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Spin Flagellum, Spin

This month in Current Biology Vol 18 No 16, Howard C. Berg writes a “Quick guide” to the Bacterial Flagellar motor. In it he outlines what is currently known of these amazing structures.

“The flagellar motor is a remarkably small rotary electric motor that includes a stator, drive shaft, bushings, mounting plate, and a switch complex. The motors are powered by protons or sodium ions, that flow through channels from the outside to the inside of the cell. Depending upon the configuration, the rod, hook, and filament are driven clock wise or counter clock wise. Other components include a rod cap, discarded upon rod completion, hook cap, discarded upon hook completion, hook-length control protein, and a factor that blocks late-gene expression.”

As ”nothing in biology makes sense except in the light of evolution”, Berg concludes with a few brief comments.

“Is the flagellar motor unique? Yes and no. As a device that powers flagellar rotation, yes. As a device composed of rings, rods, and external filaments, no. There is a homologous structure, called the needle structure, assembled by the same kind of transport apparatus, used by pathogenic species (such as Salmonella) to inject virulence factors into eukaryotic cells. Some argue that the flagellar rotary motor evolved from the needle structure, but it was probably the other way around, since flagellated bacteria existed long before their eukaryotic targets. Perhaps they evolved from a common ancestor. What was the rotary motor doing before the helical propeller was invented, if indeed that was the order of events? Serving as a secretory apparatus that acquired the ability to spin? Packaging polynucleic acids into virus heads? Food for thought.”

Recently Nature Reviews Microbiology volume 6 June 2008 p 455 has a review of the regulation of Flagellar construction, where the authors say “The bacterial flagellum, one of the most remarkable structures in nature: a complex self-assembling nanomachine” where “dozens of proteins, many of which have intrinsic self-assembly properties, need to come together in an ordered assembly process to complete these molecular nanomachines.”

These authors also need to remind us of the inescapable compelling logic of evolutionary biology:

“Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system. We only need to be reminded that evolution demands that changes occur on the existing structure — no starting from scratch. It is fair to say that we are at long last making a dent in our understanding of how this evolutionary process might have occurred for the reducibly complex bacterial flagellum and the beautiful result it has produced.”

The flagellum is obviously too complex to have been designed. It must have evolved. The logic is inescapable.

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98 Responses to Spin Flagellum, Spin

  1. If it’s too simple, darwinismdidit. If it’s too complex, darwinismdidit.

    Great.

  2. With apologies to biologists who do not suffer from biology logic, I think we need to require that undergraduates majoring in biology be required to take a course in symbolic logic.

  3. I don’t think it’s the flagellum that is spinning here.

  4. idnet

    Do I detect a note of sarcasm in your closing line:

    The flagellum is obviously too complex to have been designed. It must have evolved. The logic is inescapable.

    I wonder if Nature realizes that a year or two ago they published a tedious review article by Nick Matzke where he opines that the T3SS preceded the flagellum in phylogenetic sequence. Is there any peer review going on at Nature? It seems like almost anyone should realize, as Berg does in this article, that evolution won’t produce a predatory weapon like the T3SS until evolution has produced a prey to use it on. Matzke’s horrible logic was equivalent to saying that the design of anti-aircraft missiles preceded the design of aircraft. Like DUH.

  5. Me sarcastic? Never!

  6. (speechless)

  7. omg!

    That has to be one of the most stupid comments I’ve ever read. That journal should be embarrased.

    Then again, what should we expect from people that apparently reject intelligent design a priori… an equally thoughtless gesture.

  8. DaveScot,

    Please forgive my ignorance, but can you explain more fully the reasoning behind your objection to Matzke’s logic on T3SS? Was he actually saying that there were no prey around?

  9. This must be understood, the “this system in nature is so staggeringly complex in form and function that it renders speechless our best engineers, therefore it can only be a creation of natural selection and random genetic mutation and aren’t these IDist idiots to even consider an alternative” non-thinking is not an abberation, an anomaly in evolutionary thinking, it is evolutionary thinking. That is it is evolutionary logic in a nutshell. It applies across the board in the natural sciences. But how to make sense of this counter-intuitive “thinking” in evolutionary biology? Well it is a psychological necessity, I mean to even consider abandoning their god of scientific materialism, simply unthinkable, so they don’t think…

    Even (in fact especially) ten year old children yet to be indoctrinated into a scientific materialist worldview get how counter-intuitive such mental convolutions are when describing ever more complex systems in nature, yet the PhDs’ from Cornell, Stanford and Berkeley are the last people to get it naturally. As the saying goes “you have to have your PhD before you don’t get it.”

    The Native Americans were right, the Trickster Coyote’s shadow looms over every aspect of the world and humanity and in the discipline of evolutionary biology his shadow looms large, Coyote stands a hundred feet tall and his howling can be heard for hundreds of miles around, but you have to know how to listen…

  10. This reminds me of phlogiston logic. Phlogiston is given off during combustion, so the ash weighs less than the original material. When it was demonstrated that a metal (like zinc or tin), when heated and combusted in a bell jar filled with oxygen, yielded ash that weighed more than the original metal, it was proposed that phlogiston could have negative weight.

    So, phlogiston has positive weight except when it has negative weight. By similar logic, Darwinian mechanisms produce a result, except when they produce the opposite result, and when something is too complex to have been designed, it must have evolved by Darwinian means.

    Finally, it seems that the bacterial flagellum is a structure of great complexity. In an attempt to understand why, it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system.

    An Intel CPU is a structure of great complexity, so surely a designer would have fashioned a simpler structure? What kind of logic is this?

    If anything is the enemy of science, it is Darwinian logic.

  11. Is it possible that the T3SS did evolve from the flagellum? Since the T3SS has fewer of the components of the flagellum, it’s possible that evolution did in fact destroy several components leading to the new structure. And there wouldn’t have to be any new structures involved to simply secrete something. That could involve transport mechanisms that already existed for the virulent factors.

    I find it interesting that the simpler T3SS may have evolved from the flagellum and is also pathogenic. I’ve been wondering if every pathogen is actually an evolutionary derivative of something created for a positive biological purpose. All pathogens could have started out performing a function, but a random mutation knocks out a key system which specifies the structure’s function. More information means more specification. If you knock out some information, the system becomes less specified and able to infect species it was never meant for, causing a disease. Am I making sense?

  12. portishead

    can you explain more fully the reasoning behind your objection to Matzke’s logic on T3SS? Was he actually saying that there were no prey around?

    Many people, including me, pointed out to Matzke (before he submitted for publication) that the T3SS is a weapon used by predatory prokaryotes to inject toxins into their eukaryote prey. The commonly accepted order of phylogeny is that prokaryotes were around for about 2 billion years before the first eukaryote showed up on the scene. During all those 2 billion years prokaryotes had strong survival need for locomotion to move upstream in nutrient gradients. The flagellum thus, in any reasonable explanation, preceded the T3SS by billions of years.

    Matzke pointedly ignored that in his desperation to find a simpler precursor for the flagellum so he went right ahead with a fatally flawed thesis that the flagellum descended from the much simpler T3SS when everyone and his brother had pointed out to him that was almost certainly not true. Nature went right ahead and published the nonsense as well such is their zeal to cast doubt on anything that comes out of the ID camp.

  13. @11.

    I am not sure what perspective you are coming from, but *if* there is a designer, he/she/it/they are responsible not only for designing the ‘good things’ in biology, but also many of the ‘bad things’ in biology. Behe says as much in EoE regarding Malaria, and there are many more examples of complex ‘negative’ organisms (Parasitology comes to mind). It is not necessary for pathogens to have originated from a ‘positive’ organism from either a design or evolutionary point of view.

    Re: “species specific” pathogens. The worry with many pathogens is that they become zoonotic, animal diseases infecting humans. This is the worry with Avian Influenza, that a strain that can infect humans will mutate and spread (has it yet? I have not kept up with the news).

    “More information means more specification” -> actually, it is possible this is not the case. See the thread on UD (and TT) about the ‘universal genome’. However, more expressed information means more specification (which is probably what you meant, rendering this last para useless:/ heh).

    http://www.uncommondescent.com.....f-metazoa/

  14. I thought someone would say that, but I know it’s not necessary. It’s perfectly reasonable that pathogens were designed to do exactly what they do. Any Christian (as I am), reading through the Old Testament would have to immediately come to grips with God being responsible for killing people. My point is that it makes sense that the original blueprints of a designer did not include pathogens. So in order to make pathogens, the designer drew upon pre-existing structures.

    It might be possible that they evolved through Darwinian or other evolutionary means (front-loading perhaps) as well. But either way this is a question ID can pursue that Darwinists won’t.

    As to specific pathogens, that’s my point exactly. The natural limits on these pathogens are being removed, suggesting a loss of specificity. That is something we know Darwinian processes can do. A designer could do it just as well, sure. What we have not seen is any increase in specificity or information, even though it appears to us as if pathogens are “evolving”.

  15. For people who claim not to believe in ID or a designer, they seem to know plenty about what this designer couldn’t, shouldn’t, and wouldn’t do. Do you think they acquired this knowledge scientifically?

  16. DaveScot,

    Thanks for the note at (12) – fascinating stuff. I take it that T3SS is a part of prokaryotes that is only used for predating on eukaryotes (i.e. it doesn’t work on other prey, only eukaryotes)?

  17. “it is not necessary to resort to intelligent designers, because surely a designer would have fashioned a simpler structure and gene regulation system”

    This is the obligatory bow of the Darwinist brain’s normal reasoning faculties to the absurdities of the Darwin idol.

    What have real designers fashioned in real life? Electric motors that look uncannily like the somebody ripped off the original plans for the flagellum.

    The design is so obvious that Crick just had to say, “Biologists must constantly keep in mind that what they see was not designed, but rather evolved.”

    Darwinian ‘logic’ here is tantamount to insanity. For mentally ill folks usually live in some deep form of denial of reality or inability to distinguish reality from imagination. That’s exactly what we witness here in the article.

  18. Portishead

    re; function of t3ss only to prey on eukaryotes

    Yes, that is correct. See here.

  19. DaveScot,

    You’re absolutely right about the lack of logic that T3SS should have evolved before the eukaryotic targets in which it injects effectors. According to the literature, it appears however that the evolutionary scenario which has most support is that both systems (flagellum and the type III secretion system) evolved independently from an ancestral system involved in bacterial protein export.

    Wong et. al. (2007) wrote a review that touches on this [1] and so did also McCann and Guttman [2], if you want to learn more about their arguments. Mark Pallen and Gophna U Volff has also written a book chapter that addresses this issue [3].

    1. Wong T, Amidi A, Dodds A, Siddiqi S, Wang J, Yep T. Evolution of the Bacterial Flagellum. MICROBE-AMERICAN SOCIETY FOR MICROBIOLOGY, 2007

    2. HC McCann, DS Guttman. Evolution of the type III secretion system and its effectors in plant-microbe interactions. New Phytol, 2008
    3. Pallen MJ, Gophna U. Bacterial Flagella and Type III Secretion: Case Studies in the Evolution of Complexity. Genome Dyn. 2007

  20. You guys might find this interesting:
    Scott Minnich actually predicted that they would find the Flagellum doing “double duty” as a secretory mechanism for virulence. Look around the 8:30 mark on the video:

    Bacterial Flagella – A Paradigm for Intelligent Design 4/6

    http://www.godtube.com/view_vi.....76f8304ecf

    Bacterial Flagella – A Paradigm for Intelligent Design 5/6

    http://www.godtube.com/view_vi.....14bc8d6337

  21. Make that the 6:00 minute mark of the first video,,, it is also very interesting that Dr. Minnich is very frank in stating that his “design” perspective allowed him to make the “correct” prediction!

  22. Hi Bornagain,
    That’s been a favourite point of mine.
    Of course if you use it in an argument you will hear the lament “well, I don’t see how the design perspective was necessary…anyone could have made the prediction.”
    The point is, of course, that we know the design perspective was central because the man who made the prediction said it was, and we know that he is the one who did make the prediction independently.

    And then his work becomes twisted as evidence against design. Funny.

  23. Penitents of denial, the proud, always “Nature” incurred,
    insanity-littered was fella
    reconsidered just flagella
    Instance for another smelling like turd
    Evidence in for theory that was backward.

    OK, I was just trying to see what else besides logic could run backward. I happened to choose a limerick. See? No problem, as long as you are willing to TORTURE IT TO DEATH to meet your needs.

    Don’t worry Darwinists, anything can go backward . . . everything will be fine . . . peer review is just weiver reep going the other way, it will all make sense (ignore for now that it makes little sense); it will all be fine. . . it just takes time.

  24. Devil’s Advocate sez:

    The TTSS injects eukaryotes now but back then it injected other prokaryotes. And BTW those prokaryotes are no longer around.

    (However we still cannot explain how the TTSS came about because it is irreducibly complex.)

  25. As a software engineer I can’t count the number of times I’ve worked on someone else’s code (or even my code that I had not visited in a long time) and thought, “Why did he (or I) do it that way? There’s a much simpler, more efficient way to do it.” So I modify the code and the program goes down in flames. Upon further inspection I realize that the “inefficient, unnecessarily complex” code was actually the only way to do it, for reasons that were not immediately evident.

    So, when I hear Darwinists in their infinite wisdom making claims about how biological systems are inefficient and unnecessarily complex (as in “too complex to have been designed”), and that they know it could have been done better, I can only assume that they have no experience in designing complex, functionally integrated systems. I imagine they would be more than happy to offer their opinion about how write a computer program when they know nothing about software engineering.

  26. parlar

    Nice try but no cigar.

    I have an even newer paper (2008) finding that the T3SS, just like we said all along, came from the flagellum, not an ancestor they both had in common. You can read it here.

  27. DaveScot,
    Thanks for pointing me to this interesting paper. I think, however, that you may partly have misunderstood its conclusions and implications. The paper you refer to does not in any way demonstrate that flagellum preceded the T3SS.

    First of all, let me say that your statement about devolution, as you call it, being simpler than evolution indeed is very correct. The paper actually provides a good demonstration of this.
    What it shows is that genes required to build the flagellum are lost in an environment where the flagellum is no longer needed (in this case, inside another cell). In fact, in bacteria that establish host-restricted and less complex lifestyles, a large array of gene functions are always found to become degraded and ultimately lost. This is because gene functions need to be maintained by selection – otherwise they are unavoidably inactivated by random genetic drift.

    The interesting point in this paper is, however, that some genes in the flagellum apparatus are consistently (conspicuously!) retained, namely those shared with the T3SS. Note that it does NOT convert the flagellum to a T3SS. The T3SS is a specialized apparatus with a needle structure that can inject effectors (proteins) through membranes into different cellular compartments. The retained genes can merely move proteins out of the bacterium. The authors speculate that the retained genes might support symbiotic interactions by exporting proteins out from the bacterium to the host organism.

    If the conclusions in the paper are true, two things are evident: First, since a subset of its components exhibits an altogether different (protein exporting) function, then the flagellum can obviously not be “irreducibly complex” (!). Second, in agreement with phylogenetic data, it suggests that this primitive protein export system existed first and that that the flagellum and the T3SS independently evolved from it.

    Just to clarify this point, if the T3SS evolved from the flagellum, we’d expect from phylogenetic analysis that the T3SS would exist as a recently diverging branch in a flagellum tree. This is not the case.

  28. T3SS would exist as a recently diverging branch in a flagellum tree

    Recently? A billion years ago is hardly recently.

  29. DaveScot:

    Ok, relatively speaking. The point being that there would be both more deeply diverging as well as more recently diverging branches of flagella sequences. Of course, the same argument goes for T3SS preceding the flagellum, which is likewise unsupported by the data. Instead, the tree demonstrates two major branches that coalesce at the root.

  30. Another clarification of the last statement (very important!).
    The phylogenetic tree of T3SS sequences and flagella sequences contains two major branches: One major branch with T3SS sequences and one major branch with flagellum sequences. These major branches coalesce at the root. This provides a good indication that these branches have different origins.

  31. trag @11:
    Somewhere online (no link) I had read a paper where the author discussed the previous 3 (at that time) simplest (smallest genome) life forms that had yet been discovered. Each originally had been touted as possibly the earliest independent life, but had eventually been determined to have devolved from more complex life forms. The author wanted to suggest that all viruses had actually been parts of previously viable independent life forms that eventually had devolved to viruses.
    No idea if that is in any way supportable, but might fit in with the idea that originally there hadn’t been “negative” organisms.
    However, even in the sea, where 1 life form eats another, not quite sure what means bad and good.

  32. tragicmishap, es58:

    It is actually true that many pathogens demonstrate evidence of degenerative processes acting on their genomes: Some examples are Yersinia pestis (bubonic plague), Bordetella pertussis (whooping cough), Francisella tularensis (rabbit plague), Mycobacterium leprae (leprosy). The list is long.

    Common for all such pathogens is also that they are more specialized than their undegenerated relatives.
    Taking it to the extreme, bacteria that are intracellular endosymbionts (being extremely specialized and restricted) all have extremely small genomes.

  33. OFF:

    Could you guys recommend me some articles about using parts of the flagellum motor in nanotechnology?

  34. parlar

    You’re still either not up to speed on the evidence or not willing to acknowledge the bits that don’t support your case.

    Far, far more prokaryote species have flagella than have a T3SS which was also evidence presented to Matzke before he submitted his hypothesis for publication.

    And here’s another paper explicitely suggesting that the t3ss is a descendent of the flagellum.

  35. First, since a subset of its components exhibits an altogether different (protein exporting) function, then the flagellum can obviously not be “irreducibly complex” (!)

    That is a very common misconception. Read:

    http://www.uncommondescent.com.....ock-in-it/

    http://www.discovery.org/scrip.....38;id=1831

  36. If the flagellar motor was designed and not evolved step-by-step over time via natural selection what is the ID hypothesis of how it got into prokaryotes in the first place? Was it placed whole within an existing strain of microorganism? (i.e., there was a generation of prokaryotes without flagellar motors followed by a generation of prokaryotes _with_ fully functioning, fully formed flagellar motors) Or did the structure build up slowly over time, according to non-natural selection rules? (i.e., successive generations of microorganisms developed portions of the flagellar motor piece-by-piece according to some pre-existing non-NDE plan, but the entire structure was not operational all at once.)

    Or is there some other method that I’m missing? This is not something I’ve seen a lot of discussion about. Given that structures like the flagellar motor are irreducibly complex how are they instantiated in the creature that contains them?

  37. what is THE ID hypothesis

    Before anyone discusses this further I want to note there isn’t such a thing as “THE ID hypothesis” but there are ID-compatible hypotheses. So despite this question being outside the scope of core ID it is a valid question. Considering the timescales involved, the hard part is determining which hypothesis is correct. So it’s a matter of examining the evidence and attempting to narrow down the possibilities until one, or as few as possible, remains.

    More on this topic:

    How does the actor act?

  38. successive generations of microorganisms developed portions of the flagellar motor piece-by-piece according to some pre-existing non-NDE plan, but the entire structure was not operational all at once

    That “might” be viable if there exists a realistic indirect pathway. A recent conversation on UD where the hypothetical indirect pathway of the bacterial flagellum is discussed:

    http://www.uncommondescent.com.....ent-289741

    The end of this conversation puts the problem in perspective:

    http://www.uncommondescent.com.....ent-290187

    Other major points:

    http://www.uncommondescent.com.....ent-290408

    http://www.uncommondescent.com.....ent-289702

    http://www.uncommondescent.com.....ent-212175

    But while Darwinian mechanisms have trouble making leaps in the “islands of functionality” a designed plan “shouldn’t” have that issue since even large informational/functionality gaps can be bridged.

  39. Thanks for the links. I’ll check those out.

    Although it’s possible that a precisely detailed account of an ID-compatible mechanism may be impossible (given an unknown creator and potentially unknowable technology) I think it’s useful to find a general description in order to bolster the core ID hypothesis. A general description of the process gives you something to predict and test for and provides ID with experimental backing.

    For example, if the mechanism is “fully functional IC objects appear all-at-once, fully functional” then we should expect to see major changes in species within single generations. If the mechanism is “slow accumulation of non-functional pieces of an IC object” then we might expect to see half-finished non-functional structures in organisms (ex., a quarter of a flagellar motor in this generation, a half of a motor in a later generation, 3/4 later than that, etc.)

    This is very simplistic of course but still useful in making ID a compelling argument. After all, saying that “A designer did it” is describing a mechanism at a very high level, in the same way that NDE says “random change over time” did it. The more that can be said to support the supposition that a designer did it, the better.

  40. After all, saying that “A designer did it” is describing a mechanism at a very high level, in the same way that NDE says “random change over time” did it. The more that can be said to support the supposition that a designer did it, the better.

    Trimbach. I think you’ve hit the nail on the head. In fact, I believe my first post to UD, a couple of years ago, asked this question: “When and how would you expect ‘design’ to appear?” I’ve come to understand that ID currently isn’t developed enough to have a hypothesis about this.

    I don’t think this deficiency should disqualify ID, though. In fact, if the notion of “design” is given credence, this is a logical next step for exploration.

    The same want of a mechanism applies in psychology. Once credence is given to “mind” as an entity which is able to influence brain function in some way, the same question applies: “How and when is ‘mind’ able to influence ‘brain?’”

    Neuroscientists haven’t really looked in that direction, since it’s seemed simpler simply to explain away ‘mind’ as an emergent property. But once the existence of “mind” becomes a credible variable, new horizons of research will open.

    We’ve hardly just begun! This is the heuristic value of ID. At least that’s how I see it…

  41. Okay, y’all want a hypothetical mechanism a hypothetical designer used to used to insert complex specified information into the DNA of living organisms…

    Retroviruses and phages.

    Any questions other than wanting to know the address of the designer’s lab and the brand of lab equipment he/she/they used to assemble the viruses or the fuel economy of the aircraft used to disperse the CSI vectors?

    If you want us to play the evolution game where anything we can imagine happening in the past, as long as it’s physically possible, is as good as experimental demonstration then we can play that game too. We’d prefer to rise above the fabrication of stories that our opponents call evolutionary biology but I suppose when in Rome we should do as the Romans do and just start making crap up that goes far beyond the actual evidence.

  42. 42

    DaveScot,

    I think that is a bit of a cop-out. First of all, the question wasn’t how is any CSI inserted, it was how was the flagellar motor inserted in particular, which is a very different question indeed.

    Furthermore, your answer just begs the question of how the retroviruses or phages were made in the first place.

    Now it’s fair enough to say we don’t know but I don’t think your answer flies.

  43. Winston Macchi

    The retroviruses and phages were made in a lab on the dark side of the moon, packaged in cannisters for aerial dispersal, and boosted from the moon to the earth by magnetic rail guns. The genes that make up the parts of the flaggellar motor and control its assembly where inserted into existing bactreria by custom designed bacteriophages.

    You think that’s a copout? Now you know how we feel about our opponents claiming that a random dance of atoms did the same thing. Chancedidit. Isn’t that just precious? It’s just so superior to Godidit. Somehow. I’m still trying to figure out the difference between chancedidit and godidit. Help me out there. Or how about if we both just forget about imaginary scenarios and focus on what can be demonstrated? As criminal investigator Sgt. Joe Friday on Dragnet famously said when interviewing witnesses, “Just the facts please.” We’re all waiting for an experimental demonstration that chance & necessity can build complex biological structures like the bacflag. Good luck with that. In the meantime we’ve already demonstrated that intelligent agents with expertise in biochemistry can purposely alter DNA with custom designed sequences – it’s called genetic engineering.

    If you want to know who designed the designer we’ve figured that out too. Who designed the designer is the same agency that created the material in materialism. Isn’t this fun? It’s hard to believe evolutionary biologists get away with pretending their woolgathering isn’t fiction, getting paid to make it up as they go along, and teach it to the gullible like its proven fact just as well tested as gravity. What a joke.

  44. 44

    DaveScot,

    Isn’t the point that ID is better science than your opponents? So why would you settle for explanations that are just as weak?

  45. The retroviruses and phages were made in a lab on the dark side of the moon, packaged in cannisters for aerial dispersal, and boosted from the moon to the earth by magnetic rail guns. The genes that make up the parts of the flaggellar motor and control its assembly where inserted into existing bactreria by custom designed bacteriophages.

    I know you’re being facetious but even this hypothesis is useful since it can be tested. Does the dark side of the moon show evidence of laboratories and rail guns in the past? Is there evidence of bacteriophages inserting (or capable of inserting) fully functioning IC components? Do we see evidence of Species X without a flagellar motor followed by Species X with a flagellar motor within a period of time consistent with infection? Do we see IC structures appearing in the absence of bacteriophages? Is this theory consistent with the observed behaviors of bacteriophages in the present? Etc. etc.

    We have observed enormous amounts of evidence for an Old Earth. We have observed that life forms have appeared gradually over a long, long period of time (no life at all before Time X, no Eukaryotes before X+1, no fish before Time X+2… the whole “Tree” of life). These are “just the facts.” NDE posits a mechanism of how these observed facts occurred, and this mechanism is subject to testing. Whether this mechanism is a compelling explanation or not depends on the extent that tests support this explanation. Surely this explanation is not compelling to ID-ists, but it is compelling to the vast majority of scientists. Saying “chancedidit” is initially no more compelling than “goddidit” until you add in test and observations of the proposed mechanisms. If ID wants to convince people it needs to tell a compelling story, a story that is also backed by tests and observations.

    Stating the conclusion up front (“this was designed”) and ignoring the how may be correct but it’s not compelling. It’s like my old Calculus class where a right answer got less points than a wrong answer unless you showed your work. ID needs to show its work on how to get from A to B or (in my opinion) it will continue to be marginalized in the scientific community.

  46. All, fascinating stuff, but I need clarification. OK, the flagellum rotary motor is too complex to have randomly evolved. So how did it get here? What is ID saying that keeps it from simply espousing a God of the Gaps? My intentions are to blog about this on my website at http://www.sophiesladder.com, which you might want to visit.

  47. “Saying “chancedidit” is initially no more compelling than “goddidit” until you add in test and observations of the proposed mechanisms.”

    One problem is, you’re not actually testing if ‘chancedidit’. At most, you’re searching for mechanisms and events, and if you can find evidence of them – hell, if you can just dream them up, many times – you file it under chance regardless of what you find or imagine.

    Your ‘chancedidit’ is no more testable than ‘goddidit’. The only difference is this position, philosophical and untestable at its core, gets stamped and passed off as scientific while questioning it is forever branded unscientific. Leading to a tidy hypocritical position where detecting design in nature is unscientific, but detecting the lack of design is somehow scientific.

    I personally think ID can’t really be scientifically proven or disproven. But if it’s scientific to say ‘Aha, by looking at the data, I can determine that there was no design involved!’, it’s entirely scientific to say ‘Aha, by looking at the data, I can determine that there was design involved!’

    Sure, such a view may be ‘marginalized in the scientific community’. But frankly, who cares? Even the scientific community doesn’t care what the scientific community thinks when it comes to ID. The concern is what people at large think, and even that concern seems to (strangely) boil down to ‘Will they say they believe in darwinian evolution?’ Not even ‘Do they understand the theory and mechanisms and debates?’ but a personal commitment to it.

  48. Trimbach

    I know you’re being facetious but even this hypothesis is useful since it can be tested.

    Genetic engineering, also known as intelligent design, has already been proven to be a capable mechanism. No further testing of its capacity is required.

    Does the dark side of the moon show evidence of laboratories and rail guns in the past?

    It is not, even in principle, possible to look everywhere. So even if my story is true, we could simply be missing the evidence for it. How do we know when to stop searching? Just so, it is not possible to show chance incapable of doing things that are physically possible and evolution theory leverages that to absurdity. For instance, it’s possible that chance alone could assemble a microprocessor. The odds against it are so long that we don’t reasonably expect it has ever happened in the history of the universe. The study of how matter behaves in bulk, including predicting how it will behave in the future starting from a given state in the present, is called statistical mechanics and is virtually ignored in evolutionary biology. It’s physically possible for a flagellum to become assembled by random chance. How do we know when to stop searching?

    Is there evidence of bacteriophages inserting (or capable of inserting) fully functioning IC components?

    Not just evidence, it’s an established fact. A bacteriophage is a fully functional IC component in its own right and some of them operate by inserting genetic material into the host genome which causes the host to manufacture copies of the phage.

    Do we see evidence of Species X without a flagellar motor followed by Species X with a flagellar motor within a period of time consistent with infection?

    Any direct evidence of flagellar saltation billions of years ago would be unrecoverable given the reality of fossilization. However, we can look for evidence of a gradual process that should still be occuring today. We don’t see half formed flagella today. Maybe we just haven’t looked hard enough. When do we know when to stop looking?

    Do we see IC structures appearing in the absence of bacteriophages?

    Phages are everywhere in vivo so there is no absence of them in the wild. In vitro where we can artificially remove them we have not observed the de novo formation of any IC structures.

    Is this theory consistent with the observed behaviors of bacteriophages in the present?

    Absolutely yes.

    We have observed enormous amounts of evidence for an Old Earth.

    Agreed.

    We have observed that life forms have appeared gradually over a long, long period of time (no life at all before Time X, no Eukaryotes before X+1, no fish before Time X+2… the whole “Tree” of life).

    Keeping in mind that lack of evidence is not proof of lack and the obstacles in the way of organic structures being preserved in quantities where we can reasonably expect to discover them billions of years later this might easily be wrong.

    However, we do know that the fossil record we have so far discovered is a record of saltation where new species with fully formed distinctions characteristic of their kind appear abruptly in the fossil record, remain stable (unchanging) for an average of about 10 million years, then abruptly disappear from the record. This is known as “the trade secret of paleontology”.

    These are “just the facts.” NDE posits a mechanism of how these observed facts occurred, and this mechanism is subject to testing.

    Actually chance & necessity is not subject to confirmation testing of it happening in the past. The only thing that can be tested is what it can under do under observation in the present. Actual observation of NDE in trillions of opportunities to produce heritable change is the focus of Behe’s “Edge of Evolution”. It didn’t do much.

    Whether this mechanism is a compelling explanation or not depends on the extent that tests support this explanation.

    It has failed all tests to produce novel cell types, tissue types, organs, and body plans. How should we know when to stop testing? I put to you that testing has virtually stopped with no success in any of the above categories yet the theory is not abandoned. Why?

    Surely this explanation is not compelling to ID-ists, but it is compelling to the vast majority of scientists.

    It’s not compelling to any objective observer.

    Saying “chancedidit” is initially no more compelling than “goddidit” until you add in test and observations of the proposed mechanisms.

    True. But when we say intelligent agency did it, instead of “god”, we can at least test the possibility. I assert that the test is successful and is embodied in the discipline known as genetic engineering. So it has been adequately demonstrated that the mechanism of intelligent agency can get the job done. In contrast, the mechanism of chance & necessity has never been demonstrated as able to get the same job done.

    If ID wants to convince people it needs to tell a compelling story, a story that is also backed by tests and observations.

    It IS backed by tests and observations.

    Stating the conclusion up front (”this was designed”) and ignoring the how may be correct but it’s not compelling.

    It’s compelling to a vast majority of objective observers. That’s why there is still a raging controversy today. Only a tiny fraction of observers in academia and elsewhere with a vested interest in preserving the status quo are not compelled by it. Most people know a machine when they see one and also know that machines don’t create themselves. It requires years of indoctrination into evolutionary dogma to sway people into the belief that complex machines can create themselves.

    It’s like my old Calculus class where a right answer got less points than a wrong answer unless you showed your work. ID needs to show its work on how to get from A to B or (in my opinion) it will continue to be marginalized in the scientific community.

    We already have shown our work. Genetic engineering, which IS intelligent design operating in the present, is well established. Where the work needs to be shown is chance & necessity getting from point A to point B. And when we try to point out the lack of any demonstration in this regard to the chance & necessity narrative in science textbooks our opposition resorts to legal chicanery to keep it out. Why legal chicanery? The answer to that is quite simple – there’s no scientific defense for the chance & necessity narrative.

  49. nullasalus: ” personally think ID can’t really be scientifically proven or disproven.”

    Why do you think that?

  50. StephenB,

    The same reasons as ever – I think questions of agency and intention, especially on the scale ID supposes, are just not something that can be investigated or ruled upon and still be science. I think evidence of design is present and extremely abundant, but the debate falls under philosophy. Same old reasons I always give.

    I’m still open to having my mind changed about it all, but I view the problems of materialism and ‘darwinism’ differently. We saw a sample of it here in action – ‘We can test for chancedidit, but not goddidit!’ Well, no. We can’t. And pretending that we not only can, but have, is one of the reasons I have little sympathy for the claims that ID is a threat to science.

    Davescot actually provides one of the reasons I take the position I do: We humans can genetically engineer. We can create simulations, plan in advance, orchestrate natural processes towards certain ends, etc. And our knowledge not only grows, but we have the minds to entertain what a truly superior mind (or minds) would be capable of producing: Everything we see and have seen. So when it comes to awkward ideas of utter inexplicable chance to explain anything – cosmological coincidences, evolutionary events, convenient natural structures, etc – I take a version of LaPlace’s tact. “I have no need for that hypothesis.”

  51. I’m sympathetic when you say that design cannot be proved—ID seeks the best explanation—only if we actually saw it all happen could we say we have absolutely proved it. It’s theory based on fact. We’re not saying—as the Darwinists do about Darwinism—that the theory IS fact.

    But I do get tired of arguments over whether ID is or is not “science”. The distinction between science and nonscience is overwraught and silly, that is, unless you intend like the rest of them to cast Darwinism on the side of fact, of evidence driven theory, and throw ID into the realm of wishful thinking and irrational nonsense.

  52. DaveScot,

    This response became too long, sorry about that.

    I recognize that there are many things about biology that we don’t understand. One thing that really puzzles me, for example, is the relative short time that life had to get started. But that doesn’t mean that I instantly buy religious (or the ID proxy) arguments for how it happened.
    Admittedly, a significant problem in evolutionary theory (which IDists take careful note of) is that historical events cannot be proved, simply because we cannot turn back time to see what actually happened. It is likewise clear also that major evolutionary feats happen extremely rarely, often just once, in an earth-sized test tube over billions of years, which make probabilities difficult to estimate. We’re also kind of biased by the end result. Most of the time, however, we can quite easily reconstruct plausible chains of events of how things likely could have happened.
    I did my homework regarding ‘irreducible complexity’ (IC), and found that I indeed had misunderstood the concept, please excuse my ignorance.
    Here is the definition that I found:
    “By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system, because any precursor to an irreducibly complex system that is missing a part is by definition nonfunctional. An irreducibly complex biological system, if there is such a thing, would be a powerful challenge to Darwinian evolution.” (Darwin’s Black Box p39.)
    Thus, if the ORIGINAL function of a complex structure disappears by the removal of one subpart of it, then that would establish that evolution couldn’t have done it. (indirectly supporting that a maker must have constructed it.)
    The reasoning of this argument is appealing if you are inclined to accept the concept of a creator, but is logically flawed as I’ll demonstrate. The more conservative connotation that I intuitively thought it had, namely that subparts of the system would at all not be allowed to have other (previous) functions, actually made more sense. It would still suffer from the same logical flaw, but it would be more impressive.
    The logical flaw lies in the test implied in the first sentence of the cited paragraph. The principal reason comes from the fact that a molecular complex (AB) evolves together. Original functionality in one part A is likely to disappear if a second part B exists that performs that function more efficiently. If B did not perform it more efficiently, evolution would not have promoted this complex AB. The reason why A doesn’t keep the function is that (purifying) selection pressure is required to maintain protein functions; otherwise they are degraded by genetic drift. And if B does the job, selection doesn’t make A keep the function. Simple enough. So, if you remove B and test the function of A, you will often find that it cannot do anything.
    Behe’s argument can therefore not be used as an evolutionary test.
    I can now imagine arguments that purifying selection and genetic drift is just Darwinist complicated wish-thinking, but I assure you that these are well-established facts with tons of concordant evidence behind.
    Just to briefly re-connect to the previous discussion on the flagellum: the paper that you refer to from the year 2000 was written and coordinated (last name authorship) by Milton Saier Jr., who was also last name on the review in Microbe by Wong et. al. (2007) that I referred to earlier in this conversation. Apparently, he changed his mind.
    Actually, I’m not really sure what this significance is of the progression of these appearances. If the flagellum appeared first (I’ll gladly admit that it very well might), and that the T3SS then would be partly derived from flagellum components, wouldn’t that still require evolution? Or how does ID then explain that the T3SS later came about? How does this support the ID case?
    To really disprove evolution, you would have to find a credible way to deal with the massive amounts of data that supports it in all corners of biology and paleontology. How can the progressions in fossil records be dealt with in a credible way? What about the real-time observations that we make every day on the spreading of antibiotic resistance (adaptive phenotypes)? What about data that demonstrates increased genetic drift in small populations? What about data that demonstrates how new pathogens have come into existence by import of pathogenicity traits (such as genes for T3SSs). Actually, what about molecular data that demonstrates phylogenetic relationships between taxa? From an ID perspective, this must be extremely weird. Homology must be devastating.

  53. DaveScot

    Genetic engineering, also known as intelligent design, has already been proven to be a capable mechanism. No further testing of its capacity is required.

    That fact that we (21st century homo sapiens) can do genetic engineering shows that we have the capacity in theory, but since we weren’t around the billions of years ago when flagella appeared we know it wasn’t us. :-D

    It is not, even in principle, possible to look everywhere. So even if my story is true, we could simply be missing the evidence for it.

    Absolutely true. But the point I’m trying to make has to do with the strength of the argument. We’re never going to get the full story about anything that happened in the past, but what we can do is collect whatever it is we can collect, using current hypotheses to narrow the search whenever possible. Make a hypothesis, create a test for the hypothesis, and go forth and see what you find. The better the hypothesis, the better the test, the more convincing that the hypothesis is true. Any hypothesis that is consistent with lots and and lots of different tests and lots and lots of data makes that hypothesis much more convincing than one that doesn’t.

    How do we know when to stop searching?

    Well, never. People in general and scientists in particular are curious creatures and given that perfect knowledge of everything is practically unattainable, there’s never a shortage of things to investigate. Scientists continue to investigate even well-established and well-proven phenomena looking for exceptions and applying new level of precision.

    Just so, it is not possible to show chance incapable of doing things that are physically possible and evolution theory leverages that to absurdity.

    I don’t think that NDE relies on chance, I think rather they take existing mechanisms that capably explain a certain set of phenomena (“microevolution”, whatever that means to you) and extrapolates that that also solves a certain other set of phenomena (“macroevolution”). That extrapolation may not be warranted, and may not even be strongly verifiable for certain cases (the unlikely preservation of ancient flagella, for example), but it is, demonstrably, compelling for many people.

    I put to you that testing has virtually stopped with no success in any of the above categories yet the theory is not abandoned. Why?

    Because a more convincing hypothesis hasn’t been presented? This is what I’m talking about: if ID is to supplant NDE it needs to be more convincing. It is demonstrably less convincing than NDE at present. Why is that?

    [NDE is] not compelling to any objective observer.

    and

    Only a tiny fraction of observers in academia and elsewhere with a vested interest in preserving the status quo are not compelled by it. Most people know a machine when they see one and also know that machines don’t create themselves. It requires years of indoctrination into evolutionary dogma to sway people into the belief that complex machines can create themselves.

    That’s a very big claim. Are you saying that the real reason for the popularity of NDE is brainwashing? Wow…. that’s very tin-foil-hat of you.

    Think about the geocentrists. I happen to think anyone who believes the Earth is the center of the Universe is completely off their rocker, and they are certainly in the (distinct) minority of people in general and scientists in particular. But oddly enough there’s no really good way to prove them wrong because it is possible given a certain choice of reference frame that the Earth really is the Center of the Universe. There’s a non-zero chance they might be right. But the common opinion is that these people are wackaloons. How does ID avoid this level of marginalization? How can the ID story be told in a way to make it compelling to the scientific community and the general population? I hear your frustration that you think everything’s already been done that needs to be done, but clearly that’s not true.

  54. —–nullasalus: (Why don’t you think that ID is science) “The same reasons as ever – I think questions of agency and intention, especially on the scale ID supposes, are just not something that can be investigated or ruled upon and still be science. I think evidence of design is present and extremely abundant, but the debate falls under philosophy. Same old reasons I always give.”

    In effect, you are saying that you think questions of agency and intention are not science because you think they are not science. That is not really an answer. ID says that a DNA molecule contains empirically based, observable patterns that manifest themselves as functionally specified complex information FSCI. Under the circumstances, design is the best inference because our experience confirms that each time FSCI is present, intelligence was the cause. And you say that is not science because…………

  55. —–Rude: “But I do get tired of arguments over whether ID is or is not “science”. The distinction between science and nonscience is overwraught and silly, that is, unless you intend like the rest of them to cast Darwinism on the side of fact, of evidence driven theory, and throw ID into the realm of wishful thinking and irrational nonsense.”

    Actually, nullasalus is skeptical of both Darwinian claims and ID science. The problem is that he equates the fantasies of the former with the reasonableness of the latter.

  56. Rude,

    “But I do get tired of arguments over whether ID is or is not “science”. The distinction between science and nonscience is overwraught and silly, that is, unless you intend like the rest of them to cast Darwinism on the side of fact, of evidence driven theory, and throw ID into the realm of wishful thinking and irrational nonsense.”

    First, I don’t think ID is wishful thinking or irrational nonsense. I see it as a powerful perspective and the most defensible position to take with regards to nature and existence philosophically/rationally. Don’t mistake my thinking that design can’t be ruled in or out scientifically as a belief that there is no evidence for design, or that there aren’t powerful reasons to affirm design in nature. Probably more powerful than any of the TEs I’m aware of argue, and possibly most of the ID proponents.

    Second, I don’t see Darwinism and ID as mutually exclusive – unless we’re talking about the warped, philosophy-laden ‘Darwinism’ StephenB routinely and rightly talks about, where purposelessness, a lack of guidance, etc are required by the theory. Those are examples of an abuse where extraneous philosophy is infused into the science, and passed off as 100% science. I see evolution, mutation, etc as yet more tools available in a designer’s suite (We’ve used evolutionary principles in the creation of transistors, etc already – and I don’t have to tell UD regulars how often we refer to nature for design schematics). So again, I take a position that oddly enough may be stronger than what Behe takes – I don’t limit design considerations to IC structures, etc. I see design in even scenarios where Behe would accept gradualism and evolution as sufficing to explain the non-IC structures. Call it “design all the way down”.

    Lastly, and I think ultimately, I see science as a very limited enterprise. It can accomplish great things (And also a lot of terrible things, but such is life), it’s given us access to quite a lot of useful technologies (And the flipside, some devastating ones), but I think there are questions – many intellectual spheres – where its usefulness taps out quickly. And I don’t see this changing.

  57. StephenB,

    “In effect, you are saying that you think questions of agency and intention are not science because you think they are not science.”

    Let me try to make my reasoning clearer. Your example will provide a good way to frame the explanation.

    “That is not really an answer. ID says that a DNA molecule contains empirically based, observable patterns that manifest themselves as functionally specified complex information FSCI. Under the circumstances, design is the best inference because our experience confirms that each time FSCI is present, intelligence was the cause. And you say that is not science because………”

    Because you’re underestimating what an atheist can and will dream up to explain anything and everything. I know atheists aren’t the only critics of ID, but it’s the atheist reply which most of those criticisms unconsciously focus on.

    Think of it this way: To the atheist, anything an omnipotent, omniscient God can do, ‘nature’ can do either directly or by a proxy. Directly meaning it can just happen with no guidance whatsoever (Is the universe fine tuned? Well, then there are probably multiple universes! Is the Origin of Life an event of fantastic unlikelihood? Well, then we just got lucky. Etc, etc.) By a proxy, meaning ‘By some intelligent agent who is not God, and who in turn was created unintentionally by nature’. This can be the observer themselves (“Did I just witness a miracle? No, clearly I’m either mistaken about nature or hallucinating.”), large groups of observers (“Did thousands of us just witness a miracle? No, clearly we’re either all mistaken about nature or this is a case of mass hallucination.”), or an intelligent entity who is not God, and who likely came about through unintentional natural processes as well (“Clearly aliens did this. Or the Sysop who is running the simulated universe we’re all in. Or humans with secret technology. Or…”)

    I see no way to scientifically distinguish between the atheist explanation and the theist explanation. Now, I can see one explanation as more persuasive than the other – I think theism, or at least some form of deism, wins hands down every time when it comes to fundamental questions of nature like this – but if there’s no scientific test between the two perspectives, that is that. Both theism and atheism (Which is just, really, a mindless God) cannot be falsified. Science can’t settle that fight – it can barely assist with it indirectly.

  58. nullasalus: Excuse me, but I think you may have missed my question. Here it is again:

    ID says that a DNA molecule contains empirically based, observable patterns that manifest themselves as functionally specified complex information FSCI. Under the circumstances, design is the best inference because our experience confirms that each time FSCI is present, intelligence is the cause.

    You have stated many times that ID is not science. Please tell my why the above is not a scientific argument.

  59. StephenB,

    Taken in reverse.

    “You have stated many times that ID is not science. Please tell my why the above is not a scientific argument.”

    Small point, but no. I’ve said I don’t believe claims of design or no-design are decidable by science. So it’s not just ID, and I’m not stating it as incontrovertible fact – it’s simply my view. I also think some of the issue centers around what a person defines science to be (Hence my position that, if someone claims science demonstrates a lack of design, then questions of design must be scientific by their measure – and therefore claims that science demonstrates the presence of design must themselves be scientific by the same measure. And my continual complaints that ID is treated to a double standard.)

    “ID says that a DNA molecule contains empirically based, observable patterns that manifest themselves as functionally specified complex information FSCI. Under the circumstances, design is the best inference because our experience confirms that each time FSCI is present, intelligence is the cause.”

    “Please tell my why the above is not a scientific argument.”

    What are you defining ‘a scientific argument’ as here? I’m not arguing that you can’t make reference to scientific knowledge to bolster or attack a design claim, or even a philosophical claim for that matter. But I don’t think such arguments are themselves ‘science’ – I guess you could say I go by the falsification standard. How do you falsify the claim that FSCI patterns don’t arise from non-intelligent sources? Watch one spontaneously develop in nature? But even if you did, how do you know you didn’t just witness an intelligence creating the FSCI, either in a front-loaded way or through some kind of intervention?

  60. —–nullasalus: Are you saying that your standard for science is falsifiability? Is that your argument that ID is not scienc? Are you saying that ID cannot be falsified and is therefore not science?

  61. StephenB,

    “Are you saying that your standard for science is falsifiability? Is that your argument that ID is not scienc? Are you saying that ID cannot be falsified and is therefore not science?”

    Sure, I’d say my standard for science is falsifiability. It’s a vague limit, but I think it’s a practical one.

    No, I’m not saying ‘ID cannot be falsified and is therefore not science’. You keep putting it in a way that makes it sound like I’m militant or certain about this – really, I’m open to being corrected. Hey, even particular ID claims may be falsifiable – Behe’s comes to mind, though I’m in no way prepared to judge his scientific claims. I’ve said in the past that I’m certainly open to the idea that some kinds of design are detectable (though attributing said design to God is a whole other matter, scientifically.) I’ve also said that I think it’s very hard to, say… justify SETI as science in action, or a scientific endeavor, while at the same time arguing ID is never itself scientific.

    Again, it always goes back to the atheist God-equivalent. You have guys like Dawkins insisting that we don’t see design in nature – but we absolutely see illusions of design. I think passing off that claim as a scientific viewpoint is an abuse of science, especially when the inverse (‘Those aren’t illusions, you’re actually seeing design’) is immediately ruled out. But how do you scientifically propose to demonstrate or falsify design when you have people willing to imagine what amounts to an omnipotent but mindless force as a counter-example?

  62. —–nullasalus: “No, I’m not saying ‘ID cannot be falsified and is therefore not science’. You keep putting it in a way that makes it sound like I’m militant or certain about this – really, I’m open to being corrected.”

    I am not saying that you are “militant,” I am simply saying that you don’t believe ID is science and I still do not understand why. If you were open to being corrected, you would have already acknowledged ID methodology as science, and that would be the end of it.

    Only recently have you proposed “falsifiability” as your standard, so only recently have I asked you about it. If, indeed, falsifiability is your standard, it would seem that you would acknowledge that ID is science, since ID is obviously falsifiable. Yet, you do not accept ID as science, so evidently you have some other standard.

    If you like, we can use your own working definition of science, since you must have one. So, would you be willing to define science, and then explain why ID doesn’t meet that definition.

    My definition of science and its method is as follows:

    science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe.

    scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses.

    Obviously, ID meets that standard, but you don’t believe that ID is science. So, obviously, you have another standard. Would you share it?

  63. If ID isn’t science then neither is chance & necessity. Confirmation of the chance & necessity hypothesis as the mechanism behind the origin and diversification of life constitutes the falsfication of the design hypothesis. Conversly confirmation of the design hypothesis constitutes the falsification of the chance hypothesis.

    It is a true dichotomy that the origin and diversification of life either did or did not involve intelligent agency. There’s no third option. Either both are science or both are not science. Takes yo pick. No double standards.

  64. DaveScot,

    I agree with you fully, and I take the second choice. I think I’ve been saying as much here. I have tremendous sympathy for ID precisely because I believe a double standard has been in play for a long time, and the reaction to ID has been particularly furious and obsessive in some quarters precisely because ID forces that dilemma to be realized. Whether the choice is to drop both C&E (or other forms of it) and ID as scientific conclusions or agree both views are scientific ones, it’s a step down from what was previously the norm: C&E being viewed as scientific, while ID is not. Thanks in large part to the efforts of ID proponents, it’s now much harder to hold that position without the flaw being noticed.

    That said, I look at the sidebar: “Hence, ID needs to be vigorously developed as a scientific, intellectual, and cultural project.” Whatever my misgivings about the first goal listed, I happily and enthusiastically support the second two goals. And my misgivings about ID as science aren’t rooted in ID so much as the perception of science. I don’t think science can rule on what many people believe it can – not just chance versus ID, but many other things (morality, aesthetics, etc.)

    Anyway, that’s it for me tonight. I’ll gladly respond more to StephenB tomorrow – and if I’m derailing this thread, my apologies. Please inform me as much and I’ll quiet up quickly.

  65. In following this discussion, there seems to be one point that is being completely overlooked: when speaking of the origin of the bacterial flagellum, you’re not just simply asking for the origin of a structure, you’re asking for the origin of life itself. The first form of “life” we know about is bacteria. Since bacteria having no flagella would lack motility, they would be unlikely to survive; hence, we’re dealing with an original structure. (Yes, there are bacteria which lack the flagella, but they survive only through the presence of other forms of life. This wouldn’t have been the case initially.)

    So, if you’re asking how ID explains the bacterial flagellum, you’re indirectly asking how life began. Darwinism has no answer for that. Our answer would be that it was somehow designed and constructed. IOW, the complexity of structure—and, hence, its improbability—is so immense as to be beyond ‘chance’ events.

    As to the T3S system, it is quite conclusively derivative. I’ve just looked at a 2005 review article, and it is abundantly clear, from molecular phylogenies and such, that the flagellar structure existed first. (Physiology 20: 326-339, 2005)

  66. nullasalus

    Your comments are appreciated. I don’t care where you sit with regard to ID science or pseudoscience as long as you don’t apply a double standard. I fall on the side that both the chance and design hypotheses are good science and encourage further research to resolve the dispute.

    The reason I think that way is because we haven’t observed under controlled conditions any unexplainable genetic transformations actually happening and I doubt that we ever will. Everything so far actually observed happening in organic evolution is explained by statistical mechanics without resort to ignoring impossibly long odds. What can’t be explained in terms of statistical mechanics all happened in the past. When I’m presented with the argument “well, what happens if we observe in a lab CSI forming de novo won’t you just claim it’s an act of design accomplished by your invisible creator/God”. Actually I won’t make that claim and I hope that every means possible will be used to find a material explanation congruent with statistical mechanics. If it’s under controlled conditions we can look for a cause and I’m confident we’ll find an explanation congruent with statistical mechanics. I don’t think that observation will happen but if it does we can address it when it does. In the meantime there’s nothing to analyze. We’re talking about a hypothetical observation. We could just as well talk about how we’d explain an apple falling from a tree and hovering in midair defying gravity. Why waste time talking about something that hasn’t happened and likely won’t ever happen? It’s just woolgathering. Discuss actual observations. Just the facts, please. So what we have are design inferences made on actual, existing molecular machines in living cells. I encourage the design doubters to keep seeking non-design explanations because the harder they search and fail the stronger the design inference becomes.

    The basic problem here boils down to what Karl Popper exemplified with the Black Swan hypothesis. He states that the no Black Swan exists in nature and that is a valid scientific hypothesis even though we can never be sure we’ve searched everywhere in nature. We can’t prove that no black swan exists in nature but finding a single black swan will falsify the hypothesis. Lots of things in science can’t be proven but they can be disproven. ID states, for instance, that there is no non-intelligent process that can bring about the de novo formation of a bacflag. Obviously we can’t prove that because we can never be assured beyond doubt that we’ve simply overlooked a non-intelligent mechanism that can reasonably explain it. But the design hypothesis can be falsified by demonstrating (not just speculating but actually demonstrating) a single non-intelligent process able to perform the task. That non-intelligent process would be Popper’s Black Swan. In the meantime, until and if a single black swan is found, the hypothesis that the black swan doesn’t exist remains a valid scientific hypothesis. The chance pundits, when they object to this, merely demonstrate their lack of confidence in their ability to locate a black swan. I understand their lack of confidence. I don’t have any confidence in their finding it either.

  67. DaveScot,

    I dont know if you read my entry above. Bud I’d really like to see some credible statistical mechanic, or ID for that matter, explaination for, say, spreading of antibiotic resistance or the existence of DNA homology.

    Why not address the evidence without the rethorics?

  68. parlar

    What you ask for requires reading some books not some blog comments.

    Read Behe’s “Edge of Evolution”, Sanford’s “Genetic Entropy”, Mike Genes “The Design Matrix”, and Graville Sewell’s papers on thermodynamics.

    I’d also recommend (although I have not yet but I’ve been following its development over the past year and am in contact with the authors) downloading and running Mendel’s Accountant. I was waiting for a working Windows version and it looks as if that’s been released now.

  69. parlar,

    Personally I don’t have the time to respond at length…never mind that your objections are very common and have been discussed before at length. As such most of my response is copy and paste.

    spreading of antibiotic resistance

    Micro-evolution. No “special ID explanation” required. Why, do you hold the misconception that ID proponents consider everything in evolutionary biology to be false?

    Behe had this to say:

    Intelligent design is a good explanation for a number of biochemical systems, but I should insert a word of caution. Intelligent design theory has to be seen in context: it does not try to explain everything. We live in a complex world where lots of different things can happen. When deciding how various rocks came to be shaped the way they are a geologist might consider a whole range of factors: rain, wind, the movement of glaciers, the activity of moss and lichens, volcanic action, nuclear explosions, asteroid impact, or the hand of a sculptor. The shape of one rock might have been determined primarily by one mechanism, the shape of another rock by another mechanism.

    Similarly, evolutionary biologists have recognized that a number of factors might have affected the development of life: common descent, natural selection, migration, population size, founder effects (effects that may be due to the limited number of organisms that begin a new species), genetic drift (spread of “neutral,” nonselective mutations), gene flow (the incorporation of genes into a population from a separate population), linkage (occurrence of two genes on the same chromosome), and much more. The fact that some biochemical systems were designed by an intelligent agent does not mean that any of the other factors are not operative, common, or important.

    and

    I think a lot of folks get confused because they think that all events have to be assigned en masse to either the category of chance or to that of design. I disagree. We live in a universe containing both real chance and real design. Chance events do happen (and can be useful historical markers of common descent), but they don’t explain the background elegance and functional complexity of nature. That required design.

    you say:

    or the existence of DNA homology.

    ID proponents typically interpret homology as compatible with universal common descent, common descent from multiple LUCAs, or Designer Information Reuse (which is itself compatible with multiple scenarios).

    http://biology.plosjournals.or.....&ct=1

    Read this article where they’re seeing multiple bushes, not a tree. They even discuss the biases used to resolve this bad picture for Darwinists like long-branch attraction:

    “Thus, a priori expectations of obtaining fully resolved topologies combined with the use of large amounts of data (which generate high support values) can make trees out of bushes.”

    And it keeps getting worse:

    “recent analyses of some key clades in life’s history have produced bushes and not resolved trees.”

    “The patterns observed in these clades are both important signals of biological history and symptoms of fundamental challenges that must be confronted.”

    “Wolf and colleagues omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom”

    “The evidence presented here suggests that large amounts of conventional characters will not always suffice, even if analyzed by state-of-the-art methodology.”

    They even discuss the “high frequency of independently evolved characters” aka convergent evolution.

    I think it would help the conversation to differentiate between Darwinian Common Descent and Common Descent compatible with ID hypotheses (which is fine with the above picture of bushes and not a consistent TOL). For example, you wouldn’t expect to find the same information being used in divergent lines from a Darwinian viewpoint if they’re geographically isolated or if the divergence supposedly took place a very large amount of time before.

    Instead of resolving a tree we’re getting bushes since we cannot find the gradual informational links that would be expected of Darwinian Common Descent. Continuing the theme of “islands of functional information”, these bushes could also be called “archipelagos of functional information” which must be bridged by informational leaps. Designed mechanisms could bridge (or traverse) these informational leap, thus producing Designed Common Descent.

    Another thing that ID proponents predicted is homologous information where none would be expected if Darwinian mechanisms were responsible for macro-evolution. Like the platypus, for example, whose genome is a patchwork of mammal, reptile, and bird.

    Chromosomal sex determination in the platypus was also discovered to be a combination of mammal and bird systems. Yet TO says:

    “birds are thought to have evolved from dinosaurs in the Jurassic about 150 million years ago, and that mammals are thought to have evolved from a reptile-like group of animals called the therapsids in the Triassic about 220 million years ago. No competent evolutionist has ever claimed that platypuses are a link between birds and mammals.”

    In the past I’ve mused what might happen if the genomes for animals not considered to be related were compared. My predication would be that we’d find evidence for front-loading, other scenarios, and information re-use in general. I personally want to see a comparison of North American flying squirrels and Australian sugar gliders.

    Often the the convergent evolution storytelling card is played…you’d think Darwinist would have run out of cards in that deck by now. Universal common descent from a single LUCA may be true itself but the historical narratives we have now may not be true themselves. Some ideas like land mammals to whales may have never existed (or persisted to this day) if the bearded buddha had never posited his bear story. If front-loading and universal common descent are both true then why couldn’t the whale have evolved entirely in the ocean and received the mammal-like features from internal information?

    I have my personal preferences but I also have no problems with multiple LUCAs and other narratives. Directed panspermia (front-loading with no further design interaction), intelligent evolution, progressive creation, separate creation (possibly combined with more limited front-loading), it doesn’t matter. As long as intelligence is involved as the data shows and the evidence is compatible with a scenario.

  70. DaveScot,

    Thanks for the reply and the kind words. For me, the issue is not a stark choice between design or statistical mechanics – even if the latter can explain what is seen, you’re still left with questions of why systems function in the way that they do to provide those statistics, how systems can be designed in ways to make certain patterns more/less likely, etc. On the flipside, even if we do observe biological structures that defy appeal to statistical mechanics, you already know the typical responses – “Well, we just got extremely lucky! Maybe there are multiple universes even.” or “Clearly we’re just missing something, and science will up and die if we think otherwise.” This gets worse since the fight isn’t really over pure science besides, or even what kind of research is done – it’s also about wanting people to reject certain possibilities out of hand because they’re too congruent with worldviews that are unacceptable.

    StephenB,

    “If, indeed, falsifiability is your standard, it would seem that you would acknowledge that ID is science, since ID is obviously falsifiable. Yet, you do not accept ID as science, so evidently you have some other standard.”

    Maybe you missed my saying this: Hey, even particular ID claims may be falsifiable – Behe’s comes to mind, though I’m in no way prepared to judge his scientific claims.

    But let’s say Behe’s claims are accurate. There really does seem to be an edge to evolution, and claims are made which could be falsified by research (Say speculation about mutation rates and possibility are made and tested.) As DaveScot said, what evolution cannot explain are (at least by and large) past events. Saying ‘this event/structure could not have come about through known mechanisms of evolution according to what we know’ does not mean you’ve proven design, anymore than ‘this could have come about through evolution’ proves a lack of design. You can argue that you’ve at least inferred it – I’d agree. But the question of design or a lack of design in nature still goes beyond science.

    Maybe we’re talking past each other. I’m not arguing that nothing an ID proponent (or an ID opponent) can propose as an experiment is scientific by my standard. Propose something which can be falsified, engage in research/testing, and I’ll say you’re doing science. Say you infer design based on what you’re seeing, and I may even agree with what you infer. But when you start talking about inferring design or a lack of design, that is when you’re no longer doing science by my view.

    So let me ask this: “The bacterial flagellum could/could not have come to be without design.” Is this, to you, a falsifiable statement? To me it isn’t – even if you show a definite and past-plausible evolutionary or material mechanism that could have conceivably resulted in the bacterial flagellum, you still have the design of the overall system, the historical pattern, etc to contend with. Design speculation never goes away, and in fact may become even stronger depending on the conditions required to enable those mechanisms. And even if you show that no known evolutionary or material mechanism could have resulted in what we see, despite considerable research, the claim always will linger – we missed something, it was just luck, or in the most extreme case, ‘maybe it was designed, but not by who you think’.

  71. —–nullasalus: “Maybe we’re talking past each other. I’m not arguing that nothing an ID proponent (or an ID opponent) can propose as an experiment is scientific by my standard. “

    Perhaps, but we must establish what it is that you are calling a standard. To say that ID is or is not science is to say that it does not conform to whatever standard or definition of science we are talking about. So, you can’t logically say that science doesn’t meet your standard unless you disclose that standard. Or, are you saying that “falsifiability” is your sole standard?

    —–“Propose something which can be falsified, engage in research/testing, and I’ll say you’re doing science. Say you infer design based on what you’re seeing, and I may even agree with what you infer. But when you start talking about inferring design or a lack of design, that is when you’re no longer doing science by my view.”

    Are you saying that all logical inferences are philosophical and no logical inferences are scientific? Or, are you saying that a design inference can be scientific UNLESS it leads to “design?” How would you justify either assertion?

    Actually, my favorite comment on this subject comes from Dave Scot, who once asked a question something like this: If the Red Sea parted down the middle, could science legitimately TRY investigate the matter? I say yes. If you are going to say no, which I assume is the case, then your answer needs to be grounded in something, namely your definition of science and the scientific method.

    —–“So let me ask this: “The bacterial flagellum could/could not have come to be without design.” Is this, to you, a falsifiable statement?

    In this case, I think that you are imposing a philosophical formulation (“come to be”) on a scientific construct (falsifiability). Only a scientific construct can be scientifically falsified. On the other hand, the statement can be philosophically falsified by simply pointing out that something cannot come from nothing. The scientifically falsifiable statement is that the bacterial flagellum is “irreducibly complex.” That is why Behe devised the term—it has the requisite scientific dimensions. If, for example, Nick Matzke keeps plugging away and finds his evolutionary pathway to complexity, then “irreducible complexity” has been falsified. Such a discovery would confirm the fact that the bacterial flagellum is not irreducibly complex.

    Even so, I don’t accept falsifiability as a standard of science. I submit that science is exactly what I said it is:

    science: a branch of knowledge conducted on objective principles involving the systematized observation of and experiment with phenomena, esp. concerned with the material and functions of the physical universe.

    scientific method: principles and procedures for the systematic pursuit of knowledge [”the body of truth, information and principles acquired by mankind”] involving the recognition and formulation of a problem, the collection of data through observation and experiment, and the formulation and testing of hypotheses.

    Because I have offered my standard, I can reasonably claim that ID conforms to it.

  72. StephenB,

    “So, you can’t logically say that science doesn’t meet your standard unless you disclose that standard. Or, are you saying that “falsifiability” is your sole standard?”

    More or less. If someone has an idea that explains what we see in the world, but there’s no way to falsify it, that’s not the stuff of science by my view.

    “Are you saying that all logical inferences are philosophical and no logical inferences are scientific? Or, are you saying that a design inference can be scientific UNLESS it leads to “design?” How would you justify either assertion?”

    No, it’s back to falsifiability – and I don’t think design of the type ID explores can be subject to falsification (Remember, I’m not saying this about every idea an ID proponent advocates). And again, no, this holds true both for ‘design’ and ‘lack of design’ – I’m just as critical of the latter, moreso because I think it’s the established viewpoint, and those who hold said viewpoint while criticizing ID are hypocrites.

    “If, for example, Nick Matzke keeps plugging away and finds his evolutionary pathway to complexity, then “irreducible complexity” has been falsified. Such a discovery would confirm the fact that the bacterial flagellum is not irreducibly complex.”

    But the bacterial flagellum could still be the result of design even if such a pathway could be found. (And I notice that many ID opponents claim that such pathways HAVE been found. I’m not in the position to judge the arguments of either side, so I take a hands-off approach to this.)

    So in this case, I would hesitantly agree that ‘the bacterial flagellum is irreducibly complex’ is a falsifiable statement. While ‘the bacterial flagellum was/was not designed’ is not.

  73. —–nullasalus: “No, it’s back to falsifiability – and I don’t think design of the type ID explores can be subject to falsification (Remember, I’m not saying this about every idea an ID proponent advocates). And again, no, this holds true both for ‘design’ and ‘lack of design’ – I’m just as critical of the latter, moreso because I think it’s the established viewpoint, and those who hold said viewpoint while criticizing ID are hypocrites.”

    OK—no double standard. Fair enough.

    Let’s remember, though, that your standard for science is arbitrary. In effect, you are accepting a faddish and constricted definition, which you “more or less” subscribe to. That is an awful lot of equivocation. At the same time, you totally ignore my definition as if it doesn’t deserve a second look, even though it contains a lot more tradition, a lot more public support, a lot more information, and a lot more explanation than yours. Under the circumstances, I don’ think that you don’t have a very solid basis for challenging ID’s scientific status.

    —-“But the bacterial flagellum could still be the result of design even if such a pathway could be found.”

    No, not really. If the evolutionary process is completely autonomous and unassociated with an intelligent agency, which is what Matzke and the other Darwinists are proposing, then it cannot be designed. The whole point of their enterprise is to find a logical alternative to design and characterize its conception as an “illusion.” Of course, it is possible that an intelligent agency could design evolutionary pathways, but that would be intelligent design, the very thing that Darwinists have ruled out in principle.

    —–“So in this case, I would hesitantly agree that ‘the bacterial flagellum is irreducibly complex’ is a falsifiable statement.”While ‘the bacterial flagellum was/was not designed’ is not.

    If you falsify irreducible complexity, you falsify the design hypothesis. Put another way, if it is irreducibly complex, then it is reasonble to conclude that it was probably designed, since it is our experience that all things known to be irreducibly complex are also known to be designed.

  74. StephenB,

    “Let’s remember, though, that your standard for science is arbitrary.”

    If that’s your view, so be it. I’d be more interested in defending my view on science another time, but I’m glad at least we can agree I avoid double standards.

    “No, not really. If the evolutionary process is completely autonomous and unassociated with an intelligent agency, which is what Matzke and the other Darwinists are proposing, then it cannot be designed. The whole point of their enterprise is to find a logical alternative to design and characterize its conception as an “illusion.” Of course, it is possible that an intelligent agency could design evolutionary pathways, but that would be intelligent design, the very thing that Darwinists have ruled out in principle.”

    And the Darwinists step outside of science the moment they “rule it out in principle”, because they’ve now gotten into the wonderful and unfalsifiable world of philosophical and theological speculation. So I’d reject the classification of evolution as ‘completely autonomous and unassociated with intelligent agency’ as a scientific statement, and I stand by the view that whether or not the bacterial flagellum is IC, the question of design v no-design cannot be settled by science. I will admit that whether the bacterial flagellum is IC is a question which itself may be scientific, but those two declarations are distinct.

    “If you falsify irreducible complexity, you falsify the design hypothesis.”

    You falsify the design hypothesis with regards to a specific view and claim of design on the table. You do not falsify design/no-design as a live and (in the former’s case) very powerful argument philosophically. This is stepping into an area of science-abuse that I abhor – ‘If earth isn’t 6000 years old, there is no God!’ and ‘If evolution is true, there is no God!’ type challenges and lines in the sand that I see no reason to accept, and every reason to reject.

  75. —–nullasalus: “And the Darwinists step outside of science the moment they “rule it out in principle”, because they’ve now gotten into the wonderful and unfalsifiable world of philosophical and theological speculation. So I’d reject the classification of evolution as ‘completely autonomous and unassociated with intelligent agency’ as a scientific statement, and I stand by the view that whether or not the bacterial flagellum is IC, the question of design v no-design cannot be settled by science. I will admit that whether the bacterial flagellum is IC is a question which itself may be scientific, but those two declarations are distinct.”

    You seem to have forgotten the reason I brought it up in the first place. You stated as follows: —

    -“But the bacterial flagellum could still be the result of design even if such a pathway could be found.”

    No, in fact, it could not. There are only two options: evolution associated with intelligent agency (designed) and evolution unassociated with intelligent agency (not designed). A Darwinian pathway to complexity is totally incompatible with design because it is unassociated with intelligent agency.

    —–”I’d be more interested in defending my view on science another time, but I’m glad at least we can agree I avoid double standards.”

    Your view on science is the main point at issue. How one defines science determines whether one accepts ID as science. So, I will ask the relevant question again: If the Red Sea parted, could science legitimately try to investigate the matter?

  76. Patrick,

    Thank you for your extended answer. I greatly appreciate the effort, now I begin to understand the ID ideas better.

    I did not understand that ID accepts evolution as an important force, and that instances of design may be rare. In other words, when credible evolutionary models exist, they’re likely to be true, and when we don’t understand how things happened, that’s a sign of design.

    The only problem is that the examples you provide have, according to evolutionary theory, highly sensible explanations that are supported by evidence.

    The difficulties in phylogenetic analysis that you highlight are indeed very real; either inabilities to at all find reasonably supported evolutionary hypotheses, or the misleading problem that strong support can be obtained for incorrect hypothesis when large datasets are used. The limitations of our methods do not prove that trees don’t exist, however.

    I’ll explain the problems:

    1. Phylogenetic inference commonly uses of Markov rate matrices and make assumptions on, for example, time-reversibility, which are not always realistic. Different lineages can also experience different evolutionary rates (heterotachy). These issues can be problematic, especially at deeper phylogenetic levels where the phylogenetic signal is weak because of saturation effects. Biases can significantly influence the end result or you might not get any reliable result at all.

    2. Lateral gene flow will naturally influence phylogenetic relationships, simply because different genes will have different evolutionary histories.

    3. A phenomenon called lineage sorting can also result odd phylogenies for individual genes. This occurs when genes have been duplicated earlier in history and copies are differentially inherited in different lineages. Lineage sorting is a very real evolutionary process with tons of evidence to back it up.

    http://people.bu.edu/msoren/Maddison.pdf

    I would also be extremely surprised if lineage sorting could not explain all the oddities of the platypus. In fact, in figure 4 of the genome paper for this animal they provide an inheritance scheme for beta-defensin peptides which illustrate the effects of lineage sorting.

    http://www.nature.com/nature/j.....e06936.pdf

  77. StephenB,

    “You seem to have forgotten the reason I brought it up in the first place.”

    “No, in fact, it could not. There are only two options: evolution associated with intelligent agency (designed) and evolution unassociated with intelligent agency (not designed). A Darwinian pathway to complexity is totally incompatible with design because it is unassociated with intelligent agency.”

    And you’re forgetting my response: Science is not capable of ruling on design of this nature. Are you honestly, truly taking what amounts to a New Atheist scientism view here? ‘If science cannot demonstrate it, it did not happen, and is therefore false.’? If so, I vehemently disagree with you.

    So yes, there are only two options: Designed evolution, and not designed. And I say that whether evolution is design or not designed, especially when God is in the picture, is a question that science is incapable of answering in either direction.

    “Your view on science is the main point at issue. How one defines science determines whether one accepts ID as science. So, I will ask the relevant question again: If the Red Sea parted, could science legitimately try to investigate the matter?”

    I believe this was already asked of me, and I gave an answer. I’ll try to give another: It depends on the context. A claim that the Red Sea parted in conditions not ideal to observation (once, thousands of years ago, lacking in scientific detail)? Likely not, or not in any decisive way. In better conditions? Well, then it depends on the conditions. Could science propose mechanisms for parting the Red Sea in general? Sure, though that’s getting into questions of technology as well.

    Still: “If science cannot demonstrate it, it did not happen.” Is this your view?

  78. Short on time so I’ll only respond to this:

    In other words, when credible evolutionary models exist, they’re likely to be true, and when we don’t understand how things happened, that’s a sign of design.

    ID is not “we don’t know”. The positive case for ID is discussed in the books Dave mentioned as well as on Bill’s site http://www.designinference.com

  79. Nalluasalus: “Science is not capable of ruling on design of this nature. Are you honestly, truly taking what amounts to a New Atheist scientism view here? ‘If science cannot demonstrate it, it did not happen, and is therefore false.’? If so, I vehemently disagree with you.”

    No. I believe that more can be learned through non-scientific means than through science, and I certainly don’t subscribe to New Atheist scientism, inasmuch as I am an ID theist. That is not the issue. The point is that science is not needed to determine is something is logically impossible. You stated,-“But the bacterial flagellum could still be the result of design even if such a pathway could be found.” It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency. If a Darwinian pathway to an organism was found, then that organism could not have been designed. That is why finding one would falsify claims about “irreducible complexity” I press the issue not to be irksome, which I fear is happening, but because this is what all the fuss is about.

  80. “It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency.”

    Are you calling me stupid! When I ‘design’ something using a genetic algorithm then according to you I am not an intelligent agent.

    There’s a reason you’re getting ignored…a genetic algorithm requires intelligence’s involvement in order to function. Darwinian evolution is supposedly independent of intelligence. You yourself admitted in the past that genetic algorithm are limited and thus could not directly equate to biology in order for Darwinian evolution to work. You seem to believe there is some “unknown factor” which allows biology to exceed the limitations of GAs. – Admin

    Put another way – If the universe was designed by an intelligent agent such that life might (or would) evolve, then it is not really an intelligent agent.

  81. Nalluasalus: “Science is not capable of ruling on design of this nature.

    Do you believe that the science of archeology can detect design in an ancient hunter’s spear or from the writings on a caveman’s wall? Do you believe that science can be used to decipher hieroglyphic writing?

  82. —–”Put another way – If the universe was designed by an intelligent agent such that life might (or would) evolve, then it is not really an intelligent agent.”

    If the universe was designed by an intelligent agent such that life would evolve, then it is obviously an intelligent agent. What does that have to do with Darwinian mechanisms which, by definition, have nothing to do with an intelligent agent?

  83. “Do you believe that the science of archeology can detect design in an ancient hunter’s spear”

    We know human beings exist and that they manipulate the environment in ways that, so far, appear to be unlike anything else, so it is quite reasonable to use what we know about humans to detect their influence on objects we find. It doesn’t always work though, people still worship vaguely human looking stains or other naturally occurring simulacrum thinking they are intentional creations.

  84. StephenB,

    “It is not logically possible that a Darwinian pathway to evolution could be designed, because a Darwinian evolutionary pathway by definition is one that was not associated with an intelligent agency.”

    And I say, again, that insofar as ‘Darwinian evolution’ rules on the involvement of agency at that level, it is outside of science.

    Let’s assume the darwinist case for something, unwarranted as it may be. Let’s say Celltype-B. We know that Celltype-B evolved from Celltype-A from darwinian mechanisms – in this case, just mutations and natural selection (Let’s ignore neutral drift, etc for this case). We know with certainty this is what happened. Was Celltype-B therefore not designed?

    Many darwinists will say ‘Absolutely not. NS+M was sufficient for Celltype-B to come about.’ My response is: You cannot rule out front loading. You cannot rule out design of the very laws that allow NS+M to provide the result we know we see. If you assert mutation is random, at best you can assert “for all practical purposes random” which is tantamount to saying you are in the dark about what went on behind the involved mutations. It’s a statement of ignorance, and it has to remain so when you examine the mechanics deep enough, because you get to a question of, ultimately, determinism and indeterminism. Pleading the overall pattern fits a stochastic result doesn’t help because a single guided result in the pattern would poison the well.

    At best you can get to ‘Well, we don’t need to make an appeal to design. What happened happened, and the general development happens with enough regularity for us to rely on practically.’ And that’s true, for both design and a lack of design. Assume the universe just happened to spit out all the right laws and properties to give what we see without forethought. Assume that there’s fundamental ex nihilo randomness and indeterminacy at work in the world. Assume you’re seeing the work of a powerful deity who orchestrated all the laws and properties in advance. Assume the deity works constantly and subtly. Assume chance explains everything. You can reconcile all the views with the results. And therefore, you need not appeal to any of them for what you see – and the questions therefore are extraneous to the science.

  85. “…Darwinian mechanisms which, by definition, have nothing to do with an intelligent agent?”

    Fair point, so the flagellum could have evolved in exactly the way that EvoBiologists think it did, except that if the universe was designed for evolution to work then the theory of evolution is wrong, even though it works in exactly the way they describe…

    I wasn’t aware that the theory of evolution is an attempt to provide a naturalistic explanation for the origin of the universe.

    Darwinian mechanisms do not ‘by definition’ have nothing to do with an intelligent agent because the theory does not provide an explanation for how those mechanisms came to exist – if the universe was designed for evolution then Darwin was basically right, the mechanisms he proposed work.

  86. StephenB,

    “Do you believe that the science of archeology can detect design in an ancient hunter’s spear or from the writings on a caveman’s wall? Do you believe that science can be used to decipher hieroglyphic writing?”

    Really depends on the context. Perfect example: The Divje Babe flute. Is it a flute, or a chew toy? There’s disagreement. Is either claim scientific? I’m not sure, even though science may be used to investigate the matter. Though it doesn’t need to be science for speculation to be insightful and warranted.

  87. Though it doesn’t need to be science for speculation to be insightful and warranted.

    That’s right. We can detect design or figure out many things without science. On the other hand, science can tell us, among other things, about the probabilities involved. Example: The more words I write in this paragraph, the less the chance that the seemingly purposeful arrangement of letters occurred by chance. If you saw them written on the planet Mars, you would infer (without science) that they were formed with purpose, but you could also measure the likelihood that they were not (through science). As the functionally specified complex information grows in quantity, the probability that it was designed increases proportionally. Science can measure that probability– it can also detect the “effects” (not the “mechanism” or “process”) of design by the texture of the patterns, which, as it turns out, is always the same (FSCI).

    Again, if you see the letters, “SOS” written on the sand, you may suspect that the “message” was designed, but you also know that it may well not have been designed. In other words, the appearance of design can be misleading. There is a reasonable chance that natural forces could have carved it out; coincidences like that happen every day. Snowflakes and moon craters, for example, appear to be designed, but are not. (Something science tells us, by the way). Since there is very little complexity in the sequence “SOS,” or very little information, science can tell us that a design inference is not really warranted. As you have suggested many times, you don’t need science to draw the conclusion. On the other hand, science can also lead us to this same kind of conclusion and can also justify that conclusion by analyzing the evidence. Science can either confirm or disconfirm our intuitions about design.

  88. —–nullasalus: “Really depends on the context.Perfect example: The Divje Babe flute. Is it a flute, or a chew toy? There’s disagreement. Is either claim scientific? I’m not sure, even though science may be used to investigate the matter. Though it doesn’t need to be science for speculation to be insightful and warranted.”

    Sorry, but the difference between a flute and a toy is irrelevant. ID has no methodology to make those kinds of distinctions. Science can detect the presence of an intelligent agent in both cases. I don’t think you understand intelligent design at all, which may be why you question the science.

    In any case, the question was this: “Can archeology detect design in an ancient hunter’s spear? The question you answered (which wasn’t asked), was “can science detect design every time.” They are two radically different questions. While the answer to the second question is “no,” the answer to the first question is obviously, “yes.” By questioning the obvious fact that archeology can detect design, which it clearly can, you are, in effect, saying that it is not a science.

  89. StephenB,

    I think we’re winding down here now. We both agree important and real truths can be explored without resort to science. Therefore, we at least agree that there are some spheres – some important ones – where science cannot delve into.

    The problem for me is that God is unlike any other designer. A given design may be the work of God, but science cannot prove or disprove that (And I believe even ID proponents agree that speculating about identity is beyond the scope of ID.) When you say “Snowflakes and moon craters, for example, appear to be designed, but are not. (Something science tells us, by the way).”, I have to disagree. Instead, at best, we can rule out any designer for snowflakes and moon craters except for God, or frankly the God-equivalent. Oddly, I think I may be in the more orthodox ID position here – I could be wrong, though I do wonder if Behe and Dembski believe that, if a given thing is not IC, it is not designed by God. Or better yet, if a given IC structure is shown not to be IC, that it demonstrates the given thing was absolutely not designed. The more reasonable conclusion seems to be ‘It’s not demonstrating the threshold of design indicators necessary for us to scientifically infer design, but there may be non-scientific considerations.’

    In fact, I could possibly get behind such a view, with such a stipulation.

  90. —–“so the flagellum could have evolved in exactly the way that EvoBiologists think it did, except that if the universe was designed for evolution to work then the theory of evolution is wrong, even though it works in exactly the way they describe…

    The question is this: Was the evolutionary pathway to complexity thought out or was it not? EvoBiologists say that it was not thought out—it just happened. Intelligent design says that it was thought out. It cannot be both thought out and not thought out (unless you are a TE and believe that a thing can be true and false at the same time.) . One side must be right; one side must be wrong.

    —–I wasn’t aware that the theory of evolution is an attempt to provide a naturalistic explanation for the origin of the universe.

    It isn’t. But the questions always seem to come up anyway.

    —–“Darwinian mechanisms do not ‘by definition’ have nothing to do with an intelligent agent because the theory does not provide an explanation for how those mechanisms came to exist – if the universe was designed for evolution then Darwin was basically right, the mechanisms he proposed work.”

    Darwinian mechanisms have no room for an intelligent agent, because the process is said to operate solely by law and chance, meaning that no purpose, direction, or design can be considered. That is what all the fuss is about: ID–says-design is real, Darwin—says design is an illusion. ID says that an intelligent agent is the MOST LIKELY cause; Darwinism says that unaided naturalistic forces are DEFINITELY the cause. (Darwinists do not allow for the possibility that they could be wrong, which is actually one of their least offensive qualities)

  91. nullasalus: Yes, I agree. It is time to wind down and reflect. You last point is a meaningful one, and it does frame the issue nicely. Is God a different kind of designer? It’s a thoughtful question, and one rapid fire answer occurs to me: He seems to have created in a way that he intended to leave clues about his existence, just as is says in Romans 1: and just as all the great scientists of the past believed. We have been talking exclusively about science, but from a theological perspective, I would say this: If God’s revelation in Scripture is not consistent with God’s revelation in nature, then we don’t really live in a rational universe.

    Thanks for keeping your sense of humor through the sprited exchanges.

  92. StephenB,

    Fair enough. I actually agree with Romans 1, believe it or not. And I believe the design in the universe is abundant and evident. I simply do not believe that it is the kind which can be specifically tested for and falsifiable.

    Nevertheless, my pleasure, and thank you for the exchange.

  93. Hey guys, can you please cool it with all the God talk and bible quotes? I understand the TE invasion got your hackles up, mine too, but I gave the worst offenders the boot. Let’s get the conversation back on things that can be weighed and measured. Unless you can put the God of Abraham on a scale and tell me how much He weighs take it offline or move it to another forum. Thanks.

  94. “a genetic algorithm requires intelligence’s involvement in order to function. ”

    Yes, I was making a point about theistic evolution, but I’ll stop now because I don’t want to get banned.

  95. Dave: I get your point, here. This thread is primarily about the flagellum and measurement, and only secondarily about definitions of science, although the latter point is relevant. Also, I get it that creationists make us look bad by claiming affinity with ID while flooding cyberspace with extraneous theological references, and we don’t want anything like that on this site. That is why I enthusiastically contend that ID is real science and vociferously challenge those who deny that fact.

    On the other hand, when someone implies that ID isn’t science because [expletive deleted] is a different kind of designer, I can hardly meet that objection without making references to [expletive deleted].

  96. By the way, Timeuas fell into that same trap, following up on JK’s and TD’s theological references. That is why I think you should give him a reprieve. He is a neo-Platonist and doesn’t normally approach things that way.

  97. StephenB and DaveScot

    After some reflection…

    I also understand the point that this discussion is about flagellum, not definitions of science, and that this is not the forum for discussing unanswerable philosophical questions about creation. Totally fair enough but if I can beg a small indulgence I would just like to quickly clarify what I was trying to say (which is not really about TE)

    StephenB, you say “I get it that creationists make us look bad by claiming affinity with ID” Yes I agree but I would add that idiots like Dawkins also make biological evolution (the theory) look bad by trying to co-opt it into justifying their atheism when in reality it does not extend to providing a naturalistic explanation for the actual origin of life, or the universe.

    When I made the point about genetic algorithms I was trying to get across the idea that although the evolutionary mechanism its self does not (according to the theory) require intelligent intervention it also does not explicitly require the laws of nature that underpin it to have a naturalistic origin.

    Put it this way, if the evo biologists turn out to be right in that the evolutionary mechanism can account for the complexity of life as we see it then it does not follow that the entire universe was an accident – indeed it may still be possible to detect intelligent design at a different level, or even to detect some intention underlying the evolutionary mechanism.

    To sum up, when creationists claim ID supports their particular beliefs they are just as wrong as atheists claiming evolutionary theory to support theirs, or ID supporters claiming that evolutionary theory categorically excludes the possibility of any intelligence or ‘plan’.

  98. —–CGUGGreyArea: “Put it this way, if the evo biologists turn out to be right in that the evolutionary mechanism can account for the complexity of life as we see it then it does not follow that the entire universe was an accident – indeed it may still be possible to detect intelligent design at a different level, or even to detect some intention underlying the evolutionary mechanism.”

    I am not clear on this point or on how you are relating cosmology to biology. What does “design at a different level mean?” I don’t know how to interpret “intention underlying the evolutionary mechanism.” Does the “intention” influence the evolutionary process? If it does, then the program has been front loaded or guided in some way. That would mean it is not Darwinistic. If it does not influence the evolutionary process, then what is its point for being there?

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