Ken Miller misrepresents Behe on cilium

[DNAunion]

DNAunion: I have a lot of posts that go together. I would appreciate it if no one responded until I have posted them all. It might take an hour or two because they'll have to be divided up into logical 12,000-char-max segments.

Concerning the fact that Kenneth Miller misrepresented Behe, I cannot continue to “debate” 3 or more people simultaneously and still cover all of the “counters” (no matter how strong or lame, how relevant or irrelevant, they might be) each of those multiple people can come up with, on all the multiple misrepresentations Miller made (after all, a single person can handle only so much stuff without becoming overwhelmed – a point some people take advantage of in such situations). And, since to demonstrate the fact that Miller misrepresented Behe I need only one solid example, I am starting this new thread and restricting it to just one of Miller’s misrepresentations of Behe – the one dealing with the cilium (which was the primary IC system being discussed in the old thread anyway, which can be found at http://www.christianforums.com/threads/29446.html ).

I will quote the actual statements made by Behe and Miller in this thread too. But before bringing them into the discussion, it would be a good idea to try to make sure that everyone has a firm grasp on the underlying principles of interest, which does not require that we look at Behe’s and Miller’s actual statements. You see, they dealt with biological matters that some people here apparently do not have a clear enough grasp of (for example, they might wonder…is there a difference between a eukaryotic cilium and a eukaryotic flagellum? If not, and since both eukaryotes and prokaryotes have flagella, then aren’t a eukaryotic cilium and a prokaryotic flagellum the same thing? Do both eukaryotes and prokaryotes have cilia, and if so, is there a difference between their cilia? How are microtubules assembled in vivo? What is a central pair of an axoneme? What is a doublet? Why is it wrong to call the central pair of an axoneme a doublet? In relation to microtubules, what do 9 + 2 and 9 x 3 mean? What are dynein arms, and what is the difference between the inner and outer arms? Etc.). In some of the following posts, we will see that more than one error in biology was made by those opposing me due to their lack of knowledge of the relevant subject matter. So, because of the unfamiliarity of at least some to the terms/concepts involved, I have attempted to paraphrase the arguments in more familiar terms, using a common, everyday system that Behe mentions in his book, that Paley used a couple centuries ago, and that even Jerry Smith brought up during our discussion in the other thread: that system is a mechanical watch. As long as the rephrasing is analogous enough to the original statements, this switch is not illegitimate – in fact, it serves a valuable role as a preliminary example aimed at clarifying concepts: an example we can refer back to as needed.

Please note that I am not claiming to have done a thorough IC analysis of a mechanical watch – I took all of one minute to figure out what parts are required and why, and so could have easily overlooked something due to the brevity of the process. But the analysis could be completely flawed and it wouldn’t matter here – what matters is whether or not someone who claims to refute those statements sticks to what was originally said. (For example, if I said something as wrong as, “The Moon is made of green cheese”, and some people claimed to refute me, they would have to stick to countering my actual statement in order to not be misrepresenting me. It is the accuracy of the counter that is important, not the correctness of the original statement).

Also, the following that deals with a mechanical watch is not meant to be an actual IC argument, so again, the accuracy of the analysis is not of concern. The mechanical watch discussion is for demonstrative purposes – the use of a familiar object to simplify the discussion in hopes of revealing the main issues that might have been getting lost for some people due to their unfamiliarity with the biological terminology that was involved in the original.

Much of what follows in the next several posts of mine are watch-analogous paraphrasings of various people’s statements and/or arguments – many of the statements are not the original ones made by the parties (I will try to be clear about which are analogs and which are actual statements).

Also, I had no access to the internet while composing these many replies. My source was a hard-copy printout of the old thread and Miller’s web page as they existed the day I stopped posting several weeks ago. So it is possible that Miller and/or some of the posters here went back and edited their statements after I took the snapshot.

 

[DNAunion]

DNAunion: This whole post uses the watch analogy to present analogs of Behe’s original statements, Miller’s “refutation”, and my original rejection of Miller’s “refutation”.

Michael Behe: Examining a typical mechanical watch we discover a variety of parts. There’s a battery that powers the system, and a set of rotating gears that work together to sweep the hour hand, the minute hand, and the second hand across the face in a circular path. Spaced evenly around the outer region of the face are the numbers 1 through 12; between each of those numbers are 4 unnumbered tick marks which indicate smaller units of time. The day, month, and year are displayed in a small inset somewhere on the face. A rubber, plastic, or metal band with a buckle or latch secures the watch to the wrist, and a glass or plastic see-through covering seals the watch, protecting it from water and dust. In order to allow the user to read the time at night, a small light comes on at the press of a button, and other buttons or small knobs allow the user to set an alarm, the date, the month, and so on.

…

If the hands of a mechanical watch are removed, while all the other parts remain, the system is unable to perform its function (without the hands, one cannot tell what time it is). … If just the gears are eliminated the hands will not be moved: they will always point to the same positions and the system ceases to function. … If (while keeping all other parts in place) the battery is taken out, the watch becomes ‘paralyzed’, and the system is once again functionless.

Now, let us sit back, review the workings of a mechanical watch, and consider what they imply. What components are needed for a mechanical watch to work? Certainly it requires a hand (i.e., a pointer); otherwise, there would be nothing to indicate the current time. Additionally it requires an energy source, such as a battery, or else the system would lie stiff and motionless. Furthermore, it requires a set of gears that connect the energy source to the hand, and that move the hand at an appropriate rate. All of these parts are required to perform one function: that of a mechanical watch. Just as a mousetrap does not work unless all of its constituent parts are present, a mechanical watch simply does not exist in the absence of a hand, an energy source, and a set of gears: remove any one of them and the system ceases to function.

Ken Miller: One of these [IC systems Behe discusses] is a mechanical watch. And, …

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Behe: “Just as a mousetrap does not work unless all of its constituent parts are present, a mechanical watch simply does not exist in the absence of a hand, an energy source, and a set of gears. Therefore, we can conclude that a mechanical watch is irreducibly complex.”
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Miller: Remember Behe’s statement that the removal of any one of the parts of an irreducibly complex system effectively causes the system to stop working. A mechanical watch provides us with a perfect opportunity to test that assertion. If it is correct, then we should be unable to find examples of functional mechanical watches anywhere that lack a mechanical watch’s basic parts.

DNAunion: Wrong! That is not Behe’s claim. What Miller goes on to show is that some accessory structures can be removed without loss of function. What Miller basically does is show that although a wristband is found on almost all watches, there are some that don’t have that “basic part”. That’s great, but a wristband is not one of the essential parts of the IC mechanical watch system – it is an add-on that can clearly be removed without loss of function.

Kenneth Miller: Unfortunately for the argument, that is not the case. There are many examples of fully-functional mechanical watches that are missing key parts. One of the most compelling is the Seikasiolex 1230 pocket watch, which lacks at least three important parts normally found in a mechanical watch: the wristband, the nightlight, and the second hand.

This diagram shows a view of the Seikasiolex 1230 pocket watch. In other mechanical watches, this “irreducibly complex” system includes a wristband, a nightlight, and a second hand. Each of these structures are missing in the Seikasiolex 1230 pocket watch, and yet the structure is fully functional.

DNAunion: So what? The first two are accessory parts, not even mentioned by Behe as being any of the required parts of the IC system. Remember what words of Behe Miller himself just quoted above? Look again.

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Behe: “Just as a mousetrap does not work unless all of its constituent parts are present, a mechanical watch simply does not exist in the absence of a hand, an energy source, and a set of gears.
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DNAunion: Removing the wristband and the nightlight still leaves the Seikasiolex 1230 pocket watch with an energy source and gears. And note that only the SECOND hand is missing – which means that the HOUR hand is still present (as can be seen in the photo). So the Seikasiolex 1230 pocket watch still has all three parts Behe says are mandatory for mechanical-watch function.

 

[DNAunion]

DNAunion: This post shows the original statements made by Behe and Miller (and me), so that people can relate them back to the above watch analogy. First, here is the link to Miller’s web page: http://www.millerandlevine.com/km/evol/design1/article.html

Now, the quotes.

Michael Behe: ”… the motor to power ciliary motion resides in the cilium itself – not in the interior of the now-missing cell. The next clue is that if (through biochemical tricks) the dynein arms are removed but the rest of the cilium is left intact, then the cilium is paralyzed, as if in rigor mortis. Adding back fresh dynein to the stiffened cilia allows motion to resume. …

… What would removal of [just] the [nexin] linkers do? … When biochemical energy was supplied to the cilium, instead of bending, it rapidly unraveled. … [Biochemists] concluded that the nexin linkers are needed to keep the cilium together when it is trying to bend.

… The dynein arms on one microtubule attach to a second, neighboring microtubule, and the dynein uses the biological energy of ATP to “walk up” its neighbor. When this happens the two microtubules begin to slide past each other. In the absence of nexin, they would continue to slide until they separated; however, the protein cross-links prevent neighboring microtubules from sliding by more than a short distance. When the flexible nexin linkers have elongated to their limit, further walking by dynein makes the nexin linkers tug on the microtubules. As dynein continues to walk, strain increases. Fortunately the microtubules are somewhat flexible, so the dynein-induced sliding motion is converted to a bending motion.

Now, let us sit back, review the workings of the cilium, and consider what they imply. What components are needed for a cilium to work? Ciliary motion certainly requires microtubules; otherwise, there would be no strands to slide. Additionally it requires a motor [i.e., dynein], or else the microtubules of the cilium would lie stiff and motionless. Furthermore, it requires [nexin] linkers to tug on neighboring strands, converting the sliding motion into a bending motion, and preventing the structure from falling apart. All of these are required to perform one function: ciliary motion. Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. Therefore we can conclude that the cilium is irreducibly complex…

… All systems that move by paddling – ranging from my daughter’s toy fish to the propeller of a ship – fail if any one of the components is absent. The cilium is a member of this class of swimming systems. The microtubules are paddles, whose surface contacts the water and pushes against it. The dynein arms are the motors, supplying the force to move the system. The nexin arms are the connectors, transmitting the force of the motor from one microtubule to its neighbor.

The complexity of the cilium and other swimming systems is inherent in the task itself. It does not depend on how large or small the system is, whether it has to move a cell or move a ship: in order to paddle, several components are needed.” (bold added, Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p63-65)

Kenneth Miller: One of these [IC biochemical systems Behe discusses] is the eukaryotic cilium, an intricate whip-like structure that produces movement in cells as diverse as green algae and human sperm. And, . . .

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Behe: "Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. Therefore we can conclude that the cilium is irreducibly complex" (Behe 1996a: 65).
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Miller: Remember Behe's statement that the removal of any one of the parts of an irreducibly complex system effectively causes the system to stop working? The cilium provides us with a perfect opportunity to test that assertion. If it is correct, then we should be unable to find examples of functional cilia anywhere in nature that lack the cilium's basic parts.” (Ken Miller from above URL)

DNAunion: Wrong! That is not Behe’s claim. What Miller goes on to show is that some accessory structures can be removed without loss of function. What Miller basically does is show that although a company logo is found on almost all mouse traps, there are some that don’t have that “basic part”. That’s great, but a logo is not one of the essential parts of the IC mousetrap system – it is merely an add-on that can clearly be removed without loss of function.

Kenneth Miller: “Unfortunately for the argument, that is not the case. Nature presents many examples of fully-functional cilia that are missing key parts. One of the most compelling is the eel sperm flagellum (Figure 3), which lacks at least three important parts normally found in the cilium: the central doublet, central spokes, and the dynein outer arm (Wooley 1997).” (Ken Miller from above URL)

DNAunion: So what? The first two are accessory parts, not even mentioned by Behe as being any of the required parts of the IC biochemical system. Remember what words of Behe Miller himself just quoted above? Look again.

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Kenneth Miller [quoting Behe]: "Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. Therefore we can conclude that the cilium is irreducibly complex (Behe 1996a: 65)”.

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DNAunion. Removing the central doublet and the central spokes still leaves the eel sperm flagellum with microtubles - those that allow the system to perform its usual function. And note that only the OUTER dynein arms are absent – which means the INNER dynein arms are still present (as can be seen in the photo). So the eel flagellum still has all three parts Behe says are mandatory for ciliary function.

 

[DNAunion]

DNAunion: This post doesn’t deal with the watch analogy. I want to point out two or three biological errors that Kenneth Miller made in his web page.

Kenneth Miller: “One of the most compelling is the eel sperm flagellum (Figure 3), which lacks at least three important parts normally found in the cilium: the central doublet, central spokes, and the dynein outer arm (Wooley 1997).” (bold added, Ken Miller from above URL)

DNAunion: Originally, I blindly followed Miller in calling the central pair the central doublet. After all, he is a biology professor with a Ph.D, and on top of that, one who is “refuting” another Ph.D. professor of biology: so one would assume that Miller would have made sure that he crossed all of his T’s and dotted all of his I’s. But a quick check showed that Miller is wrong. The central pair is not a single doublet – they are two physically separate singlets (a microtubule doublet consists of one complete tubule with a partial tubule attached to it).

But that’s not all: Miller makes another error on his web page.

Kenneth Miller: “… biologists have known for years that each of the major components of the cilium, including proteins tubulin, dynein, and actin have distinct functions elsewhere in the cell that are unrelated to ciliary motion.” (bold added, Ken Miller from above URL)

and…

Kenneth Miller: “But the individual parts of the cilium, including tubulin, the motor protein dynein, and the contractile protein actin are fully-functional elsewhere in the cell.” (bold added, Ken Miller from above URL)

DNAunion: Miller twice mentions the protein actin and calls it a major component of a cilium. But Behe doesn’t even mention actin when discussing the cilium, so why is Miller bringing that protein into the discussion as if it were one that Behe considered to be a required part?

Actually, it’s worse for Miller than that: actin is not a major component of cilia. You see, Behe is not the only scientist who doesn’t mention actin when discussing cilia. Over the last couple of days I have read dozens of pages about cilia and microtubules from two molecular cell biology texts and nowhere do I recall any mention of actin (in microfilaments, yes; microtubules, no. in motility by muscular contraction, yes; motility by cilia, no). But before claiming Miller to actually be wrong, I wanted to make double sure, so I spent several hours carefully rereading every sentence of the pertinent sections of both molecular cell biology texts. Here are the topics I reread in full.

The World of the Cell: Third Edition: Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, Benjamin/Cummings Publishing Co., 1996
Chapter 20: Cytoskeletal Structure and Function
---Introduction (p644)
---Structural Elements of the Cytoskeleton (p644-645)
---Microtubules (p648-659)
------Introduction
------Structure and Polarity of Microtubules
------The Genetics of Microtubules
------Microtubule Assembly in Vitro
------The Dynamic Instability Model of Microtubule Assembly
------Drug Sensitivities of Microtubule Assembly
------Microtubule Organization, Function, and Regulation in the Cell
------Organization and Maintenance of Cell Shape
------The Role of Dynamic Instability and Capping Proteins in Microtubule Organization
------Regulation of Microtubules by Microtubule-Associated Proteins

Chapter 21: Cellular Movement: Motility and Contractility
---Introduction (p675)
---Systems of Motility (p675)
---The Molecular Basis of Motility (p675-676)
---Intracellular Microtubule-Based Movement: Dynein and Kinesin (p678-680)
------Cytoplasmic Microtubules, Motor MAPs, and Axonal Transport
------Motor MAPs and the Transport of Intracellular Vesicles
---Microtubule-Based Motility: The Motile Appendages of Eukaryotic Cells (p702-706)
------Cilia and Flagella
------The Structure of Motile Appendages
------The Sliding-Microtubule Model for Motile Appendages
---The Bacterial Flagellum (p706-709)
------Nature’s Wheel: Locomotion by Rotation
------Flagellar Rotation and Chemotaxis

Molecular Cell Biology: Fourth Edition: Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, W. H. Freeman and Co., 2000
Chapter 19: Cell Motility and Shape II: Microtubules and Intermediate Filaments
---Introduction (p795-796)
---Microtubule Structures (p796-802)
------Introduction
------Heterodimeric Tubulin Subunits Compose the Wall of a Microtubule
------Microtubules Form a Diverse Array of Both Permanent and Transient Structures
------Microtubules Assemble from Organizing Centers
------Most Microtubules Have a Constant Orientation Relative to MTOCs
------The [gamma]-Tubulin Ring Complex Nucleates Polymerization of Tubulin Subunits
---Microtubule Dynamics and Associated Proteins (p802-809)
------Introduction
------Microtubule Assembly and Disassembly Occur Preferentially at the (+) End
------Dynamic Instability Is an Intrinsic Property of Microtubules
------Colchicine and Other Drugs Disrupt Microtubule Dynamics
------Assembly MAPs Cross-Link Microtubules to One Another and Other Structures
------Bound MAPs Alter Microtubules Dynamics
---Kinesin, Dynein, and Intracellular Transport (p809-817)
------Introduction
------Fast Axonal Transport Occurs along Microtubules
------Microtubules Provide Tracks for the Movement of Pigment Granules
------Intracellular Membrane Vesicles Travel along Microtubules
------Kinesin Is a (+) End-Directed Microtubule Motor Protein
------Each Member of the Kinesin Family Transports a Specific Cargo
------Dynein Is a (-) End-Directed Motor Protein
------Dynein-Associated MBPs Tether Cargo to Microtubules
------Multiple Motor Proteins Are Associated with Membrane Vesicles
---Cilia and Flagella: Structure and Movement (p817-823)
------Introduction
------All Eukaryotic Cilia and Flagella Contain Bundles of Doublet Microtubules
------Ciliary and Flagellar Beating Are Produced by Controlled Sliding of Outer Doublet Microtubules
------Dynein Arms Generate the Sliding Forces in Axonemes
------Axonemal Dyneins Are Multiheaded Motor Proteins
------Conversion of Microtubule Sliding into Axonemal Bending Depends on Inner-Arm Dyneins
------Proteins Associated with Radial Spokes May Control Flagellar Beat
------Axonemal Microtubules Are Dynamic and Stable


All that material on the structure, function, dynamics, and assembly of microtubules; all that stuff on cilia, flagella, axonemes, axonemal dynein, etc.; and yet nothing about actin (at least not in relation to anything of relevance. There were several very brief mentions of actin, such as in one of the introductions where microfilaments, which are made of actin, were briefly contrasted to microtubules, which are not. But the few off-hand mentions were completely irrelevant to the matter at hand: nothing that would rescue Miller).

Therefore I feel quite confident in proclaiming Miller to be wrong: it is quite clear that actin is in fact not a major component of cilia. Chalk up another biological boo-boo for Miller.

There’s a possible third error in Miller’s biology, but it’s a bit less secure than the others. None of the sources I have read use Miller’s term “central spokes”. I have been assuming that when using that term Miller is actually talking about the radial spokes the texts mention, which extend between the central pair and the outer doublets. However, this is not certain: could Miller be talking about the proteins that from a bridge between the two separate central singlets themselves? Perhaps. Or perhaps the term “central spokes” is used by some sources instead of term “radial spokes”, but just not the three that I checked. The use of the term “central spokes” may be another error on Miller’s part.

With two confirmed errors, and a third possible one, perhaps Kenneth Miller should stick to watch analogies, seeing as how he has a bit of trouble with the biology!

 

[DNAunion]

DNAunion: This post and the next (originally one post, but it exceeds the 12,000-character limit) deals with actual quotes – not watch-altered analogs. If a watch is mentioned, then it was the object being discussed originally.

A common misconception, which seems to be the source of much confusion about Behe’s concept of irreducibly complex systems, needs to be addressed.


Behe’s IC System != Whole System
Behe’s IC System = System’s IC “Core”


One mistake many people – Ken Miller, Lucasps, and other anti-Behe’ians – make is to incorrectly assume that when Behe says a system is IC that he means all parts of the system constitute the IC system. That is incorrect: for many or most systems, some parts of the complete system are simply add-on/accessory/auxiliary parts and are not counted among the required parts that comprise the IC system itself (the IC “core”, as IDists have come to call it). And anyone who actually bothered to read Behe’s book and tried to understand Behe’s position would know this.

For example, consider what Behe states about a watch.

Michael Behe: ”It is surprising but true that the main argument of the discredited Paley has actually never been refuted. Neither Darwin nor Dawkins, neither science nor philosophy, has explained how an irreducibly complex system such as a watch might be produced without a designer.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p213)

DNAunion: So Behe has explicitly classified a watch as being an irreducibly complex system. If we accepted what many of Behe’s detractors claim, then Behe would be saying that every single part of a watch is required for it to function. But this is clearly not what Behe holds. In fact, on page 216 he points out that Paley should not have discussed the watch cover when arguing design because a watch cover is not part of the (core) IC system itself, but merely a convenience added onto it.

Michael Behe: “The problems start when Paley digresses from systems of necessarily interacting components to talk about arrangements that simply fit his idea of the way things ought to be. The first hint of trouble comes in Paley’s opening paragraph, when he mentions that the watch’s wheels are made of brass to prevent rust. The problem is that the exact material, brass, is not required for the watch to function. It might help, but a watch can function with wheels made of almost any hard material – probably even wood or bone. Things only get worse when Paley mentions the glass cover of the watch. Not only is the exact material not required, but the whole component is dispensable: a cover is not necessary for function of the watch. A watch cover is simply a convenience that has been attached to an irreducibly complex system itself.” (bold and contained italics added, Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p216)

DNAunion: Note that Behe – after stating that a watch is an irreducibly complex system – explicitly says that a watch cover, though surely part of the watch, is not part of the irreducibly complex system. A watch cover (or a wristband, or a nightlight) is a part that is added onto the IC watch system itself – an auxiliary part appended to the “core”. Thus, there is a “core” system within the watch that is IC, onto which accessory/auxiliary parts – such as a watch cover, or a wristband or nightlight, etc. - can be added.

This is an important point. Contrary to what we would be led to believe by Behe’s detractors, we see that the whole system (the whole watch) is not what Behe claims is IC, just a subdivision of it – the “core”. And only the subset of parts that comprise the core are the required parts: the other parts, while surely parts of the system as a whole, are not parts of the IC system itself. So removing such auxiliary/accessory parts and retaining system function does nothing to refute the concept of IC.

We can see Behe’s implicit statements of an IC core in other places in his book. For example, Behe states that swimming systems – such as the cilium and prokaryotic flagellum – are irreducibly complex. He introduces his readers to the subject by discussing a person swimming at a local pool and noting that that person’s swimming system has the same basic parts’ requirements as that of a cilium: a paddle (legs and hands/microtubules), a motor (skeletal muscles/dynein), and connectors (bones/nexin). However, he also points out that for humans, vision, though beneficial to swimming, is not part of the swimming system itself: vision is an auxiliary system that merely improves the swimming system (the former is not required for the latter to function).

Michael Behe: ”The neighborhood pool scenario illustrates the requirements for swimming. It also shows that efficiency can be improved by adding auxiliary systems to the basic swimming equipment. … A direction-finding system (such as eyesight) is also useful for swimming; however, it is not the same thing as the ability to swim. In the story you could do the backstroke for a while and still advance through the water. Eventually, an inability to sense the surroundings can lead to accidents. Nonetheless, one can swim sighted or one can swim blind.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p56)

DNAunion: As Behe continues his introduction to swimming systems, he again notes that parts that are not required for function can be found in a system as a whole.

Michael Behe: ”When a real-life system has more than the theoretically minimum number of parts, then you have to check each of the others parts to see if they’re required for the system to work.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p57)

DNAunion: Thus one must test to see if any “extra parts” (those other than the ones included in the theoretically minimal set of parts) are required for the system to function: if they aren’t, then they aren’t part of the IC system itself.

Even when Behe is discussing non-IC systems, he still indicates that parts that are not required for the system to function can be found in the system as a whole.

Michael Behe: ”First, we should note that the function of the bombardier beetle’s defensive apparatus is to repel attackers. The components of the system are (1) hydrogen peroxide and hydroquinone, which are produced by the secretory lobes; (2) the enzyme catalysts, which are made by the ectodermal glands; (3) the collecting vesicle; (4) the sphincter muscle; (5) the explosion chamber; and (6) the outlet duct. Not all of these components, though, are necessary for the function of the system. Hydroquinone itself is noxious to predators. A large number of beetle species synthesize quinones that are not even secreted, but which “taste bad”. Initially a number of individual beetles are chewed up and spit out, but a predator learns to avoid their noxious counterparts in the future, and thus the species as a whole benefits from this defense.

Hydroquinone alone, then, has the defensive function that we ascribed to the entire system. Can the other components be added to the bombadier’s system in such a way that function continuously improves? It would seem that they can.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p34-35)

DNAunion: So the other 5 parts of the bombadier beetle’s defensive system are auxiliary parts – add-ons that merely enhance or improve the “core” of the system.

And again, when discussing the vertebrate eye, an integrated system of systems, Behe indicates that one should not confuse everything present as being a single system – there are accessory parts tacked on to the “core”.

Michael Behe: ”The function of the retina alone is the perception of light. The function of the lens is to gather light and focus it. If a lens is used with a retina, the working of the retina is improved. Similarly, the muscles that focus the lens or turn the eye function as a contraction apparatus, which can be applied to many different systems. Tear ducts and eyelids are also complex systems, but separable from the function of the retina.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p38)

DNAunion: Thus, the retina would be the closest thing to the core system here, onto which the other auxiliary parts – a lens, muscles to alter the shape of the lens, etc. – are added. The auxiliary parts would not be required for the core system to perform its function.

Another system that Behe lists only a subset of parts as being the core of the IC system is the cilium. Although the answer is obvious to anyone who actually tried to understand Behe, the following question is at the heart of the controversy: when Behe says that the cilium is irreducibly complex, does he claim that the whole cilium is IC, making all parts present in a typical cilium required for function?

Absolutely not. Behe’s statement about the cilium being irreducibly complex is just like his statement that a watch is irreducibly complex. In both, what he is addressing is the IC “core” itself. Any auxiliary/accessory parts that may be present are not included as parts of the irreducibly complex system itself (the IC “core”), and removing even all of them while retaining function would not refute Behe in the least.

One might wonder, “Does Behe actually limit his statements about the cilium to just a few parts that comprise an IC ‘core’”? Yes. Behe explicitly creates a subset consisting of just three required parts that together form the IC system itself: the microtubule “paddles”, the dynein “motors”, and the nexin “linkers”. A fuller quote can be found in a previous post in this thread – this is a condensed one.

Michael Behe: ”Now, let us sit back, review the workings of the cilium, and consider what they imply. What components are needed for a cilium to work? Ciliary motion certainly requires microtubules; otherwise, there would be no strands to slide. Additionally it requires a motor [i.e., dynein], or else the microtubules of the cilium would lie stiff and motionless. Furthermore, it requires [nexin] linkers to tug on neighboring strands, converting the sliding motion into a bending motion, and preventing the structure from falling apart. All of these are required to perform one function: ciliary motion. Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. …

… All systems that move by paddling – ranging from my daughter’s toy fish to the propeller of a ship – fail if any one of the components is absent. The cilium is a member of this class of swimming systems. The microtubules are paddles, whose surface contacts the water and pushes against it. The dynein arms are the motors, supplying the force to move the system. The nexin arms are the connectors, transmitting the force of the motor from one microtubule to its neighbor.

The complexity of the cilium and other swimming systems is inherent in the task itself.” (bold added, Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p64-65)

DNAunion: The other parts of a cilium – such as the central pair, central spokes, etc. - are shown in a diagram of a cilium on page 60 of Behe’s book, but they are not listed as being parts of the IC system when Behe creates his explicit list of required parts: the central pair and central spokes aren’t parts of the IC core.

 

[DNAunion]

DNAunion: Second half of the above post...

When Behe briefly returns to the cilium in a later chapter, he again lists just the three parts mentioned above.

Michael Behe: “The function of the cilium is to be a motorized paddle. In order to achieve this function microtubules, nexin linkers, and motor proteins all have to be ordered in a precise fashion. They have to recognize each other intimately, and interact exactly. The function is not present if any of the components is missing.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p204)

DNAunion: So twice Behe restricts his list of required parts for a cilium to those three (microtubule “paddles”, dynein “motors”, and nexin “linkers”). They form the IC “core”.

Let’s go back and take another, slightly different, look at what Behe stated on page 57 of his book. Keep in mind the three required parts of the cilium Behe lists in two separate locations, as well as his saying that the cilium is a member of the class of swimming systems.

Michael Behe: “Mechanical examples of swimming systems are easy to find. My youngest daughter has a toy wind-up fish that wiggles its tail, propelling itself somewhat awkwardly through the bathtub. The tail of the toy fish is the paddle surface, the wound spring is the energy source, and a connecting rod transmits the energy. If one of the components – the paddle, motor, or connector – is missing, then the fish goes nowhere. …

Keep in mind that we are discussing only the parts common to all swimming systems – even the most primitive. Additional complexity is frequently seen. … When a real-life system has more than the theoretically minimum number of parts, then you have to check each of the other parts to see if they’re required for the system to work.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p57)

DNAunion: Here we have two more indications that Behe does not consider the parts that Miller “removed” to be parts of the IC cilium system itself.

Already mentioned:
(1) Behe lists only three parts of the cilium as being part of the IC system itself (microtubule “paddles”, dynein “motors”, and nexin “linkers”)

Two new ones:
(2) Let’s ask ourselves, “What parts are common to all cilia, even the most ‘primitive’”?

Microtubule “paddles”? Yes.
Dynein “motors”? Yes.
Nexin “linkers”? Yes.
Central pair? No.
Central spokes? No.

So in addition to Behe’s explicitly stated subset consisting of just three parts, we have another indication that only the first three parts listed comprise the IC system itself (the “core”) with the other parts being accessory/auxiliary add-ons (and therefore, not parts of the IC system itself).

(3) Let’s ask ourselves, “What parts constitute the theoretical minimum subset of parts required for ciliary function?” Behe already answered this on pages 63-65, listing each of the three required parts and what role each one serves in completing the system function: that minimal theoretical subset consists of just the first three listed above (those with the answer, Yes). Since the central pair and central spokes are not included in the theoretically minimal set of parts required for ciliary action, one would need to test to see if they are required for the system to work. Are they required? No, there are multiple known examples of functional cilia that lack them. So are the central pair and central spokes part of the actual IC system itself? Nope. Thus, another – a third - indication that the central pair and central spokes are not to be considered parts of the IC system.

In summary, the parts of a cilium that Miller “removed” were ones that Behe never, in any way, claimed were required for ciliary function. In addition, at least three lines of evidence indicate that Behe considers those parts that Miller “removed” to not be part of the IC core (the dynein outer arms come close, but no cigar, since the dynein inner arms remained). What Miller “removed” were auxiliary/accessory parts added onto the core IC system itself. As such, Kenneth Miller’s eel-sperm-flagellum counterexample and accompanying “refutation” are to be rejected as invalid misrepresentations of Behe’s position.

 

[DNAunion]

DNAunion: I won’t bother with the watch analogy for this one, but we can see why it could be useful for some people.

Jerry Smith: By the way, we never really determined whether the “missing parts” [central pair, central spokes, dynein outer arms] from the eel sperm flagellum should be considered [parts of the IC system] except by showing that a system simpler that the eukaryotic cilium does not possess them.

DNAunion: Here’s one problem with your biology (and another to come - one reason the watch analogy might be preferable for you, when possible).

The eel sperm flagellum is a eukaryotic “cilium”. An eel is a eukaryote, and its sperm are eukaryotic cells. And in eukaryotes, cilia and flagella are the same thing (well basically – there are several insignificant differences based on length, number present, and stroke pattern. But for our purposes they are the same thing: they are both plasma membrane-enclosed cell extensions that contain a central shaft called an axoneme that is composed of, typically, 9 outer doublet microtubules surrounding a central pair of singlet microtubules, with dynein arms extending clockwise from each A tubule of one outer doublet to the B tubule of its neighbor, with neighboring doublets also being linked by nexin, and so on.).

What that means is that we have an example of a eukaryotic cilium that is simpler than the typical eukaryotic cilium, and the simple one lacks the central pair and central spokes and dynein outer arms. Since Behe stated that we are to consider only the parts that are common to all instances of the system, taking even the most primitive form into consideration, then we have determined that the central pair, the central spokes, and the dynein outer arms are not parts of the IC system itself. They are accessory/auxiliary parts, not parts of the IC core.

Therefore, contrary to what Ken Miller would like us all to believe, removing all three of those accessory parts does not refute Behe at all.

Jerry Smith: “You neglected to answer my question – the only question I think could be used to test whether [those “missing parts”] belong in the category or not. The question I am talking about is perhaps the only one that Behe has given us that we can use to check this theory. If you remove the hub, spokes, and linking arms from the eubacterial cilia – does it, or does it not, continue to function?? Unless you can give us a pretty good reason to believe that it does continue to function, your whole book is based on a premise not in evidence. If it does not function, then Miller is quite right to treat them as part of the IC core of the cilium, and his refutation is then very strong (and the charge of misrepresentation moves into the fast lane of the sewer line).

I honestly don’t know if the eubacterial cilium could function without one or more of those complex and interdependent parts. I suspect that it could not, and that your tome o’rants is based nothing on your desire to pick fights.

I could be wrong. If the eubacterial cilium could function without those parts, then, at least on this point, Miller’s refutation is poor – and it remains for you to demonstrate that his poor refutation is evidence of misrepresentation.” (bold added)

DNAunion: There’s your lack of understanding of biology getting in the way again: eubacteria don’t have cilia or even microtubules. Thus, your whole ‘challenge’ gets tossed out.

We can’t look to eubacteria, sorry. Hey, let’s look at eukaryotes again. We already know from just above that the “missing parts” are not required to have a functional eukaryotic cilia, and that they should not have been considered parts of the IC system itself.

 

[DNAunion]

DNAunion: Addressing a different part of Jerry Smith’s statements I quoted in my last post. I will intermingle the watch analogy. The quotes of Jerry Smith I post are not watch analogs but are his actual words (except for those words enclosed by [], which were used to eliminate his errors).

Jerry Smith: “I honestly don’t know if [a] cilium could function without one or more of those complex and interdependent parts. I suspect that it could not, and that your tome o’rants is based nothing on your desire to pick fights.

I could be wrong. If [a] cilium could function without those parts, then, at least on this point, Miller’s refutation is poor – and it remains for you to demonstrate that his poor refutation is evidence of misrepresentation.”

DNAunion: As we have seen, a cilium could function without those parts. Thus, you have as much as admitted that Miller’s refutation is poor (it’s actually worse than poor – it was dead in the water from the get go). That leaves it to me to show that Miller misrepresented Behe. Okay. But it’s actually easier to see (at least for the open minded and impartial) than to explain, but here goes.

Miller claimed to have “refuted” Behe by removing parts (wristband, nightlight, and second hand – or the central pair, central spokes, and dynein outer arms) from an “irreducibly complex” system and having that system still retain function. For that counter to Behe to be valid, Miller would have to have removed parts that Behe stated were required for the IC system to function (if Miller simply removed parts that Behe holds as merely beneficial – that is, not required - then Miller would not have been refuting Behe at all). Thus, Miller’s claim of effectively countering Behe indirectly stuffs into Behe’s mouth the statement that the wristband, the nightlight, and the second hand – or the central pair, the central spokes, and the dynein outer arms - are all required parts of the IC system itself. But Behe did NOT list those as being parts required for function, and in fact more than one of his statements show them not to be. Therefore, Miller has misrepresented Behe.

Think about it like this. Using the watch analogy, what if Behe had said, “An hour hand is required for function, but a wristband is just a convenience and is therefore not required for function”. Obviously, Miller could not “refute” Behe by showing a watch that functioned without a wristband; to refute Behe, Miller has to remove a required part – the hour hand – and have the system still retain function. By claiming to have “refuted” Behe, Miller implicitly, but surely, labels the wristband as a required part according to Behe (it is Behe who Miller claims to “refute”, after all, and not himself). In this imagined example, we see that labeling the wristband as being required doesn’t work because of Behe’s explicit labeling of the wristband as a mere convenience. But, since in the “real discussion” Behe did not explicitly state that the wristband was not required – though multiple lines of evidence clearly indicate that such would be his position – Miller feels free to “interpret” Behe as he sees fit, then turn around and “refute” his own personal, clearly incorrect interpretation of Behe.

I challenge anyone to present a quote from Behe where he says, or unavoidably implies, that the central pair and central spokes are required for ciliary function.

Doing so would surely win the case for my opponents, hands down. Yet no one has done that so far, why not? Because they can’t. People like Miller just ASSUME what they want about Behe’s position, and then go on to “refute” their own misconceptions. If Behe did not explicitly reject notion X – even if he implicitly rejected it by multiple means - some of his opponents feel free to claim that Behe proposed notion X, then go on to “refute” Behe by showing notion X to be wrong. That is misrepresenting Behe.

Jerry Smith: “By the way, a faulty refutation is not necessarily equal to a misrepresentation. Miller never portrays Behe as specifically listing the parts that are missing from the eel flagellum as being I/C.”

DNAunion: Miller does indirectly stuff those words into Behe’s mouth. Again, consider how utterly useless Miller’s “refutation” of Behe is if Miller is claiming only to have “removed” parts that Behe considers to be nonessential add-ons: not parts of the IC core and not required for function. To claim to have effectively countered Behe, Miller must be claiming that Behe claims the “missing parts” are required parts of the irreducibly complex system itself.

Now, one more time on the flawed refutation vs. misrepresentation thing, this time using fictitious exchanges involving the watch analogy.

Flawed refutation: accurate representation

Michael Behe: The three parts required for a mechanical watch to function are a hand (to indicate the current time), an energy source (such as a battery - to power the system), a set of gears (to convert the energy of the battery to motion of the hand). Remove any one of those three parts and the IC mechanical watch will cease to function.

Kenneth Miller: Unfortunately for Behe, that is not true. Here we have the Seikasiolex 1230 pocket watch, and it doesn’t have an energy source: yet it still functions. How can that be? It can’t be, if we believe Behe – yet, there it is.

Michael Behe: Looking at the schematic shows that it does indeed have a battery – it is just incredibly small and is concealed, and therefore not visible if one simply opens the watch and looks inside.

Flawed refutation: misrepresentation

Michael Behe: The three parts required for a mechanical watch to function are a hand (to indicate the current time), an energy source (such as a battery - to power the system), a set of gears (to convert the energy of the battery to motion of the hand). Remove any one of those three parts and the IC mechanical watch will cease to function.

Kenneth Miller: Unfortunately for Behe, that is not true. Here we have the Seikasiolex 1230 pocket watch, and it doesn’t have a wristband, a nightlight, or a second hand: yet it still functions. How can that be? It can’t be, if we believe Behe – yet, there it is.

DNAunion: It is the latter, which involves a misrepresentation, that is analogous to Miller’s actual “refutation” of Behe.

 

[DNAunion]

DNAunion: A short one, dealing with the watch analogy.

LiveFreeOrDie or Jerry Smith: Let’s suppose for the sake of debate that Miller did address a piece other than one of those Behe meant were required. Miller still wouldn’t be to blame - Behe was too vague.

DNAunion: No, Behe wasn’t vague – he listed only three parts when stating which ones were required (basically, a battery, a set of gears, and a hand). Yet, somehow, all three of the parts Behe listed as being required for function were present in Miller’s counterexample “refutation” (how could that be?).

And looking at it from a different point of view, two of the pieces Miller removed weren’t even in Behe’s list of three required pieces. Miller missed the target from both sides.

That Miller can point out a mechanical watch that lacks a wristband – a part obviously not included in the list of 3 required parts Behe gives – demonstrates nothing in the way of refuting Behe on this issue. It does demonstrate, however, that Miller misrepresented Behe – how else could Miller claim to have effectively countered Behe by using his example, which clearly cannot contradict Behe in the least if one sticks to what he actually said.

 

[DNAunion]

DNAunion: This one doesn’t deal with a cilium or a watch, or with what Behe or Miller said, or with IC systems, or with anything else important related to the debate. Why? Because Morat chose not to contribute anything worthwhile – just to try to “mock” me.

Morat: [DNAunion’s] not fooling Jerry. He’s not fooling Lucaspa. He’s not fooling LFoD. If I’m any guide to the lurkers, he’s not fooling me.

Is he fooling himself?

DNAunion: Wow, Morat, what a substantive contribution! <snicker> Is that really the best counter you could come up with?

Do you really think it’s all about how many people one has on his/her side – that “popularity” is the determining factor as to which position is the correct one? Well, unfortunately for you, that’s not the way things work. Popularity in a single thread, at a single site, or even in the whole human population, is not what determines what is and is not “truth”. True facts are facts, no matter how many or how few people are “fooled” into believing them.

Miller misrepresented Behe – that is a fact. And it is a fact regardless how many people stubbornly refuse to be “fooled” into believing something so obvious and unavoidable.


*************************

PS: Let’s see how your method of determining “the truth” works, in the hands of your “opponents”.

This is a Christian board, right. So we can safely assume that Christians outnumber all others here, including Pagans, atheists, etc. Therefore, basically, any statements of Christian belief that are stated at this site are correct…right Morat? After all, the Christians could get more people to “vote” for their own team and thereby make their position “the truth”.

So Morat, now by your own logic, you are forced to accept that Jesus was actually born of a virgin, that Jesus actually was the Son of God, that Jesus actually was resurrected, and that Jesus actually did perform miracles. Right? I mean, no one can successfully argue against those “truths” – nope, not according to you Morat – according to you, they’re as good as unquestionable facts, because an opposing side wouldn’t have enough people here to make their own position correct.

You, Morat, have now given Christians here the only tool they will ever need to refute any non-believer or science that might counter in any way any Christian claim: they just need to be sure to have more people from their side post the Christian position, then say to the opponent, “You aren’t fooling ChristianX, you aren’t fooling ChristianY, and you aren’t fooling ChristianZ. Are you fooling yourself?” I mean, how could anyone ever hope to overcome such a completely devastating counter? The logic is just too overwhelming!

 

[DNAunion]

DNAunion: In the next several posts I will address Lucaspa’s statements on the cilium. There’s an awful lot of stuff, so I don’t know into how many posts this will have to be split.

First, using the watch-analog (fictitious) exchanges.

Lucaspa: Ah, Behe may not have been vague in the passage you quote, but Behe is inconsistent in what he says about the IC mechanical watch. Sure, on page xxx he lists just those three parts as being required. But on page yyy he says that it takes more than those parts alone to assemble a mechanical watch, pointing out that if you take a battery, gears, and a pointer/hand and throw them into a factory that does not produce watches, no functioning mechanical watch will be assembled.

DNAunion: So what? Assembly of a system and its subsequent functioning are clearly not the same thing. Of course there are parts that are needed to assemble a watch that, after they perform their assembling function, are no longer required for the watch itself to function. Otherwise, we’d all be carrying around watch factories on our wrists.

DNAunion: That introduces one of the problems with Lucaspa’s claim (it will be dealt with more below). Now for the real stuff, dealing with cilia – END OF WATCH ANALOGY.

Lucaspa: This is one instance where Behe says different things in different places.

For instance, go to page 72 in Darwin’s Black Box:

*********************************
Behe: Above I noted that the cilium contains tubulin, dynein, nexin, and several other connector proteins. If you take these and inject them into a cell that lacks a cilium, however, they do not assemble to give a functioning cilium.
*********************************

Lucaspa: So, it’s not just the 3 proteins that constitute the “irreducible complexity” of the system. Provide those and you don’t have the cilium, which is the irreducibly complex system, not just the 3 proteins. Instead, you have to have the complete structure of the cilium, which includes all the parts in Figure 3-2.

DNAunion: Nope.

Several problems. As a quick introduction to some of them, note that in the quote you present Behe has switched to talking about (1) assembly and not function, and talking about (2) tubulin and not microtubules, and talking about (3) assembly in vivo and not beating in vitro. You are comparing apples to oranges and then claiming that Behe is being inconsistent.

(I originally tried to address the problems with Lucaspa’s counter one at a time, but I kept ending up bringing at least one of the others into the discussion).

First, Note that Behe says that tubulin, dynein, nexin, “and several other connector proteins” are not enough to assemble a functioning cilium in a cell that lacks cilia. As I pointed out in the watch analogy response, what is required to assemble something and what is needed for it to function once assembled can clearly be two very different things. And since Behe switched to talking about tubulin instead of microtubules, the cell first has to get tubulin to polymerize into stable microtubules before we can even think about them becoming bundled together and making a cilium.

In cells, which was what Behe made reference to in your quote, microtubules are assembled from dimers consisting of alpha-tubulin and beta-tubulin by MTOCs (microbutule organizing centers). For cilia, the MTOCs are basal bodies. Now, when Behe mentions ciliary function in relation to IC on pages 63-65, he talks about the in vitro beating of cilia that have been stripped from the cell – ciliary function in the absence of basal bodies and other cellular components. Thus, although basal bodies may be used by cells for the assembly of cilia, they are not required for ciliary function. In addition, several proteins associated with MTOCs are used by cells to initiate assembly of microtubules, but are then (apparently) not needed for a cilium to function once assembled.

Here are some quotes that validate different parts of the above paragraph.

First, some showing the roles that microtubule-organizing centers (MTOCs) play in relation to microtubule assembly and organization in cells.

”Microtubules commonly originate from a structure called a microtubule-organizing center (MTOC). An MTOC serves as a site at which microtubule assembly is initiated and as an anchor for one end of these microtubules. … Some types of cells have many MTOCs. For example, ciliated cells have an MTOC, called the basal body, at the base of each cilium.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p648)

”The centrosome or MTOC plays an important role in controlling the organization of microtubules in cells. The most important aspect of this role is probably the MTOC’s ability to nucleate and anchor microtubules.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p656)

”For axonemes to participate in movement, they must be stable structures anchored by at least one end. As noted already, a cilium or flagellum is anchored at its cytosolic end to a basal body. In addition to its anchoring role, the basal body serves as a nucleus for the assembly of flagellar microtubules. Recall that the basal body has nine triplet microtubules. The nine A and B tubules of these triplets appear to initiate assembly of the nine outer doublet microtubules of the cilium or flagellum by growing outward from the basal body during elongation of the axonemal shaft.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p822)

DNAunion: Now one that shows that although cells use MTOCs/basal bodies to assemble and organize microtubules, the MTOCs/basal bodies are not required for ciliary function once the cilium has been assembled (which we already know Behe stated).

”Axonemes of isolated cilia and flagella that lack their basal bodies and membranes can be induced to beat if ATP is added to the medium…” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p705)

 

[DNAunion]

DNAunion: Continuation of my reply to Lucaspa: no wacth analogy.

Next a couple quotes on two other proteins – gamma-tubulin and pericentrin - used by cells to nucleate (initiate) microtubule assembly. Note that the protein gamma-tubulin, though obviously a tubulin, is not a protein part of a microtubule (microtubules are composed of alpha,beta-tubulin dimers).

”Despite its amorphous appearance, the pericentriolar material of an MTOC is an ordered lattice that contains many proteins that are necessary for initiating the assembly of microtubules. One of these, [gamma]-tubulin, was first identified by studies designed to discover proteins that interact with [beta]-tubulin. Subsequent studies demonstrated that [gamma]-tubulin and the lattice protein pericentrin are part of the pericentriolar material of centrosomes; it has also been detected in MTOCs that lack a centriole. The finding that introduction of antibodies against [gamma]-tubulin into cells blocks microtubule assembly implicates [gamma]-tubulin as a necessary factor in nucleating polymerization of tubulin subunits.

… These observations provide additional evidence that [gamma]-tubulin plays a key role in directing microtubule assembly in vivo.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p800-802)

”The pericentriolar material has not been completely defined but contains at least two proteins, pericentrin and [gamma]-tubulin, that are needed for the nucleation of microtubules in vivo.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p655)

DNAunion: So a cell uses MTOCs called basal bodies, as well as associated proteins such as gamma-tubulin and pericentrin, to get microtubule assembly started. But there’s still a problem. Microtubules spontaneously disassemble except in very high concentrations of alpha,beta-tubulin dimers. For a microtubule to serve its function in a cilium, it must be a stable, lasting structure. Other proteins are needed during assembly to prevent the growing microtubule from depolymerizing from the tip as fast as it is growing.

”We have seen that cellular microtubules exhibit dynamic instability; they grow out from the centrosome and then disassemble. … One way to [stabilize microtubules] is to “capture” and protect the growing plus end of the microtubule. Capping proteins perform this function: Microtubules with capped plus ends are more stable than those that are uncapped. Thus, the distribution of stable microtubules in a cell is determined by both the position of the MTOC and the distribution of capping proteins that capture and stabilize newly formed MTs.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p656-657)

DNAunion: Finally, various proteins that are found in association with microtubules (MAPs) play various roles, one of which is stabilizing MTs from disassembly.

”Although [alpha and beta] tubulin is the main component of microtubules, a variety of other proteins are known to be involved in microtubule structure, assembly, and function. These microtubule-associated proteins (MAPs) account for 10-15% of the microtubule mass.

MAPs add another level of regulation to the organization and function of microtubules in cells. … MAPs are also important in regulating MT assembly, most likely by binding to the growing plus end of a microtubule, thereby stabilizing it against disassembly. Most MAPs have been shown to increase MT stability, and some also stimulate MT assembly. The many different kinds of MAPs differ mainly in how they link microtubules together or to other structures and how their effects on microtubules are regulated.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p657)

 

[DNAunion]

DNAunion: Another continuation of my reply to Lucaspa: again, no watch analogy.


The next three quotes on MAPs don’t deal specifically with axonemal microtubules, but they still have relevance.

”One major family of MAPs, called assembly MAPs, is responsible for cross-linking microtubules in the cytosol. These MAPs are organized into two domains: a basic [that is, non-acidic] microtubule-binding domain and an acidic projection domain. In the electron microscope, the projection domain appears as a filamentous arm that extends from the wall of the microtubules. This arm can bind to membranes, intermediate filaments, or other microtubules, and its length controls how far apart microtubules are spaced.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p807)

”Transfection of cultured insect cells with either the [MAP] tau gene or the MAP2 gene induces growth of microtubule-filled processes. These observations indicate that both Tau and MAP2 accelerate polymerization of tubulin subunits, as well as contribute to cross-linking of microtubules.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p809)

DNAunion: So in cells MTOCs/basal bodies, gamma-tubulin, pericentrin, capping proteins, and MAPs playing roles in assembling microtubules. Yet it is explicitly stated that MTOCs/basal bodies are not required for cilia to beat, and no mention is made of gamma-tubulin or pericentrin playing essential – or any other - roles in the functioning-once-assembled cilia.

We can see that Behe’s explicitly mentioning tubulin and not microtubules in the quote Lucaspa presented does represent a change in what Behe is discussing. In a cell, having alpha- and beta-tubulin (the two tubulins that comprise microtubules) is not the same thing as having microtubules. In addition, there is the large change in Behe’s discussing the assembly of a cilium in vivo, in Lucaspa’s quote, as opposed to the functional beating of a pre-assembled cilium in vitro as Behe references when discussing the IC biochemical system. Apples and oranges – two different discussions - not an inconsistency.

 

[DNAunion]

DNAunion: Another continuation of my reply to Lucaspa: no watch analogy.

Are basal bodies, pericentrin, and gamma-tubulin absolutely required for microtubules to form? Basal bodies aren’t, and apparently, neither are the other two (though I could be wrong about that – the books I read are a bit vague on this). In vitro studies have shown that if alpha,beta-tubulin dimers are present in high enough concentration, along with GTP and Mg2+, and are kept at a high enough temperature (such as 37 degrees C), they will spontaneously join end-to-end to form an oligomer, which will continue to grow until becoming a polymer called a protofilament, and several of these will associate laterally to form a sheet, which will then curl up into a tube to form a short microtubule, onto which more alph,beta-tubulin dimers will be added, at a rate faster than they are removed, thus leading to a net increase in size. But there are problems carrying this over to cells.

First of all, the microtubules would be located in the cytosol and would not form projections that extend outwards from the cell, so could not make contact with the surrounding aqueous environment. Second, the microtubules would not be linked together by dynein, and without a motor to power them, they could not bend or generate a force. Third, the microtubules would not be anchored so any force imposed upon them would just make them move about within the cytosol. Fourth, even if we assume that dynein did link the microtubules together and could serve as a motor, with the microtubules being unanchored (in the cytosol) they could not generate a force sufficient for function since their pushing against an organelle or other sizable inclusion would cause the microtubules to move as much if not more than the object they were pushing against. It’s clear that microtubules that formed in a cell simply by having tubulin dimers in a high enough concentration could not function as cilia.

But there’s more. Microtubules formed spontaneously in vitro are not stable structures (but the microtubules of axonemes are), they “suffer” from dynamic instability. In general, dimers are not just added to the two ends of a microtubule, they are also removed from both ends. Whether a given microtubule shows net growth, net shrinkage, or temporarily remains the same overall size, depends upon several factors. And if certain conditions are not met, a microtubule can disassemble catastrophically (here’s a basic overview. Each alpha,beta-tubulin dimer binds GTP when it gets incorporated into the elongating microtubules. But over time, the GTP gets hydrolyzed to GDP, weakening the linkage between successive alpha,beta-dimers. Hydrolysis occurs at a fairly constant rate, so the “older” dimers – typically those nearer the (-) end – tend to have GDP instead of GTP bound. The stability of the “old” part of a microtubule is weakened and that of the whole microtubule can depend heavily on the stability of the (+) end, with its bound GTPs. If the (+) end does not grow sufficiently fast, the GTPs there may be hydrolyzed to GDPs leading to a rapid collapse of virtually the whole microtubule). And the whole population is not necessarily in the same state at the same time: one microtubule can be undergoing growth while its neighbor is disassembling. Basically, for a population of in vitro microtubules to grow in size requires (among other things) that the concentration of alpha,beta-tubulin dimers be above a critical concentration. But as microtubules are formed from alpha,beta-tubulin dimers, their levels diminish. If the level of dimers falls below the critical concentration, then the population of microtubules will shrink by depolymerization. The phenomenon of dynamic instability is not confined to just in vitro microtubules; it occurs to microtubules within cells too (that’s one reason why cells use capping proteins, certain MAPs, and MTOCs).

And there is a fifth problem. Assuming stable individual microtubules did form in a cell, they still have to associate with each other (as well as with other parts, such as dynein and nexin) in order to form an axoneme. So the next question is, “Will the individual microtubules come together or will they remain separate?” Unless other proteins interact with them to cause them to bundle together, they will remain separate. As Behe notes:

Michael Behe: ”… microtubules do not aggregate with one another without help from other proteins. There is a good reason for this: microtubules have a number of jobs to do in the cell. For most jobs, single, unassociated microtubules are needed. For other jobs (including ciliary motion), however, bundles of microtubules are needed. So microtubules lie around individually, like the rods from the game of pick-up sticks, unless purposely bundled together for a particular job.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p62)

 

[DNAunion]

DNAunion: Another continuation of my reply to Lucaspa: no watch analogy.


DNAunion: And there’s another problem. Even assuming that individual cytosolic microtubules form, and are stable, and somehow get bundled together, in a cell that does not possess cilia, an axoneme still hasn’t been formed. There are other structures that rely upon bundled microtubules, such as the axons and dendrites of neurons. And it is specific MAPs that determine which type of bundled arrangement will form.

For example, in neurons, the MAP Tau produces axons and MAP2 produces dendrites. When Tau or MAP2 are injected into cells that aren’t neurons, those cells form axon-like or dendite-like processes respectively.

”The importance of MAPs for neurite formation can be demonstrated by introducing MAP2C or tau genes into a nonneuronal cell line that cannot normally make either protein. These cells are normally rounded, but when the tau gene is introduced and expressed, these cells extend single long processes that look remarkably similar to nerve axons. In contrast, when the MAP2C gene is introduced and expressed, several shorter processes form that resemble nerve dendrites.” (Wayne M. Becker, Jane B. Reece, and Martin F. Poenie, The World of the Cell: Third Edition, Benjamin/Cummings Publishing Co., 1996, p658)

DNAunion: And it works the other way around too. If cells that normally form axons and dendrites are deprived of tau or MAP2C, then they do not form axons or dendrites, respectively.

”The importance of Tau in promoting axon growth was further confirmed by the finding that cultured neurons microinjected with DNA encoding tau antisense RNA are unable to grow an axon. Expression of tau antisense RNA inhibits translation of tau mRNA and thus reduces the intracellular level of Tau. Similar experiments with MAP2 antisense RNA shows that MAP2 is critical to formation of dendrites.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p809)

DNAunion: Based on the preceding quotes, getting an axoneme instead of an axon or dendrite by bundling microtubules together would require the presence of the appropriate “axoneme-making” MAP. Yet a cell that lacks cilia would probably not posses that protein.

So in cells, many proteins are used during the stages of assembling microtubules (let alone bundling them together, and then going further to assemble a full cilium), but at least some of them are not required for a cilium to function once it has been assembled. And if the basal bodies and assembly proteins are bypassed, by having microtubules form spontaneously due to a high enough initial concentration of tubulin, they will not be anchored, they won’t be stable, they won’t be capable of generating a force, they won’t project outward from the cell, and they won’t be bundled together: in short, they won’t form a cilium.

Another point. Behe lists some of the possible functions that the proteins other than tubulin, dynein, nexin, and the several other connector proteins he mentions, might be needed for in order to assemble functional cilia in cells that lack them.

Michael Behe: ”Other tasks for which the proteins might be required, however, include attachment of the cilium to a base structure inside the cell; modification of the elasticity of the cilium; control of the timing of the beating; and strengthening of the ciliary membrane.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p72)

DNAunion: As we have seen, the first function – attachment of the cilium to a base structure inside the cell – is not required for ciliary action (remember, Behe discusses ciliary action in relation to beating cilia that have been separated from cells, and a quote from another source also stated that basal bodies are not required for cilia to beat). Thus whatever proteins serve this function may be needed for assembling a cilium in a cell but are (likely) not required for ciliary function. And the last function Behe mentions here is also not required because the cilia he mentions when discussing ciliary function in vitro had had their membranes removed. Also, the function of adjusting the elasticity of the cilium would be a matter of improving upon minimal function and not a necessity; so it too would not be required for ciliary function.

So no, Behe is not being inconsistent. He is talking about two different things. When listing microtubule “paddles”, dynein “motors”, and nexin “linkers” as the three required parts of the IC cilium, Behe mentions ciliary action as the ability of a cilium separated from a cell to beat, which occurs well after the cilium has been assembled. When later talking about these other proteins, Behe is talking about the assembly of a functional cilium, in a cell, with that cell being one that does not possess cilia originally, when handed tubulin instead of microtubules, etc. Lucaspa is confusing apples with oranges in more ways than one (confusing assembly with function, the system as a whole with the IC core, in vivo requirements with in vitro requirements, …).

 

[DNAunion]

DNAunion: Another continuation of my reply to Lucaspa: no watch analogy.

There’s more. Leaving aside the other problems in Lucaspa’a argument for a minute (see the tons of stuff above), he hasn’t in any way shown that if one were to take all the individual parts shown in Figure 3-2 and simply inject them into a cell that lacks a cilium that a functional one will be assembled. Lucaspa would need to do at least that for his claim of needing all the parts in Figure 3-2 to be in the least bit valid based on the failure of tubulin, dynein, nexin, “and several other connector proteins” to assemble a cilium in vivo.

And even if Lucaspa did happen to somehow manage doing that, it still would not show that the parts Miller “removed” are actually required for a cilium to function – in fact, no one can possibly demonstrate that because Miller’s own example shows that the central pair, central spokes, and dynein outer arms are not required to have a functional cilium. And the fact that multiple examples of functional cilia without central pairs exist has been stated in other texts.

”Although the 9 + 2 [9 outer microtubule doublets and 2 central microtubule singlets] is the fundamental pattern of virtually all cilia and flagella, the axonemes of certain protozoans and some insect sperm show some interesting variations. The simplest such axoneme, containing three doublet microtubules and no central singlets (3 + 0) is found in Daplius, a parasitic protozoan. … Other axonemes consist of 6 + 0 or 9 + 0 arrangements of microtubules. These atypical cilia and flagella, which are all motile, show that the central pair of singlet microtubules is not necessary for axonemal beating and that fewer than nine outer doublets can sustain motility, but at a lower frequency.” (bold added, Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p819-820)

DNAunion: To go further (though we need not), we could ask ourselves whether or not the central pair, central spokes, and other connecting proteins are included in Behe’s inject-them-into-a-cell-and-you-wont-get-a-cilium statement. Well, here’s the quote of Behe that Lucaspa posted.

Michael Behe: “Above I noted that the cilium contains tubulin, dynein, nexin, and several other connector proteins. If you take these and inject them into a cell that lacks a cilium, however, they do not assemble to give a functioning cilium.” (italics added, Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p72)

DNAunion: What are the “several other connector proteins”? Well, here’s something that Behe said earlier.

Michael Behe: “In photographs of a cilia taken by an electron microscope, several different types of connectors can be seen tying together the individual microtubules (see Figure 3-2). There is a protein that bridges the two central single microtubules in the middle of the cilium. Also, from each of the double microtubules, a radial spoke projects toward the center of the cilium. The structure ends in a knobby mass called the spoke head.” (Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p62)

DNAunion: So even the central spokes and other proteins that connect to the central pair are included in Behe’s statement that injecting “tubulin, dynein, nexin, and several other connector proteins” into a cell that lacks cilia will not result in a functional cilium being assembled. In the statement Lucaspa quoted, Behe is not talking about the IC core – he is talking about the larger picture, as his statements make clear. In fact, look at how he follows up – just a paragraph or so later - his statement Lucaspa quoted and his remarks about the other functions those other proteins would play in assembling a functional cilium in vivo.

Michael Behe: “New research on the roles of auxiliary proteins cannot simplify the irreducibly complex system.” (bold added, Michael Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution, Free Press, 1996, p73)

DNAunion: Again Behe indicates that there is an irreducibly complex “core” to the cilium onto which auxiliary proteins are added. Behe is not talking about the IC “core” system itself when he makes the statement about assembling a cilium in vivo that Lucaspa quoted.

Now if the central pair or central spokes were in fact required for ciliary action, then they would be part of the IC system Behe is discussing (and he would have included them in his list of required parts for a cilium). But since, for the central pair and the central spokes, we know:

1) they are not part of the theoretically minimal set of parts needed for function
2) they are not required in order to have a functional cilium
3) they are not common to all cilia
4) Behe does not list them as being in the subset of three parts required for function

then we know they cannot be part of the IC system and therefore must be auxiliary parts/proteins.

 

[DNAunion]

DNAunion: Another continuation of my reply to Lucaspa: no watch analogy.


Okay, so the fact that the central pair and central spokes aren’t part of the IC (core) system is settled. But what ever happened to the dynein outer arms? Are they required parts or not? Obviously they are not. Otherwise, Miller wouldn’t have been able to point to a functional cilium that lacked them. In addition, there are these quotes.

”Genetic studies of mutant Chlamydomonas with abnormal motility reveal that the inner- and outer-arm dyneins contribute differently to the waveform and beat frequency of an axoneme. For example, the absence of one set of inner arms affects the waveform of flagellar beating. In contrast, mutant flagella lacking outer arms have normal waveforms but slower beat frequencies. Thus the outer-arm dyneins accelerate active sliding of the outer doublets but do not contribute to bending. In contrast, the inner-arm dyneins are responsible for producing the sliding forces that are converted to bending; this suggests that inner-arm dyneins are essential for bending.” (bold added, Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p821)

”… removal of outer-arm dyneins by treatment with high-salt solutions reduces the rate of ATP hydrolysis, microtubule sliding, and beat frequency of isolated axonemes by 50 percent. When the extracted outer-arm dyneins are added back to salt-stripped axonemes, both the ATPase activity and the beat frequency are restored, and electron microscopy reveals that the outer arms have reattached to the proper places.” (Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore, and James Darnell, Molecular Cell Biology: Fourth Edition, W. H. Freeman and Co., 2000, p820)

DNAunion: Thus the dynein outer arms serve primarily as enhancers: in their absence the cilium still bends and still beats (though at a slower, but still sufficient for minimal function, frequency).

However, even if one were to come across a functional cilium that had dynein outer arms but no dynein inner arms, that still would not refute Behe. He stated that dynein motors were required – he did not specify the inner arms. As long as dynein motors exist – both inner and outer, only inner, or only outer – then Behe is not refuted. My point in presenting the preceding two quotes was simply to show that not only did Miller not remove the dynein “motors”, but that he removed the lesser of two possibilities, making his “refutation” of Behe just that much weaker.

 

[DNAunion]

DNAunion: Last part of continuation of my reply to Lucaspa: no watch analogy.

In light of all the preceding information I posted, let’s go back to look at Lucaspa’s statements towards the end of his post one at a time.

Lucaspa: Provide those and you don’t have the cilium, which is the irreducibly complex system, not just the 3 proteins.

DNAunion: No, the IC system is the functional core of the cilium - consisting of the microtubule “paddles”, the dynein “motors”, and the nexin “linkers” - with the other parts being accessory/auxiliary parts tacked onto the core. Together, the core (the actual IC system itself) and the other add-on parts form the whole cilium.

Lucaspa: Instead, you have to have the complete structure of the cilium, which includes all the parts in Figure 3-2.

DNAunion: No. The quote of Behe that Lucaspa presented does not justify this assertion. It’s Lucaspa’s own personal misinterpretation of Behe that leads him to express this faulty conclusion.

Lucaspa: Now, since Behe defines an IC system “I mean a single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.” – Michael J. Behe “Molecular Machines: Experimental Support for the Design Inference” http://www.arn.org/docs/behe/behefig1.gif , it is reasonable to conclude that the parts in figure 3-2 are necessary since Behe claims the entire cilium is IC.”

DNAunion: No, Behe does not claim that the entire cilium is IC, any more than he claims an entire watch is IC (see my earlier post in this thread about the common misconception you just fell prey to. Try looking for,
Behe’s IC System != Whole System
Behe’s IC System = System’s IC “Core”).

And what is funny is how Lucaspa completely overlooks the obvious. The definition he himself quoted and used to “prove” his point said, “… where removal of any one of the parts causes the system to effectively cease functioning.”, yet, somehow, Lucaspa claims that the central pair and central spokes are parts of the IC system even though we all know that they are absent from some cilia that are fully functional. Wow, what blinders he’s wearing! If’n it’d ben a snaik, it’d bit‘m.

Lucaspa: What you are trying to do in defending Behe is to use one part of Behe to limit liability to 3 proteins.

DNAunion: No, the problem is that what you are trying to do in attacking Behe is to use two sections of Behe’s book where he is discussing two different things – apples and oranges - to try to create the illusion that Behe was inconsistent. One of your goals in doing so is to thereby expand his “liability” to whatever extent you want, that is, the whole cilium.

Lucaspa: But that isn’t what Behe is claiming, because those 3 proteins are not, in themselves, sufficient to make a cilium.

DNAunion: And making something and its subsequent functioning are two different things, and Behe was talking about in vivo vs. in vitro, and Behe did include the central spokes and (indirectly) the central pair in his statement, and so on. You’re mixing apples and oranges to concoct a claim that Behe contradicted himself when he didn’t.

Lucaspa: If the whole cilium or flagellum is an IC system, as Behe claims…

DNAunion: No, that is not what Behe claims. The IC system itself – the IC core - is a subset of the full system. Onto the IC core, additional accessory/auxiliary parts are added and together, the two – the core and the add-ons – form the whole system, with the whole system not being IC (since accessory parts can be removed without the system ceasing to function).

Lucaspa: …then all parts have to be necessary because that is how Behe defines an IC system.

DNAunion: Your “if…then” argument is not valid because your premise is wrong.

Lucaspa: So when Miller can find cilia and flagella without some of the components, that contradicts Behe’s claims.

DNAunion: Nope, not at all. All that does is contradict your and Miller’s misrepresentations of Behe’s claims.

 

[DNAunion]

DNAunion: A bit off topic - basically an afterthought side note that arose from parts of Lucaspa's and other anti-Behe'ians arguments.

Lucaspa tries to use his self-perceived instance of inconsistency on Behe’s part to show that Behe is “wrong” (Behe said “X” on page x, but said “Y” on page y, so he’s inconsistent, and that means, he’s wrong). Others have complained that Behe doesn’t give absolutely solid definitions for some of his terms and so his argument on which they are based is overly vague and useless. I wonder if these people would extend similar logic to other scientists? For example, if Darwin said two different things about the same topic on two separate pages, and in the process made his central theme vague and ambiguous, would they then consider Darwin to be wrong? If so, then those people would have to consider Darwin’s whole “Origin of Species” pretty much useless because (in addition to Darwin’s main topic being the origin of species, a term he readily admits has multiple distinct meanings) Darwin is inconsistent in his definitions of the term Natural Selection, which is the underlying principle of the entire book.

Charles Darwin: ”Owing to this struggle [for life], variations, however slight and from whatever cause proceeding, if they be in any degree profitable to the individuals of a species, in their infinitely complex relations to other organic beings and to their physical conditions of life, will tend to the preservation of such individuals, and will generally be inherited by the offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term Natural Selection, in order to mark its relation to man’s power of selection. But the expression often used by Mr. Herbert Spencer of the Survival of the Fittest is more accurate, and sometimes equally convenient.” (Charles Darwin, The Origin of Species by Means of Natural Selection Or The Preservation of Favored Races in the Struggle for Life, The Modern Library, 1998, p88)

Charles Darwin: ” … can we doubt (remembering that many more individuals are born than can possibly survive) that individuals having any advantage, however slight, over others, would have the best chance of surviving and procreating their kind? On the other hand, we may feel sure that any variation in the least degree injurious would be rigidly destroyed. This preservation of favourable individual differences and variations, and the destruction of those which are injurious, I have called Natural Selection, or Survival of the Fittest.” (Charles Darwin, The Origin of Species by Means of Natural Selection Or The Preservation of Favored Races in the Struggle for Life, The Modern Library, 1998, p108)

DNAunion: You see, in the first quote Darwin considers natural selection to be the retention of advantageous individual differences only, whereas in the second quote Darwin considers natural selection to be both that and also the elimination of detrimental individual differences. (Hmmmmm….Darwin was inconsistent in his definition of his central term, and the other most important term, species, is also ambiguous…does that mean Creationists can now run around legitimately claiming that Darwin’s whole argument is too vague and too ambiguous, and therefore useless and meaningless? Is it true that what’s good for the goose is good for the gander?)

Other examples come to mind. I don’t have quotes – but hey, I’m not going to let that stop me.

Some physics texts will, on the one hand, make the blanket statement that the speed of light is constant, but then, on another page, rely on changes in the speed of light to explain rarefaction. Those same physics texts may state on one hand, as a blanket statement, that no thing can travel faster than light; but then, on another page, state the some things can travel faster than light (this is possible when light passes through certain media). If one quotes just the isolated statements one catches the authors in two self-contradictions. But did the authors really err? Or does the problem reside with the reader?

Here’s a helpful tip for all of us to remember. Anytime you come across an apparent self-contradiction or internal inconsistency in someone else’s statements, you should take it as an indication that you may have somehow misunderstood what was being said in one or both of the statements. Some careful rereading and, if needed, proper interpretation using each statement’s surrounding context should be attempted before claiming that the author is inconsistent, wrong, or has contracted himself.


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PS: Thought of one more. Many electronics texts state the fact that a potential difference (voltage) is required to generate a current through a closed circuit; yet on another page the same authors say that in a series circuit the total voltage drop across all resistors is equal to the circuit’s total voltage. See the problem? Suppose the total voltage is 120 v and there are two 60 ohm resistors in series, giving a current of 1 amp through each resistor. The voltage drop across the first resistor is v = ir = 1 amp * 60 ohm = 60 volts. The voltage drop across the second resistor is also v = ir = 1 amp * 60 ohm = 60 volts. So the first resistor “sucks up” 60 v of the 120 volts, leaving 60 v; and the second resistor “sucks up” all those remaining 60 v. That means there is no potential difference between the rest of the circuit (that which follows resistor 2) and the battery, so no current can flow from the second resistor to the battery. But if no current can flow between those two points, then the series circuit is an open circuit and no current can flow through any of the circuit. But we just said that each resistor has a current of 1 amp flowing through it. There’s an internal inconsistency here: but the self-contradiction is only apparent.

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PPS: That's it - I'm done for now. Feel free to respond (but please, first take the time to review the material I posted that is relevant to what you address).

 

[Jerry Smith]

Hey, a one-man circus!

Don't worry, I'm not going to rain on your parade. I just want to acknowledge my mistake in typing "eubacterial" where "eukaryotic" was intended. It makes no difference to my "core argument" (note my "core argument" is not the same as my "whole argument." LOL!)