Uncommon Descent Serving The Intelligent Design Community

Flagellum Evolution


Nick Matzke at Panda’s Thumb, what evidence is there that the type III secretion system appeared in nature before the flagellum? If the flagellum coopted the ttss then the ttss must predate the flagellum. The ttss mediates elaborate interactions with plant and animal hosts of the bacteria. The flagellum on the other hand is for locomotion, not parasitic or pathogenic relationships with more complex cells. The flagellum is useful absent more complex organisms in the environment while the ttss is not. It seems to me quite likely that the flagellum appeared in nature before the ttss. Probably billions of years before as the following supports:

J Mol Microbiol Biotechnol. 2000 Apr;2(2):125-44.

Phylogenetic analyses of the constituents of Type III protein secretion systems.

Nguyen L, Paulsen IT, Tchieu J, Hueck CJ, Saier MH Jr.

Department of Biology, University of California at San Diego, La Jolla 92093-0116, USA.

Multicomponent Type III protein secretion systems transfer gram-negative bacterial virulence factors directly from the bacterial cytoplasm to the cytoplasm of a host eukaryotic cell in a process that may involve a single energy-coupled step. Extensive evidence supports the conclusion that the genetic apparatuses that encode these systems have been acquired independently by different gram-negative bacteria, presumably by lateral transfer. In this paper we conduct phylogenetic analyses of currently sequenced constituents of these systems and their homologues. The results reveal the relative relatedness of these systems and show that they evolved with little or no exchange of constituents between systems. This fact suggests that horizontal transmission of the genes encoding these systems always occurred as a unit without the formation of hybrid gene clusters. Moreover, homologous flagellar proteins show phylogenetic clustering that suggests that the flagellar systems and Type III protein secretory systems diverged from each other following very early duplication of a gene cluster sharing many (but not all) genes. Phylogenies of most or all of the flagellar proteins follow those of the source organisms with little or no lateral gene transfer suggesting that homologous flagellar proteins are true orthologues. We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems.

Update: I found this paper by Scott Minnich and Stephen Meyer to be extremely helpful in understanding the relationship of the TTSS and the flagellum.

Thought Provoker just doesn't have the right spirit for our little community and won't be with us any longer. Fare thee well, Thought Provoker. DaveScot
The full abstract from the Matzke and Pollen article read:
In the recent Dover trial, and elsewhere, the 'Intelligent Design' movement has championed the bacterial flagellum as an irreducibly complex system that, it is claimed, could not have evolved through natural selection. Here we explore the arguments in favour of viewing bacterial flagella as evolved, rather than designed, entities. We dismiss the need for any great conceptual leaps in creating a model of flagellar evolution and speculate as to how an experimental programme focused on this topic might look.
I find that last sentence rather interesting. Without having read the full article (because I can't get it), the indication here seems to be that all this paper really does is attempt to "speculate" (interesting word choice in itself) on how research into the issue of flagellar evolution might look. In other words, this paper itself isn't presenting any actual lab results that would lead us closer to a detailed, testable model of how the flagellum evolved. Even more interesting, though, (if one reads between the lines), is the implication here that no such experimental programs have existed to date, or if they have, they have not been successful. That would seem to fly in the face of all the claims that the evolution of the flagellum is a problem long since solved by biologists. Indeed, I have often seen long lists of research studies posted on blogs and around the net that supposedly demonstrate the detailed, testable model of flagellar evolution. Apparently, either Matzke and Pollen are unaware of all these research studies, or all those oft cited studies really don't provide the model as claimed. If its the former, they are in good company as Behe himself was accused of not being aware of them when he wrote Darwin's Black Box. If the latter, then several biologists and other participants in internet disussions are grossly misinformed. Either way, though, the abstract seems to be a pretty strong indication that in the 10 years since Behe's book was published, evolutionary biologists have still not solved the riddle of flagellar evolution in Darwinian terms, nor has a detailed, testable (and potentially falsifiable) model been developed. Further, it seems to also be the case that there really hasn't been any detailed structure as to how a biologists would even go about conducting the experimental research, since this paper offers "speculations" as to how such research "might" go. To me, this looks like a frank admission that no one has a clue how the flagellum evolved, which is exactly what Behe claimed in his book, and for which he has endured 10 years of mocking and excoriation from Darwinists. Matzke and Pollen are to be congratulated for being honest enough to admit that Behe was right after all. DonaldM
trrll: No, the IDist argument is a pure argument from incredulity: No the IDists argument is one from knowldge: "We know what intelligent agencies are capable of coupled with the knowledge of what nature, operating freely, is capable of."
]“Thus, Behe concludes on the basis of our knowledge of present cause-and-effect relationships (in accord with the standard uniformitarian method employed in the historical sciences) that the molecular machines and complex systems we observe in cells can be best explained as the result of an intelligent cause. In brief, molecular motors appear designed because they were designed” Pg. 72 of "Darwinism, Design and Public Education"
It is the anti-IDists who argue from ignorance guided by dogma: "We don't know what mutations caused what changes and perhaps we never will but we know evolution did it." You can't even tell us what mutations caused what changes or whether or not mutations can cause the changes required if evolutionism were indicative of reality. IOW evolutionism is dogma based on ignorance. And again you display willful ignorance by stating the following: I cannot think of a selectable pathway by which this can have evolved; therefore none exists.” Again ID is not anti-evolution. And "selectable" is very subjective- selectable by what? Ya see alleged IC structures could have evolved by an ID mechanism similar to the mechanism in "Evolving Inventions" SciAm Feb 2003. And you could falsify that statement, as oposed to your continued whining, by demonstrating RM&NS can account for such structures. But I can understand why you would rather whine... Joseph
Ofro, Sorry, I cannot let you off so easily. The telephone thing of course I experience often enough, but for a person to walk in and answer something that she heard so clearly that she thought it had been spoken to her, and responded as such, only then to suddenly realize that what had just happened was impossible is quite something else. And at the same time, the younger daughter is shocked to find someone speak an exact answer to an exact thought that she had just had. There had been no tension before my daughter went out to the car. As soon as she did, my younger daughter apparently began the train of thought as in, "how convenient." Another time, same younger daughter was feeling upset and wanted to talk with an old family friend on the other coast and strongly thought that she wished she could talk with him. A day or so later he called, and he said, "The other day I was in the shower getting ready to go somewhere, and I heard someone telling me to call, and it sounded like your voice." avocationist
ofro: if you are not already bored by the topic, see my comment #23 on the "selfish gene" thread which has moved to the next page. avocationist: thank you for your kind words. I think you misjudge your own eloquence, though, which far exceeds mine. I have really enjoyed your exchanges with Carlos over on the other thread. Turtle down and all that! tinabrewer
"A big part of that argument is the claim that no subset of a structure could have been useful for any other purpose." That is the anti-IDists’ claim. IDists make no such claim
No, the IDist argument is a pure argument from incredulity: "I cannot think of a selectable pathway by which this can have evolved; therefore none exists." This is a remarkably broad claim—to be able in one's mind to imagine every conceivable pathway through the enormous multidimensional maze of possible mutational pathways, evaluate them for fitness, and conclude that no viable pathway exists. One bit of evidence, albeit somewhat weak evidence, that might be offered to support such an assertion would be if it could be shown that the components of the structure were so specifically adapted to this function that they could contribute to fitness in no other possible way. If this could be shown, it would certainly support the argument that the structure is IC. Lacking this, we are left with nothing at all other than the insistence of ID theorists that we trust in their ability to foresee every possible pathway. trrll
avocationist and tinabrewer: I agree with you, just about everybody had a similar experience that all of a sudden we thought of somebody or of something happening, good or bad, followed by just that happening. It has happened to me numerous times in the past few months that in just about the moment when I was going to dial my wife’s cellphone, she called me (and vice versa), or, just as I walked into my office, she called. That just begs the question; how come? Deep inside, we all would love to come to the conclusion that there was some physical/field/thought/spiritual/etc connection. But we have to ask ourselves seriously and honestly: how often did we have a similar thought, and nothing happened? This is very difficult for an untrained individual to answer accurately, and that is why I will not accuse anybody of lying about such an occurrence. Try it out on yourselves: whenever you come up with a random thought, make it a conscious effort to recognize it, “record it” so to speak, and see if anything actually happened as a consequence (mark that down again in your memory). I am confident that you will recognize soon that these random thoughts are not followed up by miraculous happenings, and the few mouth-dropping moments are chance events. Now, that is different from situations like my phone calls, since we happen to call each other fairly frequently, especially when it is time to go home together. And, avocationist, I am quite sure that your situation was a similar one; which youngster would not think about the chance of getting out of a chore, or worse, about her sibling trying to that? I may not even accuse a self-proclaimed psychic claiming to have a vision, although I admit I will be extremely suspicious. Just yesterday, on “The Infinity Mind” on Public Radio, a psychiatrist described a mentally disturbed person who became a pretty good “psychic” because he was able to put himself so well into the other person’s situation. My private decision about a person’s honesty will eventually depend on how far-going and how often such claims are made. We all agree that there are plenty of charlatans who lie and cheat in order to dominate somebody or get their money. As an aside, an amazing feature of our brain is that it can come up with all kinds of associations while it is churning in the background, and only some of these eventually surface as thoughts. Just as example for this surprising phenomenon: metabolic brain scanning studies have demonstrated that in anticipation of an action such as moving an arm, certain brain centers become active before the individual actually “knows” he/she made this decision. So while I have no objections to two people having the romantic notion of connecting mysteriously; it can be a sign of a personal bond that holds them together. However, from a scientific standpoint I can give it no credence. I agree, one should not call this supernatural. Or natural. It's just not there. Now I am really off-topic…. ofro
Tina, Everything is natural. its just that the material aspect of reality which we currently inhabit makes up a tiny fraction of the whole reality, As usual, you have explained very lucidly and logically what I express so poorly. I said almost this very thing on a thread yesterday. Your paragraph (post 56) explains why I keep insistig that there is no such thing as supernatural, while fully agreeing with Joseph that nature cannot cause itself. Ofro: One time I was shopping in a place where you pack your own groceries. Older daughter went to the car to fetch something just as I began to pack them with younger daughter. Younger daughter had some resentment, as she generally helped me greatly with projects while her sister always was busy. The car was visible, across the glass, but we could not see her and it was not in hearing range. Anyway, nobody spoke a word, because I stood there next to younger daughter. Suddenly, older sister burst in and answered her sister thus: "I am not trying to get out of work! I had to go to the car!" Both of their mouths dropped open, as they realized that she had responded to a thought, not a spoken word. And of course, younger sister was not making it up, as her jaw dropped as well, that she was thinking exactly that angry thought moments before. You might try looking up Ervin Lazslo "Science and the Akashic Field." And remember, I do not believe in supernatural. avocationist
Ofro: I don’t think you meant to address me with your reply (second time already). But I am honored to be confused with trrll. He is much more eloquent in his arguments than I. I hope he doesn’t mind. D'oh- My apologies to both I am so poor I can't even pay attention... Joseph
Joseph, I don't think you meant to address me with your reply (second time already). But I am honored to be confused with trrll. He is much more eloquent in his arguments than I. I hope he doesn't mind. ofro
Ofro: The argument that the flagella did not evolve is of course a classic argument from incredulity Again it isn't that it did not or could not "evolve". That I have to keep stating that just demonstrates a lack of caring for reality. Also without supporting data to say it could "evolve" via any method is faith, not science. And pointing to alleged homologs is not supporting data. Ofro: A big part of that argument is the claim that no subset of a structure could have been useful for any other purpose. That is the anti-IDists' claim. IDists make no such claim: Irreducible Complexity is an Obstacle to Darwinism Even if Parts of a System have other Functions From "No Free Lunch": IC- A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system. Numerous and Diverse Parts If the irreducible core of an IC system consists of one or only a few parts, there may be no insuperable obstacle to the Darwinian mechanism explaining how that system arose in one fell swoop. But as the number of indispensable well-fitted, mutually interacting,, non-arbitrarily individuated parts increases in number & diversity, there is no possibility of the Darwinian mechanism achieving that system in one fell swoop. Minimal Complexity and Function Given an IC system with numerous & diverse parts in its core, the Darwinian mechanism must produce it gradually. But if the system needs to operate at a certain minimal level of function before it can be of any use to the organism & if to achieve that level of function it requires a certain minimal level of complexity already possessed by the irreducible core, the Darwinian mechanism has no functional intermediates to exploit. I suggest you take a step back and actually try to learn about ID from IDists. Then enter the discussion. Joseph
The flagellum on the other hand is for locomotion, not parasitic or pathogenic relationships with more complex cells.
In evolution, a protein or structure is not really "for" anything. It is selected because it increases fitness, but the reason it increases fitness may vary from time to time. The argument that the flagella did not evolve is of course a classic argument from incredulity: "I can not envision any way in which the precursors of such a structure could be selectively advantageous, therefore no pathway exists." This is, of course, fundamentally a weak argument, because cells evolve in a "landscape" of a huge number of dimensions (degrees of freedom) and humans often have trouble finding their way around in just 3 dimensions. Indeed, even fairly simple genetic algorithms frequently discover solutions that humans are unable to find, and do so by pathways that cannot readily be reconstructed. Behe used to define as IC a structure that does not work if any part is removed. Unfortunately for Behe, this is a testable hypothesis, and a number of systems that he claimed to be IC were shown not to qualify by his definition. He has since modified the definition such that "An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations)." Since it is impossible at present (and in the foreseeable future) to test the selective value of every possible series of mutational steps in an evolutionary pathway, this is an untestable (and hence nonscientific) hypothesis. Essentially, Behe waves his hands, and says, "I think that there must have been an unselectable step in the evolution of this structure." A big part of that argument is the claim that no subset of a structure could have been useful for any other purpose. So the demonstration of secretory systems that use a set of proteins with homology to the flagella undermines Behe's argument whether or not those systems preceded or followed the flagella. While Matzke's case is a good one, it would not be surprising if the precursor to both the flagellum and TTSS served a different function from either. A recent review in science points out how vertebrate cells use a cilium (which in protozoa is used for locomotion) for sensory purposes. trrll
Thought Provoker: It looks like we are working our way to agreement. However, using an ID proponent’s definition for “evolution” is as unfair as using an evolution proponent’s definition for “Intelligent Design”. It isn't "an ID proponents definition for "evolution"". The book I took it from was reviewed by ID critics and anti-IDists. They even have several chapters in the book relating their position on ID. In a letter to Kansas signed by 38 Nobel Laureates we see the following:
"Logically derived from confirmable evidence, evolution is understood to be the result of an unguided, unplanned process of random variation and natural selection."
And then there is Richard Dawkins who gave us "the blind watchmaker". Thought Provoler: What if the experiment results in barely functioning flagellum that appear quickly through an unexpected process? I will spread my wings and fly away- just kidding. I would find it very interesting, as I would think anyone would. It may open up genetic engineering again (with few exceptions it (ge) appears to be a bust). Why start with the bac flag? Why not start by trying to get a TTSS to evolve in a population that didn't have one? It's like a work-out program- start light then start increasing the resistance. Joseph
To Joseph, It looks like we are working our way to agreement. However, using an ID proponent's definition for "evolution" is as unfair as using an evolution proponent's definition for "Intelligent Design". That being said... I find it informative that you agree there is at least some validity in an experiment that starts preloaded with T3SS and other flagellum components (unassembled). I find it disturbing if there is an expectation of immediate, concrete answers. This usually is a sign that one or both sides are trying to play to the populous instead of investigating the nuanced results typical of scientific experiments. If done well, this flagellum experiment would undoubtedly raise more questions than it would answer. Appropriately, people will question the significance and implications of the results. You foreshadow this with "it is cheating a little bit" and "getting a bac flag is useless if it doesn't function". What if the experiment results in barely functioning flagellum that appear quickly through an unexpected process? Ending on a positive note... thank you, Joseph, for the opportunity to explore this. It would also be interesting to hear from other people (both sides). Who sees the recent interest in the flagellum challenge as a good thing? Thought Provoker
tinabrewer: I know, we are probably getting into off-topic territory (sorry, everybody). To stay brief, I’ll just address your question about the notion of an information-bearing field. Any kind of information transfer between two entities requires either matter or energy. (I hope I am not stepping on too many physicists’ and engineers’ toes by going out of my expertise and commit errors). Easy examples are light (electromagnetic field) and sound (mechanical effects) since we can detect them with our own eyes and ears and we have instruments to measure them. For frequencies outside our own detectable range we have developed detectors. There are other physical means to transfer information, such as through pure electrical or magnetic fields, theoretically also by means of gravitational fields/forces, plus a few exotic ones derived from quantum physics. And that is about all that can be found in the physics books. I can’t think of any physical mechanism by which humans can transmit mental energies or thoughts. If there is such a capability of the brain, it has to be recorded by some physical instrument or through some other physical manifestation of its action before it is acceptable to science. So far every effort to demonstrate mental effects has failed miserably under closer scrutiny (such as making it reproducible). Sorry about being such a sober pedant. In turn, I am more than content just enjoying the beauty of nature using my built-in retinal and cochlear detectors, at times supplemented by a microscope or similar instrument. ofro
ofro: I also need to look at life from a logical perspective. To me, the "supernatural" doesn't exclude logic or defy it in any way. Everything is natural. its just that the material aspect of reality which we currently inhabit makes up a tiny fraction of the whole reality, and our tendency is to overvalue the sense impressions we recieve from matter and undervalue our inner perceptive capacity. What is undervalued is underused. What doesn't get used gets weak. Its very logical, and no different from the material to the spiritual. If I sit on the couch all day, am I going to be muscular and fit? No. If I do this for long enough, i may even begin to doubt that things like running and jumping are possible! Similarly, if I refuse to use my spiritual insight/intuition, and even deny its existence, then it makes perfect sense that this capacity will become weaker and weaker over time. I am glad you looked up the work of Sheldrake, but of course I disagree with your assertion that telepathy and extrasensory perception are hocus pocus. Although this was not the aspect of Sheldrake's ideas I was referring to, rather to the idea of 'morphic resonance', I think the ongoing controversy over these types of skills, which in my view are entirely natural and not at all mysterious, is a little like the controversy over ID vs. NDE. The skeptics and proponents are working from such totally different positions that mutual understanding is highly unlikely. I myself have frequently experienced quite striking pre-cognitive events. You could assume I am lying, but I know you are too kind to do that. So, the next best thing is to assume that some OTHER, more NATURAL (read: material) explanation must exist. I disagree, but am not at all invested in convincing anyone of this. Frankly, its just not interesting enough its so common. Anyway, I would like to ask you (although we'll probably get stopped for being so TOTALLY off-topic) why you so completely dismiss the idea of an information-bearing field? Why does this idea seem unnatural to you? Just because we cannot measure or see it? I would question that standard given the history of science alone. tinabrewer
Lack of experimental data for evolutionism: First I should start off by clarifying when I say evolutionism I am referring to evolution #6: The meanings of evolution, from "Darwinism, Design and Public Education": 1. Change over time; history of nature; any sequence of events in nature 2. Changes in the frequencies of alleles in the gene pool of a population 3. Limited common descent: the idea that particular groups of organisms have descended from a common ancestor. 4. The mechanisms responsible for the change required to produce limited descent with modification, chiefly natural selection acting on random variations or mutations. 5. Universal common descent: the idea that all organisms have descended from a single common ancestor. 6. “Blind watchmaker” thesis: the idea that all organisms have descended from common ancestors solely through an unguided, unintelligent, purposeless, material processes such as natural selection acting on random variations or mutations; that the mechanisms of natural selection, random variation and mutation, and perhaps other similarly naturalistic mechanisms, are completely sufficient to account for the appearance of design in living organisms. Is there any experimental data that demonstrates that a population of bacteria can "evolve" into anything but bacteria? No. Is there any experimental data that demonstrates that a population of inverts can "evolve" into a population of verts? No My point about Dr Behe's proposed experiment is that it should have been started years ago. Why should evolutionists run the experiment? Because it would refute an ID icon but more importantly it would substantiate THEIR claims. Now if Dr Behe went into a lab and genetically engineered a bac flag would that confirm ID? No. In Dr Behe's words:
If I conducted such an experiment and no flagellum were evolved, what Darwinist would believe me? What Darwinist would take that as evidence for my claims that Darwinism is wrong and ID is right? As I testified to the Court, Kenneth Miller claimed there was experimental evidence showing that complex biochemical systems could evolve by random mutation and natural selection, and he pointed to the work of Barry Hall on the lac operon. I explained in great detail to the Court why Miller was exaggerating, was incorrect, and made claims that Barry Hall himself never did. However, no Darwinist I am aware of subsequently took Hall’s experiments as evidence against Darwinism. Neither did the Court mention it in its opinion. The flagellum experiment the Court described above is one that, if successful, would strongly affirm Darwinian claims, and so should have been attempted long ago by one or more of the many, many adherents of Darwinism in the scientific community. That none of them has tried such an experiment, and that similar experiments that were tried on other molecular systems have failed, should count heavily against their theory.
Thought Provoker: How about an experiment that starts with all the building blocks including a fully functional T3SS to see if this evolves into an \”irreducibly complex\” flagellum? That would work, even though it is a cheating a little bit. It would work because the assembly instructions are at least just as IC as the structure. Then there is the communication link that controls the structure- IOW just getting a bac flag is useless if it does not function. Thought Provoker: From my view of the world, it looks like the flagellum challenge has been accepted and is being worked. And that is a good thing. And in the words of Dr Behe:
In pointing out that not much research has been done on the Darwinian evolution of irreducibly complex biochemical systems I should emphasize that I do not prefer it that way. I would sincerely welcome more research (especially experimental research, such as done by Barry Hall--see my discussion of Hall's work in the essay on the "acid test" at this web site) into the supposed Darwinian origins of the complex systems I described in my book. I fully expect that, as in the field of origin-of-life studies, the more we know, the more difficult the problem will be recognized to be.
Ya see every time we take a closer look the better ID looks... Joseph
To Joseph, Thank you for your reasoned response. I will attempt to return the favor. First, I find it difficult to accept the statement \"Evolutionism is pretty much void of experimental data...\". What are your criteria for this statement? How are you dismissing all the experiments performed with fruit flies, E. coli, etc? Let me respectfully suggest there is a significant amount of experimental data that is pertinent to evolution, even if you feel the bulk of this data is irrelevant. Your presumption there are labs already set up to run Behe\'s evolution experiment belies the idea of a field that is \"pretty much void\" of experimentation. IMO, the suggestion that it would be meaningless for Behe to run his own experiment is only partially correct. If Behe were to run the experiment and document the results, the burden of proof would shift to the evolutionists. They would have to explain why the experiment didn\'t show what Behe claimed it did or rerun the experiment themselves to show, if done correctly, you get the expected results. This brings us to why scientists aren\'t just performing Behe\'s experiment. Why should they? Behe is convinced of experiment\'s significance, not them. However, I think we are getting to the point that an experiment with flagellum will be performed soon, but probably not the one Behe suggested. Once people like Pallen and Matzke formulate a detailed hypothesis, there will be motivation for testing it. How about an experiment that starts with all the building blocks including a fully functional T3SS to see if this evolves into an \"irreducibly complex\" flagellum? From my view of the world, it looks like the flagellum challenge has been accepted and is being worked. For those that don\'t like the direction the research is taking, I suggest they hurry up and perform their own research and experiments. We would all benefit from the knowledge. Thought Provoker
To Thought Provoker, I know I shouldn't speak for Scott but my impression (inference) of what he said was that the time for "talking" is over. And if they really want to refute ID they should do so experimentally. Dr Behe provided a possible experiment that would, if successful, refute an icon of ID (the bac flag) and at the same time substantiate their claims. However they not only refused to do such an experiment but turned it around as if IDists should be conducting it! Right- who would believe Dr Behe if he did that experiment and a bac flag did not "evolve"? That is the crux of the matter. Evolutionism is pretty much void of experimental data largely due to (alleged) time constraints. So in its place they take a little variation and just add eons of time. IOW "sheer-dumb-luck" plus father time can accomplish amazing things. Interesting but hardly scientific. All that said your point is what needs to be emphasized- that being open discussions- challenges met and challenges failed- regardless but do so in the hopes of finding the reality to our existence. Joseph
"We should all be eager for “actual molecular biologist[s]” to study and discuss evidence of the natural process that lead to the flagellum." From what I gather, Pallen is fairly respected, well published, and has a wealth of knowledge in bioinformatics and genomics. The only thing he has in common with Matzke is simply a love for Darwinism (He was the host of "Darwin Day" at the University of Birmingham). I am curious to see Pallen's take on the matter, and to see if he has anything new to add. chunkdz
Scott wrote... "C’mon folks, why are we even still discussing the rediculous [sic] notion that the flagellum could have come about via Darwinian mechanisms?" The reason this subject is of interest because it is something scientifically tangible. It provides an opportunity to explore the predictive nature of both ID and evolution. More importantly debating this topic helps inform and define what is meant by the term "Intelligent Design" by various proponents. At its core, the flagellum embodies the concept that if it looks designed it probably is. It also presents the challenge/opportunity to evolution proponents to hypothesize how this came about naturally. Why should anyone be surprised when evolution proponents start making predictions about the origin of the flagellum and testing those predictions? In my opinion debating this is both very topical and constructive (as opposed to arguing about who is and isn’t a true Christian). I read with interest Joseph's comments (even checked out his blog). This is an example of the positive aspects in discussing this. I can understand the position that the existence of the flagellum isn't "anti-evolution" is designed the same way that the earth/moon system is designed. They both came about via natural processes but, if I understand correctly, Joseph and other ID proponents are arguing that it is unlikely, if not impossible, that either came about from “sheer-dumb-luck”. Unless ID wants to remain a simple variant of a “God in the gaps” argument, its proponents need to encourage discovery and discussion. We should all be eager for “actual molecular biologist[s]” to study and discuss evidence of the natural process that lead to the flagellum. This, of course, might be problematic for those whose real agenda is the promotion of the supernatural. Thought Provoker
Scott: C’mon folks, why are we even still discussing the rediculous notion that the flagellum could have come about via Darwinian mechanisms? Mick Natzke’s homology/co-option canard has been demolished numerous times and in numerous places. Nick's point, this time, is to show there are much more what he calls homologous proteins than the 10 in the TTSS. However his use of "homology" is very questionable. However I agree with chunkdz: Cant wait to hear from some actual molecular biologists on this. Joseph
DaveScot: There are definitely predictions made by common descent. The biggie is that all life shares a common genetic code. That's funny because common design would also predict a common genetic code. DaveScot: That’s not to say other hypotheses can’t predict the same thing but none of the alternatives that I’ve seen have the evidentiary weight behind them that common descent does. Seeing that we don't know what makes an organism what it is it is pretty clear that CD doesn't have any evidentiary weight except to assume CD and then set out to find what someone considers as confirming data.
First, evolution does not predict that life would arise precisely once on this planet. If there were two or more unrelated systems of life, then evolutionary theory would effortlessly accommodate that situation.[3] Second, even if life originated precisely once, then evolutionary theory would still not predict biologic universals. Shortly after life’s origin, nothing prevented life from branching and leading separate lineages to higher life forms entirely lacking the known biologic universals. Third, evolutionary loss and replacement processes could prevent biologic universals. If one organism is a distant ancestor to another, then nothing in evolution predicts the two must share similarities. If evolution were true, then distant ancestors and descendants (as well as sister groups) can be totally different. Evolution never did predict biologic universals, it merely accommodated them. (ReMine, 92-93.)
There is yet another reason that the universality of the genetic code is not strong evidence for evolution. Simply put, the theory of evolution does not predict the genetic code to be universal (it does not, for that matter, predict the genetic code at all). In fact, leading evolutionists such as Francis Crick and Leslie Orgel are surprised that there aren’t multiple codes in nature. Consider how evolutionists would react if there were in fact multiple codes in nature. What if plants, animals, and bacteria all had different codes? Such a finding would not falsify evolution; rather, it would be incorporated into the theory. For if the code is arbitrary, why should there be just one? The blind process of evolution would explain why there are multiple codes. In fact, in 1979 certain minor variations in the code were found, and evolutionists believe, not surprisingly, that the variations were caused by the continuing evolution of the universal genetic code. Of course, it would not be a problem for such an explanation to be extended if it were the case that there were multiple codes. There is nothing wrong with a theory that is comfortable with different outcomes, but there is something wrong when one of those outcomes is then claimed as supporting evidence. If a theory can predict both A and not-A, then neither A nor not-A can be used as evidence for the theory. When it comes to the genetic code, evolution can accommodate a range of findings, but it cannot then use one of those findings as supporting evidence. (Hunter, 38.)
------------------------------------------------------------------------------------- chunkdz: Haven’t read the most recent paper, but Matzke’s argument seems to hinge on homology. Homology as defined by Matzke and Pallen that is. Is there any other kind? ;) Joseph
Casey, "With regards to the flagellum at least 2/3 of the parts are not known to be shared with any other structure therefore might not be even a sub-part of another system at all." -Casey Luskin (2006). “Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum.” Evolution News & Views. April 19, 2006. This and several other quotes bring Matzke to the blanket conclusion: "Summary: All the IDists think that 3/4 of the flagellum proteins are “unique”, i.e. do not share homologies with other proteins. All they are aware of is the homologies to T3SS, which they usually mention while rebutting Kenneth Miller. Casey Luskin, a late example, cuts the number to 2/3, probably because he is dimly aware that there are some other homologous proteins out there, perhaps because several of us ID skeptics have been mentioning this point repeatedly for several years." Haven't read the most recent paper, but Matzke's argument seems to hinge on homology. Homology as defined by Matzke and Pallen that is. Structural similarity and "easily postulated" ancestral use seems to qualify. chunkdz
DaveScot “It appears to me the best explanation is that the LUCA had a complex genome designed to evolve into myriad different forms.” (For the more casual reader: LUCA stands for “last universal common ancestor”; I had to look it up myself, too). The problem I have with this concept is that I don’t see an accounting of the amount of starting DNA that is presumably necessary to enable this extensive radiation into the many past and existing life forms. After all, if I understand this scheme correctly, the mutations are more or less directed, so information must also be stored about the genetic responses to all possible different environments that might occur on earth, then and in the future. One possibility is that all that information still exists in all life forms, and with the proper conditions and given enough time, each of them could mutate into a any other form that is pre-programmed in LUCA’s database. We can safely eliminate this possibility since there are bacteria with a near-minimal gene set and other species with an amazingly large genome. So there must be at least some instances where genomic information was lost during evolution into another species. In fact, the genomes in the different phyla appear so different that it is unlikely that there would ever be an interconversion of body plans by mutation. In terms of accounting, I don’t know how to fit your scheme to the observation that the genome size varies so greatly among different species. Would you see a correlation between genome size and “evolvability”? Let’s go to a specific case that I had mentioned previously without getting a response. According to several good lines of evidence, the cetaceans and artiodactyls have common ancestry. Here we have a case where a species that became specialized to live and move on solid ground eventually mutated into animals specialized to live in the three-dimensional world of water. According to your scheme, there should be no problem for LUCA eventually evolving into the land-dweller. A lot of LUCA’s complex genomic was probably lost along the way, i.e. the database of possible genetic features to respond to future environmental eventualities most have been reduced. But now the artiodactyl undergoes another drastic shift into a different environment. That required a considerably different set of instructions to get to this point. So perhaps one of my starting assumptions about your scheme is wrong. You probably accept RN&NS to a certain extent, but it seems to me that you are placing a limit somewhere short of mainstream evolutionary schemes. Either way, according to your scheme there still must be a lot of genetic information left in us mammals that we haven’t even started thinking about yet. ofro
C'mon folks, why are we even still discussing the rediculous notion that the flagellum could have come about via Darwinian mechanisms? Mick Natzke's homology/co-option canard has been demolished numerous times and in numerous places. Here are few of them: http://www.discovery.org/scripts/viewDB/filesDB-download.php?id=389 http://www.arn.org/docs2/news/wd_still_spinning.htm http://www.designinference.com/documents/2004.01.Irred_Compl_Revisited.pdf Scott
DaveScot, you are commenting on a response to tinabrewer that I made a while ago but that hasn't shown up yet. Is the spam filter staring to zero in on me? ofro
Joseph There are definitely predictions made by common descent. The biggie is that all life shares a common genetic code. We've only confirmed this with a tiny fraction of the life on this planet so in principle it's a falsifiable prediction - i.e. an organism is found with a drastically different genetic code. There are very few biologists who won't confidently predict that all life shares that code. That's not to say other hypotheses can't predict the same thing but none of the alternatives that I've seen have the evidentiary weight behind them that common descent does. There's an as yet unbroken law in biology that living things only come from other living things. It's the weight of that law that makes me reject abiogenesis without extraordinarily strong evidence showing that it's possible and plausible and that also causes me to reject alternatives to common descent. DaveScot
ofro writes My mind needs to see a natural, logical structure in a phenomenon, and supernatural phenomena are foreign to that logic. Mine too! What about design do you think must be supernatural? I look at living things from an engineering point of view and I don't see anything about it that requires a designer to have supernatural powers. It's just chemistry and intelligent agents, as demonstrated by us, have the ability to accomplish things with chemistry that would never otherwise happen. Do you think humans are supernatural? I don't. Artificial is what I call it, not supernatural. DaveScot
tinabrewer: I appreciate your comments. I have been enjoying your posts and their kind and moderate tone. They are refreshing among the brashness that abounds (could that be testosterone-related?), even if I don’t necessarily agree with everything you post. My mind needs to see a natural, logical structure in a phenomenon, and supernatural phenomena are foreign to that logic. Philosophical aspects of life are reserved to the contemplation time window between putting my head on the pillow and falling asleep, and they are kept separate from natural science. In my mind, what the ID folks here need is a constant reminder (sometimes a sledgehammer seems inadequate) of their tendency to over-interpret a scientific observation and to call for (what appear to me are) supernatural explanations when they are not necessary. The current thread “How Random is Random Mutation” is an excellent case in point. I looked up Rupert Sheldrake, and what I read made me cringe (sorry about that). Some of that stuff he talks about, like telepathy or the feeling of being observed, is total hocus pocus that has never withstood any scientifically controlled test. So while it would be really cool to transfer our morphic fields onto other people (just imagine a telepathic blog site without having to sit in front of a computer screen), there is absolutely no evidence for that. I prefer being totally enthralled by all the (nearly) incredible intricateness and apparent ingenuity of nature and enjoying our mental capacity to recognize it and try to figure out how it works. ofro
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