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Author
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Topic: What ID Proof Must Look Like.
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Pim van Meurs
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Member # 541
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posted 04. April 2004 18:39
Scott, good questions. My claim is that bacterial mutations are not 'forward looking' nor that when mutations arise they are preferentially beneficial to the environment.
Two examples:
1. Luria and Delbruck showed that mutations pre-existed in the genome. But until they introduced a new challenge these variations seemed to not be selective. You ask if these mutations were pre-existing and that the non-resistant bacteria somehow mutated. Again this seems an interesting but for the discussion irrelevant scenario. In the alternative scenario mutations were neutral and given the presence of the 'threat' they became detrimental.
2. Adaptive mutations. For a while researchers thought that particular mutations arose preferentially in response to a challenge. Later it was established that mutation rates increased in response to the challenge, allowing the bacteria to explore possible solutions. But in the end it was random mutations and selection that led to the 'solution'.
A good indepth intro to Luria and Delbruck
Cairns argued that Luria and Delbruck do not rule out the existence of non-random mutations and he performed the first experiments that suggested adaptive mutations.
The presence of neutrality in the genetic code however is an important contributor to two opposite factors: robustness to mutations and evolvability.
Due to the neutral nature of most mutations, the genotype can explore phenotypic space and it has been found that most protein/RNA structures are close in this neutral space, that is only a few non random mutations are needed to reach another protein RNA structure. The scale free nature of genetic networks combined with the neutrality of mutations (or perhaps they are cause and effect?) results in a remarkable evolvability of the genome. This neutrality may also explain the observed phenotypical stasis followed by rapid changes.
If the claim is that the mutations are non random wrt future challenges then one needs to explain how the genome knows about these challenges? If the claim is that the genome is 'prepared' for future challenges then it is hard to claim that mutations happen preferentially for future challenges. Especially when these future challenges for all practical purposes are unpredictable.
[ 04. April 2004, 18:49: Message edited by: Pim van Meurs ]
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zenheadache
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posted 04. April 2004 22:24
1.
Pim: As far as Zen's attempt to 'prove' design, it seems that he is rejecting that science is tentative...
Not at all. I understand and appreciate the tentativeness of the scientific approach. But there are plenty of scientists who talk about the tentativeness only when called on the carpet, and who make claims of far greater confidence when not challenged.
Pim: ...but despite pointing out that we may not understand the mechanisms of mutations which therefor make it appear random, the same may apply to his approach namely the interpretation of useless.
Again, I disagree. The uselessness of a part MAY be defined by observing or inferring its uselessness ALONE, but NOT in conjunction with other parts which contribute to some functioning irreducibly complex molecular machine. The flagella’s rotor, by itself, could perhaps be demonstrably useless, but conjoined to a stator and flagella, it suddenly has a use.
Pim: Perhaps useless is defined best by 'that which we do not understand yet'? Any conclusions based on such ignorance should be made carefully. Certainly proof seems to be too strong a concept here.
This would have to be decided by the nature of any future discoveries, and the confidence we have in what can be inferred from them. But, given the appropriate discovery, i.e, one that fits my assembly line model, we may “tentatively” have a great deal of confidence in design that could be called “proof.”
2.
Zen: There is no evidentiary or purely logical reason why we must accept the pre-experimentally mutated bacteria which survived as examples of random mutation AT ALL.
Pim: Of course not, we can always posit an intelligence which saw these experiments coming. But that is not much of a scientific explanation really. So is it a false disjunction that Luria's experiments had two options only?
IF there is a designer, THEN it is a false disjunction if the choices do not include that possibility. What I think you are heading toward is a form of argumentum ad ignorantium, i.e., that because we do not know x, x should be excluded from the list of possibilities. Of course if we do that, then we should also exclude random mutation on the same grounds, for the reasons I have already given.
Pim: Perhaps Zen can help us understand what the evidence of intelligence is in this experiment? A scientific approach or a philosophical approach?
The evidence of intelligence in the experiment is the same evidence of intelligence on the factory assembly line. To observe parts coallescing either within a single organism, or through several different organisms, which have no immediate function, and which then suddenly GET one by some final part falling into place is EXACTLY the same as watching a car being built by robots in an automotive factory where it is then driven out the door by a worker.
As for whether this is a scientific approach or a philosophical approach, it is actually both. Science is a species of philosophy, one that might require an evolution in its basic premises in order to fully explain the world. But I really don’t want to go too far off on a tangent here.
3.
Zen: What is assumed to be random in this experiment fits perfectly what we would expect to find if evolution is being guided by intelligence.
Pim: Why? Seems a bit ad hoc to me. Are you saying that intelligent guidance can predict the future?
What I am saying is that intelligence predicts the future and DESIGNS responses to it BEFORE the future arrives. This is no great mystery. It is what we ALL do every day in our own lives. In recent years there has been great concern about future asteroid impacts, and we now have in place a good number of people that we did not have before whose job it is to look for these things, hopefully to find them far enough in advance that we shall have enough time to deflect that rare LARGE one on a bullseye path to earth. The fact that we are now standing watch has produced many news reports on misses and near misses lately, you may have noticed. That is due mostly to the fact that we are looking for them much more earnestly now than before, and finding ones we were ingorant of before we came awake to the dangers. This is intelligence in action. We are seeing , not what IS, but what MIGHT BE, and DESIGNING responses to it in advance.
4.
Zen: Therefore, contrary to what is claimed, the question I asked remains unanswered: Is it really random, or does it simply look that way to us? unfortunately, the experiment cannot answer the question.
Pim: What it can answer is that these mutations appear to be random and that such is well explainable scientifically.
This is an Occam’s Razor type argument. And what I have to say about that is this: The set of facts which explains a thing will always be the simplest in REALITY, but not necessarily the simplest in our understanding. In other words, it may well be that X can be explained well scientifically, but this does not mean the explanation is correct. It does not follow that the simplest explanation is the correct one, because the reality may be more complex than our understanding, for which our understanding is merely a simplistic reflection. The simplicity of an explanation is not enough to prove a theory correct.
I am not sure if there is a textbook fallacy called the argument from simplicity, but there should be if not.
5.
Zen: Anticipation is an indication of intelligent design.
Pim: Yes, these smart bacteria surely saw Luria and Delbruck's experiments coming :-)
Very funny, but I’m sure you know that’s not what I meant :-)
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Rex Kerr
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posted 04. April 2004 23:22
If there is some intelligence that mutates bacteriophage resistance genes in bacteria whose descendants will be placed on bacteriophage at some point in the future, at a constant rate, independent of the time into the future, then I am happy to call the product of that intelligence "random".
The success of the Luria-Delbruck experiment relies on the fact that mutation rate is constant across generations.
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Argon
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Member # 276
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posted 05. April 2004 12:42
I think it is interesting that the addition of chemical mutagens or treatment with ionizing radiation would appear to make the bacteria more 'intelligent', w.r.t. the increasing the likelihood that a strain would acquire mutations for resistance to bacteriophages and streptomycin. I can imagine the little 'bugs' thinking: "Hmm... I just got blasted with some alpha particles, maybe the intelligent response would be to develop resistance to a specific antibiotic."
![[Wink]](wink.gif)
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Pim van Meurs
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Member # 541
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posted 05. April 2004 14:20
quote:
Pim: As far as Zen's attempt to 'prove' design, it seems that he is rejecting that science is tentative...
Zen: Not at all. I understand and appreciate the tentativeness of the scientific approach. But there are plenty of scientists who talk about the tentativeness only when called on the carpet, and who make claims of far greater confidence when not challenged.
I have found little evidence for these claims but perhaps I am hanging out with the 'wrong' crowd?
quote:
Pim: ...but despite pointing out that we may not understand the mechanisms of mutations which therefor make it appear random, the same may apply to his approach namely the interpretation of useless.
Zen: Again, I disagree. The uselessness of a part MAY be defined by observing or inferring its uselessness ALONE, but NOT in conjunction with other parts which contribute to some functioning irreducibly complex molecular machine. The flagella’s rotor, by itself, could perhaps be demonstrably useless, but conjoined to a stator and flagella, it suddenly has a use.
Zen misses the point. Uselessness is infered from our ignorance of function but that does not mean that there is NO function, even by itself. In other words interpretation of usefulness is fraught with the same problems.
quote:
Pim: Perhaps useless is defined best by 'that which we do not understand yet'? Any conclusions based on such ignorance should be made carefully. Certainly proof seems to be too strong a concept here.
Zen: This would have to be decided by the nature of any future discoveries, and the confidence we have in what can be inferred from them. But, given the appropriate discovery, i.e, one that fits my assembly line model, we may “tentatively” have a great deal of confidence in design that could be called “proof.”
Seems to me that Zen has an innovative definition of the term proof. Since science rarely deals in proof, I find the claim that our ignoranc may be proof of something rather elucidating.
quote:
Zen: There is no evidentiary or purely logical reason why we must accept the pre-experimentally mutated bacteria which survived as examples of random mutation AT ALL.
Pim: Of course not, we can always posit an intelligence which saw these experiments coming. But that is not much of a scientific explanation really. So is it a false disjunction that Luria's experiments had two options only?
Zen: IF there is a designer, THEN it is a false disjunction if the choices do not include that possibility. What I think you are heading toward is a form of argumentum ad ignorantium, i.e., that because we do not know x, x should be excluded from the list of possibilities. Of course if we do that, then we should also exclude random mutation on the same grounds, for the reasons I have already given.
Even if there were a designer, it is not a false disjunction for logical reasons. I find it also interesting that Zen raises the argument ad ignorantium here but fails to apply it correcly to his own argument about usefulness or lack thereof. Luria's experiments showed that variation was pre-existing, the logical interpretation is that this variation is 'random wrt immediate fitness'. That it may be non-random wrt future fitness is irrelevant. Zen suggests that it was an intelligence that caused these variations, but so far this is an appeal to lack of evidence to support such a claim. Not that I am denying the possibility just pointing out that if Zen is arguing that mutations in the past were made knowing the future that Zen seems to have a special form of intelligence in mind which precludes a scientific interpretation.
quote:
Pim: Perhaps Zen can help us understand what the evidence of intelligence is in this experiment? A scientific approach or a philosophical approach?
Zen: The evidence of intelligence in the experiment is the same evidence of intelligence on the factory assembly line.
Sort of like an egg growing into a full organism? Seems intelligence becomes a little meaningless under such a definition. Since Zen was suggesting that this 'intelligence' was aware of future challenges/needs, I would be interested in what kind of intelligence can foresee the future?
quote:
Zen: What is assumed to be random in this experiment fits perfectly what we would expect to find if evolution is being guided by intelligence.
Pim: Why? Seems a bit ad hoc to me. Are you saying that intelligent guidance can predict the future?
Zen:What I am saying is that intelligence predicts the future and DESIGNS responses to it BEFORE the future arrives.
So intelligence forsaw the Luria experiments? Fascinating. A bit ad hoc but it does give me a better understanding as to what kind of intelligence Zen has in mind.
quote:
Zen: Anticipation is an indication of intelligent design.
Pim: Yes, these smart bacteria surely saw Luria and Delbruck's experiments coming :-)
Very funny, but I’m sure you know that’s not what I meant :-)
What else could you have meant then? You suggested that the mutations were intelligently designed, but for what?
Perhaps it's time to discuss a recent paper by Caporale?
NATURAL SELECTION AND THE EMERGENCE OF AMUTATION PHENOTYPE: An Update of the Evolutionary Synthesis Considering Mechanisms that Affect Genome Variation Annu. Rev. Microbiol. 2003. 57:467–85
quote:
Yet intrinsic variations in the physical-chemical properties of the DNA sequence context, and its interactions with polymerase, proofreading, repair, and recombination machinery, alter the probability of distinct types of mutation along a DNA sequence. Darwin “called [the] principle, by which each slight variation, if useful, is preserved, by the term Natural Selection” and asked “why should we doubt that variations in any way useful to beings ... would be preserved, accumulated, and inherited?” (26). Variations in the probability of mutation along a genome can be
“in any way useful to beings” and thus “preserved, accumulated, and inherited.”
this leads Caporale to suggest that
quote:
34). If the challenges that confronted genomes were unprecedented and completely random, it would be hard to disagree with the statement that selection “lacks foresight.” However, to the extent that classes of challenges and opportunities tend to recur, a response that is better than random can be favored by selection (17, 18, 88). Examples of recurring challenges include host/pathogen battles, access to valuable information encoded by other genomes, and the evolution of new members of gene families.
While this of course does not preclude 'intelligent design', it seems that nature itself may be 'intelligent' enough where mutations themselve evolve.
As Caporale puts it so well
quote:
The research reviewed here leads to the conclusion that, under the pressure of natural selection, a “mutation phenotype” evolves in which, first, certain classes of mutation are more probable than others and, second, some of the more probable classes of mutation can have an increased probability of being useful, or at least
not harmful, compared with completely random mutation (15, 18). (This is not the same as suggesting that a genome “knows” that it if it replaces a particular A with a G, it will be able to digest a specific sugar.)
[ 05. April 2004, 14:28: Message edited by: Pim van Meurs ]
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zenheadache
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posted 05. April 2004 19:41
Pim: I have found little evidence for these claims but perhaps I am hanging out with the 'wrong' crowd?
Is that an anecdote?
Zen: Again, I disagree. The uselessness of a part MAY be defined by observing or inferring its uselessness ALONE, but NOT in conjunction with other parts which contribute to some functioning irreducibly complex molecular machine. The flagella’s rotor, by itself, could perhaps be demonstrably useless, but conjoined to a stator and flagella, it suddenly has a use.
Pim: Zen misses the point.
:-)
Pim: Uselessness is infered from our ignorance of function but that does not mean that there is NO function, even by itself. In other words interpretation of usefulness is fraught with the same problems.
Really? We can come to know greater judgement about the function of a V8 cylinder head sitting in the dirt of a junk yard, all by itself, even if we have never seen one before and do not know what it is, other than to say that it MIGHT have a use that we do not know about right there on the grass? I hadn’t realised how weak was our capacity to know. While you are correct that there might always be some purpose to that V8 head—the junkyard owner might use it for a stool, for instance—I had thought we would be able to come to some sort of confident decision on the nature of such things even if such judgements fell short of being absolutely certain. I had thought we both realised the fluidity of our knowledge base, and that the fluidity does not stop us from making judgements of various levels of confidence? But we needn’t use so extreme an example. Open the hood of your car, start your engine, and look at what happens. You will find all sorts of mechanical parts under your hood, some of them moving, but most of them not. Now, if I removed your alternator and tossed it on your driver’s seat when you weren’t looking, you would no doubt wonder what the heck that “thing” was doing on your seat. When your car stalls, and you looked under the hood, you might be able to infer with a GREAT deal of certainty that I had removed this strange part and put it on your seat, that it might fit the empty space you now see in the engine compartment, and that it’s loss has something to do with your car not running well. Would the situation be so bad that you could come to no confident conclusion about the uselessness of the alternator on your front seat, and the usefulness of the alternator when properly connected in that space next to your engine, even though you know nothing about engines and how they operate?
Pim: Seems to me that Zen has an innovative definition of the term proof. Since science rarely deals in proof, I find the claim that our ignoranc may be proof of something rather elucidating.
Excellent, this means I can continue to believe the moon is made of cheese, unmolested by my critics. As a cheese lover, this is yet another reason for me to support a return to the moon.
Pim: Even if there were a designer, it is not a false disjunction for logical reasons.
Wrong. All that is required for a false disjunction is that you load the options to choose from in such a way as to EXCLUDE some possibilities that might be real ones. look, I could be wrong. I read the summary of Luria’s experiment through the link you posted, and it could be that some relevant facts were left out of the summary that were crucial in the paper. I responded to the summary, not the original paper. And according to the summary you posted, what the experiment proved, and what I agree that it proved, is that some of the bacteria mutated prior to the release of the bacteriophage. The experiment does not tell us that the mutations were random, which is your key claim.
Pim: I find it also interesting that Zen raises the argument ad ignorantium here but fails to apply it correcly to his own argument about usefulness or lack thereof.
Of course not, because I do not think we are making symmetrical claims. I think that we can in some cases—not all, but some—make judgements of high confidence with regards to the use of a part, or the lack of a use as I have already explained.
Pim: Luria's experiments showed that variation was pre-existing, the logical interpretation is that this variation is 'random wrt immediate fitness'.
Please do show how the logical interpretation you speak of follows from the data, and I will comment on it.
That it may be non-random wrt future fitness is irrelevant. Zen suggests that it was an intelligence that caused these variations, but so far this is an appeal to lack of evidence to support such a claim.
This is the argumentum ad ignorantium part. There is no evidence to support such a claim, therefore it cannot become one of the options of a disjunction. There is an equivocation on the word "evidence" in your statement. I think you mean evidence that is already some part of the body of knowledge called science, but that is not relevant, unless you plan to keep science insulated from the rest of the world and what it believes. That's not possible because the world IS the territory of science, and so are the people in it and what they think. Now, the reasons why I think it should be included are many. Let me TRY to explain briefly. The idea of God and religions themselves were not invented over the weekend by Joe Crackhead. It would be easy to dismiss the notion of a designer or creator if Joe Crackhead were our only source on the subject. But the FACT is that the idea of God and all the many religions have had enormous influence on world history and the lives of possibly BILLIONS of human beings over the ages. Now, it COULD be that it’s ALL hogwash. It COULD be that EVERYONE who believes or who has believed in God or a designer is flat out wrong. However, given the enormous influence of religion on world history, on current history, and no doubt in ways in your own life of which you may be barely conscious, it seems a little self serving and unscientific to deny at least the possibility that there MAY be a designer. MAYBE. And if we are willing to admit that there MAY be, then it makes no sense to make that admission on Monday, then load an experiment against that possibility on Tuesday, and then conclude randomness on Wednesday as if we never admitted anything on Monday.
Now, since this is an ISCID forum, not the Skeptical Inquirer, I am assuming, wrongly perhaps, that most of us here are willing to consider a designer as ONE of the possibilities.
In addition, it must be remembered that PROOF (sorry, but I am not afraid of that word) is not that which we start out with but that which we end up with if our inquiry is successful. For this reason, we should INVITE questions, not discourage them with hostility or contempt. We are, are we not, after the same thing, which is to get at what is really going on, correct?
I trust that neither you nor any of the other readers will attribute any sense of absolutism to my word choices which I have not specifically endorsed.
Pim: Since Zen was suggesting that this 'intelligence' was aware of future challenges/needs, I would be interested in what kind of intelligence can foresee the future?
You should have asked what kind of intelligence CANNOT see the future. I know of only ONE flavor of intelligence, which is consciousness itself, so that is the one I mean. Perhaps you had something more mystical in mind, but let me tell you what I mean by our ability to foresee the future. When I am driving on the highway, I don’t just watch the car ahead of me, but the next 3 or 4 after that one. This practise has helped me to predict what the car directly ahead of me would do, and in this way I have escaped more than one potentially dangerous accident, because I was able to see the future, and adjust to it to avoid it. I don’t mean ANYTHING different than this, nor have I said that the designer is watching over us from the clouds, anymore than the designers of the robots in the auto factory stand watch over their creations telling them what to do in this or that problem situation.
Pim: Why? Seems a bit ad hoc to me. Are you saying that intelligent guidance can predict the future?
Zen:What I am saying is that intelligence predicts the future and DESIGNS responses to it BEFORE the future arrives.
Pim: So intelligence forsaw the Luria experiments? Fascinating. A bit ad hoc but it does give me a better understanding as to what kind of intelligence Zen has in mind.
This has gone from a criticism of the assembly line approach to what kind of intelligence does Zen mean? I really do not know what you are looking for, but suspect that you already have something in mind and are trying to get me to say it without putting words in my mouth. Isn’t this a littte bit off the point? I mean are you trying to get me to say something which will cause you to reflexively dismiss everything I have said thus far?
In answer, intelligence doesn’t have to see Luria or his experiment. Intelligence doesn’t have to have an opinion on Luria or know what Luria ate for breakfast on any given day. What intelligence must do is gauge either what IS possible or what will BECOME possible, and design a response, automated perhaps, to it in the organism. The laws of physics might THEMSELVES be part of that automated response. And because there are many possibilities, intelligence has to kick out a LOT of predictive responses to cover a portion of them.
Zen: Anticipation is an indication of intelligent design.
Pim: Yes, these smart bacteria surely saw Luria and Delbruck's experiments coming :-)
Very funny, but I’m sure you know that’s not what I meant :-)
Pim: What else could you have meant then? You suggested that the mutations were intelligently designed, but for what?
Okay, I thought I would have been given more credit than that. No, one bacteria did not turn to the other and say “Holy Smokes Eugene, it looks like we’ll be doused with bacteriophage this coming Tuesday according to MY oracle...RED ALERT...RED ALERT...MUTATE! MUTATE! MUTATE.” It isn’t the BACTERIA that see anything coming, but the designer, according to which life might POSSIBLY be unfolding according to the design.
It is the appearance of what proof of THIS would look like that I tried to describe. It is the description of what the PROOF would look like that I was after, where the reality might look quite different and be UNprovably designed or not designed.
Finally, I didn’t write this to irritate anyone. So if I have done so, I do apologize. This is a forum for the free exchange of ideas, not a peer reviewed publication, so there is more latitude here to think differently and freely. Sometimes good ideas come from unlikely places.
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zenheadache
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posted 08. April 2004 21:10
Pim wrote: Zen misses the point. Uselessness is infered from our ignorance of function but that does not mean that there is NO function, even by itself. In other words interpretation of usefulness is fraught with the same problems.
Pim also wrote: I find it also interesting that Zen raises the argument ad ignorantium here but fails to apply it correcly to his own argument about usefulness or lack thereof.
The test of the fallacy ad ignorantium is whether or not a particular kind of error follows a particular kind of logical form. The basic form that it has is: “I don’t know X is true, TF it is false” or “I don’t know X is false, TF it is true.”
We could always claim there might be some other non-observed function to the parts of a molecular machine, but this does not refute the observed uselessness of the parts with regard to some known function no longer operative.
Now, nowhere in the use/useless investigation I am suggesting is this claim hiding. Example: In context A, a machine is assembled into its parts where each part is performing its use. In context B, the same machine is sitting in a pile disassembled. In context A, we have visible use, and in context B, we have none.
In both, the observation is positive. We are actually observing use and loss of use. Translated into the particular form relevant to this example, the fallacious ad ignorantium would have to read something like this:
“I do not observe X has a use, TF it has none” or “I do not observe X has no use, TF it has one.”
This isn’t the argument I am making at all. We are in fact observing the use and uselessness of the very same parts in different contexts, assembled and disassembled respectively.
In other words, true statements about each context would read: “context A: use C; context B: no use c.” These would be purely descriptive factual statements based on the observations. Or, put another way, “use” and “useless” in this context does NOT mean that a set of given parts CANNOT have any other use, BECAUSE we do not see one, but rather that a confirmed use is present in one context and not another.
Now, remember the alternator I removed from Pim’s car engine and placed on his front seat? Well the alternator could have some other PRACTICAL use: It could be used in a windmill or water wheel to generate electricity just as it did in the automobile. Notice that in this case it is performing the same function it did before. Or it could even have some WHIMSICAL use a jelly bean holder on my desk, in which case it does not perform the same function. OR it can have USABILITY: It could be melted down into aluminum, iron, and copper, and the metals transformed into something else entirely. But it CANNOT have ANY use imaginable. I cannot poke a stick through it and give it to some kid who knocks on my door at halloween as a lollipop. So there are limits on the possibilities, and therefore on our ignorance as well.
And I suspect that this is also true on the biochemical level, but I could be wrong. I don’t know. But if all the parts of a bacterial flagellum appeared one at a time, each doing nothing, but assembling with each new piece that appeared, and if they suddenly began working with some visible purpose, I would feel rather confident that this was proof of design.
As in the case of the alternator, the parts of a bacterial flagellum cannot have infinite uses. They have to be limited in number, and I’d wage a bet that the number of possibilities is very small indeed.
Pim wrote: If the claim is that the mutations are non random wrt future challenges then one needs to explain how the genome knows about these challenges?
First, I have made no claim that the genome “knows” anything at all. Perhaps Pim was thinking that the genome “knowing” is the only possible way to account for the mutation reaction; but the knowing might be external to the reaction, and the reaction automatic. A computer program, for example, doesn’t know ANYTHING. It’s merely a dead reflection of what WE know.
Second, there are two issues here. One is the question “How could X be so?” and the other is the demonstration THAT X is so, and it does not follow that we must first know HOW in order to show THAT. My article deals with how we might show THAT it happens, and I do not touch upon the how.
1. IF the bacterial flagellum was designed,
2. IF it was possible to SHOW that it was designed,
3. IF it was NOT possible to observe the designer creating the bacterial flagellum,
4. THEN what must we DETECT to confidently conclude that the bacterial flagellum was designed?
The automated assembly line is the answer I came up with. I did not consider the egg as a possibility. I was thinking about molecular machines, particularly the startling bacterial flagellum. And I assume that I am not the only one who was startled by the flagella mechanism the first time he or she saw it.
Pim seems to think that this is too ad hoc. If I correctly understood what he meant, let me address it this way: I do not mean that the bacterial flagellum was designed, but the rest of the bacteria was not designed. It may be the case that EVERYTHING in the entire universe is designed, but that design is only provable in some very small cases. I think Behe also made this point.
Pim wrote: Zen suggests that it was an intelligence that caused these variations, but so far this is an appeal to lack of evidence to support such a claim.
No, I am not appealing to a lack of evidence to support anything. I am saying that if the IDH is true, finding the assembly line might BE the discovery of the support Pim wants. But you have to look for it.
Pim wrote: Not that I am denying the possibility just pointing out that if Zen is arguing that mutations in the past were made knowing the future that Zen seems to have a special form of intelligence in mind which precludes a scientific interpretation.
The question of whether or not it is demonstrable depends on finding the evidence. We cannot automatically assume that the evidence is unavailable or impossible to get hold of. We have to look. I’m simply proposing what to look for.
What I was actually hoping for with this was for someone to tell me something like, “No way. That’s not how the bacterial flagella could have come to exist, and here’s why...”
I haven’t got that yet.
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Rex Kerr
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posted 09. April 2004 01:49
Your proposal of what to look for is a good one, but there is a problem: how are we actually supposed to identify the assembly line?
We can't look in organisms with a flagellum, because it's functional now.
We could look in organisms without a flagellum, but how would we distinguish portions of a forming assembly line from the remnants of a mutated and no longer used flagellum? [Actually, there may be ways to do this, but it would require more assumptions about how the assembly line process works.]
If we do find assembling components that don't produce a full working flagellum, is there a way to judge when we have looked enough to conclude that there isn't some function that we are missing?
These questions are difficult to answer for a structure as ancient as the flagellum. As an analogy, note that it is much easier to find a Model A Ford than it is to find the factory that built the Model A and recognize it as such. (It's only a rough analogy, granted.) If there is anything to find, it would be easier to find in a more recently developed system--blood clotting, for example.
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zenheadache
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posted 09. April 2004 21:40
Rex, thanks for the reply.
Just some questions off the top of my head:
Is there a fossil record of the bacterial flagellum? If so, when it appears in the record are there different or missing parts in the record as compared to its current form? Or when it appears is it already fully assembled and operating?
Are there any parts in other organisms which bear resemblance to the parts of the flagella mechanism, but which do NOT perform the same function? If there are parts similar in appearance, do they perform some visible function at all, or are they just hanging around as far as we can tell?
I would be especially interested in the rotor and stator parts. A part cannot have any use whatsoever, and a stator and rotor are extemely specialized parts. The number of uses they could have would have to be low, especially with regard to producing some locomotion.
Do any independently living organisms resembling these parts exist? If so, which parts and what are the differences in resemblence?
Rex wrote: We could look in organisms without a flagellum, but how would we distinguish portions of a forming assembly line from the remnants of a mutated and no longer used flagellum? [Actually, there may be ways to do this, but it would require more assumptions about how the assembly line process works.]
What ways did you have in mind?
Perhaps this problem might be solved with a bunch of people from different disciplines all working together on it.
Are there any mechanical engineers in the house?
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Rex Kerr
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posted 10. April 2004 14:36
You can't expect to see flagella in fossils--they're much too small. It's difficult to see even whole bacteria. Perhaps there would be an extremely faint impression if you got very lucky, and if it was missing the long tail, it'd be completely hopeless.
(What I had in mind was some sort of statistical genomic analysis, but without an idea of the assembly-line process, it'd be very hard to know what to predict. With an idea of the assembly-line process, it might only be hard to predict.)
Some bacteria have a "type III secretory system" that looks an awful lot like the base of the flagellum. It is functional--as the name suggests, it secretes proteins. I'll leave additional reading on the subject to you. There are a variety of threads on this forum that talk about it, for instance.
[ 10. April 2004, 14:44: Message edited by: Rex Kerr ]
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zenheadache
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posted 06. May 2004 19:00
Rex, the molecular factory proposal implies that something might produce the parts of an IC system like the flagellar motor. It might be that the mystery machine produces the system AROUND itself.
I understand that current thinking has the TTSS evolving from the flagella, rather than the flagella evolving from the TTSS. But how certain is this? If there is a molecular factory producing systems around itself, then the product could fit either hypothesis, with the only thing swaying one's judgement about which evolved from which being one's opinion.
In the bio factory I am proposing, something has to produce parts.
Can the TTSS do this? Is it capable of producing all the parts of the flagellar motor, leaving aside any other assumptions about which might have come from which? Is it POSSIBLE?
[ 06. May 2004, 19:01: Message edited by: zenheadache ]
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Rex Kerr
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posted 06. May 2004 22:42
Unfortunately, I'm not an expert on flagella or the TTSS. I shall have to leave your technical questions to others, or to your perusal of threads
on the topic here. (And threads not on the topic that subsequently were hijacked by a TTSS/flagellum debate.)
[ 06. May 2004, 22:42: Message edited by: Rex Kerr ]
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