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Author Topic: The Utility of IC
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Icon 1 posted 02. March 2002 20:34      Profile for Moderator   Email Moderator   Send New Private Message       Edit/Delete Post 
Charlie,
From now on, when you want to discuss my decisions, please send a note to this address: moderator@iscid.org

I am not questioning the truth of your statements. I am simply saying that this is not a forum to discuss groups of people and their motives. That is plain and simple. The truth of your claim is not being questioned. Its relevancy to this board is.


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Mike Gene
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Icon 1 posted 02. March 2002 20:51      Profile for Mike Gene     Send New Private Message       Edit/Delete Post 
Hello Charlie,

First, as for my "specific work" and "references," ID thinking is more of a hobby that I do mostly between the hours of midnight and 3 AM. I like how the ISCID puts it: "Retraining the scientific imagination to see purpose in nature." I am in this "retraining" phase. If you are interested, feel free to read through the dozens of essays I have posted on my web site (the url is in my profile).

Secondly, I am not interested in the socio-political side issues, thus I fail to see the relevance of your observations in the context of my posting. Let's stick to the "novel intuitions, speculations, hypotheses, conjectures, arguments, and data."

quote:
Basically, unless I am mistaken, you see design theory as a supplement to Darwinism, mostly on issues that Darwinism by its own nature is "neutral" about (of course Darwinism does not predict we are going to find every single intermediate in every single molecular evolutionary pathway). Hardly something that can reverse materialistic science, although still an empirically "useful" concept.

Indeed. It's not that I think IC will "reverse materialistic science." It's an example where IC was useful and Darwinism was not.

quote:
Finally, to get to the real scientific issues, rather than the far less exciting (to me, at least), philosophical ones, you correctly state that flgE-less flagella, even if proven to exist, being themselves IC, would not invalidate ID (although that still leaves my question open: what would?).

I don't think in terms of "validate" and "invalidate." I think in terms of "weaken" and "strengthen." What's more, I think like a traffic light. With the bacterial flagellum, the light is bright green for the design inference. To turn the light yellow, you could find a much simpler flagellum (composed of 6 parts). To turn it red, you need only account for the most of parts such that they existed prior to and independent of the bacterial flagellum. Let's contrast this with the view that the flagellum arose through non-teleological means. What data would cause us to suspect this explanation is wrong? What would cause us to suspect it was designed? In other words, what would turn the light yellow and red with regard to the non-teleological thesis?

quote:
On the other hand, you’d have a nice demonstration of how an apparently IC system (flagella with flgE) could in principle have originated from a simpler system (flagella without flgE), reaching its flgE-dependent IC status later. But if that is true for flgE, why couldn’t it also be the case for all other flagellar components?

Because not all parts are equal. Compare flgE to flgG. Compare flgE to fliE. Compare flgE to fliF. I'll explain this in my upcoming TeleoLogic articles on my web page.

quote:
What makes flgE-less flagella more IC than conventional flagella (in fact, mathematically, shouldn’t it be the reverse)? If the vertebrate complement cascade, in all its irreducible complexity, could have originated from a urochordate cascade missing some component, what precludes the urochordate cascade from having originated from a yet simpler system, and so on? In summary, what are you left with, if you take the irreducibility away from IC?

Good stuff here. To me, the issue is not about "mere IC" (just as evolution is not about "mere similarity"). Two other factors come into play. First, there is the consideration of knowing why something is IC. This is very significant in any analysis. Secondly, the big issue comes from a consideration of minimal complexity coupled to IC. If minimal complexity is IC (let's call this MIC), we have a rather interesting situation. For example, a Rube Goldberg machine is IC, but not minimally complex. We can make it simpler and simpler, but ultimately, we reach a minimal level of complexity needed to carry out the function. What do we do then?


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Mike Gene
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Icon 1 posted 02. March 2002 20:54      Profile for Mike Gene     Send New Private Message       Edit/Delete Post 
quote:
The point I want to get across, though, is that if ID will have to limit itself to be a complement to darwinism in the exploration of a subset of molecular machines, as Mike seemed to propose, then it will be quite a small achievement.

Four things.

  • I don't know why you would read such limitations for "ID" into my approach. Employing the IC analysis as I do may entail such limitations, but my teleological approach is not so one-dimensional.
  • I'm not sure we're talking about a "subset" of molecular machines. My approach may apply to all molecular machines.
  • I concede the "small achievement," but this does not detract from the significance of the achievement in light of the common belief that "IC is useless." I'm encouraged that we can agree on this.
  • Small achievements always have the potential to snow-ball. The moderator's initial comments on this thread are highly relevant.

quote:

Furthermore, by conceding that a failure in his prediction would not really affect ID theory significantly, Mike is leaving again the door open for the classic Darwinist objection that ID theory is not falsifiable.

I'm not all that interested in whether my approach is open to rhetorical counter-claims. But if this is the case, I would note that I have laid on the table the very type of data that would weaken my position (to the point where I would abandon it). Unless you or another "Darwinist" can tell me what type of data would weaken the belief that the bacterial flagellum arose through non-teleological mechanisms, it would seem I am on more solid ground on this "falsifiable" point.

quote:
Therefore, I am trying to start a discussion to see whether indeed ID theory can be used for more ambitious (and by definition, more "risky") testable predictions, with broad implications for our understanding of biology.

Then, shouldn't this discussion be in another thread?

As I see it, you've agreed with me that IC is not useless. My point is made.


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rafe gutman
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Icon 1 posted 03. March 2002 22:07      Profile for rafe gutman         Edit/Delete Post 
mike, i've been avoiding learning the specifics of the bacterial flagella, so take these comments with a grain of salt. i agree that you've made a legitimate prediction based on your understanding of this specific system, and using the concept of IC. i also agree that IC in this sense is a very real part of biochemical systems. it appears that the flagella has achieved a state similar to the roman arch; very functional and stable, but requiring all of its "core" components.

since flgE does exist in t. maritima (pseudogene or not), i'm inferring that this organism does not represent a line ancestral to the origin of the flagella, so even if the component is indeed a pseudogene, it would not necessarily mean that the flagella minus flgE represents an ancestral state of the IC flagella (including flgE). in light of this, i don't think your prediction is based on IC as it relates to origins, but rather IC as an empirically-detectable feature of extant systems. as a result, the success or failure of your prediction would not affect the IC to ID inferrence.

i do agree that your prediction is a valid one. i don't think it would hold up in all IC systems, but that isn't the point. i don't think it can be applied to ID though, as it does not relate to the origin of the system. however, since i have often stated my opinion that IC is a useless concept (on the ARN forum), i'll amend that to: IC is a useless concept, as it relates to origins.


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Mike Gene
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Icon 1 posted 04. March 2002 22:57      Profile for Mike Gene     Send New Private Message       Edit/Delete Post 
Rafe,

Thank you for acknowledging my prediction as valid and making your amendment. I think this prediction would hold up for many systems as along as the two factors I mentioned above are also considered: knowing why something is IC (reverse engineering) and minimal complexity. But one thing at a time.

Your point is that IC is a useless concept, as it relates to origins. We have to be careful here, as pronouncements of something being useless can either be a person-dependent expression or an objective observation. After all, I bet there are many grandma's who think computers are also useless.

So you need to clarify. Are you saying that you find IC to be useless as it relates to origins or are you saying IC is useless as it relates to origins. Is this judgment based on experience trying to use IC as it relates to origins or is in based on a priori considerations?

Furthermore, we have to better clarify what you mean by "relates to origins." Are we talking about the ability to prove an origin state or the ability to infer an origin state? Are we talking about utility in terms of guiding a research approach focused on origins or in terms of reaching a final conclusion about origins?

I would note that in the example I cited above, we can extend this utility into the area of phylogenetics/evolution: If we consider the structural components of the bacterial flagellum from Aquifex aeolicus, Bacillus subtilis, Escherichia coli, and Treponema pallidum, they all share the same core of 21 gene products.

Why is this?


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Mike Gene
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Icon 1 posted 05. March 2002 11:32      Profile for Mike Gene     Send New Private Message       Edit/Delete Post 
Another Example of the Utility of IC.

Let's begin with Aquifex aeolicus . This is a deep-branching, thermophilic bacterium. Its genome was sequenced in the hope of uncovering what primitive bacterium might look like [1]. TIGR lists genes by category. In my attempt to reconstruct what the first flagellum looked like, I noticed that FliM is missing from Aquifex's list of motility genes. This gene is part of the "C-ring" that forms prior to the export apparatus and also functions as the rotor. This was somewhat surprising, as FliM is found in all other bacteria that have functioning flagella. However, it was not too surprising as Aquifex do posses another component of the C-ring, FliN. It is estimated that the C-ring includes 110 copies of FliN and 35 copies of FliM. FliM is a bigger protein, around 340 amino acids, while FliN only contains about 110 amino acids. Nevertheless, in my scoring, I collapsed FliM and FliN into one component:

quote:
I've collapsed FliM/FliN into one species for three reasons reasons: a) Various studies have shown FliN and FliM to be closely related in a functional sense; b) In Bacillus subtilis, FliN is missing, but another gene, FliY, exists that appears to be a fusion of FliM and FliN (Mol Microbiol 1992 Sep;6(18):2715-23; and c) among all the groups compared, bacteria either had FliN, FliM, or both. For example, species lacking FliN had FliM. Species lacking FliM had FliN.
But then I got to thinking about this later one night. Aquifex are unusual in that they lack the Che chemotaxis system genes. These genes interact with fliM, which acts as the switch. Thus, from an IC perspective, the missing fliM is not surprising. Yet FliM is multifunctional. It is not merely part of the switch for flagellar rotation, but is an essential C-ring component needed to assemble the rest of the flagellum. So from an IC perspective in this regard, something is wrong. A flagellum doesn't need a switch, but it does need to be assembled.

So I went back and used fliM sequence from Thermotoga to BLAST the Aquifex genome. Could it be this easy? Sure enough, I got a hit with a 175-aa sequence from Aquifex, where there was 26% identical positions and 52% positives. The E value was 10^-12.

I then took this sequence and used ClustalX to align it against the FliM sequences of Bacillus subtilis, Escherichia coli, Treponema pallidum, and Thermotoga maritima. There is a decent alignment from positions 130-330 (with many invariant and conserved positions) and it appears the Aquifex FliM has thus lost its N-terminal 130 amino acids. So let's go back to IC and formulate a hypothesis: the N-terminal portion of FliM is employed in switching while sequence downstream of this deletion is crucial in assembly. Time to go to PubMed. And sure enough, this is exactly what genetic studies have uncovered [2,3].

Yet these studies suggest the residues important for switching are found in the N-terminal 20 amino acids. Aquifex has a 130-N-terminal deletion. This is slightly odd, as the size of FliM is fairly well conserved: 332 in B. subtlis, 334 in E. coli, 328 in Thermotoga, and 344 in Trepenoma. In contrast, Aquifex FliM is only 182 amino acids. The deletion might be cutting into the assembly function of FliM and IC says this can't be. In fact, I then found a study that suggests there is assembly-information in this region[4]. But wait, could FliN be filling in for this missing FliM Aquifex sequence? Afterall, FliN is missing in Thermotoga, so perhaps it contains redundant assembly information. Back to PubMed. It turns out that FliN is indeed involved in assembly [5] (one reason for it being retained in the more recently evolved type III secretion system). Yet could this function compensate for the missing sequence in Aquifex FliM?

When I originally BLASTed the Aquifex genome with Thermotoga FliM sequence, I also picked up Aquifex FliN, where an overlap of 84 residues turned up 32% invariants and 52% positives with an E value of 10^-7. What aligned with Aquifex FliN was the C-terminus of Thermotoga FliM (known to be essential for assembly).

Finally, I went back to the Aquifex sequence. FliN is 112 amino acids. If this was added to the N-terminus of FliM, the protein would be 294 amino acids in length, close to the conserved size of FliM from the other distantly related species analyzed. So I add the sequence (an Aquifex FliN-FliM fusion) and attempted to align this against the FliM sequence from E.coli. With only one 3-residues gap in Aquifex and one 2-residue gap in E coli sequence, the N-terminal amino acids (from position 10-120) of these two sequences lined up with eight invariant positions and 34 conserved positions. Not bad, if I may say. Aquifex thus apparently tolerates this large deletion in FliM because of FliN.

As we would expect from IC, the functions are all there. They've been moved about somewhat, as a consequence of Aquifex jettisoning its chemotaxis system, but they are there. In fact, the built in FliN/FliM redundancy as it pertains to assembly points to the robustness of this subsystem, making it possible for something like the Aquifex flagellum to evolve from an originally designed state that included both FliN and FliM. If so, IC has helped us track the species-specific evolution of the flagellum (not to be confused with the ultimate origin of the flagellum).

The big question is the constitution of the original flagellum. A minimal complexity consideration would have us omit FliN (the small protein) from the list, as its core function could probably be supplied by FliM (the larger protein). However, here is where other ID considerations come into play. If my thesis is that these originally designed cells were designed to evolve (front-loading evolution), then robustness, a trait of advanced engineering, comes into play and leads me to tentatively include FliN in the list. However, that's another story, thus, for the purposes of sticking close to IC, I will retain my original scoring that collapsed FliM and FliN into one component. IC simply helped me to understand, and support, the logic of this move.

1. With the new ability to decode the full DNA of a microbe, it is these high-temperature microbes that biologists have chosen for some of their first targets. Aquifex aeolicus, a denizen of Yellowstone Park that lives at 5 degrees below the boiling point of water, is the deepest branching of all known bacteria.
In the light of evidence suggesting that the oldest region of the ribosomal RNA tree lies on the branch leading into the bacterial kingdom, Aquifex provided grounds for the claim that it was the nearest living cousin of the universal ancestor. But the sequence of the Aquifex genome, reported last month in the journal Nature, has yielded only disappointments. For one thing, the microbe appears to have only one gene, called a reverse gyrase, that is not found in organisms that live at ordinary temperatures. -Wade

2. Poggio S, Osorio A, Corkidi G, Dreyfus G, Camarena L. The N terminus of FliM is essential to promote flagellar rotation in Rhodobacter sphaeroides. J Bacteriol 2001 May;183(10):3142-8.

3. Bren A, Eisenbach M. The N terminus of the flagellar switch protein, FliM, is the binding domain for the chemotactic response regulator, CheY. J Mol Biol 1998 May 8;278(3):507-14.

4. Toker AS, Kihara M, Macnab RM. Deletion analysis of the FliM flagellar switch protein of Salmonella typhimurium. J Bacteriol 1996 Dec;178(24):7069-79

5. Tang H, Billings S, Wang X, Sharp L, Blair DF. Regulated underexpression and overexpression of the FliN protein of Escherichia coli and evidence for an interaction between FliN and FliM in the flagellar motor. J Bacteriol 1995 Jun;177(12):3496-503

[ 05 March 2002, 11:33: Message edited by: Mike Gene ]

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Alex Wild
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Icon 1 posted 05. March 2002 12:51      Profile for Alex Wild   Email Alex Wild       Edit/Delete Post 
Mike,

This may just be my systematist's bias showing through, but I think it would be a worthwhile excercise to map the different aspects of the flagellar system onto a phylogeny. This would allow you to more explicitly identify which missing parts of the system in the different bacteria have been lost, which have apparently never been gained, and the order of addition of various parts. It could bring some resolution to the question of which parts of this system are essential to original function, and which have been added to the I.C. core as later developments.

Note that this should not be done using the flagellar proteins themselves, as using a tree generated on the proteins to map the evolution of the proteins is circular.

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nobody
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Icon 5 posted 05. March 2002 13:07      Profile for nobody     Send New Private Message       Edit/Delete Post 
quote:
Originally posted by Mike Gene:
But the sequence of the Aquifex genome, reported last month in the journal Nature, has yielded only disappointments. For one thing, the microbe appears to have only one gene, called a reverse gyrase, that is not found in organisms that live at ordinary temperatures.

hmmm

Who exactly was disappointed? This appears, to me, to be additional evidence for Design.

One gene may be the only difference they can locate, but perhaps that's because one single gene is not all that significant. Perhaps it is the gene regulatory network that is responsible.

http://doegenomestolife.org/roadmap/grn.html

"A major gene regulatory network in the bacterium Caulobacter is now beginning to be mapped in a comprehensive manner based on genome-wide expression analyses coupled with genetic methods [M. T. Laub et al., Science 290, 2144­48 (2000)]. Caulobacter has about 3000 genes, of which almost 20% were found to be differentially expressed during the cell division cycle. Of the 553 responding genes, 38 are likely to be direct targets of a sequence-specific DNA-binding protein called CtrA and another 144 are indirectly regulated by CtrA. A firstpass connectivity map of the CtrA gene regulatory network derived from this study is summarized in this figure. Green indicates previously known relationships, while red indicates relationships that emerged from this global gene-expression study performed using microarray technology."

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Alex Wild
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Icon 1 posted 05. March 2002 13:32      Profile for Alex Wild   Email Alex Wild       Edit/Delete Post 
Another question for Mike,

How confident are you that the Aquifex FliM deletion is really a deletion? If we take the standard Prokaryote phylogeny at face value and Aquifex is basal, it seems that we could make an equally parsimonius case that the 175-a.a. homolog of FliM you found in Aquifex is not reduced. Rather, it could also be that the longer FliM in the later-branching prokaryotes are expanded versions of a smaller, earlier gene.

Under this scenario, Aquifex isn't compensating for the loss of FliM, but the other prokaryotes have perhaps developed a different way to perform the same function, using a larger protein. I don't see any a priori reason why either story should be preferred over the other.

[ 05 March 2002, 13:35: Message edited by: Alex Wild ]

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Alex Wild
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Icon 1 posted 05. March 2002 13:47      Profile for Alex Wild   Email Alex Wild       Edit/Delete Post 
quote:
In the light of evidence suggesting that the oldest region of the ribosomal RNA tree lies on the branch leading into the bacterial kingdom, Aquifex provided grounds for the claim that it was the nearest living cousin of the universal ancestor. But the sequence of the Aquifex genome, reported last month in the journal Nature, has yielded only disappointments. For one thing, the microbe appears to have only one gene, called a reverse gyrase, that is not found in organisms that live at ordinary temperatures.
If Aquifex is supposedly a good analog of the universal common ancestor, we wouldn't expect it to have genes that other organisms lack. The presence of novel genes in Aquifex would require either multiple new gene origins in the Aquifex lineage since the time of the ancestor (rendering it a poor analog for the ancestor), or multiple losses of genes in the other prokaryote lineages. From what you've reported here, it seems that the Aquifex genome is pretty much what we'd expect if it is similar to the genome of the common ancestor.
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Mike Gene
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Icon 1 posted 05. March 2002 22:23      Profile for Mike Gene     Send New Private Message       Edit/Delete Post 
Alex,

Thanks for the phylogeny suggestion. But I should point out that I have been discussing the few areas of noise. When we consider these five distantly related bacteria, they all have the same 21 structural gene products, making it quite reasonable to infer their presence in the last detectable flagellum. The only noise involves what I have already discussed above.

As for Aquifex and last common ancestors, (which is really unrelated here, but worthy of a quick comment), many do indeed think there would have been multiple lossess of genes in the other lineages. Aquifex lives in extremely hot conditions and many accept the "hot origin of life" scenario. According to this view, the mesophilic lifestyle is secondarily derived and would involve independent loss of thermophilic information.

Now, to the really fun question:

quote:
How confident are you that the Aquifex FliM deletion is really a deletion?
About as confident as any other tentative hypothesis would be.

quote:
If we take the standard Prokaryote phylogeny at face value and Aquifex is basal, it seems that we could make an equally parsimonius case that the 175-a.a. homolog of FliM you found in Aquifex is not reduced. Rather, it could also be that the longer FliM in the later-branching prokaryotes are expanded versions of a smaller, earlier gene.

Under this scenario, Aquifex isn't compensating for the loss of FliM, but the other prokaryotes have perhaps developed a different way to perform the same function, using a larger protein. I don't see any a priori reason why either story should be preferred over the other.

Sure, but when I factor my ID thesis into the equation, there are two squishy reasons to prefer the loss hypothesis:

1. An original flagellum with both FliN and full-length FliM would be more robust, where robustness is a sign of clever/good design.

2. My thesis of front-loaded evolution provides an intellectual inertia to prefer loss explanations over gain explanations.

I'll see if I can come up with something less squishy tomorrow night.

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Alex Wild
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Icon 1 posted 06. March 2002 11:55      Profile for Alex Wild   Email Alex Wild       Edit/Delete Post 
Mike,

Since my last post I've had a chance to look up some prokaryote phylogenies to get myself oriented in the group. I'll get to that in a minute, but I'll respond to some of your other points first.

Mike: "When we consider these five distantly related bacteria, they all have the same 21 structural gene products, making it quite reasonable to infer their presence in the last detectable flagellum.'

Just want to clarify that I'm not arguing against a single origin of the flagellum. Your inference is I think straightforward. Since genes move around a good bit, each one might be considered to have a different history, and my previous post was specifically about only one of those.

"1. An original flagellum with both FliN and full-length FliM would be more robust, where robustness is a sign of clever/good design."

I don't know about this. The Good/Bad design argument is a double-edged sword. One anti-I.D. argument that I've abandoned in the past 6 months (due to logical failure) is the "Bad Design is evidence that design could not have occurred." You know this one. Wisdom teeth and the blind spot are evidence against design because a decent engineer wouldn't have made them. In truth, lacking any outside information on the designer's goals or processes I don't think we can say that wisdom teeth are incompatible with design.

However, this argument cuts the other way as well. Lacking knowledge of design goals and processes, we cannot argue that a "robust" design supports a design inference. How do we know what is "robust" in an unknown designer's eye? I'd argue that if we cannot make judgements on the robustness of wisdom teeth, we cannot make them for bacterial flagella either.

" My thesis of front-loaded evolution provides an intellectual inertia to prefer loss explanations over gain explanations. "

You aren't alone in this inference. In general, most mainstream biologists seem to favor loss over gain explanations, and for the similar reasons that loss seems easier to accomplish than gain. My instinct is to agree with you; however, empirical justification of these claims really requires that we carefully examine phylogeny.

Onto the phylogeny. Most I saw looked something like the ones presented here:

Jörg Soppa 2001. Prokaryotic structural maintenance of chromosomes (SMC) proteins: distribution, phylogeny, and comparison with MukBs and additional prokaryotic and eukaryotic coiled-coil proteins. Gene 278: 253-264.

The problem for any inference about the truncation of FliM in Aquifex is that the tree is unrooted. Two scenarios:

1. If the root falls along the single branch leading to Aquifex, then the hypothesis that the short FliM is truncated is equally parsimonius to the hypothesis that the short FliM is ancestral. I don't don't prokaryotes well, but it seems to me that the speculations of people who work in this field view this as at least a reasonable rooting.

2. If the root falls anywhere else in the tree, then the hypothesis that short FliM is truncated is more parsimonius than the hypothesis that it is ancestral.

There is a third possibility that might be a bit of a stretch but deserves mention anyway. The amino acid sequence identity that you found could simply be convergence. The match you found was not very strong. If there was strong selection on the function that FliM performs, and that function requires particular amino acids in particular positions, then it isn't impossible that what we see is homoplasy.

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Columbo
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Icon 1 posted 06. March 2002 13:18      Profile for Columbo   Email Columbo   Send New Private Message       Edit/Delete Post 
Hello Alex,

Forgive me for barging-in on an interesting discourse. If you don't mind, I'd like you to go a little further on the following thought:



However, this argument cuts the other way as well. Lacking knowledge of design goals and processes, we cannot argue that a "robust" design supports a design inference. How do we know what is "robust" in an unknown designer's eye? I'd argue that if we cannot make judgements on the robustness of wisdom teeth, we cannot make them for bacterial flagella either.



I'm a mechanical engineer, with a respectable amount of design experience behind me, so I (understandably, I hope) have certain expectations regarding "good designs." In my opinion, recognizing "robust" design is not equivelant to debunking intelligent design for "sub-optimality." If the flagellum, for instance, operates well in a range of environmental conditions, adapts to new environments, and does not tend to suffer premature (average life of the cell) catastrophic failures, then I think that it demonstrates "good design practices." None of these measures have anything to do with the whims of the designer. They have to do with the final function of the system itself. {edit: I.e. it seems to me that "good design practices" apply generally to design problems, and are not designer dependent.} However, given the potential for environmental and mutational harms, it seems that a "good design" might appear under certain conditions, or after a prolonged time, to become corrupted.

Finally (as in the case of the inverted retina) the fact that a number of competitive constraints lower the optimization of any given one (resulting in a "maximally designed system" - the best possible given all constraints), should not count against there being a designer at all (as you have correctly deduced.)

Please forgive the length of this intrusion. I hope you will elaborate a bit more.

Columbo

[ 06 March 2002, 15:03: Message edited by: Columbo ]

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Janitor@MIT
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Icon 1 posted 06. March 2002 14:47      Profile for Janitor@MIT         Edit/Delete Post 
I’ll intrude also, since Columbo stuck his foot in the door with some very interesting insights. Mike Gene may recognize my “voice,” since I’ve repeatedly begged the IDers to stop thinking like theologians and start thinking like engineers. I wonder if he shares my impression that the "default," analytical position of biologists is not “Darwinism” or “naturalism,” whatever those are, but a sort of “design-teleological” instrumentalism? Susan Oyama in The Ontogeny of Information states that the “argument from design,” “powerful and procrustean,” has never left biology. There’s a good reason for that apart from any “ontogenetic” theory. Treating living things as designs is a powerful analytical tool. It works! Engineers have 150 years experience dealing with the analytical issues inherent to “complex” systems, and a biological “theory” that ignores the methods and results will go the way of alchemy and astrology. I don’t think Mike Gene need struggle to make the case that it does work. Its written all over biology.
I wonder if the more parsimonious and self-consistent position is simply to admit that living things can be treated as designs because they are designs? But I guess that’s one for the philosophers and theologians.

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Columbo
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Icon 1 posted 06. March 2002 15:00      Profile for Columbo   Email Columbo   Send New Private Message       Edit/Delete Post 
Janitor,

I'm beginning to feel like a camel's nose here. (It never occurred to me that the camel was an engineer!) ... OH WELL, WERE HERE! What the heck!!

I do agree with with you. From the perspective of an engineer, this all seems obvious. We must be extra careful though, not to go question-begging, since so many very bright people take the subject seriously.

The thing to prove - ala the ID project, is that our intuitions are correct. (I raised the question in another string (Intuitions of Design) of the epistemological justification for grounding the proposition that biological contrivances are the works of an intelligent agent on these intuitions. If we are epistemically justified, the I think the burden of proof shifts to those that want to deny this notion.

Hmmm.... sounding somewhat theologic or philosophic. Sorry!

Columbo

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The ISCID Forums are aimed at generating insight into the nature of complex systems (e.g. biological complexity, organizational complexity, etc.) and the ontological status of purpose, especially from the vantage point of various information- and design-theoretic models.

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