since natural selection can only choose systems that are already working, then if a biological system can not be produced gradually it would have to arise as an integrated unit, in one fell swoop, for natural selection to have anything to act on. "(Behe 1996 ) In further steps the ID concept then includes the gradual non-Evolvable a structure to the existence of a designer. Although it may be true that an irreducible complex structure like the bacterial motor can not arise through evolution, and although it may be true that the bacteria engine can come only through "design" into existence, both conclusions are mE not in the horizon of scientific knowledge analysis (Scherer 2008b, see also footnote 11). The question of Evolvable a non-reducible complex structure is central to the historical evolution and should generally be answerable with the results of causal theories of evolution, which is further discussed below. It is first noted that Behe, like many writers of textbooks of evolution, only the Darwinian mechanism of evolution by mutation and selection considered. Of which will be discussed later. But even under this restriction, the situation turns out to be complex, which Behe, however, has recognized for over 10 years himself, when he writes: "not demonstrate that a system is irreducibly complex is a proof that there is absolutely no gradual route to its production . Although irreducibly complex system can not be to produced directly, one can not definitively rule out the possibility of an indirect, circuitous route. "(Behe 1996) In other words, there is no way around it, is concrete thoughts about the plausibility to make possible evolutionary paths that can range from very simple structures with well-known variation processes to so you do not yet say exactly how many essential proteins includes a specific bacteria engine. In principle, this number could be estimated but experimental. The research needed for this would include approximately the following steps: -Choose one specific organism, such as Escherichia coli -Identify (based on experimental data or in silico) all the genes involved in synthesis of the E. coli flagellum might play a role. -Create from any putative flagellum a markerless gene deletion in a Einfachmutation. Lay-down experimental procedure to test the functionality of the bacterial motor (eg, light microscopic observation, Motilitätsassay, swarming assay, electron microscopic analysis). -Define a standard by which a cell as a portable, movable or reduced non-mobile will be classified. -Diagnosis of any mutant on mobility: (i) the mutant motionless, then the gene was essential. (Ii) If the motion in whole or in limited availability, then the gene could not be essential. -Check if a mutant, whose mobility is not or only partially destroyed, possibly another gene has taken over the function of the deleted gene (eg duplicated genes engine). -Check whether limited mobility has a selective advantage to immobility. I could carry out such a research program in my department, the necessary molecular genetic methods are well established, but it would be a significant human and material resources necessary. [p. 14] complex structures like the bacterial motor lead. This is a painstaking process. Michael Behes provocative theses were the direct reason that such a model concepts by Matzke (see Section 9 have been formulated). No matter how plausible they are as individuals, we must recognize, first, that Behes stimulates critical arguments have the scientific debate. This is true even if he should not be right. Although all bacteria engines a non-reducible complex containing core set of proteins, it does not follow necessarily that, through gradual evolution, therefore resulting in principle can not. In a highly regarded publication have Liu & Ochman (2007b) proposed a core set of 24 proteins, which occurs in all previously genomsequenzierten eubacteria (see above). These core proteins were then examined in detail on their sequence similarities. The authors say that all the core proteins of the supposed "great-engine" each other more or less similar. From these similarities, they conclude that these proteins have emerged from a joint development by numerous, successive Duplikationsprozesse and that at the beginning of a single motor protein was original. However, the authors claim not believe that this motor protein has already exerted a motor function. Because the molecular motor proteins, and the pedigrees of the parties agree to some bacterial species, and because the motor genes are widespread on the eubacteria, Liu & Ochman conclude that the core proteins were created of the motor before the diversification of the eubacteria. Science, in its online magazine commented immediately positive (Cutraro 2007). First you have to state that similarity explained by common descent kann11 that one but it must not close to common ancestry. The primary literature in textbooks and many interpreted as convergences similarities highlight the problem. It is undisputed similarity, not by descent, but must be caused functional and it is obvious that this is the case at the molecular level. It would however be too long to reopen the homology discussion here, see for example, Junker and Scherer (2006), Junker (2002) and Fehrer (2009). A potential cause of functional similarity in the sense of convergence is by Liu & Ochman not even mentioned as a vague possibility. Surprisingly, this model of evolution unexpectedly harsh and basic criticism is met by evolutionary scientists. These relate to one part of the methodological errors of the work and the other on conceptual problems. A comprehensive collection of arguments and of links added Nick Matzke at Panda's Thumb collected (Matzke, nd), he himself rejects the model of Liu & Ochman from as well. Meanwhile, a correction has been published (Liu & Ochman 2007c), but it is not a smear given at the basic statement. In October 2007, commented M.Y. Galperin with respect to Panda's Thumb this publication: "... what is true in the paper by Liu and Ochman is not new, and what is new is not true "(Galperin, 2007). More friendly sounding, but its content clearly the violent criticism of Doolittle12 that rejects for various reasons the speculation by Liu & Ochman (Doolittle & Zhaxybayeva 2007). I think the main criticism that m. in the literature W. is no discussion, however, but is located on a completely different level: Liu & Ochman no mechanistic model offer for what it is supposed to have been as functionally possible that a rotary motor function is said to have formed gradually on the basis of ongoing gene duplication. Only such a hypothesis would be testable at least conceptually. This is not to say that the approach of the authors is entirely worthless. It would certainly important to recognize actually existing similarities between proteins and to ask for possible familial or functional causes. In conclusion, the speculation (of a model can not talk seriously) by Liu & [p. 15] Ochman no contribution to understanding the evolution of a bacterial engine delivers. Why such a weak one in many ways could appear in an article of the world's highest-ranking scientific journals, is the secret of the responsible editor Francisco J. Ayala. Much more interesting than the work of Liu & Ochman are approaches which, though hypothetical, but nevertheless represent intermediates containing evolutionary paths for discussion, as presented in biology didactics Nicholas Matzke. Before these are discussed, however, is its basis are presented, which is situated in the fascinating discovery of the multi-functionality of many biological structures. With increasing sequence data on the one hand, and increasing molecular insights on the other hand it is increasingly clear that biological structures can also have multiple functions. Particularly impressive is the very long-known and surprising finding that eye lens proteins (Crystalline), both structure and function can have enzymatic functions (Piatigorsky 1992, Piatigorsky 2003). Also very interesting, and of growing importance is the existence of overlapping genes (Chung et al. 2007, Liang and Landweber 2006, Loessner et al. 1999, Scherer 2008a), ie a nucleic acid sequence encodes several different proteins. Known to what extent a plausible mechanism for the evolutionary origin of these dual functions is to be discussed elsewhere. Also for the flagellum have been described other than the motor function as other functions. The flagella of the transmitted mainly by food pathogens Campylobacter jejuni and C. coli practice next to the motor function also functions in the secretion of virulence factors, the autoagglutination, the micro-colony formation / biofilm formation and the defense by the innate immune response (Guerry, 2007). In Figure 4, four functions are called. This includes the observation of multi-functionality of sub-components based model of evolution of bacteria engine as the core of the idea of evolution by mutation and co-option "(Gene 2003). This model is particularly caused by the discovery that the proteins of the bacterial motor by a similar mechanism of cytoplasmic membrane, cell wall and outer membrane Figure 4 A bacteria engine is a complex molecular machine consisting of several closely interacting small molecular machines or functions. In this picture, four functions are shown, there exist others: proton transport, ATP-cleavage, secretion and adhesion (adhesion is a simple function, not a machine). Mapping of the engine model with approval (Protonic nanomachines Project, Japan, http://www.fbs.osakau.ac.jp/labs/namba/npn/ top.html). [p. 16] to be transported, as was in the type 3Sekretionssystemen (T3SS), found 13 of pathogenic bacteria (eg (Blocker et al. 2003, 2008 Galan, Galan & Wolf-Watz, 2006, Journet et al. 2005, Pallen & Matzke 2006 ). In this he is particularly well studied because it is an important virulence factor. It is sort of a molecular syringe, with a pathogen toxins can be directly injected into a host cell ("Injektisom"). T3SS proteins but can also give directly to the cell environment. In Figure 5 is a schematic model of the type 3 secretion system of the pathogen E. coli shown 0157th It consists of about 10 proteins, is thus relatively complex. We know that the engine for bacteria belonging to the building and can secrete essential T3SS proteins that do not belong to the bacterial motor. Of particular interest is the new discovery that the protein transport T3SS not ATP, but is driven proton and thus fed by the same energy source as the rotation of the flagellum is (Galan 2008). It can therefore be speculated that not a complex bacterial motor was at the beginning, but that the simpler the structure of a "primitive" type 3 secretion system (without motor function) decline, which in many evolutionary stages additional, already receives co-opted into the cell existing proteins and altered by mutation, until finally led to the current, complex motor function (Musgrave 2004, Matzke 2006). The objection that the type 3-derived secretion apparatus and the bacteria could be original engine should not be further discussed. In addition, there is evidence of a number of other sub-functions of the bacterial motor, such as Virulenzgenregulation (Belas & Suvanasuthi 2005) or the perception of moisture (Wang et al. 2005) .14 It seems as if the flagellum also have gene regulatory functions (Anderson et al. 2009). Such dual functions do not contradict the assumption that the flagellum is not irreducibly complex, because the destruction of Proteinsekretionsapparates of the flagellum leads to loss of motor function, because the engine can not be assembled. One could even imagine that the entirety of the core proteins of each bacteria engine with regard to motor function is a non-reducible complex structure, and that the contained secretion apparatus terms of protein secretion also one - but simpler structure - non-reducible complex structure (with a different function) be could. Although the existence of secondary functions of biological structures for the modeling of potential evolutionary paths is extremely important (Fig. 5, see Schematic representation of the type three secretion system of pathogenic Escherichia coli cell (below). The pathogen attaches itself to an intestinal epithelial cells of the host (above) to . The secretion consists of an apparatus that in the cytoplasm of E. coli-synthesized proteins transported first through cytoplasmic membrane, periplasm and outer membrane. constructed by a molecular "needle" (mainly from the protein EspA), headed from the proteins and EspD EspB in the cytoplasmic membrane of the host cell inserts, go effector proteins (eg EspH, EspG) in their cytoplasm and enslave "the human cell. The disease can in extreme cases lead to death. Schema of Angelika Sell, changed, from different sources collected. [p. 17] below). Their mere existence means but not (unfortunately, the argument is quite familiar), so that the evolution of non-reducible structures had already been fully clarified. Secondary functions of parts of the bacteria motors are not an argument against the fact that these engines in their current form, one - included in terms of their motor function - substantial complex irreducible core set of proteins. Secondary functions may however serve as a basis for the development of hypothetical models with evolutionary intermediates. There is no doubt that not a bacteria engine "from nowhere" can arise through evolution. If the bacteria has emerged evolutionary engine, then there must have been intermediates, which were either fixed through selection or through neutral evolution in bacterial populations. These intermediates have to be built on existing structures, as they also can not arise de novo. A cognitive progress can be expected only if such intermediates proposed concrete and transitions between them are analyzed. The discovery that bacteria engage parts of the motor secondary functions, was an important step in this direction. Of particular importance in this context, the already mentioned ability of the bacteria in the secretion of motor proteins. We know then that the T3SS is true today for the irreducible complex motor, however, that this apparatus also has another function that is independent from the rotary engine, and could therefore arise independently. One can speculate that an entirely independent of the engines were, preliminary T3SS was used to build an engine. would in other words, the emergence of a "primitive" so that a functional T3SS, intermediate stabilized by selection on the way to the formation of the bacterial motor, and so a significant simplification of its evolution. Such intermediates were also known as basic functional states (Junker & Scherer 2006, Scherer 1983). It is the merit of Matzke (2006), the m. W. have proposed so far only speculative scenario for the evolution of the bacterial motor of which is detailed enough to be testable. In this scenario, an evolution story is told, which is well suited to be initially examined theoretically. I have Matzke evolutionary steps to this end, graphically in Figure 6 together gefasst15. Designed by Matzke scenario is a fantastic story (which is not meant pejoratively, any science thrives on creative hypotheses, more in section 12). It is based on the postulate of thought of many intermediates in a hypothetical evolutionary selektionspositiver (cumulative selection). However, the fact or the presumption is that a new or modified structure increases the fitness of its bearer, a true notwendige16, but by no means a sufficient condition to ensure that they can develop through evolution. You have such stories, therefore submit a "reality check". This is the only way aussehen17 that the various necessary conditions identified for a postulated evolutionary step as accurately as possible and the chances of evolutionary transitions can be estimated taking into account molecular and population genetic framework. The principal merit of Matzke is that you, the individual may consider him postulated evolutionary steps 1-11 (Fig. 6) in principle to known experimental data. As an example, I choose evolution step 4, and this is because it can be very good reasons: First, has the bacteria on a motor Sekretionsfunktion. This is intended to be already created some unknown way and as a starting point. Second, the scourge of a Adhäsionsfunktion, ie, the bacterial cell to bind with the scourge of surfaces. This was for various eubacteria such as Escherichia (Giron et al. [p. 18] 2002, Monteiro-Neto et al. 2003, Nather et al. 2006, Parthasarathy et al. 2007), Aeromonas (Gavin et al. 2003, Kirov et al. 2004), Pseudomonas (Lillehoj et al. 2002), Clostridium (Tasteyre et al. 2001) and Shewanella (Caccavo & Das 2002) is shown. Even in archaebacteria was one of the flagella Adhäsionsfunktion described (Nather et al. 2006), but these structures are entirely different than the eubacterial flagellum (Jarrell et al. 2009). A Adhäsionsfunktion is a selective advantage under certain conditions and could therefore establish by Darwinian evolution, function occurs before the rotation of the apparatus. Thirdly, this is only the co-option (transfer to a new context), and mutation of a single protein. Less than one protein can not be co-opted, we have here is a minimal Kooptionsschritt before us. Fourth, one could imagine that a not yet optimal Adhäsionsfunktion can perhaps be generated by a small number of mutations in a protein preadapted. Fifth, one might then speculate that from this initial adhesin by consecutive (following) mutations later developed the multimeric flagellins (building blocks of the Scourge). Evolutionary step 4, which is illustrated in Figure 7 graphically simplistic, I think one of the links on its evolutionary path described in Figure 6, which realize at first glance seem the easiest. What processes must be postulated to occur to ensure successful co-opt it? Matzke did not deal with molecular details. Especially this is crucial to a meaningful assessment, however, so I will add Matzke and in the following example to argue at this level. In Figure 8, the necessary requirements for are shown in Figure 6 outlined evolutionary step. 10.1 Präadaption of Vorläufergens should first follow the precursor protein, which is to be co-opted, some requirements so that the evolutionary process is likely. I assume therefore that this protein was pre-adapted (for example, the concept of Präadaption Junker & Scherer, 2006, and Ridley 2004). So that it possessed some structural features that target this protein to some extent for the necessary adhesion protein. These include, first, that there was a secretion, which can be detected by a secretion apparatus, this precursor protein should therefore belong to those who have evolved through the unknown way, "primitive" type 3Sekretionssystem were secreted. The second is to assume that the overall structure of the protein to a one Präadaption Adhäsionsfunktion brought. On einfachsten18 it would be that the origin of protein already had a vorangepasste domain Figure 6 Evolution of the bacterial motor by co-option and mutation by Matzke (2006). Co-option of existing proteins are shown in blue, with here are also mutations necessary. Mutation events without Kooptionsereignis ngegeben are in red. The co-opt an adhesin by a type three secretion apparatus is highlighted with a red arrow and is used here as an example to examine the requirement for this evolutionary step. [p. 19] was the only convert to a new Adhäsionsspezifität. This is not unreasonable, for example for each enzymatic function is also a binding of the substrate needed to be split. Must create a completely new Adhäsionsdomäne by mutation, but an existing substrate binding must be transformed in only a Adhäsionsfunktion. 2.10 mutations in Vorläufergen (1): gene duplication In general and for good reason it is assumed that new genes arise by duplication of existing genes, in particular, maintaining the original function and the duplicated copy is free to accept mutations by a modified or new function, without the old function is destroyed ( statements such as (Hughes 1994, Ohta 1989, Roth et al. 2007, Zhang 2003, Lynch 2002). Bergthorsson et al (2007) have described a way how a new function from a previously existing page function (so to speak a "preadaptation") in a population could be established. In more recent work is the emergence of a new position in duplicate also called Neofunktionalisierung (eg Beisswanger & Stephan, 2008, Teshima and Innan 2008). gene duplications are frequently observed events, but it is relatively likely that as a result of either a functionless pseudogene arises or that a subfunctionalization begins. This refers to a parallel change in the function of the original and the duplicated gene, so that both run together the function of the original gene (Hittinger & Carroll, 2007, Hovav et al. 2008, Lynch et al. 2001). Neofunktionalisierung but could possibly also run through subfunctionalization (He & Zhang, 2005, Rastogi & Liberles 2005). I postulate here that a preadapted Vorläufergen of the adhesion protein was first duplicated and then by mutations in a copy of a Adhäsionsfunktion has won it (Fig. 7). 3.10 mutations in Vorläufergen (2): Formation of an adhesion function How is it in duplicate, Vorläufergen preadapted to form a Adhäsinfunktion? One might think that this secreted protein precursor dietary sources of the bacterium opens (complex polysaccharides, proteins, nucleic acids) and showed for this purpose an appropriate enzymatic function. Thus polymers are broken down into monomers, which may be included. Such secreted, polymer-degrading proteins could also serve to destroy other cells. A number of such enzymes is eliminated, for example in phytopathogenic microorganisms by type 2 secretion, for example, Jha et al. (2005). The advantage is, therefore, that the precursor protein would already have a binding site. This should now only be reconstructed so that a reliable bond occurs without enzymatic activity. The selective advantage of the binding of a bacterium to an abiotic substrate or a plant surface is obvious. Is it possible to estimate the number of required mutations at the origin of protein? As a simple model, I see a polysaccharidabbauendes enzyme (those secreted enzymes are common). It has an enzymatic function, the polysaccharides into monomers or oligomers disassembled. This includes substrate binding, this domain could be converted into a Adhäsionsdomäne. If there are very similar substrates, the binding specificity or the affinity to polysaccharides by single point mutations can be changed (for Polysaccharidbindungsproteine see eg Simpson et al 2000; for enzymatic activity, there are many such cases, see Junker & Scherer 2006, page 143f). Figure 7 co-opt a preadapted adhesion protein and mutation of an existing type three secretion apparatus. The presumed secretion apparatus is very simplified blue outlines the preadapted protein, which is formed in the cytoplasm and then secreted through the Sekretionspparat is shown in yellow. It should already have a precursor Adhäsionsdomäne. According to co-opt and mutation in an adhesin binding protein now transformed to a protein on the outside of the secretion apparatus (black dumbbell) and can attach themselves out from there to an extracellular substrate. [p. 20] If you want to recreate a Polysaccharidbindungsstelle a bond for other types of carbohydrate, then there is the requisite number of mutations, however, 4:00 to 10:00 amino acid changes (Gunnarsson et al. 2004). Conditions for success in the considered here example are that (i) the enzymatic function is destroyed, (ii) maintain the binding function at the same time remains, and (iii) is such that it has a sufficiently high affinity for the substrate receives a fixed to ensure binding of the bacteria. Alternatively, one can imagine that bind an intracellular "adhesin", which may be bacterial polysaccharides konnte19 converted into a Adäsin was that recognizes an extracellular polysaccharide matrix. Perhaps the transformation to achieve the active site of the protein by only two point mutations on one or the other way. These are m. W. Although no experiments known. Such conduct might be, however, this assertion testen.20 4.10 mutations in Vorläufergen (3): Coupling of the Adhäsinproteins Sekretionsmaschine (co-option) A free adhesion protein is of no selective advantage for the cell, the protein must be linked to the cell surface. This later postulated a further evolution for the bacterial motor can be coupled to the one lying on the outside of the cell proteins of the existing Type 3 secretion apparatus erfolgen21. The issue is the reappearance of a very stable, noncovalent protein-protein coupling. How many mutations are required? The generation of new binding specificity in proteins by laboratory evolution has developed on the basis of biotechnological interest to a booming area of research (overviews in Bersthein & Tawfik, 2008, Singh & Sharma, 2006). Here the cases of interest, which is produced in a precursor structure that has already binding capacity (so-called scaffold22, Skerra 2007) a new binding domain, which in the present context only pure random processes are considered, ie the initial formation of a binding function. Optimizing Darwinian evolution, which would build on those already established functions and alter selection driven, inevitably in the course of evolution to be expected. In a series of recent works have been from existing scaffold genes frequently mutated gene libraries stochastic and won, which contains up to 1013 different variants. Hence the individuals were selected that have a new binding activity. This shows that binding domains in the sequence space are not too rare, and in respect of some bound substrates even occur relatively frequently. A few examples may be mentioned, I begin with the formation of protein binding domains that couple to medium determinants (we know very much about it, because that is biotechnologically relevant). If you Lipocalinscaffold the basis sets, then new binding domains for digoxygenin of about 15 new amino acids built up (Schlehuber et al. 2000), also from 1416 to phthalic new amino acids (Mercader & Skerra 2002), which requires about the same for fluorescein number of new amino acids (Best et al. 1999). The coupling to the secretion apparatus adhesin a high affinity protein-protein coupling is required. Also one has been won on the basis of Lipocalinscaffolds (Xu et al. 2002), about 20 new amino acids were involved. On another scaffold could be shown that a protein binding domain arising from a Polysaccharidbindungsscaffold also from 9-12 new Aminosäuscher forces. Figure 8 Composition of the conditions and changes that are being discussed for the co-option, and mutation of a precursor protein for a preadapted adhesin in the text. [p. 21] It must be remembered that contribute to binding of a bacterium to a solid substrate, even with slight movements enormous train and shear forces on the secretion apparatus, because its size relative to total cell mass is very small. This is true even when a cell forms multiple copies of the secretion apparatus. The various protein-protein interactions within the secretion apparatus are certainly not designed for these tensile forces, this problem would probably be offset by compensatory mutations. How many such compensatory mutations are needed? The answer to this question no one knows, the experimental verification would be difficult, and therefore can only be preliminary at this point a question mark. 10.6 Regulation of expression of the adhesin This creates an overall operational construct, it is necessary that the control of gene expression of the duplicated and mutated adhesin is reasonably fit. The new adhesin must be produced at about the right time and in roughly the right amount (optimizations by subsequent Darwinian evolution is no fundamental problem). The associated regulatory elements have to arise by mutation at the same time. How many changes in the promoter structure of the duplicated gene notre created for it (can Gunnarsson et al. 2004). These results must be considered in the present context, however, differentiated. From the gene libraries because of the experimental approach only höchstaffine variants were isolated. One can certainly assume that were included in the libraries even less affinity variants, which use less new amino acid changes. However, the required power in our context from the beginning to be quite stable because the binding of the bacteria to a surface by the adhesin that would otherwise be swept away by the secretion apparatus. I propose as a working hypothesis that a sufficiently strong, bind to the novel secretion apparatus only five amino acid changes in the precursor protein requires. It must be noted also that amino acid changes that lead to the coupling to the secretion apparatus, does not change the adhesion sites of the protein to the external substrate. Perhaps the number is taken five more deeply. Mutations in the secretion apparatus 10.05 The adhesion protein that is coupled to the secretion apparatus. This has a number of consequences, which are summarized in Figure 9. First, the binding of a protein to another protein inhibits the function of the first protein is often what is used in molecular biology for years, proving that a protein carries a very specific function (eg inhibition of a response by antibody binding). This would be unacceptable in our case, because of the secretion apparatus is essential to remain functional. It is therefore proposed that the secretion apparatus is first changed in the affected protein coupling by mutations so that the function of this protein is not impaired too much. Furthermore, these changes the function of other proteins of the secretion apparatus may, the binding partners of the affected secretory, are being affected too much. Perhaps this additional mutations are needed? Mutations that abolish the negative result of a previous mutation, are known as compensatory mutations (overview eg Ferrer-Costa et al. 2007). An additional complication is expected by the appearance of not acting far mechaniwendig are currently can not be estimated data-driven. Figure 9 Interactions of the secretion apparatus / adhesin with the substrate for adhesion and subsequent interactions and their importance for the interaction of various proteins of the secretion apparatus (schematic diagram), details in text [p. 22] Other hand, we postulate that the duplicated gene is transferred through nichthomologe, intrachromosomal recombination in an operon of the secretion apparatus, so that would be at the same time the temporal expression control and perhaps the quantity produced so happens to be true to some extent. How common is such a locally appropriate, double intrachromosomal recombination? Reliable data on such frequencies exist m. W. it, but I guess at less than 10-9 per cell per replication (Hülter & Wackernagel 2008). 7.10 Fixing of the two new loci in the population Often remains unmentioned in the narrative of evolutionary history a further important detail. Assuming all of the above changes are somehow come about: Well the data has to bacterial cell has yet to fulfill its competitors. This will only succeed on the one hand, if the positive selection coefficient is sufficiently strong. But regardless, there is a significant chance that, despite a positive selection coefficient of the new construction by random genetic drift disappears before she had the chance to assert itself by selection. The fixation of mutations in a population can also be made by neutral evolution, and so initially without Darwinian selection. For this reason, by multiplying the individual probabilities can be given only the probability of the emergence of a structure per cell and per generation. The potential of neutral evolution is discussed in Junker and Scherer (2006, p. 139f and 162F) and Scherer (2011, in preparation). There are reasons why the neutral theory of evolution - it is so important for the understanding of evolutionary processes - mE currently no convincing solution to the problem of macro-evolution has on the molecular basis. 10.8 Can the probability of formation of a bacterial motor can be estimated? As the above discussion has shown, the evolutionary history of Matzke be told clearly detailed. This allows only a still very rough reality check of history. Some things you can assess this data-driven, others for lack of data on the other hand still?) not (. The conclusion is m. E. obvious that the total probability considered for the evolutionary step is very small. How small? Behe writes: "However, as the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met Skyrockets toward the maximum that science allows. "(Behe 1996) That is a steep proposition. Can the "probability" or "improbability" of the evolution of a bacterial motor call a number? One could take the number of mutations estimated to be independent of each other, multiplying their individual abundances of it, and then would get a vanishingly tiny number for the simultaneous occurrence of events in a cell in one generation. Apart from the problem of neutral evolution, which makes such an assessment impossible (Junker & Scherer 2006, page 162F) that figure would imply an unrealistic accuracy of the result. You might also suggest the conclusion of this result is the evolution of the evolutionary process under discussion is refuted. Both is not my intention. It should be pointed out again that selected from evolutionary history to the formation of the bacterial motor (Fig. 6) one of the simplest and most justifiable action became aware of this discussion. The other postulated evolutionary steps are sometimes more complex. My conclusion from the discussion held in this section is therefore: It is unknown as by co-option and mutation in the course of the hypothetical formation of the bacterial motor, the gain would have an adhesin can run. [p. 23] Among other things, for the following reasons, Matzke Kooptionshypothese turns to the evolution of the eubacterial flagellum mE not as reliable scientific hypothesis. 11.1 All models are intermediates in Matzke selektionspositiv? Some of Matzke postulated evolutionary stages, it remains questionable whether the postulated evolutionary steps actually have a selective advantage. Whether, for example, the steps 5-8 in Figure 6 are selektionspositiv, reveals itself at least not at first glance, but this question should be discussed in detail. 11.2 The problem of the fundamental reconstruction of structures by mutations If one wants to assess whether a postulated evolutionary step could have something like this actually take place, then you have to enter more deeply into molecular genetics, mechanistic details, as has happened in Matzke (2006). Matzke from evolutionary history to the formation of the bacterial motor (Fig. 3) was one of the simplest and most justifiable action is selected and analyzed for the presumably necessary modifications in the structures involved. This results in a number of serious, unresolved problems. My conclusion from this discussion is: It is unknown as by co-option and variation in the course of the hypothetical formation of the bacterial motor, the gain would have an adhesin can run. Nevertheless, it could be that important factors were overlooked and that the co-option of a one adhesion protein secretion apparatus was somehow in another way. Perhaps further analysis will solve the problem. Then the problem would result as described below. 11.3 The problem of evolutionary canalization If the selection coefficient is high enough, a primitive, initial Adhäsionsfunktion prevail in a population and is also in the further course of evolution by the Darwinian selection mechanism, which is a biological law, need to be optimized. This will gradually be made by individual mutations in the binding site and elsewhere in the adhesin and the secretion apparatus. The further optimization of this process, the more difficult it is to couple to this function later, a new property, such as Pilusbildung with channel or rotation. It follows that a Adhäsionsfunktion (should they arise for) in an evolutionary dead end must lead in terms of the formation of a rotating flagellum. 11.4 The problem of the limitation of the variational space by multiple functions From Matzke is postulated that several adhesins coupled together and to enable more Adhäsinkomplexe that increase the binding function (Matzke 2006, step 3b). So that the secretion is not it impair its function, one must postulate with Matzke that the monomeric adhesins aggregate into a multimeric ring on * secretion apparatus, forming a pore through which secreted proteins find their way to the outside can. That would be a completely unnecessary and would Adhäsionsfunktion but an unknown number of additional changes to the Adhäsinproteinen need so that they bind to each other and to the secretion apparatus and can form the secretion injectisome. An increase in the number of Adhäsinproteine would be much easier to reach by the binding of adhesins to cell surface structures that affect not the Sekretionsfunktion. The underlying general problem is the limitation of space, and therefore the evolutionary variation possibilities when structures must perform a dual function (or will run later) - here a single protein that (a) an adhesion [p. 24] is already functional exercises, and (2) also form a secretion injectisome and (3 rotate) later. Either will be optimized to increase the adhesion point, or to form a secretion injectisome. Both are also very unlikely to be worthwhile because the dual role required only a few mutations. On the other hand, there will be many mutations that improve a Adhäsionsfunktion. Of the Darwinian selection process built in "optimization constraint" will not lead to the formation of an adhesive secretion injectisome, but to an optimized adhesion. But should be made contrary to the Darwinian selection theory, a secretion injectisome, the variation of room for future rotation is the same the more restricted (evolutionary channeling). 5.11 Darwinian evolution is contrary to the flagella-Evolution Evolutionary channeling and multiple functions of individual components lead to the following adhesion to a stage of evolution represents the evolution in real Adhäsinrings course not a realistic option. The problem is illustrated in Figure 10. The coupled to a Sekretionsmaschine adhesin will initially operate sub-optimal and the Sekretionsfunktion should be disturbed at first, because you must start it so, as few mutations have that first one still "primitive creates" new function. All the available experimental data on the evolution of bacteria consistently show that in this case an optimization and finally perfecting the still suboptimal functions by single point mutations. This is the evolutionary path that points in Figure 10 below. The better the optimization is, the farther away the structure in the area of the mutation actually desired new function of the secretion injectisome (which also has no obvious selective advantage). The formation of a built up from Adhäsinmonomeren secretion injectisome is associated with a significant number of changes in the secretion, the adhesins and the regulation of their expression. Such a multifactorial event will occur very, very rare, and it is in constant competition with the frequent occurrences of optimizing existing adhesin / Sekretionsfunktion. The Darwinian selection mechanism as a biological law will therefore need to ensure that the "wrong" evolutionary path is taken. Regarding the evolution of a flagellum leads to Darwinian evolution, which follows a hypothetical origin of the adhesin / secretion system, whose inevitable optimization in a selektionspositive impasse. 6.11 Hidden teleology The example of the above described formation of an initial secretion injectisome of a ring of Adhäsinproteinen is clear that Figure 10 Evolutionary sewer crosses the biological law of the Darwinian mechanism of evolution inevitably to the optimization of hypothetical, newly formed adhesin / secretion apparatus and power (thick black arrow) and away from the actually required to Flagellum evolutionary path (dotted red arrow to the right). The Matzke after lying on the evolutionary path "Adhäsionsring" (right box), also exhibits no better selection advantage. [p. 25] Matzke this ring is placed just so mentally cope, has so he can use it later as the basis for the further polymerization of Adhäsinproteinen to form a flagellum. In other words, Matzke has (not only for this step) and an unnamed reader ignorant hidden teleological (ie targeted) component is hidden in his evolutionary model in order to make the model plausible at all can. Such a thing is in the context of a naturalistic evolutionary biology actually is strictly prohibited. 7.11 Matzke model is not discussed in the literature to date As far as I know, was Matzke evolutionary model in the refereed literature and microbiological still not diskutiert.23 This is surprising because the evolution of the bacterial flagellum, the prime example in the public debate about Intelligent Design in the United States. In addition, alternative mechanistic (and hence theoretically testable mW) Evolution models for the bacterial motor not proposed until now. Can we conclude that the experts - if they ever took note of it - Matzke model holds little convincing? 8.11 Matzke waived the discussion of his own evolution model Together with Mark Pallen Matzke presented a comprehensive and readable publication in a leading journal on microbiological evolution of the bacterial motor (Pallen & Matzke 2006). connected Matzke relevant, above-discussed model of evolution, the two authors in their own work discussed but not yet as an argument benutzt.24 Nevertheless, Johannes Sikorski has recently Matzke model without any criticism or modification fully and it "impressive and resilient model for the evolution of the bacterial Flagellensystems "praised (2009, 278). This assessment corresponds to the available data (not so) and is used by the experts at least not yet supported. In Junker & Scherer (2006, pages 157-163) it was assumed that a "primitive" type 3-secretion apparatus is converted by the conversion of 16 pre-adapted proteins in a simple bacterial rotary motor, and for the conversion of a protein 10 mutations were estimated. This figure was derived from experimental work on the change of function of proteins and is about the lessons on the basis of other sources number of changes which are in Figure 8 of this work for the example of the co-option of the adhesin collected. The core allegation of Matzke model now is that these 16 proteins were not co-exist, if the evolution process can be divided into different stages selektionspositive. In Junker & Scherer (2006, page 158) were selektionspositiven intermediates such "basic functional states" mentioned. If Matzke true model, then two selektionspositive basis states would be much less far apart as in Junker and Scherer (2006, Seite162) was adopted. While they were still so far apart that remains unknown, as the distance could be overcome between the two selektionspositiven states by known factors of evolution, but that does not change the fact that to overcome gap would be much smaller than from Junker & Scherer adopted. While it is doubtful whether Matzke's model is basically effective. This is related to the angle shown in 11.3 and 11.4 facts of evolutionary canalization and the multiple functions of structures. Matzke assumes two things: First, should all be given for intermediate selektionspositiv. That would be examined in detail thoroughly (see 11.1). Secondly, Matzke assumes that upon reaching a level (for example, the co-opt an adhesin) the subsequent stage (the initial secretion injectisome Adhäsinring as) an undirected by the evolutionary process actually selectable option. However, this is in the specific example discussed just not the case - Matzke shall establish here a teleological element. This is not a viable co-opt an adhesin precursor to the formation [p. 26] a rotating flagellum (see Section 03/11 to 05/11) but in this respect is an evolutionary dead end. It looks at the current Argumentationsstand m. E. look as if Matzke model does not readily selektionspositive basis function describes conditions that lead from a primitive type 3 secretion via the smallest steps towards a bacterial rotary motor. Let there be no mistake: Despite the criticism is noted with appreciation that there is always a great merit of Matzke's model to have raised the argument to a qualitative new level. The affected section of Junker & Scherer will therefore be in a planned remake along the argument presented here, which would not exist without Matzke model reformulated. We know m. E. not far may have evolved by which evolutionary path a bacterial motor. Instead of reasonable scientific theories in such cases, sometimes ad hoc speculations voiced and considered a sufficient explanation. It does appear, particularly among amateurs, but is sometimes observed in the scientific literature. The argument often goes in the direction that a structure has adopted an assumed precursor structure to a selective advantage, which should make the whole process of evolution appear to have completely plausible. Egbert Leigh sat down with the still widely held view that the mere enumeration of hypothetical selection benefits sufficiently explain the evolution of life, a critical look (Leigh 1999). He cites first Antnonovics (1987): "Too many biologists behaved as if to imagine a use for an organ is ... equivalent to explaining its origin by natural selection without further inquiry "and then Gould & Lewontin (1979), this approach" adaptive storytelling "services. Gould and Lewontin made with that name probably a little fun of the "omnipotence claim" to the selection theory, as for example, particularly stark in Dawkins (1987, 2008), but not just appear there. Lynch (2007) comments on Dawkins acting religious absolutism rather ironically: "Dawkins' agenda to spread the word on the awesome power of natural selection has been quite successful, but it has come at the expense of reference to any other mechanisms, a view that is in some ways profoundly misleading." The concept of Molecular Evolutionary Story Telling will be here on the problem of the evolution of the bacteria used motor. This is not meant disparagingly. Only today's knowledge of the biology of bacterial transport systems and flagella allow the molecular basis of it all, such ad hocGeschichten to tell in acceptable detail. That was not even possible 10 years ago. There is a wealth of detailed biological knowledge to relate to such evolutionary histories so that we can derive testable hypotheses and research programs. That is a significant step forward not only of microbiology, but also in evolutionary biology: The more specifically an evolutionary story can be told, that is, the more subdued by Experimentalwissen molecular and genetic details can be incorporated into the story, the better they can on a theoretical or, much more be important, also tested on an experimental level. In that sense, I think Matzke evolutionary history (Matzke 2003) - for all substantive criticism - for helpful and wichtig.25 The molecular tools are always available to these and other stories told from the resulting experimental questions (for example, by stochastic protein libraries and targeted mutagenesis) to klären.26 Evolutionary story telling is by no means obsolete. It is on the contrary, an important element not only in evolutionary biology, but of the scientific research process insgesamt27. Regarding the evolution of the flagellum, today we can at least tell stories so far substantiated that one can examine these theoretically or experimentally. As shown, such an examination leads so far not satisfactory to a result. We currently do not know whether there is any plausible evolutionary paths, to allow a primitive flagellum or precursor thereof produced through natural processes. [p. 27] is to be hoped, however, Delt by no means a final argument in this matter. The presented preliminary conclusions are always subject to revision, if this is required by substantive arguments. The claim that the evolution of the bacterial motor was a settlement in principle, because of scientific data is not covered. This does not appear that an evolution of the bacterial motor would be fundamentally impossible. [Notes] 1 For a person of Nick Matzke see http://en.wikipedia.org/wiki/Nick_Matzke 2 On the macroscopic level of biology you come across the same phenomenon, such as the lavishly-equipped works "Bionics" show of Nightingale & Blüchel or "fascination Bionics - the intelligence of the Creation" impressive. 3 It would be really interesting to see whether such an attempt succeeds or whether it ends like trying to describe an angel as a "winged year-end figure. 4 eubacteria and archaebacteria have a plethora of variants of the rotary engine. 5 Mike Gene is neither creationist nor a representative of the usual ID course which is known from U.S.. 6 example, there are numerous, very negative and often personally disparaging comments on Mike Behe on the Internet, in journals and newspapers, especially book reviews. This is for the following two reasons not addressed: First, they generally contain no or no new scientific arguments. Secondly, I have decided, personally offensive publications regardless of their scientific merits in principle not to quote. 7 The North American public discussion of the bacterial motor can really only be understood against the political-religious background of the United States. The often consciously, but quite wrongly, as creationists have designated representatives of the Intelligent Design (though similar to creationism), aims to anchor its intuition and in classes in state schools. I think that is not appropriate. To achieve this goal, it would be intelligent design a scientific alternative to evolutionary theory. I do not believe that to be generated research will shed more light on this problem. Nevertheless: A story is not the reality, a speculative evolutionary history should not be confused with a scientific explanation, it may not considered a substitute for evolutionary research, and should be collected at least as verbal immunization against objective criticism. Stories are initially only just stories and highlight gaps statement. If they are good, they will stimulate the imagination and generate experiments that permit an assessment of their plausibility. In the end, one could initially only fictional, imaginative story prove to be plausible model for a process, which may be of this or similar actually played in the past. Or it turns out after a thorough examination as a fairy tale penned in biological terminology without parallel in the empirically tangible reality. Lynch (2007) is to agree when he remarks with regard to the causal theory of evolution, "Evolutionary biology is not not a story-telling exercise, and the goal of population genetics is to be inspiring, but to be explanatory." However, the explanatory power of evolutionary theories regarding the origin of novelties (macro evolution) at the molecular detail, ultimately prove. The bacteria engine has proven to date in this regard as quite bulky. Total lies neither in the scientific primary literature nor in the popular literature, even in a plausible mechanistic approaches, scientifically resilient model for the initial formation of the bacterial rotary motor. The claim that the evolution of the bacterial motor is basically clarified (Doolittle & Zhaxybayeva 2007, Liu & Ochman 2007b, Matzke 2006, Miller 2004, Musgrave 2004, Pallen & Matzke 2006, Wong et al. 2007, Sikorski, 2009) is not because of scientific data gedeckt.28 This is not to show that an evolution of the bacterial motor would be fundamentally impossible. It is not the intention of this paper, nor is it even possible to draw such conclusions. This work will be seen as another step in the critical discourse on the origin of the bacterial rotary motor. It han-that this is the case and have the justified elsewhere (Scherer, 2009). [p. 28] 8 archaebacteria contain a completely different type of engine, the is far less known than about the eubacterial flagellum. About its origin can be hardly justified under discussion due to lack of functional analysis. 9 The rotary engine of the archaebacteria is very different from that of eubacteria, but the same rules apply to the experimental search for essential genes of the engine as in eubacteria. 10 I do not hesitate to call cellular systems such as "brilliant", knowing that this is a border crossing that leads from the field of scientific terminology out. 11 Of course, it is also possible that similarity was caused by the operation of a designer. Even if that were true in the case of the bacterial motor, the argument would not belong in a scientific discussion: The work of a designer is not reproducible and not examinable process and the adoption of a designer is not falsifiable, therefore, lies beyond the horizon of scientific knowledge. 12 It should be known to the fact that Doolittle is one of the world's recognized authorities in the field is the bacterial evolution. 13 Among the prokaryotes a number of different secretion systems are known that the extrusion of proteins through the cytoplasm and possibly allow the outer membrane. Basically, these are relatively complex procedures. 14 Both functions are biologically meaningful connections with the motor function, but this leads at this point too far. 15 A corresponding to the lay stunningly convincing sounding and no problems leave open evolutionary history is at http:// www. youtube.com / watch? v = SdwTwNPyR9w available. Basically, this video is adjacent to a dumbing down of the unfortunately ignorant viewer. Here's 16 of Darwinian evolution, the speech, neutral evolution is an important, but among the laity is still no course concept and is discussed elsewhere (Junker & Scherer 2006, p. 139f and p. 162; and Scherer, 2010, formation of the bacterial motor by Neutral evolution? In preparation) 17 On these facts, I would point in 25 years, see Scherer 1983rd 18 Yet it would be easier if you already have a functional adhesion protein would be co-opted. However, this would then have been otherwise have been established, which is known by various adhesins in the outer membrane. In this case, the change in the secretion apparatus, however, would not include new functionality and thus do not lead to greater fitness. Maybe in the 19 Mureinzellwand? We know a number of polysaccharide-binding domains of bacterial enzymes. 20 This is an example of this is to bring as evolutionskritische analyzes the evolution of research forward. 21 If one asks what it did, as the narrator of the story, of course this still does not need current date in mind that the evolutionary path must lead towards the flagellum. 22 In "scaffold" (scaffold) means a protein which has a total construction has essential features that are new for the important function to be constructed. A scaffold is a sense preadapted protein, although it is not in the biotechnological usage so called. 23 The same goes for me the only previous known case, cited in the text in Internet Matzkes a refereed journal (Pallen et al. 2006). If there is other work, I am grateful for a hint. 24 Matzke's model is not even cited as a reference in the text there is no relation, only the title of Matzke's work is mentioned in the notes under "Further Information". My 25 made on Matzke constructive, further spun and much more detailed evolutionary history told me quite well. 26 you have to know that such work will need huge research funds. 27 Those who work experimentally know that many major scientific discoveries have begun with some adventurous and imaginative stories. 28 I am well aware that this conclusion is completely unacceptable, regardless of the reasons for those biologists for whom the term "evolution criticism from fundamentalist reasons basically a taboo. [References] Alberts, B., A. Johnson & J. Lewis (2008) Molecular Biology of the Cell., p. 1728. Taylor & Francis, London. Allan, E., N. Dorrell, S. Foynes, M. Anyim & B. W. Wren (2000) Mutational analysis of genes encoding the early flagellar components of Helicobacter pylori: evidence for transcriptional regulation of flagellin A biosynthesis. J Bacteriol 182: 29 5274-5277. Anderson JK, Smith TG, Hoover TR (2009) Sense and sensibility: flaggelum-mediated gene regulation. Trends Microbiol. 18,30-37 Antnonovics, J. (1987) The evolutionary dys-synthesis: Which bottles for which wine? American Naturalist 129: 321-331. Asai, Y., T. Yakushi, I. Kawagishi & M. Homma (2003) Ion-coupling determinants of Na+-driven and H+-driven flagellar motors. J Mol Biol 327: 453463. Attmannspacher, U., B. E. Scharf & R. M. Harshey (2008) FliL is essential for swarming: motor rotation in absence of FliL fractures the flagellar rod in swarmer cells of Salmonella enterica. Mol Microbiol 68: 328-341. Beatson, S. A., T. Minamino & M. J. Pallen (2006) Variation in bacterial flagellins: from sequence to structure. Trends Microbiol 14: 151-155. Behe, M. (1996) Evidence for Intelligent Design from Biochemistry. http://www.arn.org/docs/behe/ mb_idfrom biochemistry.htm. Behe, M. (2004) Irreducible complexity is an obstacle to Darwinism even if parts of a system have other functions. http://www.discovery.org/a/ 1831. Beisswanger, S. & W. Stephan (2008) Evidence that strong positive selection drives neo-functionalization in the tandemly duplicated polyhomeotic genes in Drosophila. Proc Natl Acad Sci U S A 105: 5447-5452. Belas, R. & R. Suvanasuthi (2005) The ability of Proteus mirabilis to sense surfaces and regulate virulence gene expression involves FliL, a flagellar basal body protein. J Bacteriol 187: 6789-6803. Berg, H. C. (1999) Motile Behavior of Bacteria. In.: Physics today on the web, pp. Berg, H. C. (2008) Bacterial flagellar motor. Curr Biol 18: R689-691. Berg, J. M., L. Stryer & J. L. Tymoczko (2007) Stryer Biochemie, p. 1224. Spektrum Akademischer Verlag, Heidelberg. Bergthorsson, U., D. I. Andersson & J. R. Roth (2007) Ohno's dilemma: evolution of new genes under continuous se-lection. Proc Natl Acad Sci U S A 104: 17004-17009. Bershtein, S. & D. S. Tawfik (2008) Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 12: 151-158. Beste, G., F. S. Schmidt, T. Stibora & A. Skerra (1999) Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold. Proc Natl Acad Sci U S A 96: 1898-1903. Blair, D. F. (2006) Fine structure of a fine machine. J Bacteriol 188: 7033-7035. Blair, K. M., L. Turner, J. T. Winkelman, H. C. Berg & D. B. Kearns (2008) A molecular clutch disables flagella in the Bacillus subtilis biofilm. Science 320: 1636-1638. Blocker, A., K. Komoriya & S. Aizawa (2003) Type III secretion systems and bacterial flagella: insights into their function from structural similarities. Proc Natl Acad Sci U S A 100: 3027-3030. Blüchel, K. G. & F. Malik (2006) Faszination Bionik. Die Intelligenz der Schöpfung. In. St. Gallen: Malik Management Zentrum St. Gallen, pp. 432. Bresolin, G., J. Trcek, S. Scherer & T. M. Fuchs (2007) Presence of a functional flagellar cluster Flag-2 and low-temperature expression of flagellar genes in Yersinia enterocolitica W22703. Microbioloy in press. Caccavo, F. & A. Das (2002) Adhesion of dissimilatory Fe(III)-reducing bacteria to Fe(III) minerals. Geomicrob. J. 19: 161-177. Cascales, E., M. Gavioli, J. N. Sturgis & R. Lloubes (2000) Proton motive force drives the interaction of the inner membrane TolA and outer membrane pal proteins in Escherichia coli. Mol Microbiol 38: 904-915. Cascales, E., R. Lloubes & J. N. Sturgis (2001) The TolQ-TolR proteins energize TolA and share homologies with the flagellar motor proteins MotA-MotB. Mol Micro-biol 42: 795-807. Chaban, B., S. Y. Ng, M. Kanbe, I. Saltzman, G. Nimmo, S. I. Aizawa & K. F. Jarrell (2007) Systematic deletion analyses of the fla genes in the flagella operon identify several genes essential for proper assembly and function of flagella in the archaeon, Methanococcus maripaludis. Mol Microbiol. Chevance, F. F. & K. T. Hughes (2008) Coordinating assembly of a bacterial macromolecular machine. Nat Rev Microbiol 6: 455-465. Chung, W. Y., S. Wadhawan, R. Szklarczyk, S. K. Pond & A. Nekrutenko (2007) A first look at ARFome: dual-coding genes in mammalian genomes. PLoS Comput Biol 3: e91. Cohen-Ben-Lulu, G. N., N. R. Francis, E. Shimoni, D. Noy, Y. Davidov, K. Prasad, Y. Sagi, G. Cecchini, R. M. Johnstone & M. Eisenbach (2008) The bacterial flagellar switch complex is getting more complex. EMBO J 27: 1134-1144. Cutraro, J. (2007) A complex tail, simply told. ScienceNOW 14. April. Dawkins, R. (1987, 2008) Der blinde Uhrmacher. dtv, München. Dawkins, R. (2008) Der Gotteswahn, p. 575. Ullstein, Berlin. Dembski, W. (2007) No free lunch: Why specified complexity cannot be purchased without intelligence. Rowman and Littlefield, Lanham, MD. Doolittle, W. F. & O. Zhaxybayeva (2007) Evolution: reducible complexity – the case for bacterial flagella. Curr Biol 17: R510-512. Ely, B., T. W. Ely, W. B. Crymes, Jr. & S. A. Minnich (2000) A family of six flagellin genes contributes to the Caulobacter crescentus flagellar filament. J Bacteriol 182: 5001-5004. Fehrer, J. (2009) Eine neue Phylogenie der Vögel: Was sagen die Daten wirklich? Stud. Int. J. 16: 315. Ferrer-Costa, C., M. Orozco & X. de la Cruz (2007) 30 Characterization of compensated mutations in terms of structural and physico-chemical properties. J Mol Biol 365: 249-256. Galan, J. E. (2008) Energizing type III secretion machines: what is the fuel? Nat Struct Mol Biol 15: 127-128. Galan, J. E. & H. Wolf-Watz (2006) Protein delivery into eukaryotic cells by type III secretion machines. Nature 444: 567-573. Galperin, M. Y. (2007) Dark matter in a deep-sea vent and in human mouth. Environ Microbiol 9: 23852391. Gavin, R., S. Merino, M. Altarriba, R. Canals, J. G. Shaw & J. M. Tomas (2003) Lateral flagella are required for increased cell adherence, invasion and biofilm for-mation by Aeromonas spp. FEMS Microbiol Lett 224: 77-83. Gene, M. (2003) Evolving the bacterial flagellum through mutation and cooption. In: http:// www.idthink.net/biot/index.html, files flag1 flag7. pp. Gene, M. (2007) The Design Matrix. A consilience of clues. Arbo Vitae Press, USA. Gerding, M. A., Y. Ogata, N. D. Pecora, H. Niki & P. A. de Boer (2007) The trans-envelope Tol-Pal complex is part of the cell division machinery and required for proper outer-membrane invagination during cell constriction in E. coli. Mol Microbiol 63: 1008-1025. Giron, J. A., A. G. Torres, E. Freer & J. B. Kaper (2002) The flagella of enteropathogenic Escherichia coli mediate adherence to epithelial cells. Mol Microbiol 44: 361-379. Gould, S. J. & R. C. Lewontin (1979) The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205: 581-598. Guerry, P. (2007) Campylobacter flagella: not just for motility. Trends Microbiol 15: 456-461. Gunnarsson, C. L., E. N. Karlsson, A. S. Albrekt, M. Andersson, O. Holst & M. Ohlin (2004) A carbohydrate binding module as a diversity-carrying scaffold. Prot. Eng,Design Sel. 17: 213-221. He, X. & J. Zhang (2005) Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics 169: 1157-1164. Hemminger, H. J. (2007) Mit der Bibel gegen die Evolution, p. 73. Evangelische Zentralstelle für Weltanschauungsfragen, Berlin. Hittinger, C. T. & S. B. Carroll (2007) Gene duplication and the adaptive evolution of a classic genetic switch. Nature 449: 677-681. Hovav, R., J. A. Udall, B. Chaudhary, R. Rapp, L. Flagel & J. F. Wendel (2008) Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant. Proc Natl Acad Sci USA 105: 6191-6195. Hughes, A. L. (1994) The evolution of functionally novel proteins after gene duplication. Proc. Biol. Sci. 256: 119-124. Hülter, N. & W. Wackernagel (2008) Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi. Mol Microbiol 67: 984-995. Jarrell, K. F. (2009) Pili and flagella. Current research and future trends. In. Norfolk. UK: Caister Academic Press, pp. 238. Jarrell, K. F., V. D.J. & J. Wu (2009) Archaeal flagella and Pili. In: Pili and flagella. K. F. Jarrell (ed). Norfolk, UK: Caister Academic Press, pp. 215234. Jarrell, K. F. & M. J. McBride (2008) The surprisingly diverse ways that prokaryotes move. Nat Rev Microbiol 6: 466-476. Jenal, U., J. White & L. Shapiro (1994) Caulobacter flagellar function, but not assembly, requires FliL, a non-polarly localized membrane protein present in all cell types. J Mol Biol 243: 227-244. Jha, G., R. Rajeshwari & R. V. Sonti (2005) Bacterial type two secretion system secreted proteins: double-edged swords for plant pathogens. Mol Plant Microbe Interact 18: 891-898. Jones, D. (2008) Uncovering the evolution of the bacterial flagellum. New Scientist Ausgabe 2643 vom 16.2.08: http://www.newscientist.com/ channel/life/mg19726431. 19726900.html. Journet, L., K. T. Hughes & G. R. Cornelis (2005) Type III secretion: a secretory pathway serving both motility and virulence. Mol Membr Biol 22: 41-50. Junker, R. (2002) Ähnlichkeiten, Rudimente, Atavismen. Holzgerlingen. Junker, R. & S. Scherer (2006) Evolution, ein kritisches Lehrbuch. Weyel Verlag, Gießen. Kaur, J. & R. Sharma (2006) Directed evolution: an approach to engineer enzymes. Crit Rev Biotechnol 26: 165-199. Kirov, S. M., M. Castrisios & J. G. Shaw (2004) Aeromonas flagella (polar and lateral) are enterocyte adhesins that contribute to biofilm formation on surfaces. Infect Immun 72: 1939-1945. Leigh, E. G., Jr. (1999) The modern synthesis, Ronald Fisher and creationism. Trends Ecol Evol 14: 495-498. Liang, H. & L. F. Landweber (2006) A genome-wide study of dual coding regions in human alternatively spliced genes. Genome Res 16: 190-196. Lillehoj, E. P., B. T. Kim & K. C. Kim (2002) Identification of Pseudomonas aeruginosa flagellin as an adhesin for Muc1 mucin. Am J Physiol Lung Cell Mol Physiol 282: L751-756. Liu, R. & H. Ochman (2007a) Origins of flagellar gene operons and secondary flagellar systems. J Bacteriol 189: 7098-7104. Liu, R. & H. Ochman (2007b) Stepwise formation of the bacterial flagellar system. Proc Natl Acad Sci U S A 104: 7116-7121. Liu, R. & H. Ochman (2007c) Stepwise formation of the bacterial flagellar system: Correction. Proc Natl Acad Sci U S A 104: 11507. [p. 31] Lodish, H., A. Berk, C. A. Kaiser & M. Krieger (2007) Molecular Cell Biology., p. 1296. Palgrave Macmillan, London. Loessner, M. J., S. Gaeng & S. Scherer (1999) Evidence for a holin-like protein gene fully embedded out of frame in the endolysin gene of Staphylococcus aureus bacteriophage 187. J Bacteriol 181: 4452-4460. Lowe, C. R. (2000) Nanobiotechnology: the fabrication and applications of chemical and biological nanostructures. Curr Opin Struct Biol 10: 428434. Lynch, M. (2002) Genomics. Gene duplication and evolution. Science 297: 945-947. Lynch, M. (2007) The frailty of adaptive hypotheses for the origins of organismal complexity. Proc Natl Acad Sci U S A 104 Suppl 1: 8597-8604. Lynch, M. & A. Force (2000) The probability of duplicate gene preservation by sub-functionalization. Genetics 154: 459-473. Lynch, M., M. O'Hely, B. Walsh & A. Force (2001) The probability of preservation of a newly arisen gene duplicate. Genetics 159: 1789-1804. Macnab, R. M. (2003) How bacteria assemble flagella. Annu Rev Microbiol 57: 77-100. Macnab, R. M. (2004) Type III flagellar protein export and flagellar assembly. Biochim Biophys Acta 1694: 207-217. Macnab, R. M. & J. S. Parkinson (1991) Genetic analysis of the bacterial flagellum. Trends Genet 7: 196-200. Matzke, N. J. (2006) Evolution in (Brownian) space: a model for the origin of the bacterial flagellum. In: http://www. talkdesign.org/faqs/ flagellum.html. pp. Matzke, N. J. (o.J.) Panda's Thumb website. http:// ttaxus. blogspot.com/2007/05/jcvi-evolutionary-genomics-journal-club.html. McQuiston, J. R., P. I. Fields, R. V. Tauxe & J. M. Logsdon, Jr. (2008) Do Salmonella carry spare tyres? Trends Microbiol 16: 142-148. Mercader, J. V. & A. Skerra (2002) Generation of anticalins with specificity for a non-symmetric phthalic acid ester. Anal Biochem 308: 269-277. Miller, K. R. (2004) The Flagellum Unspun. In: Debating Design: from Darwin to DNA. W. Dembski & M. Ruse (eds). New York.: Cambridge University Press, , pp. 81-97. Minamino, T. & K. Namba (2008) Distinct roles of the FliI ATPase and proton motive force in bacterial flagellar protein export. Nature 451: 485488. Monteiro-Neto, V., S. Y. Bando, C. A. Moreira-Filho & J. A. Giron (2003) Characterization of an outer membrane protein associated with haemagglutination and ad-hesive properties of enteroaggregative Escherichia coli O111:H12. Cell Microbiol 5: 533-547. Murphy, G. E., J. R. Leadbetter & G. J. Jensen (2006) In situ structure of the complete Treponema primitia flagellar motor. Nature 442: 1062-1064. Musgrave, I. (2004) Evolution of the bacterial flagellum. In: Why intelligent design fails. M. Young & T. Edis (eds). New Brundswick: Rudgers University Press, pp. 72-84. Mutschler, H. D. (2002) Naturphilosophie. Kohlhammer, Stuttgart. Mutschler, H. D. (2003) Gibt es Finalität in der Natur? In: Die andere Seite der Biologie. C. Kummer (ed). München: Books on Demand, pp. 2545. Nachtigall, W. & K. G. Blüchel (2000) Das Große Buch der Bionik – neue Technologien anch dem Vorbild der Natur., p. 398. Deutsche Verlagsanstalt, Stuttgart/München. Nather, D. J., R. Rachel, G. Wanner & R. Wirth (2006) Flagella of Pyrococcus furiosus: multifunctional organelles, made for swimming, adhesion to various surfaces, and cell-cell contacts. J Bacteriol 188: 6915-6923. Nelson, P. (2004) Interview. Touchstone Magazine 7/8. Nurse, P. (2008) Life, logic and information. Nature 454: 424-426. Ohta, T. (1989) Role of gene duplication in evolution. Genome 31: 304-310. Pallen, M. J. & N. J. Matzke (2006) From The Origin of Species to the origin of bacterial flagella. Nat Rev Microbiol 4: 784-790. Parthasarathy, G., Y. Yao & K. S. Kim (2007) Flagella promote Escherichia coli K1 association with and invasion of human brain microvascular endothelial cells. Infect Immun 75: 2937-2945. Paul, K., M. Erhardt, T. Hirano, D. F. Blair & K. T. Hughes (2008) Energy source of flagellar type III secretion. Nature 451: 489-492. Paulick, A., A. Koerdt, J. Lassak, S. Huntley, I. Wilms, F. Narberhaus & K. M. Thormann (2009) Two different stator systems drive a single polar flagellum in Shewanella oneidensis MR-1. Mol Microbiol 71: 836-850. Piatigorsky, J. (1992) Lens crystallins. Innovation associated with changes in gene regulation. J Biol Chem 267: 4277-4280. Piatigorsky, J. (2003) Gene Sharing, Lens Crystallins and Speculations on an Eye/Ear Evolutionary Relationship. Integr. Comp. Biol. 43: 492-499. Rajagopala, S. V., K. T. Hughes & P. Uetz (2009) Benchmarking yeast two-hybrid systems using the interactions of bacterial motility proteins. Proteomics 9: 5296-5302. Rajagopala, S. V., B. Titz, J. Goll, J. R. Parrish, K. Wohlbold, M. T. McKevitt, T. Palzkill, H. Mori, R. L. Finley, Jr. & P. Uetz (2007) The protein network of bac-terial motility. Mol Syst Biol 3: 128. Rastogi, S. & D. A. Liberles (2005) Subfunctionalization of duplicated genes as a transition state to neofunctionalization. BMC Evol Biol 5: 28. Ren, C. P., S. A. Beatson, J. Parkhill & M. J. Pallen (2005) The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli. J Bacteriol 187: 32 1430-1440. Ridley, M. (2004) Evolution. Blackwell Publishing, Oxford. Roth, C., S. Rastogi, L. Arvestad, K. Dittmar, S. Light, D. Ekman & D. A. Liberles (2007) Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. J Exp Zoolog B Mol Dev Evol 308: 58-73. Scherer, S. (1983) Basic functional states in the evolution of cyclic photosynthetic electron transport. J. Theor. Biol. 104: 289-299. Scherer, S. (2006a) Thesen: „Evolution und Schöpfung in der Schule“. http:// www.siegfriedscherer.de/schule.html. Scherer, S. (2006b) War Darwin unfehlbar? In: Rheinischer Merkur. Bonn, pp. 24. Scherer, S. (2008a) Hypothesen zur Evolution von Bakteriophagen-Holinen, Addendum zu Kap 16.2.2. http://www. evolutionslehrbuch.info/ teil-7.html. Scherer, S. (2008b) Intelligent Design ist keine naturwissenschaftliche Alternative zu biologischen Evolutionstheo-rien., p. 20. April 2008. http:// www.siegfriedscherer.de/idhtml. Scherer, S. (2009) Makroevolution molekularer Maschinen. Konsequenzen aus den Wissenslücken evolutionsbiologischer Naturforschung. In: Atheistischer und jüdisch-christlicher Glaube: Wie wird Naturwissenschaft geprägt? H. J. Hahn, R. McClary & C. Thim-Mabrey (eds). Norderstedt: Books on Demand, pp. 95-149. Schlehuber, S., G. Beste & A. Skerra (2000) A novel type of receptor protein, based on the lipocalin scaffold, with specificity for digoxigenin. J Mol Biol 297: 1105-1120. Sikorski, J. (2009) Die bakterielle Flagelle – Stand der Forschung zu molekularem Aufbau, Diversität und Funktion. In: Evolution im Fadenkreuz des Kreationismus. M. Neukamm (ed). Göttingen: Vandenhoeck & Ruprecht, pp. 262-301. Simpson, P. J., H. Xie, D. N. Bolam, H. J. Gilbert & M. P. Williamson (2000) The structural basis for the ligand specificity of family 2 carbohydrate-binding modules. J Biol Chem 275: 41137-41142. Skerra, A. (2007) Alternative non-antibody scaffolds for molecular recognition. Curr Opin Biotechnol 18: 295-304. Smart, J. A. (2003) On the application of irreducible complexity. http://www.iscid.org/pcid.php. Tasteyre, A., M. C. Barc, A. Collignon, H. Boureau & T. Karjalainen (2001) Role of FliC and FliD flagellar proteins of Clostridium difficile in adherence and gut colonization. Infect Immun 69: 79377940. Teshima, K. M. & H. Innan (2008) Neofunctionalization of duplicated genes under the pressure of gene conversion. Genetics 178: 1385-1398. Wadhams, G. H. & J. P. Armitage (2004) Making sense of it all: bacterial chemotaxis. Nat Rev Mol Cell Biol 5: 1024-1037. Wang, Q., A. Suzuki, S. Mariconda, S. Porwollik & R. M. Harshey (2005) Sensing wet-ness: a new role for the bacterial flagellum. EMBO J 24: 20342042. Wong, T., A. A., A. Dodds, S. Siddiqi, J. Wang, T. Yep, D. G. Tamang & M. H. Saier (2007) Evolution of the bacterial flagellum. Microbe 2: 335340. Xu, L., P. Aha, K. Gu, R. G. Kuimelis, M. Kurz, T. Lam, A. C. Lim, H. Liu, P. A. Lohse, L. Sun, S. Weng, R. W. Wagner & D. Lipovsek (2002) Directed evolution of high-affinity antibody mimics using mRNA display. Chem Biol 9: 933-942. Yokoseki, T., K. Kutsukake, K. Ohnishi & T. Iino (1995) Functional analysis of the flagellar genes in the fliD operon of Salmonella typhimurium. Microbiology 141 ( Pt 7): 1715-1722. Yu, J. & L. Shapiro (1992) Early Caulobacter crescentus genes fliL and fliM are required for flagellar gene expression and normal cell division. J Bacteriol 174: 3327-3338. Zhai, Y. F., W. Heijne & M. H. Saier, Jr. (2003) Molecular modeling of the bacterial outer membrane receptor energizer, ExbBD/TonB, based on homology with the flagellar motor, MotAB. Biochim Biophys Acta 1614: 201-210. Zhang, J. (2003) Evolution by gene duplication: an update. Trends Ecol. Evol. 18: 292-298.

I'm going from memory about the spontaneous generation. Will try to find some direct quotes in the not too distant future.

There's a quote I've been desperate to find about heart function. I remember seeing a documentary about medical history that quoted a pre-scientific anatomist saying that the function of the heart was to filter blood from one ventricle to the other. The fact that blood does not leak from one side to the other in sheep's hearts was taken as proof of divine intervention with every heartbeat. I've always wanted to find that quote, but it has eluded my searches (it would help if I could remember the name of the documentary).

Chris Lawson said: I'm going from memory about the spontaneous generation. Will try to find some direct quotes in the not too distant future.

Chris, you're likely thinking of Aelius Galenus (http://en.wikipedia.org/wiki/Galen), who was undeniably important for anatomy and physiology, but postulated structures (such as the heart-filter) which simply don't exist.

co, thanks for the Galen link. I know that Galen was an amazing scientist for his time who had the misfortune to become the Official Doctrinal Figure on medicine and thus all of his mistakes became ossified as medical canon for centuries, and now the mistakes are what he's mostly remembered for.

I'll have to look through Galen's work for that quote, but I don't know if he said it or if it was one of the many commentators who followed.

Reply to Nick Matzke's translation:

Very nice. One thing that stood out for me was Paul Nelson's repeating what Phillip Johnson was reported to have said some years ago:

"The theme has also Paul Nelson as an important representative of ID: “Easily the biggest design challenge facing the ID community is to develop a full-fledged theory of biological. We do not have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuition, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’ - but, as yet, no general theory of biological design. “(Nelson 2004).

This still holds true today. But I'm sure those at the Dishonesty Institute's puppet pseudo-science lab are hard at work on this very issue.

As for Behe's comment:

"The conclusion is m. E. obvious that the total probability considered for the evolutionary step is very small. How small? Behe writes: “However, as the complexity of an interacting system increases, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin’s criterion of failure has been met Skyrockets toward the maximum that science allows. “(Behe 1996).

So then what is the probability of winning PowerBall? It certainly isn't infinitely small, and someone wins every few weeks, a totally random affair. And he is basing in reasoning on what? Creationist assertions.

I know you hate to admit it Matzke, but you KNOW Behe was right.

In order to show that Behe was wrong, you need to demonstrate first, how many intermediate steps there are on the road to bacterial flagellum land ( I count at least 10 steps) and second, what the functions for each of these intermediate steps are. (I understand you may believe this to be an unfair burden to you (pl). However, it is crucial to your refutation of Behe. Note your first attempt at refutation with the assertion of T3SS secretion system as being a precursor to the b/f has failed, since it has been shown that T3SS is most likely a devolution of and not a precursor to the b/f).

For example, the b/f had to be built from the basal body outwards. The basal body is fixed to the inner membrane. So what was the function of the basal body fixed in the inner membrane before it added the C-Ring?

Next, what was the function of the basal body and the C-Ring before it added the MS-Ring?

After that, we need to know the function of the next intermediate step, the basal body + C-Ring + MS-Ring.

Moving along, what is the function of the basal body + C-Ring + MS-Rings + the newly added stators? Note for these intermediate steps in the flagelllum's development, the new parts are placed in the periplasmic space. What advantage would the function of these intermediate configurations be considering the fact that these new parts are neither within the cell (to presumably support internal functions) nor outside of the cell (to presumably support locomotion or defense)?

Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?

Steve P. said: Why would a scientist discard such an intuition when all the observations point in this direction?

Mike Elzinga,

Paul Davies also uses the "it's improbable therefore designed" argument as well (although he's too sophisticated to propose an anthropomorphic designer; he's more of a Spinozan, not that it stopped him taking the Templeton bait). A properly shuffled deck of cards has 8x10^67 possible orderings -- which means by Davies/Behe logic, you can't shuffle a pack of cards because any given combination is so unlikely.

Mike Elzinga said:

Steve P. said: Why would a scientist discard such an intuition when all the observations point in this direction?

By the same logic, icicle formation is also impossible. In order for a water molecule to lock into a particular position, it has to be oriented just right; exactly the right amount of energy has to be removed, and it cannot be dislodged by the impact of an air molecule whizzing by. On top of all that, the molecule has to have migrated along a path of an already improbably formed nascent icicle in order to find itself in just exactly the right position when the energy release occurs and it locks into position. Even more fantastic is the final formation of the icicle. How could it possibly be in exactly that shape with all the various bands and wrinkles along its length and with exactly those neighboring icicles of the size and shape they have? And this is just the simple stuff. How about superconductivity? How is it possible for a phonon to exactly coordinate the movement of two electrons, one with spin up the other with spin down? When this happens with billions upon billions of such pairs, the probability is astronomically small. Yet these billions and billions of electrons are chosen and paired off in “Cooper pairs” so that they become a collection of bosons that then condense into a superconducting state in which they flow through the solid material without any resistance whatsoever. If they have no resistance, how do they interact with the phonons that are singling them out and pairing them off into Cooper pairs? Ever look at the sequence of license plate numbers in the huge parking lot of a large shopping mall? What is the probability you would find that sequence? How could those cars be there; and how could those particular car owners be in that shopping mall at the same time? According to Behe’s logic, the world doesn’t exist.

For example, spontaneous generation. When it was thought to be true, it was undeniable proof of God’s creation. Now that we know it to be false, it is *lack* of spontaneous generation that is undeniable proof of God’s creation.

— Chris Lawson

...most of the chapter seems to be taken up with attempting to refute the evolutionary model for the origin of the flagellum!

— Nick Matzke

Steve P. said: I know you hate to admit it Matzke, but you KNOW Behe was right. In order to show that Behe was wrong, you need to demonstrate first....

MrG said: At least this PDF is further proof that creationism isn't just an American lunacy. Takes the pressure off ... a little bit.

Steve P. said: Why would a scientist discard such an intuition when all the observations point in this direction?

Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)?

Why would a scientist discard such an intuition when all the observations point in this direction?

That should be "do not reply to this part of my comment without first answering all of the questions above.

Steve P. said: Mr. Elzinga, I understand your viewpoint that you believe physics and chemistry account for all manner of material configurations whether they be inanimate or animate.

Yet, there are crucial differences in your icicle analogy: 1) the water molecule that accounts for the icicle is no special or particular variant of H2O.

2) the icicle is formed by only one molecule- water. It is not a configuration of numerous, disparate molecules;

the icicle does not exhibit function. The water molecules in the icicle do not move in any manner that represents work (the expending of energy in the transformation from one particular molecular configuration into another for a particular purpose i.e locomotion, catalysis, sensory perception, etc.

Really, we are talking apples and oranges here.

Rather it is that one particular protein set is configured in a particular way in juxtaposition to another, albeit different protein set configured in its own particular arrangement, and this is done several times.

But that is not what we are observing. What we do observe is particular sets of proteins configured in particular patterns, and each protein configuration are themselves configured into a meta-pattern resulting in a functional organelle.

So the question becomes ‘what causes proteins to align themselves in particular patterns and these patterns themselves arranged into meta-patterns (resulting in a pattern that begins to perform work) from a physics and chemistry POV?

So you would claim that benzene is impossible because it is arranged in a “circular pattern?”

— Mike Elzinga

What really gets me is the inefficiency and downright stupidity of the mechanism that Steve proposes. I mean really, an all knowing, all powerful god who could not do any better than to strap every organism with all of the different variations of every gene they might ever need for any possible future environment for all time. Man, what a waste.

Now if god were really that concerned, all she would have to do would be to create a mechanism whereby variation could arise my random processes and then selection could take over. That would produce the same result much more efficiently.

Notice how the lack of knowledge and lack of imagination displayed by Steve automatically translates into a lack of competence for his supposed god. Also notice the absolute reluctancee to try to find any evidence for the pooposed mechanism.

Come on dude, this should be easy. All you have to do is sequence the entire genome of any organism. Then all you have to do is to point out all of the multiple copies of all of the genes containing all of the alleles in every other individual of that species. No wait ... never mind.

The fact that Steve is willing to believe things that are demonstrable false in order to preserve some reason to believe in god is a testament to his complete lack of faith. And you know what the bible has to say about that.

Steve P. said: I know you hate to admit it Matzke, but you KNOW Behe was right. In order to show that Behe was wrong, you need to demonstrate first, how many intermediate steps there are on the road to bacterial flagellum land ( I count at least 10 steps) and second, what the functions for each of these intermediate steps are. (I understand you may believe this to be an unfair burden to you (pl). However, it is crucial to your refutation of Behe. Note your first attempt at refutation with the assertion of T3SS secretion system as being a precursor to the b/f has failed, since it has been shown that T3SS is most likely a devolution of and not a precursor to the b/f). For example, the b/f had to be built from the basal body outwards. The basal body is fixed to the inner membrane. So what was the function of the basal body fixed in the inner membrane before it added the C-Ring? Next, what was the function of the basal body and the C-Ring before it added the MS-Ring? After that, we need to know the function of the next intermediate step, the basal body + C-Ring + MS-Ring. Moving along, what is the function of the basal body + C-Ring + MS-Rings + the newly added stators? Note for these intermediate steps in the flagelllum's development, the new parts are placed in the periplasmic space. What advantage would the function of these intermediate configurations be considering the fact that these new parts are neither within the cell (to presumably support internal functions) nor outside of the cell (to presumably support locomotion or defense)? Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?

Steve P. said: I know you hate to admit it Matzke, but you KNOW Behe was right. In order to show that Behe was wrong, you need to demonstrate first, how many intermediate steps there are on the road to bacterial flagellum land ( I count at least 10 steps) and second, what the functions for each of these intermediate steps are. (I understand you may believe this to be an unfair burden to you (pl). However, it is crucial to your refutation of Behe. Note your first attempt at refutation with the assertion of T3SS secretion system as being a precursor to the b/f has failed, since it has been shown that T3SS is most likely a devolution of and not a precursor to the b/f). For example, the b/f had to be built from the basal body outwards. The basal body is fixed to the inner membrane. So what was the function of the basal body fixed in the inner membrane before it added the C-Ring? Next, what was the function of the basal body and the C-Ring before it added the MS-Ring? After that, we need to know the function of the next intermediate step, the basal body + C-Ring + MS-Ring. Moving along, what is the function of the basal body + C-Ring + MS-Rings + the newly added stators? Note for these intermediate steps in the flagelllum's development, the new parts are placed in the periplasmic space. What advantage would the function of these intermediate configurations be considering the fact that these new parts are neither within the cell (to presumably support internal functions) nor outside of the cell (to presumably support locomotion or defense)? Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?

Steve wrote:

"But that is not what we are observing. What we do observe is particular sets of proteins configured in particular patterns, and each protein configuration are themselves configured into a meta-pattern resulting in a functional organelle."

Look dude, you have been shown the evidence that organelles evolved. The fact that you refused to look at the evidence doesn't mean that it doesn't exist, it just means that you are no longer entitled to an opinion on the matter. Those of us who have looked at the evidence have concluded that you have no idea what you are talking about.

I can't believe that anyone who refuses to look at the evidence would think that their opinion was of any worth, therefore I conclude that you must not really believe this crap either.

Chris Lawson said: I know that Galen was an amazing scientist for his time who had the misfortune to become the Official Doctrinal Figure on medicine and thus all of his mistakes became ossified as medical canon for centuries, and now the mistakes are what he's mostly remembered for.

DS said: I can't believe that anyone who refuses to look at the evidence would think that their opinion was of any worth, therefore I conclude that you must not really believe this crap either.

Mike Elzinga said: It appears that all this Steve P. ever does is pop in here from time to time and sling some ID/creationist feces just to stir things up.

Steve wrote:

"Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?"

Bullpuckey. Look dude, once again, if you are unable or unwilling to look at the evidence, exactly how do you know what all of the observations point to? You do know that we have many complete genome sequences already, don't you?

I'll make you a deal. I will provide a free link to a paper that examined evolution in dog breeds. The paper analyzed dog genomes and determined the details of exactly what type of mutations were responsible for the morphological changes associated with domestication and selection for different breeds. It details the molecular mechanisms of the mutations and the lineages in which specific mutations occurred. The mechanisms are all well understood stochastic processes that produced the observed variation without any programming.

All you have to do is provide evidence for your programming hypothesis. Examine the dog genome sequences and provide evidence that the program exists. You should also be able to decode the program in order to predict exactly how dog evolution should proceed and how it can accommodate any potential environmental changes or future selection pressures. If you are unable or unwilling to provide any evidence for your hypothesis, then kindly piss off and stay pissed.

Come on dude, the complete genome sequences are readily available. All you have to do is analyze the sequences and publish your results. Fame and fortune await. You don't even have to do any lab work, that has already been done for you. I would really like to believe in this magically programmer, really I would. Here is your big chance, go for it.

Behe was a deluded moron, and so are you.

I would not be surprised if some of these schmucks are studying “evilutionist” responses in order to construct better obfuscations they can use to club rubes with.

harold said: Dale Husband -

Behe was a deluded moron, and so are you.

I must correct a major error here. By writing "was", the past tense, you imply that Behe is either dead, or even more improbably, cured of being a deluded moron. All available evidence suggests that Behe is a deluded moron.

SteveP,

I'll make this easier for you. If I provide the free link, will you at least promise to read the paper? If you read the paper, will you explain the observed level of linkage disequilibrium? You see, if all of the variation is programmed in, there is absolutely no reason for any linkage disequilibrium. If, on the other hand, the variation arose by random mutations that were acted on by selection, significant linkage disequilibrium is expected.

Now, all you have to do is explain why the observed level of linkage disequilibrium is better explained by your hypothesis than by the mutation and selection hypothesis. You claimed that "all observations point in this direction", right? So you can account for all of the observations better than the alternative hypothesis, right? Well, here is your chance. Go for it due. Wes a waitin.

Or are you just going to run away again as you did in response to the evidence for endosymbiosis? Thought so.

harold said: What probably happens with Steve P is that he sneaks into the grown-up section once in a while for one or more of the reasons above. He sees something that sets off a deeply muffled alarm bell in some obscure part of his brain. He transiently drowns it out by shouting his tick-like slogans (tick as in involuntarily repeated gesture). Then he sees the challenges rolling in, full panic takes over, and he flees back to isolation, where he fully indulges in all the rituals which help him overcome cognitive dissonance. Eventually the cognitive dissonance wears off, the fantasies of greatness begin again, and the cycle plays itself again.

Steve P,

Still nothin huh? Well, I can make it even easier. You don't even have to read the paper. Just explain the distribution of mutations observed in the different dog breeds. You know, why are there beneficial mutations in some breeds and not others? Why are there deleterious mutations in any breeds? Did god plan to cripple some dog breeds deliberately, did they do something to offend the programmer?

Once again, you should note that the observed distribution is exactly what is predicted if the mutations arose randomly by the mechanisms described and were strongly selected on. Your explanation needs to not only explain the pattern, it needs to explain it better than the alternative hypothesis.

So there you go man. Three chances to prove your hypothesis, each easier than the last. If you don't come through, some people might be tempted to concludes that you were just making up crap and you really don't have a clue about anything. Prove em wrong man, prove em wrong. Wes still a waitin.

Even human designed machines such as a computer are made of smaller parts that themselves can have functions completely unrelated to computer operations. Indeed, one must note that in biology, there are various levels of organization, with a body of an human being made of systems, the systems made of organs, the organs made of tissues, the tissues made of cells, those cells composed of organelles, those organelles made of molecules, those molecules made of atoms, and the atoms made of electrons, protons and neutrons. Thus, nothing in biology beyond the atomic level may be irreducibly complex in the sense that they cannot be taken apart and the parts examined. So why did Intelligent Design promoters come up with such an absurd scheme? Part of the reason stems from an assumption, completely unfounded, that every part of an organism must exist for only one purpose and that only one part of a more complex system must have been added at a time. There is absolutely no basis for this idea. Let us return to the analogy of the computer to understand why. The first electronic computers were invented in the 1940s and consisted entirely of vacume tubes and bundles of wires. They had no viewscreens (we call these monitors), no mice, no printers, and nothing like hard drives at all. Despite lacking these devices, they functioned quite adequatly for the needs of their time. Today, of course, such slow and bulky computers would be useless and are nothing more than museum relics. Likewise, it is possible that very simple life forms that were perfectly adapted to the environments of Earth billions of years ago could not possibly survive today because the more advanced life forms around now would eliminate them. Meanwhile, the television was invented and went through various stages, none of which involved computers. But eventually, engineers figured out how to have a primitive computer send signals to make an image on a television screen. Once that was done, television like devices could be manufactured exclusively for computers, but they were called "monitors" to make them seem special. But anyone can see that they have the same form and operate the same way as television sets, lacking only a reciever for TV signals and having wires linking to the computer instead. There is evidence that mitochondria and chloroplasts, so vital for the survival of animals and plants today, were originally free-living bacteria that took up residence inside larger cells, helping the larger cells survive better than their rivals while enjoying the larger cells' protection. Today, we cannot imagine an animal cell without mitochrondria or plant cells without chloroplasts, for they would not survive today at all. But there are bacteria even today that resemble chloroplasts and mitochondria, and cells more like ours than any bacteria (archaea) that possess neither of these organelles. Likewise, it is possible for a computer to exist without a monitor (most people have one or more, they are called calculators), and nearly everyone has a television today as well. It's just that certain computers in their specific form cannot function properly without monitors. But that is no argument that these computers' ancestors could never have functioned without monitors. We know they did. Likewise, just because something like a bacterial flagellum in its specific form may not function as flagella if one of its molecular parts is removed does not mean that it could not have come about naturally. Remember what I said about the television being modified to serve as a computer monitor? The individual molecules in the flagellum are made of the same substances as the rest of the bacteria, and with some modification the ancestors of the flagella bearing bacteria could have had different functions for the things which would only later become flagella. Assuming that flagella were always flagella and could have been nothing else explains nothing and produces nothing useful. Intelligent Design promoters claim that if something in a life form is "irreducibly complex" (removal of any part would make the whole structure fail), then that is proof of what they believe, that a higher intelligence made it. Actually, anyone that would make such a structure would be failing to prove his intelligence is superior to humans at all, because such a thing would actually be evidence of FLAWED design. Any good design of a complex machine made by humans would include backups in case something went wrong with some part of it. You'd think a creator of man and all other creatures would have demonstrated simular foresight. Natural selection, on the other hand, CAN account for irreducible complexity in an organism. Once such a system is put together, the organism would be favored by natural selection over any of the same kind that lack the irreducibly complex structure. At the same time, there would be no reason for the structure to become MORE complex than it has to be just to function. All that matters is that an organism survive long enough to reproduce itself. If it does so with the irreducibly complex structure and not without it, then it would be pointless to evolve complexity any further. An organism with more complexity than required to survive and reproduce itself would actually be wasting biological resources. So irreducible complexity of certain structures is not only NOT a good argument against evolution by natural selection, it actually SUPPORTS it and NOT Intelligent Design!

1) What would be the exact physical nature of such a "program"?

2) What would be the exact physical nature of the receptor for the environmental cue?

3) Can you look for these "programs"? Can you identifiy them and show how they are "triggered"? That would seem like a remarkably easy way for you to turn science on its ear and win a Nobel prize. Recognition of your "great genius" at last. Precisely as you constantly and obsessively fantasize. What's stopping you?

harold said: Steve P -

Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)?

1) What would be the exact physical nature of such a "program"? 2) What would be the exact physical nature of the receptor for the environmental cue? 3) Can you look for these "programs"? Can you identifiy them and show how they are "triggered"? That would seem like a remarkably easy way for you to turn science on its ear and win a Nobel prize. Recognition of your "great genius" at last. Precisely as you constantly and obsessively fantasize. What's stopping you? Please note that YOU are the one who is making this vague claim, so the onus is on YOU to provide support for it.

Why would a scientist discard such an intuition when all the observations point in this direction?

DO NOT REPLY TO HIS PART OF MY COMMENT WITHOUT FIRST ANSWERING ALL OF THE QUESTIONS ABOVE. Because it is not an "intuition" at all, but a desperate, vague, meaningless rationalization of science denial, which no observations whatsoever point to. Prove me wrong by providing good answers to my questions.

stevaroni said:

Steve P. said: I know you hate to admit it Matzke, but you KNOW Behe was right. In order to show that Behe was wrong, you need to demonstrate first....

Yawn..... No. Behe claimed, rather clearly, that the flagellum was a deal breaker because getting there was impossible. In order to refute that sweeping claim you don't have to demonstrate that you've found the path, you just have to show that at least one path exists. Once you prove it's possible to grow a flagellum, an argument that relies exclusively on it being impossible just whithers away and dies. Q.E.D.

Steve P. said: But in the case of biology, things are inverted. The space in the cup is information; and it (information) defines the shape of the ceramic material.

Now how about passing your darwinian evolution grant monies my way. Then I can hang up my textile hat and put on that white lab coat.

Shorter Steve P: "I don't know, in fact, I don't know anything or care to know anything about science. But that doesn't stop me from knowing better than all the miserable, godless scientists of the world! It's too complicated for evil Darwinian principles to create things with just yucky random chance, therefore, GOD An Intelligent Designer did it! I have no proof of this, though, but, I know it's true because my hero, Michael Behe told me so, and he knows better than all those evil godless scientists, too!

Steve P. said: Harold, Not all that surprising that you would studiously avoid trying to explain from a darwinian evolutionary POV the functional intermediate configurations of the basal proteins. C-Ring proteins, MS-Ring proteins, stator proteins, etc. Rather, you gravitated to the rhetorical question I placed at the conclusion of my remarks. You never fail to grab that bone and run with it. Why is that? As to your questions, (which I will studiously NOT avoid answering):

1) What would be the exact physical nature of such a "program"?

I have no idea. That's what makes science all that more interesting. Figuring out a way to detect programming that doesn't lend itself to DIRECT physical detection. Therefore it would have to be done indirectly. Kind of like defining the space in a cup by measuring the ceramic material surrounding that space. But in the case of biology, things are inverted. The space in the cup is information; and it (information) defines the shape of the ceramic material.

2) What would be the exact physical nature of the receptor for the environmental cue?

Ditto answer in no. 1., I have no idea. I suspect it will not be found as a single point in the organism. It would be a meta-location.

3) Can you look for these "programs"? Can you identifiy them and show how they are "triggered"? That would seem like a remarkably easy way for you to turn science on its ear and win a Nobel prize. Recognition of your "great genius" at last. Precisely as you constantly and obsessively fantasize. What's stopping you?

That is a good 21st century question that science should TRY to answer. See, ID DOES have major research potential. And yes, ID has the greatest potential to transform the way science is conducted in the 21st century. Exciting times. Now how about passing your darwinian evolution grant monies my way. Then I can hang up my textile hat and put on that white lab coat.

Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?

That is a good 21st century question that science should TRY to answer. See, ID DOES have major research potential. And yes, ID has the greatest potential to transform the way science is conducted in the 21st century. Exciting times.

Dale Husband said:

That is a good 21st century question that science should TRY to answer. See, ID DOES have major research potential. And yes, ID has the greatest potential to transform the way science is conducted in the 21st century. Exciting times.

What are you, a professional con artist?!

Mike Elzinga said: Did you ever send in a proposal to find out how “information” interacts with matter? Is it one of the four known forces in nature that have been studied in physics? You were asked this before, but you didn’t answer it. No creationist has ever answered it. Why is that?

Harold, Not all that surprising that you would studiously avoid trying to explain from a darwinian evolutionary POV the functional intermediate configurations of the basal proteins. C-Ring proteins, MS-Ring proteins, stator proteins, etc.

Sure, anything is possible. adidas says ‘impossible is nothing’. But we are not talking about possibilities here. We are asking did it in fact happen the way darwinian evolution says it did.

I know you hate to admit it Matzke, but you KNOW Behe was right.

SteveP wrote:

"I have no idea. That’s what makes science all that more interesting. Figuring out a way to detect programming that doesn’t lend itself to DIRECT physical detection.
Therefore it would have to be done indirectly. Kind of like defining the space in a cup by measuring the ceramic material surrounding that space.
But in the case of biology, things are inverted. The space in the cup is information; and it (information) defines the shape of the ceramic material.
Ditto answer in no. 1., I have no idea. I suspect it will not be found as a single point in the organism. It would be a meta-location.
That is a good 21st century question that science should TRY to answer. See, ID DOES have major research potential. And yes, ID has the greatest potential to transform the way science is conducted in the 21st century. Exciting times."

What a crock. This guy has no hypothesis, doesn't even have a clue what he is looking for. And yet he deludes himself that this crap still has major research potential! What a crock. It might be something that you can't even detect physically, but you can still perform experiments for it. Yea, right. If there is so much "research potential", what is ya waitin fer? Get to it man. Commence to expertimentin.

So to recap, no testable hypothesis, no mechanism, no predictions and no possible experiments, got it.

Here is a new flash for you Steve, we know the basic mechanism of inheritance. We figured it out one hundred and fifty years ago. If there is a secret program hidden anywhere, it's in the DNA. You won't even look there, so how would you know? Now until you have another mechanism, another real hypothesis and some real evidence, kindly piss off.

Oh and you still haven't explained any of the actual evidence that proves that you are spectacularly wrong. I'll make it even easier for you, just explain poodles. God preprogrammed poodles, right? Yea, right. Good one.

Dale Husband said: What are you, a professional con artist?!

Chris Lawson said: A properly shuffled deck of cards has 8x10^67 possible orderings -- which means by Davies/Behe logic, you can't shuffle a pack of cards because any given combination is so unlikely.

And as an ID/creationist you have bought the shtick that chemistry and physics no longer apply beyond some level of complexity.

Yet not one of you has ever been able to elucidate the law of nature that prevents the evolution of complexity and energy-driven organization all the way up to living organisms. You simply assert this doesn’t happen despite all the evidence to the contrary.

So are you claiming that the water in living organisms is different from “ordinary water?” What is it about the water molecule in living organisms that is different?

So are you claiming that more complex compounds, such as those found in organic chemistry, don’t obey the laws of chemistry and physics?

Are you claiming that particular juxtapositions of atoms or compounds exempt them from being subject to the laws of chemistry and physics? At what level of complexity does this notion of juxtaposition start overriding the laws of chemistry and physics?

So you would claim that benzene is impossible because it is arranged in a “circular pattern?”

So you are also seeming to suggest that molecules below a certain level of complexity – you gave the example of water molecules – are capable of forming icicles but more complex arrangements of atoms and molecules are not capable of doing this. Where is the boundary between those complexes that can make arrangements and those that can’t?

Where do the laws of chemistry and physics stop working in a complex system?

What is this business of “function” all about? What is it about a set of molecules having some “function” that suddenly makes them immune to the laws of chemistry and physics?

harold said: Dale Husband -

Behe was a deluded moron, and so are you.

I must correct a major error here. By writing "was", the past tense, you imply that Behe is either dead, or even more improbably, cured of being a deluded moron. All available evidence suggests that Behe is a deluded moron.

John Kwok said: The last time I checked - according to a Lehigh undergraduate who was registered in one of his advanced biochemistry classes - he most certainly is. And if anyone should doubt this, then take a look at his "musings" replete in their breathtaking inanity at his author's blog over at Amazon. Simply priceless for their consistent ignorance and stupidity IMHO:

harold said: Dale Husband -

Behe was a deluded moron, and so are you.

I must correct a major error here. By writing "was", the past tense, you imply that Behe is either dead, or even more improbably, cured of being a deluded moron. All available evidence suggests that Behe is a deluded moron.

Steve P. said:

And as an ID/creationist you have bought the shtick that chemistry and physics no longer apply beyond some level of complexity.

I am not sure why you insist on arguing around the obvious. You deny your own senses when you look at a mouse and say to yourself, 'geez it is essentially the same as a rock just softer, and it shits, and it bites, and it reproduces rapidly, and it sleeps, but it is still essentially the same as a rock.' So really, who is buying into what shtick?!

Yet not one of you has ever been able to elucidate the law of nature that prevents the evolution of complexity and energy-driven organization all the way up to living organisms. You simply assert this doesn’t happen despite all the evidence to the contrary.

And again, i say to you if life is inherent in the laws of physics and chemistry ONLY, then we should logically see all manner of life forms (and not necessarily carbon/water based) all over the universe. We DO NOT see this happening. Therefore, logically we can say that life does in fact have some element in it that is not present in inanimate matter. Whether it is a material based element in the form of higher-energy (soul perhaps) or something non-detectable with current scientific methods (information), we do not yet know. But just because it is difficult to figure out should not lead us to conclude that there is essentially no difference between the two. There is a HUGE chasm of difference. No scientist would say, sorry no we can't consider undetectable light energy, no we can't consider information as causes of functional complexity. Soul and information are on the table whether you like it or not and regardless if a way has not yet been established to confirm either. This is what 21st century science is working towards.

So are you claiming that the water in living organisms is different from “ordinary water?” What is it about the water molecule in living organisms that is different?

We are not comparing the water in your icicles to the water in organisms. We are comparing icicles to organisms. Organisms have countless unique molecules arranged in myriad configurations all interacting in coordinated ways in order to do work. Icicles have only one molecule, water. They are not arranged in myriad configurations. The do not interact in coordinated ways to do work. Different animals.

So are you claiming that more complex compounds, such as those found in organic chemistry, don’t obey the laws of chemistry and physics?

It is not the issue of obeying only laws of physics and chemistry. Both do. But organisms also obey an as yet undetermined law. This is obvious. We see it with our eyes. It is what differentiates organisms from icicles. Let us work to find out just what law organisms obey over and above the laws of physics and chemistry.

Are you claiming that particular juxtapositions of atoms or compounds exempt them from being subject to the laws of chemistry and physics? At what level of complexity does this notion of juxtaposition start overriding the laws of chemistry and physics?

No, I am claiming that molecules in organisms are arranged into meta-patterns that perform work. compounds are not arranged into meta-patterns and they do no work. Different animals again.

So you would claim that benzene is impossible because it is arranged in a “circular pattern?”

Tell me, is Benzene only found arranged in a circular pattern in nature? Or can it be found naturally in countless different arrangements?

So you are also seeming to suggest that molecules below a certain level of complexity – you gave the example of water molecules – are capable of forming icicles but more complex arrangements of atoms and molecules are not capable of doing this. Where is the boundary between those complexes that can make arrangements and those that can’t?

It is the interaction of innumerable configurations of molecules that makes the difference, not the existence of complex molecules themselves. The boundary is the million dollar question. But let us not deny that a boundary exists. It is obvious that a boundary exists. What it consists of, let us dig in.

Where do the laws of chemistry and physics stop working in a complex system?

That is not the question I try to evoke. The question is 'What is working aside from physics and chemistry that creates the boundary between inanimate and animate life." You will inevitably retort that there is no reason to ask this question. But I will point to my previous comment that if it is ONLY physics and chemistry then there is no boundary and life must pop up anywhere and everywhere all over the universe since life is an inherent property of physics and chemistry.

What is this business of “function” all about? What is it about a set of molecules having some “function” that suddenly makes them immune to the laws of chemistry and physics?

Again, they are not immune to the laws of physics and chemistry. However, they do obey at least one additional law. This is obvious. It is for inquiring minds to figure out just what that law(s) consists of.

1) What would be the exact physical nature of such a “program”?

I have no idea.

That’s what makes science all that more interesting. Figuring out a way to detect programming that doesn’t lend itself to DIRECT physical detection. Therefore it would have to be done indirectly. Kind of like defining the space in a cup by measuring the ceramic material surrounding that space. But in the case of biology, things are inverted. The space in the cup is information; and it (information) defines the shape of the ceramic material.

2) What would be the exact physical nature of the receptor for the environmental cue?

Ditto answer in no. 1., I have no idea.

I suspect it will not be found as a single point in the organism. It would be a meta-location.

3) Can you look for these “programs”? Can you identifiy them and show how they are “triggered”? That would seem like a remarkably easy way for you to turn science on its ear and win a Nobel prize. Recognition of your “great genius” at last. Precisely as you constantly and obsessively fantasize. What’s stopping you?

That is a good 21st century question that science should TRY to answer. See, ID DOES have major research potential. And yes, ID has the greatest potential to transform the way science is conducted in the 21st century. Exciting times.

Now how about passing your darwinian evolution grant monies my way. Then I can hang up my textile hat and put on that white lab coat.

No, Behe was assuming that because he couldn't imagine a way for flagella to arise via evolution, it couldn't have happened. But the universe does not have to conform to his limited imagination. Behe stupidly used a mousetrap as an example of an "irreducibly complex" structure, ignoring three obvious points: 1. Mousetraps cannot reproduce themselves. Strike one! 2. There are many ways to build a mouse trap. One can remove all the other parts and just have a sticky paper on the block of wood to trap the mouse. Strike two! 3. There are many uses for the components of a mousetrap. For example, you can use some of them as a paperclip. Strike three, you're OUT!

Behe was a deluded moron, and so are you.

Steve P. said: You will inevitably retort that there is no reason to ask this question. But I will point to my previous comment that if it is ONLY physics and chemistry then there is no boundary and life must pop up anywhere and everywhere all over the universe since life is an inherent property of physics and chemistry.

Again, they are not immune to the laws of physics and chemistry. However, they do obey at least one additional law. This is obvious. It is for inquiring minds to figure out just what that law(s) consists of.

Steve P. said: Dale,

No, Behe was assuming that because he couldn't imagine a way for flagella to arise via evolution, it couldn't have happened. But the universe does not have to conform to his limited imagination. Behe stupidly used a mousetrap as an example of an "irreducibly complex" structure, ignoring three obvious points: 1. Mousetraps cannot reproduce themselves. Strike one! 2. There are many ways to build a mouse trap. One can remove all the other parts and just have a sticky paper on the block of wood to trap the mouse. Strike two! 3. There are many uses for the components of a mousetrap. For example, you can use some of them as a paperclip. Strike three, you're OUT!

1) What the heck does reproduction have to do with the mousetrap analogy??? Strike one! 2) Have you tried to catch a mouse with sticky paper? Even roaches know to avoid them. Strike two! 3) The fact that a mousetrap can be used as a paperclip is irrelevant to the argument. Take the hook out and no mousetrap. Take off the base and no mousetrap. Take off the spring and no mousetrap. Strrrrrrrriiiiiiiike, three! You're outta heeeeea.

Behe was a deluded moron, and so are you.

Yeah, maybe so but I at least I can pitch better than you. So what does that make you, a loser?. Nah, just a poor pitcher. You ought to work on that curve ball a bit more; it comes over more like a knuckle ball. :)

Steve P. said: Tell me, is Benzene only found arranged in a circular pattern in nature? Or can it be found naturally in countless different arrangements?

Paul Burnett said:

Steve P. said: Tell me, is Benzene only found arranged in a circular pattern in nature? Or can it be found naturally in countless different arrangements?

This one of the more stupefyingly ignorant questions I've ever seen asked by a creationist. Obviously Steve knows as much about chemistry as he knows about other sciences. Yeah, Steve, at the moment there's more than a few tons of benzene "found naturally in countless different arrangements" in, on and above the Gulf of Mexico. :(

Paul Burnett said:

Steve P. said: Tell me, is Benzene only found arranged in a circular pattern in nature? Or can it be found naturally in countless different arrangements?

This one of the more stupefyingly ignorant questions I've ever seen asked by a creationist. Obviously Steve knows as much about chemistry as he knows about other sciences. Yeah, Steve, at the moment there's more than a few tons of benzene "found naturally in countless different arrangements" in, on and above the Gulf of Mexico. :(

It appears that all this Steve P. ever does is pop in here from time to time and sling some ID/creationist feces just to stir things up.

It’s not clear how far down the rube chain this Steve P. is; but he obviously doesn’t have a clue.

Steve P. said: Stevaroni, Sure, anything is possible. adidas says 'impossible is nothing'. But we are not talking about possibilities here. We are asking did it in fact happen the way darwinian evolution says it did.

MrG said:

Mike Elzinga said: It appears that all this Steve P. ever does is pop in here from time to time and sling some ID/creationist feces just to stir things up.

Look on the bright side: he more or less says his peace, argues a bit, then moves on. A troll, arguably, but if so not (by the standards we are familiar with) a particularly persistent or obnoxious one. Not in the "ban on sight" categorgy like "Mister Argumentum ad Lapidum", ChunkyDeeZee. A perceptive reader may have noticed a significant feature in Stevie P's postings in this thread, at least in the form of the dog that didn't bark. In earlier postings he couldn't restrain himself from playing the "Creationist Information Theory" card. I made a point of nailing him when he did it and I was just WAITING for him to do it again, but it looks like he has, astoundingly, actually decided that argument was SO WEAK that even a CREATIONIST shouldn't use it. Of course, a person who has concern for his credibility might then wonder if he was on the wrong track in general, but that doesn't apply here. "Once a con man ... always a con man."

Malchus -

At this point, there is a part of Steve P's brain that realizes that he tried to shit people who didn't fall for it.

He must have some anger and insecurity issues to be working his schtick here. He probably doesn't want to be just another high-fiving guy in the crowd at UD or something, or another weirdo with an unvisited crackpot web site. He wants some real attention; he wants flashing camera bulbs and humiliation for all the people who slighted him. But his bluff got called.

His unsurprising ritual to deal with this otherwise unacceptable blow to his fragile ego is to begin resorting to childish insults and juvenile sarcasm. That's an extremely common methodology for the more narcissistic creationists (yes, some are actually even more narcissistic than others) to use. "What you said sounded better than what I said, but wait! I called you a doo-doo with cooties! I win after all!"

By the way, they need to do it obsessively for hours, so don't expect it to stop any time soon.

Steve P. said:

It appears that all this Steve P. ever does is pop in here from time to time and sling some ID/creationist feces just to stir things up.

Mr. Elzinga, I do have a job. And since I am in Taiwan I have to post during working hours in order to have real time interaction with the posters here. That's why most of the time I am only able to 'pop in here'.

Second, my goal is never to stir things up. I bring a different perspective to the table. Whether you like it or not is yours to work out.

But make no mistake, my goal is not agit-prop. I am not a bible-thumping type that has a religious agenda. BUT YOU KNOW THAT ALREADY.

It’s not clear how far down the rube chain this Steve P. is; but he obviously doesn’t have a clue.

Schoolyard tactics, Mr. Elzinga? You and Dale would make a nice tag team. But alas, this is not the WWF. On second thought, .......

Stop projecting

Steve P. said: I do have a job. And since I am in Taiwan I have to post during working hours...

Thanks for the honest “I don’t know” answers, which should tell you something.

I mean, really, what kind of idiot employer would tolerate an employee who wastes company time by loafing on the Internet, trolling at a website in order to antagonize the other posters about how he is proud of being a pompous idiot who knows absolutely nothing about science, and how the people he's antagonizing are really the trolls because they're pointing out how stupid he really is?

Let me guess, your place of employment is in your parents' basement?

Paul Burnett said:

Steve P. said: I do have a job. And since I am in Taiwan I have to post during working hours...

How about that...a demonstration of creationist ethics. Say, Steve, what would your employer have to say if they found out you were slacking off during work hours and using company computers and internet connection and bandwidth for your anti-scientific blogging? Any thoughts on how that would go over with management?

Steve P. said: 1) What the heck does reproduction have to do with the mousetrap analogy??? Strike one! 2) Have you tried to catch a mouse with sticky paper? Even roaches know to avoid them. Strike two! 3) The fact that a mousetrap can be used as a paperclip is irrelevant to the argument. Take the hook out and no mousetrap. Take off the base and no mousetrap. Take off the spring and no mousetrap. Strrrrrrrriiiiiiiike, three! You're outta heeeeea.

So when IDists don’t know something, its because they are ignorant fools.

RBH said: Steve P, analogies break down when they're pushed too far, and ID's analogies break down well before they tell us anything useful. In fact, Behe's analogies are actively deceptive and his love for them is unrequited.

Steve P. said:

And as an ID/creationist you have bought the shtick that chemistry and physics no longer apply beyond some level of complexity.

I am not sure why you insist on arguing around the obvious. You deny your own senses when you look at a mouse and say to yourself, 'geez it is essentially the same as a rock just softer, and it shits, and it bites, and it reproduces rapidly, and it sleeps, but it is still essentially the same as a rock.'

Steve P. said: Dale, 1) What the heck does reproduction have to do with the mousetrap analogy??? Because it is the ability to both reproduce and pass on traits via nucleic acids that makes natural selection possible. We call such beings "alive". Mousetraps are not alive, so cannot be properly compared with bacteria or any other life form. ANY comparison between even the simplest man-made non-life form and the most complex natural life form is idiotic, and Behe, being a biochemist, really should have known better. 2) Have you tried to catch a mouse with sticky paper? Even roaches know to avoid them. Outright lie, for mousetraps that use glue are found in grocery stores. I've seen them. 3) The fact that a mousetrap can be used as a paperclip is irrelevant to the argument. Take the hook out and no mousetrap. Take off the base and no mousetrap. Take off the spring and no mousetrap. It is totally relevant in showing that things that appear irreducibly complex for one specific function can have useful forms with parts removed. So you lie outright AGAIN.

The below comment is why a lot of IDists don’t care to engage with folks here. When an IDist answers a question with an “I don”t know”, it is followed with a ‘see, that’s tells you something (i.e. meaning the poster is an ignoramous). But all the while you (pl) say scientists should be honest and admit when they don’t know something.

So when IDists don’t know something, its because they are ignorant fools. But when NDists admit they don’t know, its because they have exhausted all logical possibilities and therefore they are reasonable in their admission that they don’t know but for sure its not because they are ‘ignorant’. Nice condescending, arrogant double standard. I guess that is what you need emotionally. You just HAVE TO have that in your rhetorical toolbox.

Glen Davidson said:

So when IDists don’t know something, its because they are ignorant fools.

Yes, dolt, because IDiots don't even know how to begin to do their "science." They can't match up cause and effect at all, they explain nothing, and they make brain-damaged commments like, "In order to show that Behe was wrong, you need to demonstrate first.…". When our side says "we don't know about something" that's in a context of a theory that explains a huge number of facts already. When you say you don't know something, it's because you haven't the first clue as to how anyone even could do "ID science." No, troll, we don't have to show that Behe was wrong, he needs to come up with the first shred of evidence that his claims are right. The fact that you don't even recognize that the IDiot making the claim owes us some evidence for it indicates that you're colossally ignorant. Glen Davidson

Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)?

Steve P. said: And again, i say to you if life is inherent in the laws of physics and chemistry ONLY, then we should logically see all manner of life forms (and not necessarily carbon/water based) all over the universe. We DO NOT see this happening. Therefore, logically we can say that life does in fact have some element in it that is not present in inanimate matter. Whether it is a material based element in the form of higher-energy (soul perhaps) or something non-detectable with current scientific methods (information), we do not yet know. But just because it is difficult to figure out should not lead us to conclude that there is essentially no difference between the two. There is a HUGE chasm of difference. No scientist would say, sorry no we can't consider undetectable light energy, no we can't consider information as causes of functional complexity. Soul and information are on the table whether you like it or not and regardless if a way has not yet been established to confirm either. This is what 21st century science is working towards. We are not comparing the water in your icicles to the water in organisms. We are comparing icicles to organisms. Organisms have countless unique molecules arranged in myriad configurations all interacting in coordinated ways in order to do work. Icicles have only one molecule, water. They are not arranged in myriad configurations. The do not interact in coordinated ways to do work. Different animals. It is not the issue of obeying only laws of physics and chemistry. Both do. But organisms also obey an as yet undetermined law. This is obvious. We see it with our eyes. It is what differentiates organisms from icicles. Let us work to find out just what law organisms obey over and above the laws of physics and chemistry. No, I am claiming that molecules in organisms are arranged into meta-patterns that perform work. compounds are not arranged into meta-patterns and they do no work. Different animals again. Tell me, is Benzene only found arranged in a circular pattern in nature? Or can it be found naturally in countless different arrangements? It is the interaction of innumerable configurations of molecules that makes the difference, not the existence of complex molecules themselves. The boundary is the million dollar question. But let us not deny that a boundary exists. It is obvious that a boundary exists. What it consists of, let us dig in.

Where do the laws of chemistry and physics stop working in a complex system?

That is not the question I try to evoke. The question is 'What is working aside from physics and chemistry that creates the boundary between inanimate and animate life." You will inevitably retort that there is no reason to ask this question. But I will point to my previous comment that if it is ONLY physics and chemistry then there is no boundary and life must pop up anywhere and everywhere all over the universe since life is an inherent property of physics and chemistry.

What is this business of “function” all about? What is it about a set of molecules having some “function” that suddenly makes them immune to the laws of chemistry and physics?

Again, they are not immune to the laws of physics and chemistry. However, they do obey at least one additional law. This is obvious. It is for inquiring minds to figure out just what that law(s) consists of.

This one of the more stupefyingly ignorant questions I’ve ever seen asked by a creationist. Obviously Steve knows as much about chemistry as he knows about other sciences. Yeah, Steve, at the moment there’s more than a few tons of benzene “found naturally in countless different arrangements” in, on and above the Gulf of Mexico. :(

Uh, yeah, how can we rule out any and all possibilities in science?

Paul Burnett said:

Steve P. said: I do have a job. And since I am in Taiwan I have to post during working hours...

How about that...a demonstration of creationist ethics. Say, Steve, what would your employer have to say if they found out you were slacking off during work hours and using company computers and internet connection and bandwidth for your anti-scientific blogging? Any thoughts on how that would go over with management?

Steve P. said: Does it scare you shitless that in the 21st century, information will be 'nailed down' as a real entity, existing independent of matter? Why does it bother you to such an extreme? Why would you be scared to learn the reality that force is a cognizant, living entity that acts through information; that other cognizant, living entity? You guys are living in the dark ages. Sheesh.

Mike Elzinga said: Why are you trying to get us to do it? Are you incompetent?

if life is inherent in the laws of physics and chemistry ONLY, then we should logically see all manner of life forms (and not necessarily carbon/water based) all over the universe.

The fact that a mousetrap can be used as a paperclip is irrelevant to the argument. Take the hook out and no mousetrap. Take off the base and no mousetrap. Take off the spring and no mousetrap. Strrrrrrrriiiiiiiike, three! You’re outta heeeeea.

Steve P. said: Does it scare you shitless that in the 21st century, information will be 'nailed down' as a real entity, existing independent of matter? Why does it bother you to such an extreme? Why would you be scared to learn the reality that force is a cognizant, living entity that acts through information; that other cognizant, living entity? You guys are living in the dark ages. Sheesh.

The understanding that chemical laws AND NOTHING ELSE govern biochemistry has been a basic understanding of the subject for at least a century!

Steve P. said: Dale, Your below comment is the very reason we are not getting anywhere in the origins and biological development/activity subjects. And no, it is not an understanding. It is an apriori assumption. Nothing else. Again, in the 21st century it will be those who break out of that outdated thinking that will make the inroads into understanding underlying reality. It will not be a Coyne, Carroll, Myers, Dawkins, Provine, et al that will do this. Rather, it will be a Behe, Meyer, Dembski, Marks, Sternberg type of thinker that will break the stangle hold outdated conceptualizations have on the current scientific mindset. The fact the we are not able to elucidate the fundamental characteristics of force and information and the effects of their interaction empirically at this time is not an impediment to further research / investigation. It's just a matter of time, diligence and most of all faith, yes faith in the rationality of the universe.

The understanding that chemical laws AND NOTHING ELSE govern biochemistry has been a basic understanding of the subject for at least a century!

Mike,

You got it wrong. I am not asking you to do anything for me in the lab.

All you need to do is explain from a physics and chemistry POV, the formation of all the flagellic proteins in their peculiar configurations, the order of formation of each protein configuration, and how the meta-arrangement of all the sets of proteins must naturally result in a configuration that performs work.

It is a tall order. But so is trying to figure out how to nail down the fundamental characteristics of force and information empirically. No one said science is easy.

Steve P. said: Mike, You got it wrong. I am not asking you to do anything for me in the lab. All you need to do is explain from a physics and chemistry POV, the formation of all the flagellic proteins in their peculiar configurations, the order of formation of each protein configuration, and how the meta-arrangement of all the sets of proteins must naturally result in a configuration that performs work. It is a tall order. But so is trying to figure out how to nail down the fundamental characteristics of force and information empirically. No one said science is easy.

Steve P. said: Mike, You got it wrong. I am not asking you to do anything for me in the lab. All you need to do is explain from a physics and chemistry POV, the formation of all the flagellic proteins in their peculiar configurations, the order of formation of each protein configuration, and how the meta-arrangement of all the sets of proteins must naturally result in a configuration that performs work. It is a tall order. But so is trying to figure out how to nail down the fundamental characteristics of force and information empirically. No one said science is easy.

fnxtr said:

if life is inherent in the laws of physics and chemistry ONLY, then we should logically see all manner of life forms (and not necessarily carbon/water based) all over the universe.

Ouch. Steve that is the most monumentally ignorant thing I've seen from you, and you set the bar pretty high. Go read an organic chemistry text. Our kind of life is possible because of the nature of C,N,O,H,P, and a few others. That does not mean the presence of these elements will always lead to self-replicating molecules. But you knew that, didn't you. You knew you were being deliberately obtuse, and misrepresenting Mike's explanations. Right? As a friend said to an obnoxious individual at a party once, "What are you: a fool, or an asshole?"

It's lunchtime. I'm outta here. Later.

Steve P. said: Does it scare you shitless that in the 21st century, information will be 'nailed down' as a real entity, existing independent of matter? Why does it bother you to such an extreme? Why would you be scared to learn the reality that force is a cognizant, living entity that acts through information; that other cognizant, living entity?

Steve P. said: fnxtr, reread my comments. i am not talking about any particular type of life. Elzinga says there is no barrier between life and non-life; just a sliding scale in degree of complexity.

If so, then nothing is stopping the laws of physics and chemistry from producing all manner of life forms, whether they be carbon based, iron based, manganese based, sulfer based, whatever. If it did it once, it should be able to do it over and over again. As I have asked before, how long will we look and how much money will we spend on telescopes before we admit that we are in fact a special condition of matter produced by the laws of physic, chemistry AND an as yet to be determined other law (or laws)?

Well once again Steve runs away and never answers any of my questions. Now I wonder why that is? Who cares. Everyone can see that has absolutely nothing. What a waste of protoplasm.

Steve P. said: No one said science is easy.

Well once again Steve runs away and never answers any of my questions. Now I wonder why that is? Who cares. Everyone can see that has absolutely nothing. What a waste of protoplasm.

Steve P. said: Shit, I'm certainly not going to wait for Elzinga or Burnett to give me the scientific go-ahead to think outside the box. It is clear they can't and won't. It's all inside our heads and that is where we are headed(pardon the pun,not).

Then instead of spending all your time snarking at a bunch of us deadheaded scientists, you should be taking advantage of a clear field to run ahead of all of us and win the Nobel prize for figuring this out and demonstrating it with some convincing experiments. Hop to it, hot shot; you’re making poor use of your time.

Steve P. said: fnxtr, reread my comments. i am not talking about any particular type of life. Elzinga says there is no barrier between life and non-life; just a sliding scale in degree of complexity.

Steve P. said: All you need to do is explain from a physics and chemistry POV, the formation of all the flagellic proteins in their peculiar configurations, the order of formation of each protein configuration, and how the meta-arrangement of all the sets of proteins must naturally result in a configuration that performs work.

Steve P. said: Paul, I am the boss, you idi... Ah, that would of felt so good. Now I see why you guys can't help but to blurt epithets every so often. It's addictive, isn't it? As they say in Chinese, 'hao shuang'. I wholeheartedly apologize for that near-miss, folks. Better to get back to higher ground.

Paul Burnett said:

Steve P. said: I do have a job. And since I am in Taiwan I have to post during working hours...

How about that...a demonstration of creationist ethics. Say, Steve, what would your employer have to say if they found out you were slacking off during work hours and using company computers and internet connection and bandwidth for your anti-scientific blogging? Any thoughts on how that would go over with management?

Mike Elzinga said:

Steve P. said: Shit, I'm certainly not going to wait for Elzinga or Burnett to give me the scientific go-ahead to think outside the box. It is clear they can't and won't. It's all inside our heads and that is where we are headed(pardon the pun,not).

Apparently you missed this comment back at 9:34 PM on August 9, 2010.

Then instead of spending all your time snarking at a bunch of us deadheaded scientists, you should be taking advantage of a clear field to run ahead of all of us and win the Nobel prize for figuring this out and demonstrating it with some convincing experiments. Hop to it, hot shot; you’re making poor use of your time.

For a character with a lot of big ideas, you are certainly short on experimental programs.

Malchus said: Steve isn't planning to advance knowledge; he is relying on others to do that for him.

Malchus said: Steve isn't planning to advance knowledge; he is relying on others to do that for him.

Mike Elzinga said: It appears he just shows up here to make people angry. Typical troll.

Steve, your responses imply that you really don't understand what Behe is saying, nor do you have a clear handle on why the various unsupported analogies that Behe offers are invalid. This will require a fair amount of education on your part - are you interested? I'm more than happy to try to bring you up to speed on these basic concepts - since ignorance may be your only failing here. Consider the first point: reproduction is critical because of the method of manufacture varies between living organisms and non-living constructs. A mousetrap must be assembled; a biological organism develops using entirely natural processes. There is no reason to presume that Behe's analogy holds given the variance in the origin of the entity.

RBH, I'm curious why a heavy hitter such as yourself would take the time to enter what appears to be an 'evolving' tag team effort at discrediting my comments.

Hmmm.

Steve P. said: RBH, I'm curious why a heavy hitter such as yourself would take the time to enter what appears to be an 'evolving' tag team effort at discrediting my comments. Hmmm.

Steve P. said: You guys are living in the dark ages. Sheesh.

Dale Husband said: Laughter is truly the best medicine for stupidity. Especially when he denied that mice could be trapped with glue. I've actually seen it done, so he just came across as a lying idiot.

Steve P. said: RBH, I'm curious why a heavy hitter such as yourself would take the time to enter what appears to be an 'evolving' tag team effort at discrediting my comments.

RBH said:

Malchus said: Steve isn't planning to advance knowledge; he is relying on others to do that for him.

As is every other ID "theorist.

Darth Robo said:

Steve P. said: You guys are living in the dark ages. Sheesh.

Just checking, but did a creationist just accuse others of living in the dark ages?

Malchus said: Steve, I am puzzled how you expect to proceed with this discussion. You have admitted that you are unethical; you have admitted that you are fundamentally ignorant of the basics of biology, chemistry, and physics. You have demonstrated that you are very unclear on what Behe is arguing and why. What is left? You don't seem to possess the necessary background to facilitate an interesting discussion. How do you suggest we proceed?

Steve P. said: Paul, I am the boss, you idi... Ah, that would of felt so good. Now I see why you guys can't help but to blurt epithets every so often. It's addictive, isn't it? As they say in Chinese, 'hao shuang'. I wholeheartedly apologize for that near-miss, folks. Better to get back to higher ground.

Paul Burnett said:

Steve P. said: I do have a job. And since I am in Taiwan I have to post during working hours...

How about that...a demonstration of creationist ethics. Say, Steve, what would your employer have to say if they found out you were slacking off during work hours and using company computers and internet connection and bandwidth for your anti-scientific blogging? Any thoughts on how that would go over with management?

Steve P. said:

It appears that all this Steve P. ever does is pop in here from time to time and sling some ID/creationist feces just to stir things up.

Mr. Elzinga, I do have a job. And since I am in Taiwan I have to post during working hours in order to have real time interaction with the posters here. That's why most of the time I am only able to 'pop in here'. Second, my goal is never to stir things up. I bring a different perspective to the table. Whether you like it or not is yours to work out. But make no mistake, my goal is not agit-prop. I am not a bible-thumping type that has a religious agenda. BUT YOU KNOW THAT ALREADY.

It’s not clear how far down the rube chain this Steve P. is; but he obviously doesn’t have a clue.

Schoolyard tactics, Mr. Elzinga? You and Dale would make a nice tag team. But alas, this is not the WWF. On second thought, .......

SWT said:

RBH said:

Malchus said: Steve isn't planning to advance knowledge; he is relying on others to do that for him.

As is every other ID "theorist.

I don't necessarily have a problem with Steve P. not doing the research himself; it's clear he's not a biologist and would be operating outside his expertise. I mean this in a totally non-snarky way ... I'm certainly wouldn't be able to set up a credible research program in, say, geology because my training, research, and other professional experience has been in chemical engineering. My problem is that he seems to think he's delivered the knock-out punch to a scientific theory he does not appear to understand. He's doing this on the basis of an argument from incredulity that he seems to maintain by not educating himself about the theory to which he objects, instead relying on data he seems to be confident will be in evidence at some future date that will be produced by people who seem to have no interest in actually doing the requisite research to test their own propositions . Seriously: if design advocates actually had anything, they'd have been able to get some major publications into the mainstream peer-reviewed literature and to secure some serious federal grant support -- they've had over two decades since "intelligent design" was unveiled as the successor to "creation science."

Sigh, thus further demonstrating that: "There is no force in the Universe more powerful than the urge to reply to a troll."

Corrollary: "The force is proportional to the insensibility of the troll."

Steve wrote:

"On the contrary, your comment implies you KNOW that organisms develop organelles over a long period of time without any forsight or knowledge of what is happening within their genomes. However, this is an apriori assumption on your part.

There is nothing in what we observe to confirm that first, it takes huge amounts of time, and second that organisms built function by incrementaly small steps via undetected replicaton error or other non-directed, non-purposeful methods."

The fool hath said in his heart, there is no evidence. For the last time, you are dead wrong about this. I have provided you with the evidence, you have not bothered to look at it let alone refute it. You are hopeless and scientifically worthless.

A wise man once said that only a fool would think that willful ignorance would be a good substitute for knowledge, (and I was right). Steve steadfastly refuses to examine any evidence, He steadfastly refuses to learn about any of the findings of science. Out of sheer willful ignorance, he blindly dismisses all of genetics and evolution. What he proposes to substitute is apparently the invisible fairy hypothesis. Been there done that, got us nowhere, get over it. This is your mind on creationism folks. Weep for the fool.

HOW MANY CREATIONISTS DOES IT TAKE TO SCREW IN A LIGHT BULB?

Two. One to screw it in, the other to say that lightbulbs prove the Sun was Intelligently Designed and that astrophysicists are refusing to recognize this obvious truth.

None. "We don't have to match your pathetic level of lightbulb repair."

None. Since scientists can't validate every step of how to screw in a lightbulb, then they cannot show that lightbulbs honestly exist.

Steve P. said: fnxtr, reread my comments. i am not talking about any particular type of life. Elzinga says there is no barrier between life and non-life; just a sliding scale in degree of complexity. If so, then nothing is stopping the laws of physics and chemistry from producing all manner of life forms, whether they be carbon based, iron based, manganese based, sulfer based, whatever. If it did it once, it should be able to do it over and over again.

SUMMARY

ID/Creationists exist along a spectrum.

At one end are the intensely bigoted but locally well-adjusted types like McLeroy, formerly of the Texas Board of Education. McLeroy was able to function within his own community as a dentist, achieve elected office, and so on. His primary motivation seems to be hard core, ethnically bigoted, anti-intellectual right wing attitudes, a common motivator of people throughout modern history and worldwide. Creationism merely seems to have been part of the package for McLeroy. For a view of his entirely creationism-unrelated efforts to revise history in a right wing direction, go to your local library and read this brief passage in Harper's http://www.harpers.org/archive/2010/08/0083054 (you can see the ravings about Woodrow Wilson in the link...).

McLeroy joined a certain team that he sees as "winning" and advancing his own interests. He is intellectually dishonest and repugnant, but his self-interested social and political calculations are transparent.

At the other end of the spectrum, we have the likes of Steve P and perhaps some others I could name. While I would not rule out an underlying authoritarian agenda in any ID/creationism lover, this type appears to be more exclusively motivated by a narcissistic yet fragile ego and the problems it creates. One clear difference between a Steve P and a McLeroy is that the former actually seems to take Behe seriously, whereas the latter surely recognized "court-proofed old time religion for science class" as exactly what it is.

The precise obsessions and defenses of Steve P can be summarized with ease.

He is, ludicrously, either a re-inventor or an advocate of the archaic idea, "vitalism" http://en.wikipedia.org/wiki/Vitalism. Uproariously, he claims to believe that the atoms that are part of living things are different from other atoms. Although it is clear that this view is maximally discredited - all of modern biochemistry, genetics, and molecular biology would be impossible if it were true - he rigidly sticks to the claim. He is corrected by people along the full spectrum of scientific expertise, from research physicists (Mike Elzinga) to pathologists (myself), but clings to it.

His obsessively ritualistic defense mechanisms are merely the following -

1) Deliberate ignorance of the very subject he claims to be so interested in.

2) Construction of meaningless bafflegab sound bites using words like "meta-location" and "information", which makes him feel smart.

3) Contradiction and mockery of those who try to engage in him.

And of course, those old creationist favorite -

4) Moving the goal posts. Although Steve P is totally ignorant of the actual evidence for common descent/biological evolution, he isn't taking any chances. He's already stating that he won't accept the evidence unless "every mutation" is perfectly described. (Analogy - "I don't care if the defendant threatened the victim repeatedly, was seen pulling a gun and shooting the victim by multiple witnesses and several security videos from multiple directions, the bullet that killed the victim and the shell casing matched the gun, which the defendent admitted was his, the victim had GSR on his hands and spattered blood from the victim on his shirt, the victim attempted to flee after the shooting and was captured by the witnesses. Unless you can tell me every single step in the manufacture of the gun and bullet, including which mines the metal used came from, etc, you haven't proved the case!").

5) Subject changing - repeated attempts to imply that defenders of a straightforward scientific theory are somehow making comments about the "meaning" or "purpose" of life or the universe.

harold said: "Unless you can tell me every single step in the manufacture of the gun and bullet, including which mines the metal used came from, etc, you haven't proved the case!"

Harold,

Excellent summary. However you left one out:

6) Making up untestable crap for which there is no evidence whatsoever and expecting everyone to think that it is better than accepted explanations for which there is abundant evidence.

Of course this approach requires one to be completely ignorant of all of science and it also requires that anyone who is going to be fooled must be just as ignorant. The refusal to look at any evidence is the give away.

This guy reminds me of that wacko with the magic invisible hologram. Man, that guy just couldn't understand spatio-temporal patterns in cascades of gene expression. Instead he made up a whole bunch of crap, just because it was apparently easier for him to understand it! Stevie seem to have the same affliction. For whatever reason, he has decided that science just can't be right, (even though he has no idea whatsoever what science has discovered), so why bother to actually learn anything? Must make it kind of hard to function in modern society. More is the pity.

SInce Stevie refuses to discuss actual science, we're reduced to discussing his psycho pathology. At least that is more interesting than the magic invisible gene nonsense.

He’s already stating that he won’t accept the evidence unless “every mutation” is perfectly described.

Rich is enamored with Denton, and Denton included in "Evolution: a theory in crisis" a very misleading, although not obviously deliberately dishonest, analogy with the evolution of languages, one that is actually completely opposite from the truth of the importance and necessity of understanding that evolution occurred prior to understanding all of the steps involved (which may never happen with much life, for the obvious reasons involving lost information). Anyhow, here is the telling paragraph:

All the major Germanic languages of Europe, for example, including English, Dutch, German, and Icelandic, were already well differentiated and distinct and unlinked by transitional dialects when they first appeared in written form. Yet, despite the absence of intermediates, no linguist today doubts that all the Germanic languages descended gradually over a period of three thousand years from an ancestral proto-Germanic tongue. This is because they have been able to work out in very exact detail all the semantic, syntactic and phonetic changes which occurred along all the hypothetical pathways through which the languages evolved. The reconstruction has been taken to such an extent that the entire lexicon, grammar, and even the sound of these extinct and long dead languages can be specified at every point along all the various lineages leading back in time to the proto-Germanic source. Michael Denton Evolution: A Theory in Crisis. p. 199.

One can quibble in various ways about that paragraph, as he's almost certainly exaggerating how much we know about every single aspect of extinct Germanic languages, and most definitely is wrong that we know the "sound" of the extinct languages (we no doubt know something about the sounds, but to baldly state "and even the sound of these extinct and long dead languages can be specified at every point along all the various lineages leading back in time to the proto-Germanic source," can hardly be true). And Germanic languages are hardly the only ones we know evolved from a common source, and certainly less is known about the original Indo-European language (many roots are fairly certain, it is believed), so clearly Denton cherry-picked his "example." But those errors pale against the fact that virtually all linguists were -- and had to be in order to work out the specifics -- certain that the Germanic languages, and indeed all of the Indo-European languages, were related well before the specifics were worked out. They weren't convinced that the languages had evolved from common ancestors because all of the details were known, the details were able to be worked out because linguists were certain that the languages had evolved, and they operated very successfully within that framework to ferret out the details.

How anybody can be dull enough to think that every last bit of language evolution was known before linguists generally believed in language evolution is not easy to explain. Yet it seems to be dumb enough for the IDCreationists to believe (or at least cling to in order to avoid learning what they don't want to know), since they are amazingly impervious to the sorts of knowledge that really did convince linguists that linguistic evolutionary theory was correct, so that further information could and would be discovered about that evolution. I cringe to think of how much damage such a colossally stupid (although prejudice was probably the main source of the stupid) inversion has, likely, been able to cause.

Steve P. said: Malchus, On the contrary, your comment implies you KNOW that organisms develop organelles over a long period of time without any forsight or knowledge of what is happening within their genomes. However, this is an apriori assumption on your part. There is nothing in what we observe to confirm that first, it takes huge amounts of time, and second that organisms built function by incrementaly small steps via undetected replicaton error or other non-directed, non-purposeful methods. Rather, what we observe in reality is the very apparent and intelligent capabilities of organisms/cells to in fact manufacture specific proteins for specific purposes, detect and correct errors in replication, maintain the integrity of DNA, etc. etc. So actual scientific observations of what cells actually do does not lend to the idea that cells cannot detect replication errors in within their walls, or that they do not know how to handle these mistakes, or that they would let replication mistakes flounder in the empty spaces of the cell until such time that some fortuitous event happens that converts the unwanted proteins' homeless status into a stint at the soup kitchen.

Steve P. said: Does it scare you shitless that in the 21st century, information will be 'nailed down' as a real entity, existing independent of matter? Why does it bother you to such an extreme?

Malchus said: Steve isn't planning to advance knowledge; he is relying on others to do that for him.

Mike Elzinga said:

Steve P. said: Shit, I'm certainly not going to wait for Elzinga or Burnett to give me the scientific go-ahead to think outside the box. It is clear they can't and won't. It's all inside our heads and that is where we are headed(pardon the pun,not).

Apparently you missed this comment back at 9:34 PM on August 9, 2010.

Then instead of spending all your time snarking at a bunch of us deadheaded scientists, you should be taking advantage of a clear field to run ahead of all of us and win the Nobel prize for figuring this out and demonstrating it with some convincing experiments. Hop to it, hot shot; you’re making poor use of your time.

For a character with a lot of big ideas, you are certainly short on experimental programs.

Steve P. said: Does it scare you shitless that in the 21st century, information will be 'nailed down' as a real entity, existing independent of matter? Why does it bother you to such an extreme? Why would you be scared to learn the reality that force is a cognizant, living entity that acts through information; that other cognizant, living entity?

Steve P. said: You guys are living in the dark ages. Sheesh.

Steve P. said: The fact the we are not able to elucidate the fundamental characteristics of force and information and the effects of their interaction empirically at this time is not an impediment to further research / investigation.

Stevie P: "I believe that there's a physical quantity named INFORMATION on which my arguments are based, and though I cannot define it in any useful terms or demonstrate its reality ... well, one of these days maybe somebody will, I don't know when, so I don't have any problem with predicating my arguments on it, and it's unkind and unreasonable of you to say you don't buy it even though I can't tell you what it is you're supposed to buy."

Dale Husband said:

Mike Elzinga said: It appears he just shows up here to make people angry. Typical troll.

All he did was amuse me. Laughter is truly the best medicine for stupidity. Especially when he denied that mice could be trapped with glue. I've actually seen it done, so he just came across as a lying idiot.

DS -

Yes, thank you. I actually did say 'Construction of meaningless bafflegab sound bites using words like “meta-location” and “information”, which makes him feel smart.' But I think the way you put it - 'Making up untestable crap for which there is no evidence whatsoever and expecting everyone to think that it is better than accepted explanations for which there is abundant evidence' - may actually be even more accurate.

MrG said: Stevie P: "I believe that there's a physical quantity named INFORMATION on which my arguments are based, and though I cannot define it in any useful terms or demonstrate its reality ... well, one of these days maybe somebody will, I don't know when, so I don't have any problem with predicating my arguments on it, and it's unkind and unreasonable of you to say you don't buy it even though I can't tell you what it is you're supposed to buy." Wow...if it weren't such a long run-on, I'd use it for my second sig at AtBC. Just great stuff!

Thanks Robin. But I still feel like an idiot arguing with a "troll and damn proud of it" like SP. Like arguing with a little dog that likes to bark.

MrG said: Thanks Robin. But I still feel like an idiot arguing with a "troll and damn proud of it" like SP. Like arguing with a little dog that likes to bark.

MrG said: Thanks Robin. But I still feel like an idiot arguing with a "troll and damn proud of it" like SP. Like arguing with a little dog that likes to bark.

MrG said: Thanks Robin. But I still feel like an idiot arguing with a "troll and damn proud of it" like SP. Like arguing with a little dog that likes to bark.

Robin said: Ooops...that should be: Where did *he* (Steve P.) make the above pronouncement.

PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not.

On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

MrG said:

Robin said: Ooops...that should be: Where did *he* (Steve P.) make the above pronouncement.

I was just translating what it was he was saying into what it actually meant.

Robin said: ... you really caught the 'flavor' of his type of post and it took a few reads to even realize it was a paraphrase.

Sort of like Dembski’s: “You have to prove EVERYTHING and I don’t have to prove ANYTHING!”

Actually, Steve is worse that even that. It's more like:

I don't care how much evidence you have, I can always ignore it. Then I can keep demanding that you present more evidence while I present exactly none. And all the while I will continue to pretend that my non-explanation, (for which there is no evidence at all), is somehow better than your explanation, even though you have so much evidence that I won't look at, let alone explain.

Sure, everyone will be fooled by that.

DS said: Sure, everyone will be fooled by that.

MrG said:

DS said: Sure, everyone will be fooled by that.

I doubt very much he's trying to fool anyone. He pokes someone in the eye, lets them complain, and then pokes them in the other eye. Though that is, I suppose, fooling them in another fashion.

MrG said: PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not. On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

Malcolm said:

MrG said: PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not. On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

Malcolm said: I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

MrG said: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not.

Paul Burnett said:

Steve P. said: RBH, I'm curious why a heavy hitter such as yourself would take the time to enter what appears to be an 'evolving' tag team effort at discrediting my comments.

Nah, we're just having fun at your expense - your comments are doing a fine job of discrediting themselves, by themselves.

Paul Burnett said:

Dale Husband said: Laughter is truly the best medicine for stupidity. Especially when he denied that mice could be trapped with glue. I've actually seen it done, so he just came across as a lying idiot.

I've seen more mice (and a few rats) trapped with glue boards than snap-type mouse traps. But I wasn't going to bother mentioning it, because Steve would deny the probability.

Robin said:

Steve P. said: fnxtr, reread my comments. i am not talking about any particular type of life. Elzinga says there is no barrier between life and non-life; just a sliding scale in degree of complexity. If so, then nothing is stopping the laws of physics and chemistry from producing all manner of life forms, whether they be carbon based, iron based, manganese based, sulfer based, whatever. If it did it once, it should be able to do it over and over again.

First, you (nor anyone actually) don't know that life isn't abundant in the universe. The fact is, we haven't looked anywhere else but Mars, and even there we've looked at less than .0000000000000000001% of the available area if that. Of course, we aren't expecting to find any life on Mars because there's little, if anything, to support any kind of life organization. There just isn't much on Mars Which brings us to the second point that illustrates why your question is so abysmally absurd - chemistry and physics limit life itself. Gravity, pressure, energy sources, resources, etc...all place limits on life developing and hurdles before life impeding survival. So there is plenty stopping the laws of physics and chemistry from producing all manner of life form - physics and chemistry themselves. So I really have no idea what you think your point is here.

Steve P. said: Yeah, right Burnett. Meanwhile, you, Elzinga, Husband, MrG, Malchus, el all studiously avoid addressing the issue. Whose having more fun? Lol.

Paul Burnett said:

Steve P. said: RBH, I'm curious why a heavy hitter such as yourself would take the time to enter what appears to be an 'evolving' tag team effort at discrediting my comments.

Nah, we're just having fun at your expense - your comments are doing a fine job of discrediting themselves, by themselves.

Steve P. said: Robin, From your use of the peculiar term 'life organization' you seem to be implying that 'we' would not find 'our' kind' of life on Mars. True. But then why would you be looking for 'our' kind of life. Should we not be looking for any type of life?

Second, what makes you think that the universe's physics and chemistry laws are limited to carbon/water based organizations of animated matter?

As I have asked before, why not sulfer/nitrogen, silicon/methane, or whatever combination of elements?

Why would gravity, pressure, etc be barriers? If gravity is heavier, the life forms would develop dense bodies. If the pressure is high, the life forms may develop more resilient tissue and internal structures?

It seems you are thinking only within the carbon/water based biological box. Why is that?

Darth Robo,

Not true. I have not asked for a mutational play-by-play.

Everyone here assumes the bacterial flagellum can be explained solely with physics and chemistry.

I am waiting for that explanation from a physics / chemistry POV for how the flagellum came to be. ( saying it evolved is no different than saying 'goddidit').

The mush-like character of Steve Ps thinking pretty much reveals where his brain has been. This despite any denials he might try to make to hide his intellectual roots.

Steve P. said: Give it a rest, Elzinga. I got to where I am today because I know how to learn. Didn't know a thing about sales, not a thing about textiles 10 years ago and now here I am doing sales and textiles, doing multi-million dollar deals. Yeah, a rube baby. But not your average rube.

Steve P. said: Give it a rest, Elzinga. I got to where I am today because I know how to learn. Didn't know a thing about sales, not a thing about textiles 10 years ago and now here I am doing sales and textiles, doing multi-million dollar deals. Yeah, a rube baby. But not your average rube.

The mush-like character of Steve Ps thinking pretty much reveals where his brain has been. This despite any denials he might try to make to hide his intellectual roots.

DS said:

Steve P. said: Give it a rest, Elzinga. I got to where I am today because I know how to learn. Didn't know a thing about sales, not a thing about textiles 10 years ago and now here I am doing sales and textiles, doing multi-million dollar deals. Yeah, a rube baby. But not your average rube.

Then I guess you have no excuse whatsoever for not reading those papers now do ya? One thing is for sure, you didn't get where you are today by learning any science! Why do some people think that economic success, sometimes achieved through nefarious means, automatically imparts knowledge and competence. It is perfectly possible to be a successful businessman and yet have no clue how nature works. Indeed, that is one of the reasons why we have so many environmental problems. The fact that Stevie might have become rich by scamming the rubes doesn't mean that that is going to work with people who really are knowledgeable. Give it a rest yourself, you con artist.

Stanton said: And then there's the problem of how he's a snide ass who prides himself on allegedly making a ton of money, while having incompetent etiquette skills.

DS -

I think you are right about the con artist thing, by the way.

Successful con artists need to at least "get into the role" like actors and virtually believe themselves as they are delivering the con.

The line between sincere but harmful and narcissistic crackpots, and conscious con artists, is very blurred.

Many narcissistic, paranoid quacks and crackpots are making a fortune off the suckers. Yet a lot of them consciously "believe" themselves as much as they believe anything else.

There is a pretty clear link between this kind of mind and authoritarianism. "Truth" is determined by whomever is able to dominate and manipulate the most. Disciplined, objective, skeptical observation of reality, coupled with respect for the testable views of others, is literally meaningless to such people, the same way that the written word is meaningless to someone who has severe alexia due to a brain lesion.

They make up or glom onto some self-serving yet arbitrary construction, and try to prove its truth by tricking or cowing others, or at worst, by simply never conceding any evidence to the contrary.

And they probably think that we are doing the same thing. They probably cannot conceive of another way of thinking for physical neurological reasons, the same way a dog can probably not conceive of the concept of irrational numbers.

harold said: DS - I think you are right about the con artist thing, by the way.

harold said: And they probably think that we are doing the same thing.

Mike Elzinga said: There is a perfect example of this with Jason Lisle’s latest series over on AiG. This is especially emphasized in the second lecture of the series.

MrG said:

Mike Elzinga said: There is a perfect example of this with Jason Lisle’s latest series over on AiG. This is especially emphasized in the second lecture of the series.

You can actually sit through these videos? "It's a dirty job, but somebody has to do it."

Mike Elzinga said: You have to be amazed at folks like Barbara Forrest and Eugenie Scott who plow though this crap and document every link throughout the entire history of this stuff.

Steve P. said: Darth Robo, Not true. I have not asked for a mutational play-by-play. Everyone here assumes the bacterial flagellum can be explained solely with physics and chemistry. I am waiting for that explanation from a physics / chemistry POV for how the flagellum came to be. ( saying it evolved is no different than saying 'goddidit').

MrG said: Yeah, I feel for them. Who's the guy who has THOUSANDS of creationist tracts and takes creationist classes? The only way anyone who wasn't a creationist could stand to do that would be to regard it as something like a hobby, something like a very strange fantasy role-playing game -- except lacking polyhedral dice.

Steve P. said: Give it a rest, Elzinga. I got to where I am today because I know how to learn. Didn't know a thing about sales, not a thing about textiles 10 years ago and now here I am doing sales and textiles, doing multi-million dollar deals. Yeah, a rube baby. But not your average rube.

The mush-like character of Steve Ps thinking pretty much reveals where his brain has been. This despite any denials he might try to make to hide his intellectual roots.

Mike Elzinga said: I don’t recall anyone who has done that; but I certainly couldn’t rule it out. I can’t imagine where he would get the time (it has to be a he) or how he remains sane.

Mike Elzinga said:

Malcolm said: I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

Oops! Hit the submit button and forgot to paste the response. Another missed opportunity for Steve P. He could set up an “information detector” nearby the extraction and see if information flows out of the enzyme. If he detects an outflow from the enzyme, it died. If not, it’s alive.

Mike Elzinga said:

Stanton said: And then there's the problem of how he's a snide ass who prides himself on allegedly making a ton of money, while having incompetent etiquette skills.

He appears to be reduced to taunting, mooning, and proudly flaunting his ignorance. This seems to be one of the more frequent responses of creationist rubes when they can’t get beyond ID/creationist talking points and into the implications of exactly what those talking points imply about doing some real science. They can’t think of what to do; and then they want to blame the scientists. And then to actually have to learn some real science; now that really pisses them off. This is whole repetitive shtick is just boring. It has been going on since the late 1960s; and these rubes never catch on.

Steve P. said: Meanwhile, Elzinga continues to duck explaining the observed meta-pattern of 40 disparate proteins coming together to perform a task from a physics and chemistry POV. BTW, I have not taunted anyone here by any stretch of the definition. I have made a simple request based on your past assertions that it can all be explained with physics and chemistry and that information is not an independent entity, but an emergent property; incidental rather than instrumental.

Steve P. said: ... I have made a simple request based on your past assertions that ... information is not an independent entity, but an emergent property; incidental rather than instrumental.

SteveP didn't answer any of my questions. Now I have to go to work without knowing whether or not my ion-exchange column is going to drain the life essence from my protein.

"Meanwhile, Elzinga continues to duck explaining the observed meta-pattern of 40 disparate proteins coming together to perform a task from a physics and chemistry POV."

So you don't wanna step-by-step description of the evolutionary development of the flagellum but you do wanna step-by-step description of the evolutionary development of the flagellum?

What's the "scientific theory" of ID again?

From the Matzke PT post concerning flagellum evolution:

"ID advocates say that their position is supported by discontinuities between the flagellum and the rest of the biological world, just as a designed entity like a watch differs from an undesigned entity, such as a stone. In support of this line of reasoning, Scott Minnich in his expert witness report claimed that “the other thirty proteins in the flagellar motor (that are not present in the type III secretion system) are unique to the motor and are not found in any other living system.” As our discussion shows, this is not true. Instead, we have detected sequence homologies linking flagellar components to the rest of the biological universe (Table 1).

(Pallen and Matzke 2006, “From The Origin of Species to the origin of bacterial flagella.” Nature Reviews Microbiology advance online publication 5 September 2006.)"

Well, what about it Steve? How do you explain the sequence homologies shown in Table 1 of the 2006 paper? Please note that this flatly contradicts creationist claims. Please note that this is absolutely consistent with the model proposed for the evolution of the bacterial flagellum. Now you can pout and whine and demand more details all you want, but until you come up with an explanation for this evidence, (a better explanation than that provided by Pallen and Matzke), then no one will pay any attention at all to any of your pissing and whining and moaning.

It's simple really, either you prove that you are willing to read the scientific literature, or you automatically exclude yourself from any serious scientific discussion, period. One would think that you would have already learned that by now.

As for this hang up you have about "information", you have not even defined the term, let alone described what how it can exist if it is not composed of matter, let alone described where it comes from, how it can be detected, how it interacts with matter or why it wants to make a flagellum. In short, you got nothin. Look man, no one cares if you believe that the flagellum evolved or not. If you have no evidence for your own hypothesis it will be ignored, period. And by the way, why do you think that there is no information in DNA? You do Know that DNA actually, you know, exists, right?

Look dude, if you want to play tennis you need a racquet. Showing up without one and laughing at the racquet your opponent brings isn't going to get you on the court. Oh yea, you need some balls to. Game, set and match to science.

DS asks Steve P, "why do you think there is no information in DNA?"

Did Steve really say that? I'd like the answer, myself. I thought that there was nothing much useful in DNA except lists in genetic code of the series of amino acids in various proteins (plus switches to access the lists.) I didn't think DNA actually did anything except reproduce itself and store information. And what about messenger RNA? I thought it carried messages from the DNA in the nucleus to the ribosomes where the proteins are created. What else could a message be, if not information? Have I missed something vital here?

Steve P. said: Meanwhile, Elzinga continues to duck explaining the observed meta-pattern of 40 disparate proteins coming together to perform a task from a physics and chemistry POV. BTW, I have not taunted anyone here by any stretch of the definition. I have made a simple request based on your past assertions that it can all be explained with physics and chemistry and that information is not an independent entity, but an emergent property; incidental rather than instrumental.

Mike Elzinga said:

Stanton said: And then there's the problem of how he's a snide ass who prides himself on allegedly making a ton of money, while having incompetent etiquette skills.

He appears to be reduced to taunting, mooning, and proudly flaunting his ignorance. This seems to be one of the more frequent responses of creationist rubes when they can’t get beyond ID/creationist talking points and into the implications of exactly what those talking points imply about doing some real science. They can’t think of what to do; and then they want to blame the scientists. And then to actually have to learn some real science; now that really pisses them off. This is whole repetitive shtick is just boring. It has been going on since the late 1960s; and these rubes never catch on.

John Kwok said: If you need a simple illustration as to how information can be an emergent property that's just incidental, check Ken Miller's "Only A Theory: Evolution and the Battle for America's Soul". In one of the early chapters Ken does discuss this at length and has an excellent illustration:

hoary puccoon said: DS asks Steve P, "why do you think there is no information in DNA?" Did Steve really say that? I'd like the answer, myself. I thought that there was nothing much useful in DNA except lists in genetic code of the series of amino acids in various proteins (plus switches to access the lists.) I didn't think DNA actually did anything except reproduce itself and store information. And what about messenger RNA? I thought it carried messages from the DNA in the nucleus to the ribosomes where the proteins are created. What else could a message be, if not information? Have I missed something vital here?

Mike Elzinga said: Then there are those really, really complicated molecules that are pushed around by “information” and contain “information” that makes them “function.” These are the “alive” ones that scientists can’t explain.

Steve P. said: ...and that information is not an independent entity, but an emergent property; incidental rather than instrumental.

MrG said:

Mike Elzinga said: Then there are those really, really complicated molecules that are pushed around by “information” and contain “information” that makes them “function.” These are the “alive” ones that scientists can’t explain.

Oh, silly me, I was wondering all along what they meant by "information". It's nothing new, it's just "elan vital". How dense of me to have missed it. But if they wanted to resurrect to "elan vital", they should have just said so.

Steve P. said: Therefore, logically we can say that life does in fact have some element in it that is not present in inanimate matter. Whether it is a material based element in the form of higher-energy (soul perhaps) or something non-detectable with current scientific methods (information), we do not yet know.

MrG said: Oh, silly me, I was wondering all along what they meant by "information". It's nothing new, it's just "elan vital". How dense of me to have missed it. But if they wanted to resurrect to "elan vital", they should have just said so.

SWT said: Interesting that you mention this ... I thought of elan vital when I read the following in one of Steve P.'s posts in this very thread ...

hoary puccoon said: DS asks Steve P, "why do you think there is no information in DNA?" Did Steve really say that? I'd like the answer, myself. I thought that there was nothing much useful in DNA except lists in genetic code of the series of amino acids in various proteins (plus switches to access the lists.) I didn't think DNA actually did anything except reproduce itself and store information. And what about messenger RNA? I thought it carried messages from the DNA in the nucleus to the ribosomes where the proteins are created. What else could a message be, if not information? Have I missed something vital here?

Steve P. said: Meanwhile, Elzinga continues to duck explaining the observed meta-pattern of 40 disparate proteins coming together to perform a task from a physics and chemistry POV. BTW, I have not taunted anyone here by any stretch of the definition. I have made a simple request based on your past assertions that it can all be explained with physics and chemistry and that information is not an independent entity, but an emergent property; incidental rather than instrumental.

Mike Elzinga said: Then there are those really, really complicated molecules that are pushed around by “information” and contain “information” that makes them “function.” These are the “alive” ones that scientists can’t explain.

DS said: (Steve P) wants to play tennis, but he still has no balls. He's just a con artist, what a racquet.

hoary puccoon said: The only problem is that the entire field of molecular biology has consisted of proving one "alive" molecule after another actually operates by ordinary chemistry, just like salt does.

MrG said:

SWT said: Interesting that you mention this ... I thought of elan vital when I read the following in one of Steve P.'s posts in this very thread ...

Yeah, it jumped out at me then, too. It fits perfectly. I would bet that you could take most "creationist information theory" arguments, switch "elan vital" for "information", and they would work (I use the term loosely) just as well.

Robin said:

John Kwok said: If you need a simple illustration as to how information can be an emergent property that's just incidental, check Ken Miller's "Only A Theory: Evolution and the Battle for America's Soul". In one of the early chapters Ken does discuss this at length and has an excellent illustration:

Indeed. Actually if one just thinks about if for even a few seconds, one can come up with a number of examples. Think about a baseball hit by a batter: the flying baseball clearly has different information than a stationary ball sitting on the ground. Was that information in the ball all the time? Clearly not. In the air? Nope. In the bat or the batter? I don't think so. The field? Yeah right. No, the different 'information' is a product of the system itself and is not an entity unto itself.

I just had a horrifying thought.

The DI is a DisInformation laser. Dr. Evil has poured his money into a technological application of “misinformation” flow to take apart the brains of the public.

If that is true, “disinformation” is an anti-boson that can be concentrated into a highly incoherent beam that generates complete mental havoc when it is shined on compliant rubes.

MrG said: The fall of vitalism sheds some interesting light on, ahem, "contemporary controversies" since it demonstrates the fail of "gap logic". It is easy to forget now that life processes themselves were once thought, at least by a faction, to be based on a "mysterious something extra." Life processes turned out to be chemistry, no more and no less. Having lost that battle, the "mysterious something extra" has now retreated to the ORIGIN of life processes. That's the problem with gap logic: the best it can do is hold its ground until it is finally forced to take another step back.

DS said: Just ignore all of the findings of science and hope that no one notices that the gap has already closed.

Mike Elzinga said: I just had a horrifying thought. The DI is a DisInformation laser. Dr. Evil has poured his money into a technological application of “misinformation” flow to take apart the brains of the public. If that is true, “disinformation” is an anti-boson that can be concentrated into a highly incoherent beam that generates complete mental havoc when it is shined on compliant rubes.

Somehow I think of Scotty trying to balance the information and disinformation flow to the (only too appropriately named) warp engines.

"The dilithium crystal kinnae take much more, Captain." Oh, am I looking forward to seeing more of Simon Pegg in that role.

Mike Elzinga said: I just had a horrifying thought. The DI is a DisInformation laser. Dr. Evil has poured his money into a technological application of “misinformation” flow to take apart the brains of the public.

MrG said: Somehow I think of Scotty trying to balance the information and disinformation flow to the (only too appropriately named) warp engines. "The dilithium crystal kinnae take much more, Captain." Oh, am I looking forward to seeing more of Simon Pegg in that role.

DS said:

Steve P. said: Give it a rest, Elzinga. I got to where I am today because I know how to learn. Didn't know a thing about sales, not a thing about textiles 10 years ago and now here I am doing sales and textiles, doing multi-million dollar deals. Yeah, a rube baby. But not your average rube.

Then I guess you have no excuse whatsoever for not reading those papers now do ya? One thing is for sure, you didn't get where you are today by learning any science! Why do some people think that economic success, sometimes achieved through nefarious means, automatically imparts knowledge and competence. It is perfectly possible to be a successful businessman and yet have no clue how nature works. Indeed, that is one of the reasons why we have so many environmental problems. The fact that Stevie might have become rich by scamming the rubes doesn't mean that that is going to work with people who really are knowledgeable. Give it a rest yourself, you con artist.

Steve P:

I don't care how rich you are or how you got that way. If you refuse to look at the evidence, you have no right to an opinion regarding scientific issues, period. To pretend otherwise is simply intellectually dishonest.

If you are really so proud of your supposed ability to learn, then why don't you demonstrate your prowess by actually, you know, learning something?

DS said: Steve P: I don't care how rich you are or how you got that way. If you refuse to look at the evidence, you have no right to an opinion regarding scientific issues, period. To pretend otherwise is simply intellectually dishonest.

If you are really so proud of your supposed ability to learn, then why don't you demonstrate your prowess by actually, you know, learning something?

DS said:

Steve P. said: Darth Robo, Not true. I have not asked for a mutational play-by-play. Everyone here assumes the bacterial flagellum can be explained solely with physics and chemistry. I am waiting for that explanation from a physics / chemistry POV for how the flagellum came to be. ( saying it evolved is no different than saying 'goddidit').

Well Stevie boy, when you have read the relevant papers on the subject and demonstrated that you understand them, then you will be entitled to an opinion on the subject. Until then, demanding that anyone explain anything to your satisfaction is a a vacuous strategy at best. Now, once you have read those papers, perhaps you would care to explain the similarities observed between the various genes. Notice that this data makes perfect sense if the flagellum actually evolved through gene duplications and cooption. What is your explanation? How does it better account for the evidence? Times a wastin. Commence to splain boy. Unless of course you are just an ignorant con artist who is hell bent on wastin everyones time with nonsense.

Stanton said:

DS said: Steve P: I don't care how rich you are or how you got that way. If you refuse to look at the evidence, you have no right to an opinion regarding scientific issues, period. To pretend otherwise is simply intellectually dishonest.

Actually, SteveP's claiming of allegedly bringing a new and different point of view (that GODINTELLIGENT DESIGNER poofed everything together, instead of evil, godless random chance poofing everything together for no good reason), while simultaneously pounding his chest about how he doesn't need to look at or present any evidence beyond his own willful ignorance makes him just plain dishonest, as well as stupid and hypocritical.

If you are really so proud of your supposed ability to learn, then why don't you demonstrate your prowess by actually, you know, learning something?

The day SteveP sits down to read anything science-related, by his own free will, in an intellectually honest manner, will be the week after the Sun swallows up the Earth and Moon.

Malcolm said:

MrG said: PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not. On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

Steve P. said: Stanton, Same repetitive spiel, different day. I guess your and DS' definition of learning is accepting Darwin's idea of small, incremental, non-directed, unguided steps building genomes. If one doesn't accept this axiom, then one can't learn anything in biology, right? So Stanton, what are the mechanics of a bacterium co-opting say an F1F0 ATP synthase to create a stirring filament? How does 'selection' make the first insertion? I.E, how does selection provide the parts and what compels the genome (from a Darwinian POV)to put these new parts in a specific position ? And once the insertion is made, how is the modification recorded in the genome? If you KNOW the material, why not explain it to me in your own words, from memory? You can rattle off the details in a few of paragraphs, I'm sure.

Stanton said:

DS said: Steve P: I don't care how rich you are or how you got that way. If you refuse to look at the evidence, you have no right to an opinion regarding scientific issues, period. To pretend otherwise is simply intellectually dishonest.

Actually, SteveP's claiming of allegedly bringing a new and different point of view (that GODINTELLIGENT DESIGNER poofed everything together, instead of evil, godless random chance poofing everything together for no good reason), while simultaneously pounding his chest about how he doesn't need to look at or present any evidence beyond his own willful ignorance makes him just plain dishonest, as well as stupid and hypocritical.

If you are really so proud of your supposed ability to learn, then why don't you demonstrate your prowess by actually, you know, learning something?

The day SteveP sits down to read anything science-related, by his own free will, in an intellectually honest manner, will be the week after the Sun swallows up the Earth and Moon.

Steve P. said: Hey Malcolm, Why would you believe that I think your enzyme is alive? The key take-away here is that the bacterium and your liver can both 'utilize' the enzyme to do work. Can a snowflake or a crystal do this? If not, why not? What do they lack that prevents them from utilizing the enzyme?

Malcolm said:

MrG said: PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not. On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

Stanton said: The day SteveP sits down to read anything science-related, by his own free will, in an intellectually honest manner, will be the week after the Sun swallows up the Earth and Moon.

Steve P. said: Third, any number of people can attest to my integrity. I'm on facebook so talk to my family and friends. Get a background check. Whatever you need.

SWT said:

Steve P. said: Meanwhile, Elzinga continues to duck explaining the observed meta-pattern of 40 disparate proteins coming together to perform a task from a physics and chemistry POV. BTW, I have not taunted anyone here by any stretch of the definition. I have made a simple request based on your past assertions that it can all be explained with physics and chemistry and that information is not an independent entity, but an emergent property; incidental rather than instrumental.

Seven year ago Nick Matzke published a paper proposing a detailed mechanistic explanation for the origin of the flagellum, with additional material published a couple of years later. Each step in his explanation is completely consistent with mainstream chemistry and physics. If you won't take the time to read Nick's paper, why should Mike Elzinga waste time trying to explain it to you? At this point, if you want to be taken seriously, you need to propose substantial, specific challenges to what Nick has presented -- not the rhetorical equivalent of "Nuh uh, I don't believe it."

1) How are you defining “information?” 2) Why do you think “information” exists independent of matter? 3) Why do you think “information” can interact with matter?

SWT,

PS I was not referring to you with that scared remark. However, there are those that do NOT want to go down that road. Cultural 'constraints' seems to weigh heavy on some minds.

If force and information are found to have intelligent properties ie are living, then it will bring science and theology together again. But we can't have that now, can we?

By the way, my full name is Stephane Henri Joseph Claude Proulx aka Steve Proulx, or Steve P. I was born in Laval, Montreal, Canada, moved to the states when I was 4, living in Springfield, Ma for a couple of years, East Hartford, Conn. for a couple of more years, and the rest in Southwest Florida.

Malchus said: Unfortunately, Steve, what you require is remedial education in basic science. You know so little of the actual material; so little about the basics of chemistry, biology, and evolutionary theory, that no explanation can be done in a few paragraphs. You will need to start at the ground up. Stanton's point is well-made: you simply don't understand enough about science to understand what you're trying to discuss. And might I suggest and plagiarism from other websites - sites with material written by people far better educated than yourself - is fundamentally dishonest?

Steve P. said: Stanton, Same repetitive spiel, different day. I guess your and DS' definition of learning is accepting Darwin's idea of small, incremental, non-directed, unguided steps building genomes. If one doesn't accept this axiom, then one can't learn anything in biology, right? So Stanton, what are the mechanics of a bacterium co-opting say an F1F0 ATP synthase to create a stirring filament? How does 'selection' make the first insertion? I.E, how does selection provide the parts and what compels the genome (from a Darwinian POV)to put these new parts in a specific position ? And once the insertion is made, how is the modification recorded in the genome? If you KNOW the material, why not explain it to me in your own words, from memory? You can rattle off the details in a few of paragraphs, I'm sure.

Stanton said:

DS said: Steve P: I don't care how rich you are or how you got that way. If you refuse to look at the evidence, you have no right to an opinion regarding scientific issues, period. To pretend otherwise is simply intellectually dishonest.

Actually, SteveP's claiming of allegedly bringing a new and different point of view (that GODINTELLIGENT DESIGNER poofed everything together, instead of evil, godless random chance poofing everything together for no good reason), while simultaneously pounding his chest about how he doesn't need to look at or present any evidence beyond his own willful ignorance makes him just plain dishonest, as well as stupid and hypocritical.

If you are really so proud of your supposed ability to learn, then why don't you demonstrate your prowess by actually, you know, learning something?

The day SteveP sits down to read anything science-related, by his own free will, in an intellectually honest manner, will be the week after the Sun swallows up the Earth and Moon.

Steve P. said: SWT, 1) A template 2) Force moves 'through' information creating matter. So matter is the 'emergent property' of the interaction between information and force. 3) Information interacts with matter by constraining it. [eric - for reference, here's the question list]

1) How are you defining “information?” 2) Why do you think “information” exists independent of matter? 3) Why do you think “information” can interact with matter?

eric said: Information is defined as a template? What does that even mean?

Steve P. said: DS; What make you believe that I have not read the 'relevent' papers? Because I don't except gene duplication, cooption, and selection as 'answers'? No shit?

Einstein taught us that energy equals matter and light, but because matter can be condensed down to a very small space if you remove all the empty space between the elementary particles, we can mostly ignore matter. Therefore energy is light, and we are all made of energy -- not matter, or at least so little matter, you can ignore it. Stephen Hawking then came up with string theory, which tells us that all matter, which we can ignore, is made of vibrating strings. We are made of energy. All diseases are therefore caused by unhealthy energetic states, and all disease can be treated by returning the body to a previous healthy energetic states. This can be done with homeopathy, which extracts the energy out of stuff and places it in a small pill that can be used at any time.

Malchus said:

Unfortunately, Steve, what you require is remedial education in basic science. You know so little of the actual material; so little about the basics of chemistry, biology, and evolutionary theory, that no explanation can be done in a few paragraphs. You will need to start at the ground up. Stanton's point is well-made: you simply don't understand enough about science to understand what you're trying to discuss. And might I suggest and plagiarism from other websites - sites with material written by people far better educated than yourself - is fundamentally dishonest?

Thing is, for all of the time he has put into making stuff up, or accepting creationist nonsense uncritically, he could have gotten a real science education by now. The fact that he obviously doesn't think that science is important enough to understand speaks volumes about his basic approach to understanding reality. Just criticize others and demand more and more evidence from them while providing none for your own ideas, that seems to be the basic approach. And this guy wonders why no one will take him seriously.

Y'know, come to think of it ... homeopathy is supposed to work by administering extremely dilute quantitities of the toxin or whatever that is supposed to cause the illness.

The criticism made of this is that the quantities are so low that they can have no serious physical effect ... but of course they OBVIOUSLY contain "information" about the toxin.

I'm almost tempted (but no way I will do it) to play Loki Troll and try to sell homeopaths on adopting information theory as part of their package. It would have its useful aspects to spread the tactic around the lunatic fringe.

Here is a news flash for Steve. We know where information is stored in the cell. We know where it comes from. We know how it is copied and passed on. We know how it controls development, metabolism and reproduction. The fact that Steve never bothered to learn what is already known about modern biology automatically invalidates any objections he might have to the current theories. He can try to redefine information all he wants, but he has no viable alternative and no evidence. Reality doesn't care what he thinks and neither does anyone else.

eric said:

Steve P. said: SWT, 1) A template 2) Force moves 'through' information creating matter. So matter is the 'emergent property' of the interaction between information and force. 3) Information interacts with matter by constraining it. [eric - for reference, here's the question list]

1) How are you defining “information?” 2) Why do you think “information” exists independent of matter? 3) Why do you think “information” can interact with matter?

None of your answers actually answer SWT's questions. Its just gabble. Information is defined as a template? What does that even mean? F=ma is a testable, useful definition. Shannon entropy is a testable, useful definition of something like information. But your definition is neither testable nor useful. What is the SteveP information content of this sentence, and how does one calculate it?

DS said: Here is a news flash for Steve. We know where information is stored in the cell. We know where it comes from. We know how it is copied and passed on. We know how it controls development, metabolism and reproduction. The fact that Steve never bothered to learn what is already known about modern biology automatically invalidates any objections he might have to the current theories. He can try to redefine information all he wants, but he has no viable alternative and no evidence. Reality doesn't care what he thinks and neither does anyone else.

When asked: How are you defining “information?” Steve P. replied: A template . then continues with : These are plenty good foundational starting points to do science. If I were a biologist, I would be searching for that template in mathematical terms; and also: To be sure, science is starting to realize that information is in fact real, and can only be understood with the mind, not 'found' out there somewhere, or written on a molecule somehow.

Steve wrote:

"To be sure, science is starting to realize that information is in fact real, and can only be understood with the mind, not ‘found’ out there somewhere, or written on a molecule somehow."

So Steve, are you saying that there is no information in DNA? Really? Is that what you are saying? Really?

Dude, you just claimed that information was a template, remember? Are you saying that DNA is not a template? Really" Is that what you are saying? Really?

Poor Steve P. Philip Bruce Heywood’s Quantum Computer already got there first.

No Nobel for Steve.

In other words, SteveP thinks that the evolution of bacterial flagella is impossible because he doesn't want to understand how evolution works.

So, why does he insist that he has a legitimate viewpoint to bring to science when he hypocritically refuses to learn about science to begin with?

Mike Elzinga said: Poor Steve P. Philip Bruce Heywood’s Quantum Computer already got there first. No Nobel for Steve.

Steve P. said: Malchus, You're being evasive again.

If you can't explain it in your own words, what makes you believe that I should accept that YOU understand the material. It seems like so much arrogant posturing on your (pl) part, not mine.

As to your plagarism accusation, please do point out specific material plagarized and from what sites.

Otherwise, please leave off with your erroneous accusations.

Bullshit Malchus,

Admit it. You are reluctant to explain it because you know where it will lead.

Come on, Malchus. What are you worried about? Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right?

Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know.

You've (pl) got nothing to fear whatsoever.

Mike Elzinga said:

Stanton said: The day SteveP sits down to read anything science-related, by his own free will, in an intellectually honest manner, will be the week after the Sun swallows up the Earth and Moon.

Every taunting ID/creationist I have ever seen in over 40 years fits pretty much the same profile; especially when they get cocky and try to start barroom brawls. They don’t understand any science despite their claims. They have a pretty standard set of misconceptions and misrepresentations they picked up from reading ID/creationist crap. They then go out and demand answers to nonsensical questions based on these misconceptions. When they don’t get answers, they take great pride in their belief that they stumped the “evolutionists.” The leaders over at AiG even brag about their “victories.” AiG and the ICR are pushing harder than ever the notion of “same evidence, different perspectives.” They even have a formal program of “not being ashamed.” It sounds plausible to rubes who don’t know that ID/creationist “science” never works in the real world. This is typical of pseudo-science followers in general. They never test it; they never find out if it describes reality. And they sure as hell never make an attempt to grasp real scientific concepts. I don’t believe there is a cure for this disease; it’s a sectarian/hermetically-sealed form of brain-death. There is no point in trying to revive them any more. Better to adopt a triage strategy and direct one's energy toward those for whom there is some hope.

We know where information is stored in the cell. We know where it comes from. We know how it is copied and passed on. We know how it controls development, metabolism and reproduction.

Way to read those papers Stevie.

More bullshit from Stevie. Here is what it looks like :

CAT

Steve P. said: Bullshit Malchus, Admit it. You are reluctant to explain it because you know where it will lead. Come on, Malchus. What are you worried about? Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right? Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know. You've (pl) got nothing to fear whatsoever.

And this guy wonders why no one will take him seriously.

DS said: Way to read those papers Stevie.

Let' go DS.

Come on now, don't be coy. You can do it. show me your brilliance. Don't want to waste all that science.

Steve P. said: Let' go DS. Come on now, don't be coy. You can do it. show me your brilliance. Don't want to waste all that science.

DS said: Way to read those papers Stevie.

Stanton said:

Steve P. said: Bullshit Malchus, Admit it. You are reluctant to explain it because you know where it will lead. Come on, Malchus. What are you worried about? Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right? Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know. You've (pl) got nothing to fear whatsoever.

If you're supposed to be this big-shot millionaire fabric salesman, why do you insist on constantly coming back to taunt us about how we've wasted our lives understanding science?

Stanton said:

DS said: Way to read those papers Stevie.

Steve taunts us, and he mocks us, yet he constantly denies taunting and mocking us. Seriously, why do the administrators allow him to continue posting here?

Steve P. said: Stanton, There you go again, repeating that misrepresentation DS started. FYI, I am not taunting you. I am asking you to explain the modular construction of the flagellum in your own words.

Stanton said:

Steve P. said: Bullshit Malchus, Admit it. You are reluctant to explain it because you know where it will lead. Come on, Malchus. What are you worried about? Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right? Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know. You've (pl) got nothing to fear whatsoever.

If you're supposed to be this big-shot millionaire fabric salesman, why do you insist on constantly coming back to taunt us about how we've wasted our lives understanding science?

Stanton said:

DS said: Way to read those papers Stevie.

Steve taunts us, and he mocks us, yet he constantly denies taunting and mocking us. Seriously, why do the administrators allow him to continue posting here?

Steve P. said: Stanton, There you go again, repeating that misrepresentation DS started. FYI, I am not taunting you. I am asking you to explain the modular construction of the flagellum in your own words.

Steve P. said: Well Geez Stanton, I wonder why. Maybe because it is I that am on topic? And it is you (pl) (ironically) that wants to derail the thread to avoid talking about the development of the flagellum? Funny, isn't it. An ID proponent on topic and Darwinian evolutionists derailing the topic to keep the IDist from talking about the flagella. Go figure.

Stanton said:

DS said: Way to read those papers Stevie.

Steve taunts us, and he mocks us, yet he constantly denies taunting and mocking us. Seriously, why do the administrators allow him to continue posting here?

Steve P. said: DS, You should know by now that I am not the least concerned if you take me seriously or not. Just explain in your own words how the bacterium co-opts the F1F0 ATP synthase; how the protein that will become the stirring filament finds its way into the ATP synthase; and how an additional protein gets attached to the stirring filament to become a proto-flagellum. As well, how does this new configuration get recorded in the genome in order for it to be duplicated? Simple, straight forward questions.

And this guy wonders why no one will take him seriously.

Steve P. said: More bullshit, this time coming from DS. Okay, DS, I'll play. Show me information. What does it look like?

We know where information is stored in the cell. We know where it comes from. We know how it is copied and passed on. We know how it controls development, metabolism and reproduction.

My apologies: "explaining".

Steve P. said: Bullshit Malchus,

Admit it. You are reluctant to explain it because you know where it will lead.

Come on, Malchus. What are you worried about?

Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right?

Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know.

You've (pl) got nothing to fear whatsoever.

Malchus said:

Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know.

Exactly. Perhaps you have some self-awareness after all. But without the background in science - biology, chemistry, and evolutionary biology - you simply are incapable of understanding the explanation. You've already admitted your ignorance, and you've already proven that you don't care to remedy it.

Steve P. said: DS, You should know by now that I am not the least concerned if you take me seriously or not. Just explain in your own words how the bacterium co-opts the F1F0 ATP synthase; how the protein that will become the stirring filament finds its way into the ATP synthase; and how an additional protein gets attached to the stirring filament to become a proto-flagellum. As well, how does this new configuration get recorded in the genome in order for it to be duplicated? Simple, straight forward questions.

And this guy wonders why no one will take him seriously.

PS SP

Signal sequences specify the subcellular localization of cellular products such as proteins. That is where the information is found and how it gets into the genome. Take a course in molecular biology if you want to understand it. Until you admit that you were wrong about endosymbiosis, I have no reason to try to educate you about anything else.

Malchus said:

Steve P. said: Bullshit Malchus,

Your dishonesty and intellectual vacuity? Hardly.

Admit it. You are reluctant to explain it because you know where it will lead.

I am reluctant to explain it because you are incapable of understanding it. It's really that simple. I cannot help the fact that your ego appears to be considerably larger than your mouth.

Come on, Malchus. What are you worried about?

I'm not actually worried about it. I have dealt with the scientifically ignorant and ethically dishonest before, I will deal with them again. You are a nobody on the internet; no one actually cares what you think. I realize that bothers your ego, and I'm sorry, but it's the truth.

Isn't it better that I don't understand it. If I am clueless, then I am powerless as well to critique your explanation. And if I attempt to, it will just make me look plain silly, ignorant, and stupid, right?

This is logically incoherent. If it's better you don't understand it, then fine: we're done, since you already don't understand it. Problem solved, I think.

Now go ahead and put your toes in the water. Its nice and warm. No sharks in the water. Just a stupid creo who doesn't know that he doesn't know.

Exactly. Perhaps you have some self-awareness after all. But without the background in science - biology, chemistry, and evolutionary biology - you simply are incapable of understanding the explanation. You've already admitted your ignorance, and you've already proven that you don't care to remedy it.

You've (pl) got nothing to fear whatsoever.

Indeed. I don't. You don't inspire much more than pity, I'm afraid.

DS,

DNA is just a string of amino acids held together by phosphates and sugar. That's all it is.

Where is the information? Show me the location.

Mike Elzinga said:

Stanton said:

DS said: Way to read those papers Stevie.

Steve taunts us, and he mocks us, yet he constantly denies taunting and mocking us. Seriously, why do the administrators allow him to continue posting here?

Matt seems to be busy and doesn’t monitor his threads as much as do some of the others. I suspect the trolls notice this and exploit it. I would suggest just letting the troll starve.

Observe the progress of this.

Steve demands that something be explained. He is referred to scientific papers that explain it. Next he demands that the scientific papers be explained, demonstrating that he has not understood them - if he read them at all. This process can continue indefinitely, of course. Any explanation can be followed by "yes, but why...", as any five-year-old knows.

This fact is explained to him - that if he wishes to learn the fundamentals of the subject, it will be necessary for him to, well, learn the fundamentals of the subject. He immediately concludes from this that nobody actually knows the explanation.

In a very trivial way, Steve is on to something here, but it's so esoteric and so far removed from useful discourse as to be nugatory. He is like someone demanding to know how a steam engine works, and not being satisfied with explanations about steam pressure on pistons, regulated by valves. Before he's finished, he will be demanding full details on the causation of the laws of thermodynamics, and of exactly how steel functions at the subatomic level to produce the properties of rigidity and tensile strength - and sooner or later, will come to the end of knowledge. That must happen. Human knowledge is finite, after all. If you keep going long enough, you'll find its limit.

In this transaction, Steve is hoping that nobody will notice that this is not about the actual explanation he says he seeks; it's about his acceptance of it. If he is allowed this, all he has to do is not understand and not accept. His ignorance and his incredulity are two sides of the same coin. The one is necessary to the other - and it's important to him to preserve the incredulity, so he'll fight to retain the ignorance.

He is also hoping that nobody will notice that he is being grossly inconsistent, to the point of complete dishonesty, about what he accepts. His own explanations are so vague as to be meaningless: information is "a template". "Force" is something that moves through information. It creates matter, somehow. He demands explanations many orders of magnitude more precise and fulsome than these, receives them, and then complains that they are not precise and fulsome enough to suit him.

Steve has been called on his dishonesty and invincible ignorance. The game is over. But he'll be back because, in a very perverted sense, he's right. If he can't be convinced, he wins - in a sense. It's a worthless sense, but it's all he's got, so he'll go with that. And it won't affect his life at all. He'll happily gobble up the fruits of biological research at the biochemical level, and he doesn't need to know how it's done, or how evolutionary theory provides the basic insights for it. Ignorance is bliss, in these matters, for Steve.

I wonder if he's got the grace to thank his God that it is not so for everyone?

Steve P. said: DS, DNA is just a string of amino acids held together by phosphates and sugar. That's all it is. Where is the information? Show me the location.

Dave,

You are absolutely right. However, in all fairness, both Malchus and myself have already told Steve that no one cares what he thinks and that no one cares if he is convinced of anything, He has absolutely no possibility of convincing anyone of anything, so no one cares if he displays his ignorance.

Here is a guy who thinks that DNA is composed of amino acids, (after having been told at least twice that that was wrong), and yet he still thinks that the fact that he doesn't believe that there is any information in DNA will convince someone of something!

The fool hath said in his heart, there is no information.

Steve P. said: No, Malchus. Its very simple.

Matzke's article is nothing but speculation and you know it. That's why you won't take the bait. You know you know squat about how the flagellum came to be. Matzke all but admits it.

You want people to take speculation and conjecture as some sort of iron-clad, you-can-take-it-to-the-bank guarantee.

Nothing beats straight talk and that is what is lacking in your (pl)comments. You and Elzinga keep singing the same song.

So you guys are the new mandarins now, I see. Science is so complicated that the average joe needs years of schooling to be able to even talk to you.

"We would tell you, if only you could understand. But alas, science is too much for you, I'm afraid."

Sounds eerily like the theocrats of old.

You want people to take speculation and conjecture as some sort of iron-clad, you-can-take-it-to-the-bank guarantee.

Steve P. said: Hey Malcolm, Why would you believe that I think your enzyme is alive?

The key take-away here is that the bacterium and your liver can both 'utilize' the enzyme to do work.

Can a snowflake or a crystal do this?

If not, why not? What do they lack that prevents them from utilizing the enzyme?

Malcolm said:

MrG said: PS: On looking over what SP seems to mean by "information", he seems to define it as "a physical parameter that distinguishes life from nonlife" -- the two otherwise sharing the same laws of physics and chemistry differing only in that one is alive and the other is not. On this basis, "information" becomes rather hard to tell from "elan vital", and in effect "information" becomes a revival of a century-old argument that ended up being a famous bust.

I wonder what SteveP would think of the enzyme I was purifying at work today. It was expressed in a bacterial cell, but is now in an aqueous buffer. Is it alive? It has the same function and activity now as the same enzyme in rat liver. If it is alive, what about the the substrate I add to test for activity? What about the product? If it isn't alive, what about the identical version of it in his own liver?

I mentioned this before; and I also put a note over on the Bathroom Wall (where this “conversation” should be taking place).

I just finished looking at the four-part series over on AiG called “The Ultimate Proof of Creation” by “PhD” Jason Lisle.

Some of the trolls who show up here lately are apparently drinking from this most recent cesspool over on AiG.

It’s extremely nauseating to sit through; but it appears to be the most extreme form of siege mentality from the creationists yet.

Lisle is explaining and demonstrating how to shut off every possible source of evidence and knowledge that comes from outside their sectarian world view. All logic and rational thought is asserted to come from their sectarian interpretation of the world; therefore no other source knowledge and evidence can be trusted. The projection and demonizing in this series is way over the top.

I think all of us have known people who are mentally ill; but AiG is starting to look more and more like
Jonestown.

I knew I should have previewed that.

The "The the lack of enzyme's substrate." is of course the answer to why the snowflake can't utilise the enzyme.

Mike Elzinga said: I mentioned this before; and I also put a note over on the Bathroom Wall (where this “conversation” should be taking place). I just finished looking at the four-part series over on AiG called “The Ultimate Proof of Creation” by “PhD” Jason Lisle. Some of the trolls who show up here lately are apparently drinking from this most recent cesspool over on AiG. It’s extremely nauseating to sit through; but it appears to be the most extreme form of siege mentality from the creationists yet. Lisle is explaining and demonstrating how to shut off every possible source of evidence and knowledge that comes from outside their sectarian world view. All logic and rational thought is asserted to come from their sectarian interpretation of the world; therefore no other source knowledge and evidence can be trusted. The projection and demonizing in this series is way over the top. I think all of us have known people who are mentally ill; but AiG is starting to look more and more like Jonestown.

All logic and rational thought is asserted to come from their sectarian interpretation of the world; therefore no other source knowledge and evidence can be trusted.

they are taught this from birth, and this also explains much of the entire anti-science attitude in much of the US.

there was a review paper on the subject published in Science a couple years back:

http://www.rci.rutgers.edu/~deenasw/Assets/bloom&weisberg%20science.pdf

Steve P sez:

You should know by now that I am not the least concerned if you take me seriously or not.

IOW...

IGNORE ME

Ichthyic said: Steve P sez: You should know by now that I am not the least concerned if you take me seriously or not. IOW... IGNORE ME

Malcolm said:

Steve P. said:

The key take-away here is that the bacterium and your liver can both 'utilize' the enzyme to do work.

Here you show your complete ignorance of biochemistry. I 'utilize' the enzyme to do work, the exact same work it would be doing inside a cell, in a reaction tube.

Actually, I'll go further than that. The key take-away here is that the enzyme reacts with its substrate in exactly the same way it would if it were obeying the laws of physics. It does this whether in vivo or in vitro. Given that all of the functions within the cell are regulated by enzymes, at what point is SteveP's magical 'information' supposed to take over? More importantly, what is it supposed to explain?

That time I did preview. It still managed to remove the text I was trying to quote.
Oh well, I'm sure that SteveP's massive intellect will allow him to work out the comment to which I was alluding.

Arrrggggggg!

I still managed to...

Definitely time for sleep.

DS said: If you want more details about the evolution of the bacterial flagellum, why don't you ask Nick to explain it to you. Of course his hypothesis is speculative. Of course he doesn't have all of the answers. So what? At least he knows the structure of DNA! Maybe if you actually read the paper, instead of just complaining about what it doesn't contain, then maybe you would get some clue. Maybe you would be able to explain the sequence homologies between the type III secretory system and the bacterial flagellum. Maybe you would realize that people have actually proposed and tested hypotheses about flagellar evolution while all you have done is sit on the sidelines and whine.

Steve P. said: Stanton, Same repetitive spiel, different day. I guess your and DS' definition of learning is accepting Darwin's idea of small, incremental, non-directed, unguided steps building genomes. If one doesn't accept this axiom, then one can't learn anything in biology, right? So Stanton, what are the mechanics of a bacterium co-opting say an F1F0 ATP synthase to create a stirring filament? How does 'selection' make the first insertion? I.E, how does selection provide the parts and what compels the genome (from a Darwinian POV)to put these new parts in a specific position ? And once the insertion is made, how is the modification recorded in the genome? If you KNOW the material, why not explain it to me in your own words, from memory? You can rattle off the details in a few of paragraphs, I'm sure.

Insights into the evolution of the bacterial flagellum have been gained from the homologies between flagellar proteins and those functioning in other systems (13). For example, the sequence similarity between flagellum-specific ATPase FliI and the β-subunit of ATP synthase led to the speculation that flagellum possibly evolved from this highly conserved, membrane-bound enzyme, whose subunits rotate during catalysis of ATP from ADP (14). Because the flagellar motor proteins MotA/B are homologous to the motor proteins in the Tol-pal and TonB systems (15), the flagellum was hypothesized to have originated as a simple proton-driven secretion system (16). Most significantly, there are well established sequence and structural homologies between bacterial flagella and the type III secretion system (TTSS) demonstrating that the two apparati derive from a common ancestor (17). Most evidence, including their much broader phylogenetic distribution, supports the view that the flagellum arose much earlier that the TTSS, which are largely limited to Proteobacteria (18–20). Here, we take advantage of complete genome sequence data to trace the history of each gene involved in the assembly and regulation of the bacterial flagellum. Our results show that flagellum originated very early, before the diversification of contemporary bacterial phyla, and evolved in a stepwise fashion through a series of gene duplication, loss and transfer events. In this article, we focus on the evolution of the core set of flagellar genes that is uniformly present in all flagellated bacteria. The later evolving and lineage-specific components of the flagellar gene complexes remain to be addressed.

Although sequence similarities among some of the rod and hook proteins were noted in early analyses (24), the degree of paralogy for the ancestral set of flagellar genes, and its implications for the origins of the bacterial flagellum, have gone unrecognized. From a phylogeny of these core proteins, it is possible to reconstruct the order in which they appeared, which in turn, can help elucidate the progression by which the flagellum was originally formed. Based on their relationships and on the physical locations of proteins forming the flagellum, the rod, hook, and filament proteins originated in an order that mirrors the “inside-out” flagellar assembly process (2, 3). The earliest proteins are proximate to the cytoplasmic membrane with later proteins situated distally, first spanning the outer membrane and then giving rise to structures (i.e., the hook, junction, filament, and capping proteins) that extend outside of the bacterial cell. Thus, the flagellum represents a case whereby its order of assembly recapitulates its evolutionary history.

The origins of complex organs and organelles, such as the bacterial flagellum and the metazoan eye, have often been subjects of conjecture and speculation because each such structure requires the interaction and integration of numerous components for its proper function, and intermediate forms are seldom operative or observed. However, the analysis of biological complexity has changed with the application both of genetic procedures that serve to identify the contribution of individual genes to a phenotype and of comparative sequence analyses that can elucidate the evolutionary and functional relationships among genes that occur in all life-forms. As with the evolution of other complex structures and processes (29–32), we have shown the bacterial flagellum too originated from “so simple a beginning,” in this case, a single gene that underwent successive duplications and subsequent diversification during the early evolution of Bacteria.

Steve P. said: Ichthyic. Just what you are doing now I suppose, ignoring me. Got it.

Steve P. said: No, Malchus. Its very simple. Matzke's article is nothing but speculation and you know it. That's why you won't take the bait. You know you know squat about how the flagellum came to be. Matzke all but admits it.

* Homologies (as evidenced by expected values <1e05) can be confirmed by retrieving the relevant flagellar protein sequences for Escherichia coli K-12 or Salmonella enterica Typhimurium LT2 and carrying out the following: ||performing a BLASTp search at the NCBI site under default conditions. ‡performing multiple PSI-BLAST iterations at the NCBI site under default conditions; §performing multiple iterations of PSI–BLAST at the NCBI site under default conditions, except for adjusting the threshold for inclusion to 0.05 and restricting the taxonomic scope to Enterobacteriaceae, starting with the protein sequences for FlgB, FlgL; ¶These similarities fail to achieve unequivocal significance using BLAST/PSI–BLAST under any of the above conditions, but are supported by other structural or functional considerations. T3SS, type III secretion system.

DS said:

Steve P. said: Ichthyic. Just what you are doing now I suppose, ignoring me. Got it.

Until you admit that you don't know anything about the structure of DNA and show some real evidence of reading the papers on flagellum evolution and endosymbiosis, until you admit that there is information in DNA, or at least try to provide some meaningful definition of information that excludes DNA, then yes CONSIDER YOURSELF IGNORED. In the words of Maxwell Smart: So, the old: demand evidence, then refuse to read the papers, then claim I read the papers, then make up some mystical crap, then demand more evidence, then demand that others explain things to me when I don't have the faintest clue, then run away and claim victory when everyone gets fed up with me and refuses to respond: routine. TIme for the cone of silence.

Rich,

No problem. Go for it. I am just fed up with this fool jerking people around. Maybe that is what he was going for, but I don't care anymore. Anybody who brays about how great they are at learning and then continues to claim that DNA is made of amino acids, even after admitting that that was not true, is too ignorant to be redeemable. Either he really is this stupid, or he is just yanking chains. Either way, there is no possibility that such as this will ever be convinced by evidence. However, this does seem like the perfect opportunity to present evidence that someone else might learn something from.

As for the specific question about the F1F0 ATP synthase, that association is also found in the type III secretory system. So I guess the question really boils down to how macro molecular complexes are assembled. A lot is known about how such processes work, so this doesn't really represent any particular challenge for the evolution of the bacterial flagellum. Ironically, this particular structure and the associated sequence homologies is one of the strongest lines of evidence for the endosymbiotic origin of mitochondria and chloroplasts. Go figure.

Steve P. said: Science is so complicated that the average joe needs years of schooling to be able to even talk to you. "We would tell you, if only you could understand. But alas, science is too much for you, I'm afraid." Sounds eerily like the theocrats of old.

Steve P. said: I know you hate to admit it Matzke, but you KNOW Behe was right. In order to show that Behe was wrong, you need to demonstrate first, how many intermediate steps there are on the road to bacterial flagellum land ( I count at least 10 steps) and second, what the functions for each of these intermediate steps are. (I understand you may believe this to be an unfair burden to you (pl). However, it is crucial to your refutation of Behe. Note your first attempt at refutation with the assertion of T3SS secretion system as being a precursor to the b/f has failed, since it has been shown that T3SS is most likely a devolution of and not a precursor to the b/f). For example, the b/f had to be built from the basal body outwards. The basal body is fixed to the inner membrane. So what was the function of the basal body fixed in the inner membrane before it added the C-Ring? Next, what was the function of the basal body and the C-Ring before it added the MS-Ring? After that, we need to know the function of the next intermediate step, the basal body + C-Ring + MS-Ring. Moving along, what is the function of the basal body + C-Ring + MS-Rings + the newly added stators? Note for these intermediate steps in the flagelllum's development, the new parts are placed in the periplasmic space. What advantage would the function of these intermediate configurations be considering the fact that these new parts are neither within the cell (to presumably support internal functions) nor outside of the cell (to presumably support locomotion or defense)? Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?

Steve P. said: 2) Have you tried to catch a mouse with sticky paper? Even roaches know to avoid them. Strike two!

Steve wrote:

"Without this knowledge, how can we say with any scientific confidence that the bacterium did not contain within its genome a pre-existing program for the expression of a flagellum waiting to be triggered by an environmental cue (like cecal valves in lizards)? Why would a scientist discard such an intuition when all the observations point in this direction?"

So you can add the word "genome" to the list of things that Steve doesn't understand. First he claims that the genome contains a preexisting program, then he denies that there is any information in DNA! Oh well, I guess if you really think that DNA is composed of amino acids, it probably shouldn't be too surprising to find out that you don't know what a genome is.

Dale Husband said: If he knows or can say nothing truthful about mousetraps (or roaches), how can he understand or acknowledge the ideas of complex biochemistry?

Mike Elzinga said: It probably is not possible to move an ID/creationist beyond his Tinkertoy understanding of chemistry and physics... It it’s complicated, it has to be designed; that’s it.

Mike Elzinga said:

Dale Husband said: If he knows or can say nothing truthful about mousetraps (or roaches), how can he understand or acknowledge the ideas of complex biochemistry?

It probably is not possible to move an ID/creationist beyond his Tinkertoy understanding of chemistry and physics. That would actually involve some real learning in their part; something they are programmed not to do. All ID/creationists think of atoms and molecules as inert objects that just drift around and have chance encounters. That these could ever form anything complex is incomprehensible to creationists precisely because “it’s all spontaneous molecular chaos down there.” This particular troll doesn’t even understand bond angles in water, let alone polymer fibers. It it’s complicated, it has to be designed; that’s it.

All science is tentative. If you don’t understand that, you don’t understand science

Science doesn’t explain everything. We’re fine with that. That’s why we do research. Creationists wrongly imply that any gap in science should be filled by God. They won’t say that any more, probably because they know how stupid it sounds out loud, but really, that’s where Steve P. is going with all of this. His entire argument is based on the creationist strawman structure of “if you can’t explain the details, then God did it.”

Steve:

Bullshit. You haven't got a clue. Go get educated then maybe someone will care what you think, but it won't be me.

Care to guess what the structure of DNA is again? I could make it multiple choice. It's so amusing to watch you display your ignorance so proudly.

As for your own bullshit, you haven't even got a hypothesis let alone any details. Your double standard is so ridiculous that even you must see how bat shit insane it is.

Steve P. said:

All science is tentative. If you don’t understand that, you don’t understand science

Speculative and tentative are different animals.

Science doesn’t explain everything. We’re fine with that. That’s why we do research. Creationists wrongly imply that any gap in science should be filled by God. They won’t say that any more, probably because they know how stupid it sounds out loud, but really, that’s where Steve P. is going with all of this. His entire argument is based on the creationist strawman structure of “if you can’t explain the details, then God did it.”

On the contrary. What I am saying is that if you can't explain the details, you are not in a position to assert that the idea of small, incremental, unguided, undirected change caused by random mutations, builds function, is correct. Rather, if you cannot explain the details, then the correct position is "It is inconclusive". It is clear that my personal viewpoint is that an intelligent cause is behind the proactive capabilities of genomes, but until I can 'nail down' the fundamental causes in an empirical way, then I too can only say "It is inconclusive."

DS said: As for your own bullshit, you haven't even got a hypothesis let alone any details. Your double standard is so ridiculous that even you must see how bat shit insane it is.

Steve drifts back to agnosticism, for the nonce. But of course that isn't what he really thinks.

What he says is right, but only superficially. In explanation, details are important. Knowing as precisely as possible what happens, and how, is what science is for, and about. Fine.

But what level of detail? In explaining the operation of an internal combustion engine, is it necessary for me to go into subatomic physics to explain why the gasoline vaporises and explodes, but the steel of the pistons does not? Am I required to traverse the cloudy regions of string theory to understand these reactions? Must I undergo a post-doc program in the mathematics of turbulence to understand the role of the carburettor? Must I trace the course of every electron in the starter motor to understand the process of ignition?

And if I am required to do the equivalent of that with biochemistry, why does Steve think he can get away with vague handwaving like "force acts through information to create matter"? The two are so plainly, so obviously not equivalent that pretending that they're equivalent can only be put down to deception.

Maybe Steve is deceiving himself, and he really believes this. Maybe it's knowing falsehood, and he hopes to deceive others. There's no way of knowing from here. But what can be said is that he is attempting to deceive.

Steve P. said: On the contrary. What I am saying is that if you can't explain the details, you are not in a position to assert that the idea of small, incremental, unguided, undirected change caused by random mutations, builds function, is correct.

So, my serious questions to you are: 1) How are you defining "information?"

A template

2) Why do you think "information" exists independent of matter?

Force moves ‘through’ information creating matter. So matter is the ‘emergent property’ of the interaction between information and force.

3) Why do you think "information" can interact with matter?

Information interacts with matter by constraining it.

But in the case of life, it would be the other way around, where information determines the arrangement of molecules (physics and chemistry can account for the molecules themselves, but NOT their arrangement into specific patterns that function within an integrated whole); i.e. the space determines the shape of the cup. To be sure, science is starting to realize that information is in fact real, and can only be understood with the mind, not ‘found’ out there somewhere, or written on a molecule somehow.

On the contrary. What I am saying is that if you can’t explain the details, you are not in a position to assert that the idea of small, incremental, unguided, undirected change caused by random mutations, builds function, is correct.

"We don't need your pathetic level of detail"

-William (DR DR) Dembski

I quote, for those who are unfamiliar with the game Steve P is playing.

carry on.

refresher course, anyone?

http://pandasthumb.org/archives/2005/06/id-in-their-own-1.html

sound familiar now?

:)

SWT said: Physics and chemistry do, observably, account for the arrangement of matter into specific patterns.

The basic premise of Intelligent Design is that some inventions in biology are impossible to make via natural selection, therefore they must have been designed by an intelligence. All that is needed to refute it is to show that it is indeed possible for complex inventions in biology to arise via natural selection.

Logically, of course, the IDists only have to find one example where evolution could not have created some structure or process found in living things. One such would be enough to show that evolution is not all there is, and hence it would be necessary to consider some other agency.

But they have not done that. And note that they must show that evolution could not possibly have come up with the goods. It is not enough to say that it's unlikely, and it's certainly not enough to say that they can't think of a way. It must be clearly impossible, and their peers must be convinced that it is, or no cigar. And no Nobel, either.

Dave Luckett said: Observe the progress of this...

A template

phhht said: My serious questions to you are (after SWT): 1) How do you define "information?"

A template

Where does a "template" come from? ...

Dave Luckett said: Logically, of course, the IDists only have to find one example where evolution could not have created some structure or process found in living things. One such would be enough to show that evolution is not all there is, and hence it would be necessary to consider some other agency. But they have not done that.

phhht said: My serious questions to you are (after SWT): 1) How do you define "information?"

It's clear that people like Steve P. or even Michael Behe don't have a clue how molecular motors work because it requires you to understand randomness and thermodynamics. Molecular motors unlike classical ones operate in thermal bath dominated by thermal noise. Trying to move in a particular direction is like walking in a hurricane. In fact, these motors are sometimes referred to Brownian motors as in random Brownian motion. When the ID proponent looks at such a motor they naively think propellor on a boat when they really operate on an electrochemical gradient. See the H+ channel in the diagram below:

http://en.wikipedia.org/wiki/File:ATPsynthase_labelled.png

You mean FoF1 ATP Synthase is a molecular motor? Yep, it just runs backwards using the protonmotive force to synthesize ATP http://en.wikipedia.org/wiki/Electron_transfer_chain.

People who actually design nanoscale motors often use the biological motors as a model and surprise, surprise they use randomness. Because the motor events are stochastic, molecular motors are often modeled with the Fokker-Planck equation or with Monte Carlo methods. Hint: when you see an engineer use the word Monte Carlo consider what happens there, gambling. MCMC like the Fokker-Planck equation are stochastic analysis techniques because the behavior being studied is basically random. I find it ironic in the extreme the very example used to disprove randomness is at its base random!

Steve P. said: On the contrary. What I am saying is that if you can't explain the details, you are not in a position to assert that the idea of small, incremental, unguided, undirected change caused by random mutations, builds function, is correct.

Rather, if you cannot explain the details, then the correct position is "It is inconclusive".

Coincidence? Given their "access to the same literature" we had, where Graham Johnson at Scripps so brilliantly worked out the real motion of kinesins, I am simply blown away that the "Intelligent Design" animators slavishly made the hands of their kenesins move exactly as we did, even though we intentionally left out the stochastic Brownian motion which actually characterizes the tractive force and periodic pedicle placement of these tiny motivators. We simply did not have the time or budget to render these, and a dozen other details, to the level of insanity we would like to have done! This was, after all, an underfunded proof-of-concept piece. The cellular biology that serves as "filler" material, between scenes copied from Inner Life, is riddled with biological errors. Imagine "Intelligent Design's" depiction of protein synthesis without ribosomes!

On the contrary, Blinn.

Homology has nothing to say about the bacterium's ability to assemble the 40 different proteins of the flagellum (or the several proteins of the pilia, or any of the other organelles Matzke compares), each set of proteins into a specific pattern, and each pattern into a larger pattern (which I have referred to as a meta-pattern) which in turn produces work.

In order to refute Behe, you need to show for each organelle, how a missing protein will not render the organelle function-less. Matzke has not done this. He imagines that each organelle is a progression in complexity from pilia to flagellum. But to get around the stumbling block of showing how each addition of different proteins results in a functional organelle, he appeals to co-option.

However, appealing to co-option is begging the question of how the bacterial cell can co-opt a complex organelle (like ATP synthase, itself having no explanation), while at the same time it is seemingly powerless to recognize gene replication errors (but we already know this is not true because cells can in fact detect errors and make repairs), which results in excess protein production, is powerless to clean up the mess, and moreover, stands by while these homeless proteins align themselves over time into a functioning system.

You can't have it both ways.

Rather, the logical, consistent position based on what we observe, is that neither the gene duplication is in error, nor is the organelle co-option random, nor the flagellum the result of cobbling, fumbling, lucky hits.

Your position is inherently the hardest to defend precisely because you cannot reconcile the contradictions associated with the Neo-Darwinian evolutionary mindset.

Steve P. said: appealing to co-option is begging the question of how the bacterial cell can co-opt a complex organelle (like ATP synthase, itself having no explanation), while at the same time it is seemingly powerless to recognize gene replication errors (but we already know this is not true because cells can in fact detect errors and make repairs), which results in excess protein production, is powerless to clean up the mess, and moreover, stands by while these homeless proteins align themselves over time into a functioning system.

Time for me to chime in.

First point: you are using the word "organelle" incorrectly, Steve P. An organelle is a membrane-bounded space within a cell. The flagellum is a cellular structure.

Second point: you appear to have fundamental misconceptions about what happens in a cell at the molecular level. What actually happens is wasteful and inefficient; RNA is transcribed and immediately degraded. Polypeptides are translated and transported directly to a lysosome and recycled. Spurious protein aggregates form and sometimes cannot be eliminated by the cell (Lewy bodies). Multi-subunit proteins assemble incorrectly, but are still transported to their normal cellular location. Lastly, and most pertinent to your objections, INCORRECTLY assembled protein complexes work just fine.

My dissertation research demonstrated that final point. I created mutations in all 4 of the subunits of the (adult form) nicotinic acetylcholine receptor (nAChR). I then expressed those mutant genes in Xenopus oocytes and studied the assembly, transport, and function of the quaternary protein incorporating mutant and MISSING subunits. I was still able to get electrical current flowing through the cell membrane in response to acetylcholine (the normal function of the nAChR) even when one of the four subunits was missing. Thus, at the molecular level, a cell IS the result of "cobbling, fumbling, lucky hits."

Vaughn

You know, the thing I don’t get about creotards claiming it’s sooooooo unlikely that “random processes” can generate a bacterial flagellum without any sort of (presumably divine) “guidance” is that they overlook the size of the population over the timescales involved.

Even if we take their straw- based hominid of evolutionary processes as gospel, they are apparently unaware (given that most bacterial reproduction cycles are measured in hours) that even granting a laughably 6000-year-old Earth and only 1 original bacteria created de novo, there have been at least 2^2,189,999 individual bacteria that have existed (positing 1 bacterial generation per day for 6000 years, beginning with a single ur-bacteria; I trust someone credible will correct me if I’m committing mathematical murder here).

Which seems to me more than enough instances of “random” genetic variation to develop all kinds of really, really, really, really unlikely stuff.

Steve P. said: On the contrary, Blinn. blah, blah, blah, ...

Rich Blinne said: Hint: when you see an engineer use the word Monte Carlo consider what happens there, gambling. MCMC like the Fokker-Planck equation are stochastic analysis techniques because the behavior being studied is basically random. I find it ironic in the extreme the very example used to disprove randomness is at its base random!

I see Steve P. the pompous moron has not shown us exactly where God's fingerprints are in Lenski's citrate-metabolizing Escherichia coli, nor has he explained how saying God poofed bacterial flagella into existence is supposed to be a scientific explanation.

Or how anybody but the bacteria themselves gain anything from the alleged bioengineering of their parts...

Stanton said: I see Steve P. the pompous moron has not shown us exactly where God's fingerprints are in Lenski's citrate-metabolizing Escherichia coli, nor has he explained how saying God poofed bacterial flagella into existence is supposed to be a scientific explanation.

Steve also did not answer any of my questions, including the one about the structure of DNA. Although he claims that he really good at learning, he still hasn't bothered to learn even that.

Now, you can add "organelle" to the list of terms that he doesn't understand. That list is getting pretty long.

As for his hand waving dismissal of the homology data, he completely ignores the implications of this data and continues to demand more details, even though he has still provided none in support of any alternative. Once he can explain the homology data and the fact that flagellar proteins did indeed evolve by gene duplication and co-option, then he can quibble about the exact steps in the process. Fortunately, satisfying his criteria for acceptance of a hypothesis is unnecessary.

Henry J said: Or how anybody but the bacteria themselves gain anything from the alleged bioengineering of their parts...

Rich Blinne said:

Stanton said: I see Steve P. the pompous moron has not shown us exactly where God's fingerprints are in Lenski's citrate-metabolizing Escherichia coli, nor has he explained how saying God poofed bacterial flagella into existence is supposed to be a scientific explanation.

Just in case Steve P. is Google impaired: http://myxo.css.msu.edu/lenski/pdf/2008,%20PNAS,%20Blount%20et%20al.pdf My guess is Steve for Figure 1 would have a line at generation 31,500 with the label "Goddidit".

The population expansion between generations 33,000 and 33,500 (Fig. 1) was triggered by one or more mutations that improved citrate utilization, rather than by the growth of the original Cit+ mutant.

Steve P. said:

All science is tentative. If you don’t understand that, you don’t understand science

Speculative and tentative are different animals.

Science doesn’t explain everything. We’re fine with that. That’s why we do research. Creationists wrongly imply that any gap in science should be filled by God. They won’t say that any more, probably because they know how stupid it sounds out loud, but really, that’s where Steve P. is going with all of this. His entire argument is based on the creationist strawman structure of “if you can’t explain the details, then God did it.”

On the contrary. What I am saying is that if you can't explain the details, you are not in a position to assert that the idea of small, incremental, unguided, undirected change caused by random mutations, builds function, is correct. Rather, if you cannot explain the details, then the correct position is "It is inconclusive". It is clear that my personal viewpoint is that an intelligent cause is behind the proactive capabilities of genomes, but until I can 'nail down' the fundamental causes in an empirical way, then I too can only say "It is inconclusive."

Yet you take seriously the claim that an Intelligent Designer must have made the flagella from scratch, which involves the discovery of nothing.

Can you show that co-option is not possible? If not, STFU.

And you can't speak of "ATP synthase" as an organelle (it's an ENZYME, idiot!) without getting laughed at. And if cells are so good at detecting and repairing errors in their genomes, how do you explain things like Down's Syndrome, hemophilia, and hundreds of disorders and deformities known to arise in humans and other organisms due to mutated genes?

You are a liar. You have no business telling us what a contradiction is when you get caught telling falsehoods as we have already noted here.

Dale Husband said: So you [Steve P.] are agnostic? That's great, so am I. But then you wouldn't be so eager to assert Intelligent Design, would you? Once you assume there must be an Intelligent Designer, you stop saying, "It is inconclusive," and attempt to fill the gap of knowledge with belief in that Designer. Which makes your above statement a lie. Please note that carefully: ALL SELF-CONTRADICTORY STATEMENTS ARE LIES!

Steve P. said: Your position is inherently the hardest to defend precisely because you cannot reconcile the contradictions associated with the Neo-Darwinian evolutionary mindset.

Go Malchus!

SteveP still hasn't told us where the cut-off point is, where physics and chemistry fail, and beyond which magic is required for life.

Using religion to explain biology is like hiring a poet to predict the weather.

fnxtr said: Using religion to explain biology is like hiring a poet to predict the weather.

Malcolm said: SteveP still hasn't told us where the cut-off point is, where physics and chemistry fail, and beyond which magic is required for life.

mrg said:

Malcolm said: SteveP still hasn't told us where the cut-off point is, where physics and chemistry fail, and beyond which magic is required for life.

Oh, he knows he's talking baloney. We know he's talking baloney. He knows that we know he's talking baloney. He just think's it's fun to talk baloney.

Mike Elzinga said:

fnxtr said: Using religion to explain biology is like hiring a poet to predict the weather.

“Red sky in the morning, sailors warning. Red sky at night, sailor’s delight.”

Mike Elzinga said:

fnxtr said: Using religion to explain biology is like hiring a poet to predict the weather.

“Red sky in the morning, sailors warning. Red sky at night, sailor’s delight.”

fnxtr said:

Mike Elzinga said:

fnxtr said: Using religion to explain biology is like hiring a poet to predict the weather.

“Red sky in the morning, sailors warning. Red sky at night, sailor’s delight.”

"That's not writing, that's just typing."

mrg said:

Malcolm said: SteveP still hasn't told us where the cut-off point is, where physics and chemistry fail, and beyond which magic is required for life.

Oh, he knows he's talking baloney. We know he's talking baloney. He knows that we know he's talking baloney. He just think's it's fun to talk baloney.

Rich Blinne said: I'm an evangelical Christian. As such, I believe in an intelligent designer as a religious and philosophical position.

Malcolm said:

mrg said:

Malcolm said: SteveP still hasn't told us where the cut-off point is, where physics and chemistry fail, and beyond which magic is required for life.

Oh, he knows he's talking baloney. We know he's talking baloney. He knows that we know he's talking baloney. He just think's it's fun to talk baloney.

I'm not so sure. I think that SteveP may be a perfect example of the Dunning-Kruger Effect.

phhht said: Rich, I'm an evangelical atheist. As such, I believe there is no supernatural. For example, I believe there are no gods. To my mind, philosophically, what cleaves the religious from the naturalistic word view is a truth model. As I understand it, the religious world view is based on truth revealed by some supernatural being. Characteristics of such truths are often inerrancy, inconsistency, and assumed immunity to logical question. The naturalistic world view, on the other hand, eschews certainty and inerrancy, and demands logical question. Evidence, in this view, requires a consensus on what we call reality; that is, repeated observation of well-defined and -predicted phenomena. Such evidence can be overturned if there is contradictory evidence, or irreproducibility, or fraud, etc, and it often is. This is all part of a process which seeks error, and works to correct it. I'd like to hear your thoughts on these questions.

Rich Blinne said: I'm an evangelical Christian. As such, I believe in an intelligent designer as a religious and philosophical position.

Malcolm said: I'm not so sure. I think that SteveP may be a perfect example of the Dunning-Kruger Effect.

Steve P. said: Your position is inherently the hardest to defend precisely because you cannot reconcile the contradictions associated with the Neo-Darwinian evolutionary mindset.

stevaroni said:

Steve P. said: Your position is inherently the hardest to defend precisely because you cannot reconcile the contradictions associated with the Neo-Darwinian evolutionary mindset.

No, ID is inherently the hardest to defend precisely because it cannot reconcile the contradictions observed with objective, measurable, reality.

Dale Husband said:

phhht said: I'm an evangelical atheist...

Rich Blinne said: I'm an evangelical Christian...

Is this where we get into the "only atheists can truly oppose the idea of Intelligent Design" assumption? Or is it that you think that the religious and naturalistic views should never be allowed to mix and their followers have nothing to learn from each other?

I’d prefer to hear your thoughts on the issues outlined above,

you must not know Dale then. Frankly, if you did, I rather doubt you would.

Ichthyic said: I’d prefer to hear your thoughts on the issues outlined above, you must not know Dale then. Frankly, if you did, I rather doubt you would.

phhht said: I'd prefer to hear your thoughts on the issues outlined above, rather than subject-changing questions.

Dale Husband said:

phhht said: I'm an evangelical atheist...

Rich Blinne said: I'm an evangelical Christian...

Is this where we get into the "only atheists can truly oppose the idea of Intelligent Design" assumption? Or is it that you think that the religious and naturalistic views should never be allowed to mix and their followers have nothing to learn from each other?

Ichthyic said: you must not know Dale then. Frankly, if you did, I rather doubt you would.

phhht said: Rich, I'm an evangelical atheist. As such, I believe there is no supernatural. For example, I believe there are no gods. To my mind, philosophically, what cleaves the religious from the naturalistic word view is a truth model. As I understand it, the religious world view is based on truth revealed by some supernatural being. Characteristics of such truths are often inerrancy, inconsistency, and assumed immunity to logical question. The naturalistic world view, on the other hand, eschews certainty and inerrancy, and demands logical question. Evidence, in this view, requires a consensus on what we call reality; that is, repeated observation of well-defined and -predicted phenomena. Such evidence can be overturned if there is contradictory evidence, or irreproducibility, or fraud, etc, and it often is. This is all part of a process which seeks error, and works to correct it. I'd like to hear your thoughts on these questions.

Rich Blinne said: I'm an evangelical Christian. As such, I believe in an intelligent designer as a religious and philosophical position.

Dale, you are in my opinion wrong to reject the idea that the word "atheism" may mean "lack of belief in God", rather than "rejection of the idea of the existence of God". It can mean the former, and anyway there's no point in arguing about the definitions of words. Instead we need a word that signifies specifically "rejection of the idea of the existence of God". I propose "antitheism".

Icthyic, I believe, would not object to a description of his views as "antitheist", for example, as a subset of "atheist". There is a considerable faction, I think, of that persuasion. Although I would prefer the term "agnostic" to describe my own belief, I would not object to "atheist" with the rider "not antitheist".

But the rest of what you say makes sense to me. The argument appears to me to hinge on accurate descriptions of belief or acceptance of ideas. We need more precise vocabulary.

Icthyic, I believe, would not object to a description of his views as “antitheist”, for example, as a subset of “atheist”.

minor correction:

I would not object to a description of my views as anti-theistIC, or anti-theism.

theists in general I have no objection to, it's their theology that inevitably sucks.

;)

Correction noted and applied. "Antitheistic" it is.

phhht said: Rich, I'm an evangelical atheist. As such, I believe there is no supernatural. For example, I believe there are no gods. To my mind, philosophically, what cleaves the religious from the naturalistic word view is a truth model. As I understand it, the religious world view is based on truth revealed by some supernatural being. Characteristics of such truths are often inerrancy, inconsistency, and assumed immunity to logical question. The naturalistic world view, on the other hand, eschews certainty and inerrancy, and demands logical question. Evidence, in this view, requires a consensus on what we call reality; that is, repeated observation of well-defined and -predicted phenomena. Such evidence can be overturned if there is contradictory evidence, or irreproducibility, or fraud, etc, and it often is. This is all part of a process which seeks error, and works to correct it. I'd like to hear your thoughts on these questions.

Dale Husband said: Your statement about "what cleaves the religious from the naturalistic word view" is a logical error...

...because only conservatives or fundamentalists among religions insist that "Characteristics of [their] truths are often inerrancy, inconsistency, and assumed immunity to logical question."

Many who are religious are not so narrow minded, because they recognize that religious claims are made and promoted by men and are thus prone to error. They test those claims against reality, allowing what they find from nature to modify their views, thus resulting in a blending of naturalism and religion. You making an absolute distinction between the two is the fallacy known as the excluded middle or a false dichotomy.

What I find amusing about atheist fanatics is that they fail to make a distinction between beliefs in religion that are harmless and/or have NOT been disproven and those that are harmful and/or HAVE been disproven.

Then they paint ALL religion as delusional, forgetting that the true definition of delusion is "a fixed belief that is either false, fanciful, or derived from deception."

Unproven is NOT the same as false.

For something to be established as false and therefore...

Dave Luckett said: Dale, you are in my opinion wrong to reject the idea that the word "atheism" may mean "lack of belief in God", rather than "rejection of the idea of the existence of God". It can mean the former, and anyway there's no point in arguing about the definitions of words. Instead we need a word that signifies specifically "rejection of the idea of the existence of God". I propose "antitheism". Icthyic, I believe, would not object to a description of his views as "antitheist", for example, as a subset of "atheist". There is a considerable faction, I think, of that persuasion. Although I would prefer the term "agnostic" to describe my own belief, I would not object to "atheist" with the rider "not antitheist". But the rest of what you say makes sense to me. The argument appears to me to hinge on accurate descriptions of belief or acceptance of ideas. We need more precise vocabulary. Correction noted and applied. "Antitheistic" it is.

You are asserting these as fact without any evidence, and in contradiction to observation. There is in fact a well-developed theory for self-organization of chemical systems, including spatial organization. There are in fact many situations where we can see systems snap into a spatially organized dynamic state, and these transitions can be traced back to the fundamental properties of matter. Ilya Prigogine won a Nobel prize for laying the foundations of this theory, so it’s not really languishing in obscurity; when I was earning my doctorate in the 1980’s, it was well established. Similarly, Stuart Kauffmann has developed an intriguing theory for the development of complex autocatalytic systems. Physics and chemistry do, observably, account for the arrangement of matter into specific patterns.

DS said: Steve: Bullshit. You haven't got a clue. Go get educated then maybe someone will care what you think, but it won't be me. Care to guess what the structure of DNA is again? I could make it multiple choice. It's so amusing to watch you display your ignorance so proudly. As for your own bullshit, you haven't even got a hypothesis let alone any details. Your double standard is so ridiculous that even you must see how bat shit insane it is.

This is another shibboleth that marks the ID/creationist; complete ignorance of historical developments in science in which “unseen” things were surmised long before technology advanced to the point of actually allowing us to observe them. Inheritance of ancestor characteristics pointed to discrete unites of heredity. Genetics was already being mapped out long before DNA was actually observed. DNA was predicted to be a kind of quasi-crystal whose x-ray crystallographic pattern would eventually be linked to its actual structure; and it turned out pretty much as predicted. Many of the elements and their properties were predicted long before the periodic table was filled in. The same can be said of many of the elementary particles of physics. Thermodynamics and statistical mechanics show how to predict regularity from the stochastic behaviors of the underlying atomic and molecular constituents of a complex system. In many cases, that can be turned around to understand the properties and behaviors of the underlying constituents from their collective behaviors in large systems. And then we have literally millions of working examples from the fields of condensed matter physics and organic chemistry. These things are so well understood that there are entire industries build on this knowledge; including the very industry that our current troll allegedly works in. He makes his living off the work of other people; yet he appears to be completely oblivious of the physics, the chemistry, and the people who have done the research on the materials his industry uses. This has always been one of the strangest characteristics of these ID/creationists. They freely use all of the technology in society in order to spew their hatred of the underlying science that built that technology. Even when their attention is called to this fact, they deny it or simply ignore it. So it is a sectarian/political war they are waging. They don’t really give a crap about the science; they just want to be in control of everyone else.

Steve P. said: Ignore me then, DS. By the way, you DO know what I was getting at when talking about DNA. You say there is information in DNA. I asked you to explain where in the DNA molecule the information resides. Is the information located in the amino acids, in the phosphate backbone, where? DS doesn't say. Because just maybe the information in the amino acid pattern repeat is, you know, a template and not 'a thing'? Maybe it is holographic in nature but that would just be a regressive step, compelling us to ask how light energy could self-organize, expressing that organization as amino-acid patterns. If you ask that question, then it invariably brings you to all the way back to force and information. Logically, information must precede matter, not the other way around.

The occurrence of evolutionary events (such as insertions, deletions, point mutations, rearrangements, and inversion) separating two sequences sharing a common ancestor will result in the loss of their shared information. Regions of sequences which do not share a common ancestor will not share more information than would be expected at random. Here we present a mathematically rigorous universal distance based on shared algorithmic information...

Ichthyic said: theists in general I have no objection to, it's their theology that inevitably sucks.

What an asshole. The jerk wad still thinks that DNA is composed of amino acids! He has been told three times that that is not true and still he persists in his ignorance. Of course he could have easily learned the structure of DNA by now, so either he is just plain lazy, or is being intentionally provocative. Either way, he should be ignored.

FOr anyone who actually cares about information, it is obvious that there is information in the linear sequence of nucleotides in DNA. To deny this is to deny any very concept of information. Not only is there information in DNA, but we know exactly how that information is used as a TEMPLATE in order to copy DNA, direct the synthesis of proteins, determine the spatio temporal expression pattern of proteins, determine how metabolism works and determine how development works. This is also how that information is passed on from one generation to the next and how organisms change over time. It's also where we find the information that allows us to reconstruct phylogenetic relationships, another thing that Stevie doesn't understand.

Now why would anyone listen to someone who couldn't even be bothered to come up with a definition of information, let alone understand the structure of DNA. The combination of ignorance and arrogance is astonishing. And of course we eventually got around to the magic hologram hypothesis. Now how did I guess. This guy is completely clueless and just yanking chains. It would be pathetic if it wasn't so sad.

Oh and he still hasn't explained how there can be a program in the "genome" if there is no information in DNA! And now he's just plain making shit up. I never claimed that cells were "oblivious to their surroundings". I can't even imagine how anyone could contort what I wrote in order to claim such a thing. What a load of horse shit. This cretin has gone off the deep end and is sinking fast.

Steve P. said: SWT, Unfortunately, Kaufmann doesn't help your case .... he understands biology as NOT reducible to physics, in stark contrast to what posters are saying here, especially Elzinga.

The only way to falsify the conclusion (from observation) that cells actually recognize and process information is to show how several auto-catalytic systems could auto-integrate themselves into a large system (i.e. the cell). But then that's the white elephant in the room.

Steve P. said: By the way, you DO know what I was getting at when talking about DNA. You say there is information in DNA. I asked you to explain where in the DNA molecule the information resides. Is the information located in the amino acids, in the phosphate backbone, where? DS doesn't say. Because just maybe the information in the amino acid pattern repeat is, you know, a template and not 'a thing'?

Rob said: Steve P., I will ignore you as I would anyone who claims DNA is made of amino acids.

DNA is composed of which of the following?

(A) Amino acids

(B) Ribonucleotides

(C) Nucleotides

(D) Glucose

(E) Fatty acids

Now for the bonus question. Where did you get the information that allowed you to decide which answer was correct?

I told Stevie that the development of the flagellum was not a problem for molecular or evolutionary biology. In fact, we know quite a lot about it as it has been an active area of research for at least twenty years. Here is a video of the process for those who are interested:

http://stock.cabm.rutgers.edu/blast/video2.mov

It seems that the spatio temporal expression pattern of the genes responsible for producing the flagellar proteins is tightly regulated and the assembly process is controlled by enzymes and the structure of the proteins involved. It turns out that he secretory function is actually critical to flagellar assembly. The whole thing is controlled by DNA! Who would thunk it? If anyone is interested in technical details or experimental evidence, here are a few references:

Journal of Cell Science 112(21):3769-3777 (1999)

Journal of Bacteriology 181(19):6160-6170 (1999)

Plant Physiology 127:1500-1507 (2001)

Current Opinions in Microbiology 5(2):160-165 (2002)

Cell 124(5):1025-1037 (2006)

Molecular Biology and Evolution 25(9):2069-2076 (2008)

Now when Steve has demonstrated that he has read and understood all of these references, he might be in a position to demand more details, right after he describes his own alternative hypothesis in this level of detail that is. If your god is hiding in the gaps, why is he hiding? And he is getting smaller every day. Too bad for Steve, ignorance is not a gap.

Still no answer to the multiple choice question Stevie? Not enough information for you?

Steve P. said: As always, Elzinga, if all is so well understood, then please do go right on ahead and explain the development of the flagellum.

Why do you go on ad nauseum about those damn creationists? Have done with it and get on with the explanation.

By the way, contrary to your un-called for insinuations of my lack of integrity, I for one have spoken plainly and truthfully of what I do and who I am.

How does a Thermos(tm) know to keep hot things hot and cold things cold? Must be magic. Or maybe there's a mystical, incorporeal "information template" for Thermos(tm) that we just haven't found yet.

Steve P. said: Ignore me then, DS. By the way, you DO know what I was getting at when talking about DNA. You say there is information in DNA. I asked you to explain where in the DNA molecule the information resides. Is the information located in the amino acids, in the phosphate backbone, where? DS doesn't say. Because just maybe the information in the amino acid pattern repeat is, you know, a template and not 'a thing'? Maybe it is holographic in nature but that would just be a regressive step, compelling us to ask how light energy could self-organize, expressing that organization as amino-acid patterns. If you ask that question, then it invariably brings you to all the way back to force and information. Logically, information must precede matter, not the other way around.

DS said: Steve: Bullshit. You haven't got a clue. Go get educated then maybe someone will care what you think, but it won't be me. Care to guess what the structure of DNA is again? I could make it multiple choice. It's so amusing to watch you display your ignorance so proudly. As for your own bullshit, you haven't even got a hypothesis let alone any details. Your double standard is so ridiculous that even you must see how bat shit insane it is.

DS said: I told Stevie that the development of the flagellum was not a problem for molecular or evolutionary biology. In fact, we know quite a lot about it as it has been an active area of research for at least twenty years. Here is a video of the process for those who are interested: http://stock.cabm.rutgers.edu/blast/video2.mov It seems that the spatio temporal expression pattern of the genes responsible for producing the flagellar proteins is tightly regulated and the assembly process is controlled by enzymes and the structure of the proteins involved. It turns out that he secretory function is actually critical to flagellar assembly. The whole thing is controlled by DNA! Who would thunk it? If anyone is interested in technical details or experimental evidence, here are a few references: Journal of Cell Science 112(21):3769-3777 (1999) Journal of Bacteriology 181(19):6160-6170 (1999) Plant Physiology 127:1500-1507 (2001) Current Opinions in Microbiology 5(2):160-165 (2002) Cell 124(5):1025-1037 (2006) Molecular Biology and Evolution 25(9):2069-2076 (2008) Now when Steve has demonstrated that he has read and understood all of these references, he might be in a position to demand more details, right after he describes his own alternative hypothesis in this level of detail that is. If your god is hiding in the gaps, why is he hiding? And he is getting smaller every day. Too bad for Steve, ignorance is not a gap. Still no answer to the multiple choice question Stevie? Not enough information for you?

Rich Blinne said:

DS said: I told Stevie that the development of the flagellum was not a problem for molecular or evolutionary biology. In fact, we know quite a lot about it as it has been an active area of research for at least twenty years. Here is a video of the process for those who are interested: http://stock.cabm.rutgers.edu/blast/video2.mov It seems that the spatio temporal expression pattern of the genes responsible for producing the flagellar proteins is tightly regulated and the assembly process is controlled by enzymes and the structure of the proteins involved. It turns out that he secretory function is actually critical to flagellar assembly. The whole thing is controlled by DNA! Who would thunk it? If anyone is interested in technical details or experimental evidence, here are a few references: Journal of Cell Science 112(21):3769-3777 (1999) Journal of Bacteriology 181(19):6160-6170 (1999) Plant Physiology 127:1500-1507 (2001) Current Opinions in Microbiology 5(2):160-165 (2002) Cell 124(5):1025-1037 (2006) Molecular Biology and Evolution 25(9):2069-2076 (2008) Now when Steve has demonstrated that he has read and understood all of these references, he might be in a position to demand more details, right after he describes his own alternative hypothesis in this level of detail that is. If your god is hiding in the gaps, why is he hiding? And he is getting smaller every day. Too bad for Steve, ignorance is not a gap. Still no answer to the multiple choice question Stevie? Not enough information for you?

Steve, if you don't want to synthesize all this together go here: http://books.google.com/books?id=UVta7XZJHKYC&lpg=PA207&ots=E6RF7z57bv&lr&pg=PA207#v=onepage&q&f=false I realize Steve won't read this let alone understand it but it's an interesting read for the rest of us (and Google Books saves you $250).

We looked at the distribution of the 12-bp flhC deletion among other O157:NM strains and found that it occurred only in the German SF O157 strains. The absence of the 12-bp flhC deletion in the other O157:NM strains indicates that nonmotility in these strains may be due to catabolite repression or other physiological mediators (24) or to other uncharacterized genetic defects. The finding that the 12-bp flhC deletion is specific to the German SF O157 strains coincides with the presence of plasmid-encoded fimbriae genes that are unique only to this group (9), supporting previous reports that these strains are in a distinct clonal group (13, 21). The fact that the German SF O157 strains carry the H7 fliC gene (16) and can be manipulated to produce the H7 antigen also confirms their close genetic relation to O157:H7 (13, 21) and is in agreement with our evolution model that they diverged from O157:H7, in part, by the loss of motility (13, 26). As a consequence, the 12-bp flhC deletion provides a potentially useful marker with which strains in this clonal lineage may be identified and traced.

If people are believers, they don’t have any real need for them.

true; nor logic of any kind, for that matter.

of course, that depends on the definition of "need", I suppose.

How does a Thermos™ know to keep hot things hot and cold things cold? Must be magic.

fucking thermoses, how do they work?

Of course the plural is pronounced Ther-mo-SEEZ.

Ichthyic said: true; nor logic of any kind, for that matter.

Thermoses: they're hot, they're cool, they're all temperature.

(Or does that make them sound like a detergent?)

Henry J

Thanks for the link Rich. There are some very interesting references in that book chapter. I know Steve will want to read all of them right away. Seems not everyone is as ignorant as he is.

Steve P. said: SWT, Unfortunately, Kaufmann doesn't help your case. He understands his concepts to be fully speculative. Moreover, he understands biology as NOT reducible to physics, in stark contrast to what posters are saying here, especially Elzinga. He is not a reductionist, and in fact is trying to move beyond this stagnant mindset, albeit within a no-gods, natural selection is still in the game, framework. I do not see how stringing together numerous speculative concepts (epistemological and ontological emergence)in support of another speculative concept (self-organization of the bacterial flagellum) increases the likelihood of that concept being true. This IMO seems an evasion of the difficulty of reconciling the apparent ability of cells to recognize and process information, in actuality 'building' a flagellum. Contrary to what DS is saying, cells are not oblivious to their surroundings. The 'overwhelming' amount of evidence we have is that cells do in fact recognize information (read), use it (signalling), change it (insertions/deletions),transform it(work), repair it (restore original configuration), etc. The only way to falsify the conclusion (from observation) that cells actually recognize and process information is to show how several auto-catalytic systems could auto-integrate themselves into a large system (i.e. the cell). But then that's the white elephant in the room.

Steve P. said: [Kaufmann's] concepts [are] fully speculative.

Steve P. said: ...speculative concepts (epistemological and ontological emergence)...self-organization...

Rich wrote:

"One of the interesting things in the chapter I cited is the role of deletion in bacterial evolution."

Yes, I was struck by that as well. IN fact, gene duplication, co-option and deletion have all been very important processes operating in the evolution of flagella. The last paper I cited:

Molecular Biology and Evolution 25(9):2069-2076 (2008)

gives a detailed description of these processes and even presents a phylogeny with the relevant events labelled. It also discusses other aspects of the evolution of flagella and the evolution of regulatory pathways in flagellar assembly in parasites. Of course this is the same story that emerges whenever the genetics of any complex structure are investigated. The genetic mechanisms are now well understood, with gene duplication and mutational divergence almost always playing an important role, along with the evolution of regulatory elements and pathways.

Perhaps Steve could explain to us exactly why the intelligent designer included genes for flagella proteins in organisms which lack flagella or why there are defective genes for flagellar proteins in some parasites. Of course, it might be hard for him to understand the papers if he doesn't know anything about the structure of DNA. But he claimed that he is a very fast learner and so should soon be up to speed on the last sixty years of genetic research.

DS said: What an asshole. The jerk wad still thinks that DNA is composed of amino acids! He has been told three times that that is not true and still he persists in his ignorance. Of course he could have easily learned the structure of DNA by now, so either he is just plain lazy, or is being intentionally provocative. Either way, he should be ignored. FOr anyone who actually cares about information, it is obvious that there is information in the linear sequence of nucleotides in DNA. To deny this is to deny any very concept of information. Not only is there information in DNA, but we know exactly how that information is used as a TEMPLATE in order to copy DNA, direct the synthesis of proteins, determine the spatio temporal expression pattern of proteins, determine how metabolism works and determine how development works. This is also how that information is passed on from one generation to the next and how organisms change over time. It's also where we find the information that allows us to reconstruct phylogenetic relationships, another thing that Stevie doesn't understand. Now why would anyone listen to someone who couldn't even be bothered to come up with a definition of information, let alone understand the structure of DNA. The combination of ignorance and arrogance is astonishing. And of course we eventually got around to the magic hologram hypothesis. Now how did I guess. This guy is completely clueless and just yanking chains. It would be pathetic if it wasn't so sad. Oh and he still hasn't explained how there can be a program in the "genome" if there is no information in DNA! And now he's just plain making shit up. I never claimed that cells were "oblivious to their surroundings". I can't even imagine how anyone could contort what I wrote in order to claim such a thing. What a load of horse shit. This cretin has gone off the deep end and is sinking fast.

Ichthyic said: How does a Thermos™ know to keep hot things hot and cold things cold? Must be magic. f***ing thermoses, how do they work?

Steve P. said: Give it up, DS. It is YOU that errs in asserting that information is a physical thing. Information is not physical, but is conveyed through a physical medium. Different animals.

DS said: FOr anyone who actually cares about information, it is obvious that there is information in the linear sequence of nucleotides in DNA.

How many days did it take him to figure out what DNA is made of again? More evidence of reading comprehension problems; dude's practically a Creotard stereotype.

I made it a multiple choice question yesterday, AFTER I had already told him the answer.

stevaroni said: Clearly, Thermoses(tm) don't actually exist. [snip] See how easy science is when you use the AIG website for guidence?

eddie said: The Thermos is intelligently designed. So it doesn't violate the second law at all.

eddie said: And you people think you have to go to college to do science.

Steve P. said: Give it up, DS. It is YOU that errs in asserting that information is a physical thing. Information is not physical, but is conveyed through a physical medium. Different animals. Nucleotides contain no information. BUT the sequence of nucleotides does. The information is only conveyed through a physical medium as it should be since the information is building a physical structure. Just as the house in a builder's head does not reside in a single point in his brain. However, the idea of the house he is building is conveyed through the brain, which commands his hands to form the house with physical substrates. Otherwise, the house could never achieve physical form.

I really cannot get my mind around this one. I think Steve is just yanking chains. I think he is trying to see how bat shit insane he can get without some calling POE.

How is it possible to reconcile the phrase:

"Information is not physical..."

With the claim in the very next paragraph:

"Nucleotides contain no information. BUT the sequence of nucleotides does."

So, I guess the sequence of nucleotides is not a physical entity! It's not like, you know, a real physical molecule or anything! Man, this guy really doesn't understand the structure of DNA. How in hell does he think that the linear sequence of amino acids in proteins is determined? Oh wait, that's right, he thinks DNA is composed of amino acids, so I guess he couldn't have a clue about that either.

Oh and by the way, individual nucleotides can contain information as well, such as the tautomeric form they are in or whether or not they are methylated. Now why am I not surprised that Stevie did not know that either? Oh well, what can you expect from someone who claims that the genome contains a program, but there is no information in DNA. If this jackass is serious, he is seriously deluded. I'm beginning to think that he is just plain nuts and off his meds.

This is what I love.

These guys are hilarious. They say yeah sure information is not physical, but er it is in fact physical(one of Elzinga's science lessons I bet).

You know like, "Yeah sure it looks designed but you know, er it is in fact not designed".

I'm sure you guys have a mantra you keep mumbling to yourself like "It is NOT designed. It is NOT designed. It is NOT designed".

How about an "Oooooohhhhhmmm" to got with that?.

Ohhhh, but you guys got me right where you want me, huh? Coming out of the woodwork in droves now.

Rave on. Got my 3-D glasses on.

Well Stevie boy seems to have finally fallen off the deep end. Maybe he finally realized that everyone was just laughing at him. Maybe he realized that he had blown all of his imaginary credibility by repeatedly claiming that DNA was composed of amino acids. Or maybe he finally realized that physical objects can indeed contain information, it isn't just some abstract idea in someones head. It takes intelligence to interpret information, it does not take any intelligence to create it.

One last time, just to be clear, There is information in the linear sequence of nucleotides in a molecule of DNA. This information is expressed through gene regulation and transcription and translation. The information is sufficient to control all of metabolism, development and reproduction, including assembly of the flagellum. There is no magic invisible hologram. There is no consciousness or intelligence required. Real scientists understand this very well. That is why we spent three billion dollars on the human genome project. Just one more thing that Steve doesn't understand.

In any event, his record is still intact. He still hasn't read a single paper, even though he challenged people repeatedly to provide him with the "information". He still hasn't learned a single thing, including the definition of information or the structure of DNA. He still hasn't given anyone a single reason to take him seriously about, well, anything. FIne by me.

Steve P. said: Look at me! I so smart! I l337 creotard! Me contradict self every time me post! Yay me!

Steve P. said: This is what I love. These guys are hilarious. They say yeah sure information is not physical, but er it is in fact physical(one of Elzinga's science lessons I bet). You know like, "Yeah sure it looks designed but you know, er it is in fact not designed". I'm sure you guys have a mantra you keep mumbling to yourself like "It is NOT designed. It is NOT designed. It is NOT designed". How about an "Oooooohhhhhmmm" to got with that?. Ohhhh, but you guys got me right where you want me, huh? Coming out of the woodwork in droves now. Rave on. Got my 3-D glasses on.

Does it scare you shitless that in the 21st century, information will be ‘nailed down’ as a real entity, existing independent of matter? Why does it bother you to such an extreme?

So, when proven to be absolutely wrong about everything, Steve once again starts making shit up and laughing about how he was right all along. Well nobody else ever claimed that information could not be physical. JHFC, how in the hell does this guy think that CSI works? Like there isn't any information in the markings on a bullet or the spatter pattern of blood! If the is no information in DNA, how in the world can it be used to identify suspects?

Perhaps this intellectually challenged primate is just trying to play word games. Perhaps he thinks that there is somehow an important distinction between claiming that DNA IS information and claiming that DNA CONTAINS information. BFD. Who cares? The point is that DNA does contain all of the information required in order to create an entire organism, including the flagella, heart, testes and anal sphincter. JHFC you can even clone animals using nothing but an enucleated egg and a transplanted nucleus. There is no magic invisible hologram. There is no semi intelligent designer watching over every flagellum in every bacteria. If the ass hat is so frickin intelligent, why the hell can't she create a flagellum without having to supervise every time? Don't sound very intelligent like to me.

Oh well, they say ignorance is bliss, so Steve must be the happiest guy on earth. I guess that's what's really important, not you know, reality. Maybe he will read those references soon. Yea, right.

Of course information can exist without matter. JHFC on a shingle, there is information in radio waves. There is information in the spectrum of the sun. There is information in the periodicity of a pulsar. How in the hell is this supposed to mean that there can be no information in DNA? How in the hell is this supposed to mean that the magic invisible hologram controls development, or the magic invisible designer puts flagella together?

Well at least you have to admit that no one else could get so much mileage out of refusing to define the term "information". Way to go Stevie I. Wonder.

Steve P. said: And again, i say to you if life is inherent in the laws of physics and chemistry ONLY, then we should logically see all manner of life forms (and not necessarily carbon/water based) all over the universe. We DO NOT see this happening. Therefore, logically we can say that life does in fact have some element in it that is not present in inanimate matter.

Yeah, it's amazing how little life we've seen in the 99.999999... percent of the universe that we've never been to!

Gaebolga said: Wow. The stupid, it burns!