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Author
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Topic: Suggestion for selection of IC systems for study
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Argon
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Member # 276
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posted 18. May 2002 12:55
Because genomes may change over time through drift & selection and that this cumulative variation often makes it more difficult to determine the historical origins of particular genes and proteins, I think it would be very pragmatic to focus on those IC systems which have most recently emerged.
Have many people here been looking into IC systems which arose within the past 50-100 million years or earlier? These would be the most likely to provide clear-cut, uncluttered details about the development of IC systems. I have noticed that the IC systems which have more recent origins tend to also have fewer numbers of "newer" components (I'm using the IC definition first described in Behe's book here).
The recent focus on the bacterial flagellum is interesting, and it certainly represents a large, tightly-integrated system, but unfortunately its universality, age (> 1 billion years), and long period under selection tend to make questions of its origins much more difficult to conclusively resolve.
The mammalian clotting cascade is potentially more accessible (age in the range of hundreds of million years), but seems to have fallen "off the radar" in public discussions. Does it make sense to look for even newer systems to study?
This idea is relatively simple: In a fog, one sees closer objects better. It's common in science that we must often make accommodations for the resolving power of our tools and methods. In the case of biological origins, the most common obscuring factor is age. If one is interested in testing potential relationships between IC systems in biology and ID with the least noise and greatest certainty, I think the most recently emerged systems are the ones to investigate.
[ 18 May 2002, 12:59: Message edited by: Argon ]
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Mike Gene
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Member # 149
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posted 18. May 2002 23:33
Hello Argon,
You write: If one is interested in testing potential relationships between IC systems in biology and ID with the least noise and greatest certainty, I think the most recently emerged systems are the ones to investigate.
I can certainly appreciate the argument you are making, but I thought I would explain my reasoning for focusing on the flagellum.
1. My hypothesis begins with the design of the first cells. Thus, one surveys the biological features that are plausibly associated with such a design event. If I am to extend my survey for intelligent intervention into more recent times, it would seem prudent to first establish, systematically, that intervention events extended beyond the first cells. In short, I choose to work outwards from a event where I feel the case for intelligent intervention is strongest.
2. Concerning the issue of noise and IC, I think a focus on IC, as it relates to molecular machines, helps significantly to cut down on the noise. I've explained my reasoning here.
3. The decision to focus first on bacterial systems not only stems from (1) above, but it is also a fact that bacterial systems are best understood and usually simpler. For example, a PubMed search with "bacterial flagellum" turns up 1961 articles (compared to the 461 hits one gets with "blood clotting cascade"). The flagellum has been extensively studied from both a biochemical and genetic perspective. It is one of the best understood complex systems. Better yet, we now possess dozens of completely sequenced bacterial genomes, and it is my opinion that a robust IC analysis must entail genomics.
4. The lengthy time the flagellum has been in existence actually helps the IC analysis, as we can survey the effect of billions of years of evolutionary tinkering regarding this machine. This facilitates an attempt to uncover the minimal IC core of any molecular machine.
5. As I have explained (and demonstrated) before, a fruitful IC analysis is significantly helped by two factors: understanding the workings of a system (3) and pinpointing the IC core (4). Unless the recent systems you have in mind involve such information, I'm not sure how meaningful an IC analysis would be.
6. The ancient origin of the flagellum is not that much of a problem. First, according to traditional views, bacteria shared a common ancestor with archaea (and eukarya). These are outgroups that can be surveyed from homologs of the flagellar components. Of course, there are no homologs in these two domains. Secondly, unless one is willing to put a time limit on our investigation, specifying exactly when we should stop looking for clues of a gradual origin, the issue of time seems like special pleading. After all, the RNA World is much more ancient than bacterial flagellum, yet many are busy trying to reconstruct this. And Ken Miller cites the Krebs cycle as an IC system that has been worked out from a darwinian viewpoint, yet the Krebs cycle is probably older than flagella (since it is found in both archaea and eubacteria). What's more, many argue that a pathway for the evolutionary origin of the flagellum has been proposed (the type III secretory system story), clearly indicating many people are not being deterred by the ancient origin of the flagellum.
In the end, I have no a priori opposition to investigating more recent IC systems. It just seems more unworkable to me (as explained above). However, if anyone knows of any mammalian-specific IC molecular machines (or even a vertebrate-specific molecular machine), I'd be interested in hearing about it.
[ 18 May 2002, 23:39: Message edited by: Mike Gene ]
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Johan de Boer
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Member # 287
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posted 27. May 2002 20:16
I would like to add a comment to the discussion about IC systems.
Irreducible complexity appears to be the critical aspect of intelligent design. After reading quite a bit of the discussions on this issue, it occurs to me that a fundamental point is missed. Of course, when you remove a component from a complex system it may stop functioning. This is not always true, as has been shown in some cases when redundant pathway networks can accomodate for the missing pieces (e.g. to some extent the p53 gene in one of the cell's signal pathways can be removed without the terrible consequences that were predicted). However, in other systems where several proteins work together, removing one (possibly by gene knockout) most likely makes it stop working. This should not be very surprising, and the approach to this reflects a rather simple mechanical engineering mind. This is examplified by the use of a mouse trap as an IC system, even when some have demonstrated that this too may be build from the ground up.
The real problem here as I see it is that the concept of irreducible complexity is fundamentally flawed, because we look at the system in the present time. The IC approach is bound to be irrelevant for understanding the origin of a biological system that already has evolved. We should be looking at such a system as it develops, and not after the fact, for the simple reason that a developing system doesn't know where it is headed and what the parts will be or how they will work together. The final complex system (at least as it is at this moment, as changes will go on until the end of all life on earth) is not a priori the goal. The organism/system uses what it currently has available for whatever purpose it is useful and builds on that, changing along the way, without having a clue what it will look like 10 million years down the road. If somewhere down that road two or more pieces become interdependent (which is very well possible), is that irreducible? Many seem to claim this, however, I don't think this is true unless we simply look at the system at that point in time (the present I presume), but at that point the question has lost it's meaning, because the parts simply have become interdependent. The only way a truly irreducibly complex system can arise is when all components appear at the same time. This can never be established using the concept of irreducible complexity.
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Mike Gene
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Member # 149
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posted 27. May 2002 23:29
Hello Johan,
You write: The real problem here as I see it is that the concept of irreducible complexity is fundamentally flawed, because we look at the system in the present time.
That's not a problem either. See:
http://idthink.net/biot/flag4/index.html
I think the last section on Ur-IC answers your objection.
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Johan de Boer
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Member # 287
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posted 27. May 2002 23:53
Hello Mike -- I see no conflict between my statements and that section on Ur-IC. It only means that (in this case for flagelli) the system has been in operation for a very long time. I am sure there other examples of more recent systems. My point is exactly this: Once a system is formed it becomes irreducible.
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Johan de Boer
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Member # 287
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posted 28. May 2002 11:08
As a follow-up on my previous posting on IC, I would like to submit the following to consider and for discussion.
1) A complex system could be designed as an irreducibly complex system.
2) When the parts of a system that is evolving become interdependent upon each other, it has become an irreducibly complex system.
In either case, the system is now irreducibly complex, and therefore, the concept of irreducible complexity would have no predictive power either way. What systems, therefore, could be used to study IC?
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Mike Gene
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Member # 149
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posted 28. May 2002 23:28
Johan,
I was originally focused on the claim that IC analyses consider systems "in the present time." This is not necessarily true, as I show in my discussion of the flagellum that I am focused on the last detectable flagellum. You argue that "we should be looking at such a system as it develops," but this seems to beg the question in assuming it did "develop." After all, there are no homologs for the flagellar components among archaea or eukarya. You argue that IC, by itself, cannot help us decide whether something was designed or did evolve. I tend to agree with you here. But from another angle, the structural similarity between ftsZ and tubulin likewise cannot help us decide whether is reflects common design or common descent. I happen to be a person with a high tolerance for ambiguity. Yet a closer look, while considering other factors, may help tip the balance enough to make a reasonable judgment call. So you might want to check out my other essays on the flagellum (from the same web page) and several more to come. IC may not be the referee, but I think it a productive player. Its role comes into focus when we discuss specific examples rather than muse about it philosophically.
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Johan de Boer
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Member # 287
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posted 29. May 2002 12:13
Hi Mike, thanks for the followup. The problem may actually be in the examples, as both sides will simply argue for or against each of them. That is not fruitful. My main problem is simply that in principle we cannot distinguish whether a system was designed or was evolved to interdependency, because they would look the same. In that case the concept of IC has lost its explanatory power. And ICS is the main pillar of ID. I think that Behe should provide a better proof that the concept actually works. He has never done that.
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Mike Gene
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Member # 149
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posted 29. May 2002 22:24
Hello Johan,
It would seem to me that our interests are different. Apparently, you expect from IC (or some other criterion) a clear-cut way to resolve the opposing teleological and non-teleological interpretations. Since it fails to deliver, you judge the concept as being non-fruitful and think it has "lost its explanatory power." I, on the other hand, find the concept of IC to be fruitful, as I have already explained how it can be used to explore biotic reality (see my thread, "The Utility of IC"). IC, to me, is a tool to be used in a forensic manner, helping us to piece the puzzle together and arrive at a "best guess" about this ambiguous origin events.
You write: The problem may actually be in the examples, as both sides will simply argue for or against each of them. That is not fruitful.
I don't agree. It is through the dispute that fruit is generated, as most good experiments and hypotheses emerge from the interface of dispute. The lack of consensus generates the need to explore in more breadth and depth.
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