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Author
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Topic: A sequence of tests for IC
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gedanken
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Member # 594
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posted 17. March 2003 16:34
(Repeating) A REQUEST on brainstorming phase:
We have run out of page 1 of this thread. But I feel that we have not yet accumulated sufficiently clear definitions and tests for IC. I can see the possibility that this thread will have a lively discussion of the merits of these definitions. But first I want to challenge those who have studied IC and have a personal belief in its usefulness to present well reasoned cases here for tests for IC character. (I am not qualified to do so!) Remember that precise references to such reasoned arguments, and narrowly specified here are equally useful -- one does not have to quote the entire text in this thread, just a very precise reference (preferably online).
My request is to continue the brainstorming phase on through page 2 of this thread, so that we can have a chance that the very best concisely written tests for distinguishing IC cases from other cases should be presented here or linked here. (There are plenty of opportunities to challenge the application of those definitions in other threads which then provide links to this thread. Free-for-all discussion will come soon enough.)
[ 17. March 2003, 16:36: Message edited by: gedanken ]
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gedanken
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posted 17. March 2003 16:38
Micah, I don't understand the classification system well enough to classify Argon’s latest definition.
Also can someone search for a reference?
Specifically, can someone define "neutral evolutionary steps" more precisely? There are "neutral mutations" for example. (Sorry for multiple posts, wanted notice at top for specific structural purposes.)
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charlie d.
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posted 17. March 2003 16:46
Argon (et al),
it was Behe himself:
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."
(I think it was in his "Reply to my critics" thing, but I don't have the time to find right now).
Importantly, note how this definition
a) does not rule out co-option and change of function at all, and
b) does not seem to require empirical proof of every evolutionary step, but just its theoretical possibility and consistency.
For instance, according to this definition the transition from a TTSS to a flagellum would be acceptable as a selected evolutionary step, and thus would decrease the flagellum ICness by at least one degree, while according to recent arguments by Dembski and possibly even Behe that scenario does not count because it involves a change of function and is not empirically demonstrated.
[ 17. March 2003, 16:46: Message edited by: charlie d. ]
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Nel
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posted 17. March 2003 17:23
Charlie wrote:
quote:
"For instance, according to this definition the transition from a TTSS to a flagellum would be acceptable as a selected evolutionary step, and thus would decrease the flagellum ICness by at least one degree, while according to recent arguments by Dembski and possibly even Behe that scenario does not count because it involves a change of function and is not empirically demonstrated."
Actually the T3SS story, when applying Behe's Darwinian definition of IC, requires multiple unselectable steps. For example,we have to start with an M ring which only has a flagellum specific function. Then we have to follow up with a C ring which is just as flagellum specific. Outside the flagellum, it has no function. Thats a few unselectable steps right there. And then you have the problem of the 6 part export machine. There is no evidence that any subset of this export machine carries out alternative function. So thats quite a few unselectable steps right there. Then you would obviously want to add FliE since it's a great proto-filament, but FliE has no obvious role outside the flagellum either and T3SS don't need FliE. Thats another unselectable step. Then you have the rod, which is three components that are likely functionally indivisible, so adding each additional component of the rod adds more unselectable steps. With this definition of IC, evolutionary stories boil down to tornado in a junk yard making an airplane.
[ 17. March 2003, 17:45: Message edited by: Nelson_Alonso ]
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RBH
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posted 17. March 2003 18:00
Charlie and Alonso,
I think Gedanken's got a good thing going here. Let's not bog it down in premature debate and stick with his program. There will be plenty of time to do the debating once Gedanken has systematized the use of terms.
RBH
[ 17. March 2003, 18:01: Message edited by: RBH ]
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Nel
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posted 17. March 2003 18:07
RBH,
I disagree. My post shows a test for a Darwinian defintion of IC (in fact, why don't you categorize it as Darwinian?) That is exactly what Ged wanted:
quote:
But I feel that we have not yet accumulated sufficiently clear definitions and tests for IC.
Thus, I have shown that not only does the T3SS to bacterial flagellum qualify as an irreducibly complex evolutionary pathway using Argon's definition, but that it is an irreducible complex pathway of a very high degree in that it requires many unselectable steps. This is exactly what Ged wanted.
[ 17. March 2003, 18:18: Message edited by: Nelson_Alonso ]
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charlie d.
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posted 17. March 2003 19:40
It was not my intention to derail the topic. I just brought the TTSS example to illustrate what I think are the critical differences between the "evolutionary" definition and the "structural" definitions listed above. I am not interested in debating, yet again, the relationship beween TTSS and flagellum.
Personally, I think the evolutionary definition is the most scientifically interesting one, because it allows to focus on the critical evolutionary step(s) in a pathway that need to be elucidated, and because it's less subject to arbitrary definitions of components, function, etc.
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gedanken
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posted 17. March 2003 21:17
Alonso siad:
quote:
quote:
quote:
But I feel that we have not yet accumulated sufficiently clear definitions and tests for IC.
Thus, I have shown that not only does the T3SS to bacterial flagellum qualify as an irreducibly complex evolutionary pathway using Argon's definition, but that it is an irreducible complex pathway of a very high degree in that it requires many unselectable steps. This is exactly what Ged wanted.
Alonso, I looked at your initial post above, and I find discussion of a particular instance that was claimed to be IC. I find no definition anywhere in the post. And I find no concisely worded description of a “test procedure” for identifying IC. An example is exactly what I don’t want -- precisely because an example is not wording describing a generalization. How can we check, for example, that you have followed a particular “test procedure” in this specific instance, if the specific application instance is the entirety of the defining wording thereof? There would be no way to generalize, and verification on the basis of the single defining case would be question begging.
I’m not a moderator, I have simply requested that we remain in “brainstorming” mode for the remainder of this second page. I really do want generalized descriptions of tests (without specific to a particular case). These would be “definitions” of test procedure, as opposed to “definition” of the term “IC” itself.
So let me clarify what I am looking for:
Please give definitions of IC, and “test procedures” to identify IC. A “test procedure” would be similar in scope to a procedure for doing a laboratory test, except that in this instance it would probably be more of a sequence of logical examination steps. But the concept is the same as writing of a laboratory test procedure. One thing that is not part of a laboratory test procedure is a statement of the results of a particular instance of applying the test -- rather it is the procedure used to achieve those results. That is what I am looking for, clearly and concisely worded procedures for finding out whether a case to be questioned is “IC,” according to a labeled definition of IC.
Also when giving a “test procedure” description, please also refer to which labeled definition of IC is being used, according to the labels of this thread, like Micah’s labels of MP-1 or MP-2 definitions above. If a new definition of IC needs to be presented for the test procedure to be described, then include it in the post (and we can give it a succeeding definition number).
Once again - test procedures are generalized and are not based on a single example case of application. And because individual cases will in this case inevitably lead to direct argumentation, I also request that cumulative examples not be used to build a test if they can possibly be avoided.
Thanks
-------------
Now I would like to give the “evolutionary” definition a sequence label so we can refer to it. First Argon gave a definition from recollection, and then Charlie D refined it from some source (but he does not have the reference yet). We can get the reference when someone finds it -- but I don’t know how to use Micah’s classification system here, for classes of:
MP series = multiple part category
CS series = construction sequence category
CW series = Complex whole category
I suspect this would follow under “construction sequence” category (agreeing with Argon) so:
quote:
CS-1 (by Argon)
There is another criteria I've seen:
The amount of ICness in a system is a function of the number of neutral evolutionary steps required to account for its origin by natural mechanisms. The advantage is that ICness is recognized as continuous function rather than as a binary proposition. The disadvantage is that the determination requires data that is often impossible or very difficult to acquire and relies on historical knowledge of precursor states. I suppose this would put it in the Construction Sequence category.
I don't know who originaly proposed this definition but it sounds a lot like what Peter Ruest discussed in the ASA reflector hosted by Calvin College.
And
quote:
CS-2 (by Charlie D)
it was Behe himself:
"An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway."
(I think it was in his "Reply to my critics" thing, but I don't have the time to find right now).
(We can refine the attributions as they are discovered, but unless challenged as wrong category now we have names for them).
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Nel
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posted 17. March 2003 21:48
Ged,
I did use a definition, I used Argon's (which is actually Behe's definition). Secondly , the definition itself is a generalized test procedure. Find the unselectable steps in a proposed evolutionary pathway, if you find even one, the pathway is irreducibly complex.
Here I'll it lay it out for you. Here are generalized test cases for both the structural definition and the evolutionary definition.
Structural Defintion
Start with system X with parts A,B,C,D that have function F*.
To test whether this is an IC system using MP-2 I remove either A, B, C, or D from the system. If the function F* is lost then the system is irreducibly complex according to MP-2. If we remove D from the system, and function F* is preserved, then we are left with system A,B,C where D was a redundant part. We then remove A from the system, and if function F* is preserved then we have system B,C where A and D were redundant. We then remove B and if function F* is preserved then we have the system C and therefore it is not irreducibly complex according to definition MP-2.
Evolutionary Definition
We have system X with components A, B, C,D,E, G, H with function F*. We have proposed precursor called system Y with components A, B,C,D with function F1. We now study the evolutionary steps between system Y and system X. We start with A and invoke a mutation or other chance event that causes B to interact with A. If this step is functionless, it has no selective advantage and therefore it is a neutral step. We then add C, if adding C is functionless then it confers no selective advantage. Adding D confers selective advantage because we now have system Y with function F1. If we add E and it confers no selective advantage then it's a neutral step. If we add G and there's no selective advantage then it's a neutral step. If we add H and there's no selective advantage but a spontaneous , chance event that changes the function of the entire component then you have an IC evolutionary pathway. As opposed to if we had a selective advantage all the way through, where each step was functional.
[ 17. March 2003, 21:49: Message edited by: Nelson_Alonso ]
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Micah Sparacio
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posted 17. March 2003 22:15
Evolutionary Pathway IC (EP)
EP-1
An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.
Taken from Behe on evolutionary IC:
quote:
While I think that’s a reasonable definition of IC, and it gets across the idea to a general audience, it has some drawbacks. It focuses on already-completed systems, rather than on the process of trying to build a system, as natural selection would have to do. It emphasizes “parts,” but says nothing about the properties of the parts, how complex they are, or how the parts get to be where they are. It speaks of “parts that contribute to the basic function”, but that phrase can, and has, been interpreted in ways other than what I had in mind (for example, talking about whole organs that contribute to complex functions such as “living”), muddying the waters in my view. What’s more, the definition doesn’t allow for “degree” of irreducible complexity; a system either has it or it doesn’t. Yet certainly some IC systems are more complex than others; some seem more forbidding than others.
While thinking of Keith Robison’s scenario, I was struck that irreducible complexity could be better formulated in evolutionary terms by focusing on a proposed pathway, and on whether each step that would be necessary to build a certain system using that pathway was selected or unselected. If a system has to pass through one unselected step on the way to a particular improvement, then in a real evolutionary sense it is encountering irreducibility: two things have to happen (the mutation passing through the unselected step and the mutation that gives a selectable system) before natural selection can kick in again. If it has to pass through three or four unselected steps (like Robison’s scenario), then in an evolutionary sense it is even more irreducibly complex. The focus is off of the “parts” (whose number may stay the same even while the nature of the parts is changing) and re-directed toward “steps.”
Envisioning IC in terms of selected or unselected steps thus puts the focus on the process of trying to build the system. A big advantage, I think, is that it encourages people to pay attention to details; hopefully it would encourage really detailed scenarios by proponents of Darwinism (ones that might be checked experimentally) and discourage just-so stories that leap over many steps without comment. So with those thoughts in mind, I offer the following tentative “evolutionary” definition of irreducible complexity:
An irreducibly complex evolutionary pathway is one that contains one or more unselected steps (that is, one or more necessary-but-unselected mutations). The degree of irreducible complexity is the number of unselected steps in the pathway.
That definition has the advantage of promoting research: to state clear, detailed evolutionary pathways; to measure probabilistic resources; to estimate mutation rates; to determine if a given step is selected or not. It allows for the proposal of any evolutionary scenario a Darwinist (or others) may wish to submit, asking only that it be detailed enough so that relevant parameters might be estimated. If the improbability of the pathway exceeds the available probabilistic resources (roughly the number of organisms over the relevant time in the relevant phylogenetic branch) then Darwinism is deemed an unlikely explanation and intelligent design a likely one.
A note on categories. So far we have:
MP - Multiple Part
CS - Construction Sequence
CW - Complex Whole
EP - Evolutionary Pathway
All of the categories are going to overlap in certain ways. However, I am focusing on the emphasis of varying definitions in developing these categories. So, CS differs from EP in that CS focuses on the local construction sequence (the construction sequence of flagella for example) while EP focuses on the global/historical evolution of the system. Also, MP definitions usually make arguments to the effect of precluding all evolutionary designs, and put their main emphasis on the static, multi-part system that lies before us. They argue from one thing (the IC of the current system) to another (the inability of the Darwinian mechanism to reach the final state via *any pathway*) EP definitions, on the other hand, put the emphasis on specific evolutionary pathways and the necessary steps in historical development.
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gedanken
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posted 17. March 2003 23:03
Thanks, Alonso, “laying it out” was exactly what I was looking for. The “Structural Definition” test is a good example, IMO, because it uses a specific definition, but gives detail of how to go about testing the terms of that definition. So I would like to label Alonso’s test for “Structureal Definition”:
quote:
MP-2-Test-1:
Structural Defintion
Start with system X with parts A,B,C,D that have function F*.
To test whether this is an IC system using MP-2 I remove either A, B, C, or D from the system. If the function F* is lost then the system is irreducibly complex according to MP-2. If we remove D from the system, and function F* is preserved, then we are left with system A,B,C where D was a redundant part. We then remove A from the system, and if function F* is preserved then we have system B,C where A and D were redundant. We then remove B and if function F* is preserved then we have the system C and therefore it is not irreducibly complex according to definition MP-2.
Note that I am giving a naming convention -- a given test for a given definition can be labeled with the definition ID, followed by a “Test-m” identifier for the specific test description. Thus the general labeling form <Cat>-<N>-Test-<M> for IC definition <Cat>-<N>.
I would note that this can be viewed as a somewhat “logical” or armchair test. But this can be refined into an actual laboratory test if one could genetically engineer organisms in which one actually removed “parts A”, etc. from the organism, and observed the function. So this is progress over the simple definition -- a point I want to emphasize.
This test might not be a complete test for all elements of definition MP-2. Specifically it addresses MP-1 (simple or direct irreduciblility) directly in considering removal of A through D as immediately removing function. Then it addresses the “complexity” aspect of MP-2 by describing a contradicting case in which the successive reduction to the core reduces to a single part. So my question in this is whether a more generalized test procedure is needed to identify the case in which there is a “core” that is irreducible but with that core not consisting of the whole? Is this an issue where we need another test for this case?
The case where removing D from the system, and function F* is preserved, yet singly removing any of the remainder of the parts destroys function was not described. I do not know whether such a case is IC or not -- does it have a “complex IC Core” of A,B,C? Can someone add this case to the test procedure and describe how it affects the answer? And please note the importance of writing out detailed test procedures, so as to clarify our understanding.
Here is the first case, where knocking any part out kills function (assuming monotonicity):
code:
A B C D F*
======= ==
1 1 1 1 1
-------
0 1 1 1 0
1 0 1 1 0
1 1 0 1 0
1 1 1 0 0
-------
0 0 1 1 0
0 1 0 1 0
0 1 1 0 0
1 0 0 1 0
1 0 1 0 0
1 1 0 0 0
-------
0 0 0 1 0
0 0 1 0 0
0 1 0 0 0
1 0 0 0 0
-------
0 0 0 0 0
-------
And here is the second case demonstrated where part C solely and trivially supports F*, not IC due to low “complexity.” There are 4 such cases, either A,B,C, or D trivially supporting function F*.
code:
A B C D F* Knockout Step
======= == =============
1 1 1 1 1
-------
0 1 1 1 1
1 0 1 1 1
1 1 0 1 0
1 1 1 0 1 (Step 1 remove D)
-------
0 0 1 1 1
0 1 0 1 0
0 1 1 0 1 (Step 2 remove A)
1 0 0 1 0
1 0 1 0 1
1 1 0 0 0
-------
0 0 0 1 0
0 0 1 0 1 (Step 3 remove B)
0 1 0 0 0
1 0 0 0 0
-------
0 0 0 0 0 (Step 4 remove C)
-------
What about this case? I present it to ask if another test procedure needs to be written for MP-2. It is a case in which any 3 parts support the function F*, but any 2 or less will fail. I don’t know if it is supposed to show IC or not according to MP-2:
code:
A B C D F*
======= ==
1 1 1 1 1
-------
0 1 1 1 1
1 0 1 1 1
1 1 0 1 1
1 1 1 0 1
-------
0 0 1 1 0
0 1 0 1 0
0 1 1 0 0
1 0 0 1 0
1 0 1 0 0
1 1 0 0 0
-------
0 0 0 1 0
0 0 1 0 0
0 1 0 0 0
1 0 0 0 0
-------
0 0 0 0 0
-------
What is the result here, especially considering the combination table above as a whole? Also the procedure would probably need to be written in terms of testing all 16 combinations. Note this is different from the case where A,B,C are required, but D is not, mentioned previously.
Could someone consider a way to fill in this table with respect to MP-2 definition of IC? This could define a more exhaustive test for 4-part IC by definition MP-2, but the table is not well-defined because it does not capture combinatorial effects:
code:
F*==1 For how many?
A B C D NONE 1 2 3 4 5 6
======= ==== == == == == == ==
1 1 1 1 Bad x na na na na na (Trivial)
------- ---- -- -- -- -- -- --
0 1 1 1 IC ? ? ? ? na na (MP-1)
1 0 1 1
1 1 0 1
1 1 1 0
------- ---- -- -- -- -- -- --
0 0 1 1 ? ? ? ? ? ? ?
0 1 0 1
0 1 1 0
1 0 0 1
1 0 1 0
1 1 0 0
------- ---- -- -- -- -- -- --
0 0 0 1 x F F F F na na (low complexity)
0 0 1 0
0 1 0 0
1 0 0 0
------- ---- -- -- -- -- -- --
0 0 0 0 x F na na na na na (Trivial if still works)
------- ---- -- -- -- -- -- --
Bad == don’t consider this case as relevant starting point.
x == don’t care, doesn’t affect result
F == Falsify IC
IC == True IC by MP-2 (and assuming that monotonically lower number of components don’t ‘function’.)
It turns out that there are actually 16384 possible answers to what happens when one removes ‘parts’ in any of the combinations (assuming that F*==1 for all parts present “1 1 1 1”, and that F*==0 for all parts absent “0 0 0 0”). Now if one simply counts how many allow to function for each group of N knockouts (1,2,3), then there are 175 possible combinations (5 * 7 * 5). But if one assumes monotonicity -- that after a knockout that no further knockouts can restore function -- then the cases are reduced further. In that case there are 14 combinations of what can happen, simply by counting how many cases of N knockouts still function in successive trials:
code:
Knockouts IC case?
1 2 3
----------------------------------------
Functioning: 4 3 2 NOT-IC (low complexity)
4 3 1 NOT-IC (low complexity)
4 3 0 What is this case?
4 2 1 NOT-IC (low complexity)
4 2 0
4 1 0
4 0 0
3 2 1 NOT-IC (low complexity)
3 2 0
3 1 0
2 1 0
2 0 0
1 0 0
0 0 0 IC (MP-1)
I would note that this table shows that we have not yet presented a test that actually follows the words of MP-2 (as opposed to MP-1, and the trivial case of a singleton functioning part, if such a thing can exist.)
--
However, Alonso, on “Evolutionary Definition” I don’t quite see the description as a prescriptive set of steps that result in a resolution of the problem, as in a “laboratory test procedure”. Now one may not be possible, I don’t’ know. I’m not criticizing the test but rather asking if a more detailed test needs to be defined. But if we are going to label something as a “test procedure” it should in my opinion reasonably be guaranteed to give an answer, or at least its limitations should also be described in association with the test. For example the procedure could be refined to be labeled as a “falsification” procedure for EP-? definition, but one that does not give a positive answer in a complete an objective fashion.
For example the steps:
quote:
We now study the evolutionary steps between system Y and system X. We start with A and invoke a mutation or other chance event that causes B to interact with A.
Could you describe this in more detail or in terms of a larger picture? What I mean is, do you study all possible mutations that form evolutionary steps, and thus exhaustively study all evolutionary steps that are possible between system Y and system X? What I suggest is some description of how one produces the exhaustive list to study, and some estimate of its size for typical cases. (I don’t mean to get into examples, but are there billions of cases to be examined, each taking years of study, in the typical case, for example?)
Or if such procedures cannot be outlined, can you classify this test procedure and refine it as I suggested, as in listing as a falsification only for IC. Also is this intended to be using Behe’s EP-1 as Micah subsequently presented? (Or is there another evolutionary definition that should be presented?) If it is a falsification only (not a test that gives a positive answer) we could label it EP-1-Falsificaiton-1, for example, to distinguish it from a “test” that more or less gives an algorithmic set of steps to an up/down conclusion when completed.
I detect a little bit of hostility in being asked to “lay it out”, but I think this is important work in understanding IC. Thanks for this.
Because I realize from this a possibility that I had not realized before -- that a given definition might not have a procedural test that gives an up/down answer. One could simply say “just go through the terms of the definition one by one, and that is the test.” But here we see clearly the possibility that the “steps” might not be ones that can be written out as a simple up/down “procedure” to evaluate. This demonstrates the extreme importance of detailing the test procedure -- because one learn details about how to apply it to the real world that are not recognized in a strictly armchair demand to follow the terms of the definition. And I hasten to point out that even these test procedures so far are not concrete applications to actual cases and basing on actual observation of nature to give the answers -- this is a further test. But even the examining of this logical level of test procedure is very instructive. I encourage participants to continue to provide test procedures.
[ 18. March 2003, 04:03: Message edited by: gedanken ]
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yersinia
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posted 18. March 2003 03:27
In the "multiple parts required" category, I would note that various people (pro- and anti-ID both) have at times employed various methods of determining what the "parts" and "essential parts" are for an IC system.
There are at least four kinds of "required parts" that I've seen used in the molecular machine context.
quote:
Various definitions of "parts" that have been employed
1) "Logical" parts. This was fairly prominent in Behe's book although #2 (below) was also applied. E.g. a paddling machine must have a paddle and a motor (and probably a base/anchor or some such) just out of the pure logical necessity of a swimming machine; this can map to single proteins or groups of proteins, depending.
E.g., IIRC Behe defined a bacterial flagellum's parts as stator, rotor, motor (3 logical parts) but most IDists now say ~20 parts (or ~40 parts, the distribution of parts claims appears bimodal).
2) Required parts as determined by knock-out experiments/interference experiments/genetic mutations. Proteins.
3) Required parts as determined by "those parts needed in all organisms". E.g., part X might be required for function in organism A (as determined in a knockout experiment) but not in organism B (as determined by the fact that organism B has the function just fine without X). This raises the very interesting issue of how X became required in A but not B, and what this means for the ICness of both systems and the IC-->ID argument but this is another topic.
4) Required parts as in #2, but including pieces of proteins, sometimes down to individual amino acids. Subject to similar multi-organism issues as #3.
If I might be permitted just a little editorializing, no one has clarified which of the above is "right" and frankly IMO they are usually chosen arbitrarily, on the basis of whatever seems to be the greatest advantage in the topic at hand.
(The above comment applies to both sides, actually, although as the term "IC" was invented by the IDists the ID skeptics have no power to decide what the "right" one is. All they can do is complain about inconsistent usage. IMHO if you are interested in evolution then #1 is the most important (it corresponds pretty well with "minimal theoretically functional system") but I could live with #3 as well *if everyone would stick to it*.
Other common sub-terms of IC such as "function" and "system" are similarly highly ambiguous, but that is for another time...
[ 18. March 2003, 03:32: Message edited by: yersinia ]
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gedanken
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posted 18. March 2003 03:41
Yersinia, it is my contention that if any of the cases posed a difficulty for evolution, then that particular case (labeled IC) would be important. So we don't need a "right definition", any will do if it actually poses such a difficulty.
There is nothing wrong with choosing among the possible definitions to find one that poses such difficulty if it can be applied to a given case.
Where the problem occurs is when mixed definitions are applied within the same argument, without clarifying which definitions are being used. My intention here is for writers to produce multiple self-consistent definitions. Then one can ask if the definition (if found applicable) poses a difficulty for evolution. And one can ask if the given case fits the definition.
But one must ask both questions while holding the definition constant -- one cannot say that definition A clearly poses a problem for evolution if it were found in nature, and clearly we have a case of definition A' being met therefore we have an observational difficulty for evolution. That would be arguing a logical fallacy.
But there is no problem with choosing the most advantageous definition per se.
Also note that the logical procedures or actual laboratory procedures used to verify that a particular definition is being met may or may not actually verify that particular definition. (For example we have test procedures presented above that only examine certain sub-cases of the definitions given. Figuring out which sub-cases the given test procedure examines is important, so we can determine if actual real cases might cause false positives with a given test.) So we have yet another place for logical inconsistency, in that claims about reality may not actually imply that the definition being presented is actually being met. That is why I think it is so important to describe the “test procedures” in such great detail -- they are not simply “obvious” from the definitions. This is just like in laboratory science, that the actual laboratory test being designed may or may not actually demonstrate the postulated theory -- and actual laboratory procedures need to be written up and results verified. The details need to be presented in peer-reviewed literature, so that peers can examine them to see how relevant the procedures and results are to the hypothesized theories. (Here I am not asking for “results”, simply asking for the “test procedures” that are to be used, along with the definitions of the terms to be “tested”.)
[ 18. March 2003, 11:10: Message edited by: gedanken ]
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Nel
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posted 18. March 2003 22:29
Ged writes:
quote:
The case where removing D from the system, and function F* is preserved, yet singly removing any of the remainder of the parts destroys function was not described.
In fact, this was described. I mentioned that if we remove D from the system, and function F* is preserved, then we are left with system A,B,C where D was a redundant part. We then remove A from the system, and if function F* is preserved then we have system B,C where A and D were redundant. We then remove B and if function F* is preserved then we have the system C and therefore it is not irreducibly complex.
Your third case describes a system where each component had a dual redundant roles in the system making removal of any component preserve function. So in such a system where there are four components, the IC system consists of "3 parts" according to MP-2. Where component A does the work of A and B, and component B does the work of A and B such that removal of both A and B causes the system to lose F*. Removing C you still have D doing the job of C and D. Removing C still does the job of C and D.
Ged, could you describe your fourth case in a few words, it makes absolutely no sense to me. For example, this phrase:
quote:
that after a knockout that no further knockouts can restore function
A knockout, as I think you are using it, is when a gene is removed from the system causing either preservation of function (a redundant gene product) or loss of function. I've never heard of a knockout restoring function. Of course you could not be referring to knock-outs done in the laboratory. In short, if you could give a short summary of the "knock-out" table I will be able to respond. Nonetheless, that even one test case successfully delinates and IC system (the first and second one) thus far, 3 test cases show a confirmation of MP-2. Furthermore, you keep distinguishing MP-1 from MP-2 as if MP-1 states that removing any component from any component from an IC system regardless of redundancy will destroy function. A charitable reading of Behe shows this is not the case, such as when he did not mention Hageman as the part of the "IC core" of the clotting cascade. Examples of a singleton part functioning has been shown to you as Hemoglobin, Dawkins's membranes, and PPi synthase.
As for my test for EP-1, I don't understand your complaint against it other than you say that I need to test all possible evolutionary pathways.
The evolutionary pathway is not an unlimited space free for all, it is constrained by the proposed phsyical precursor given by an evolutionary proposal. Darwinian evolution requires physical precursors not imaginary ones. Thats why it was easy to test the proposed T3SS to bacterial flagellum pathway, and it was found that it was IC.
One can falsify whether a particular evolutionary pathway is IC by showing that each step is functional and therefore selectable. In this definition of irreducible complexity we can define it as some ID critics erroneously interpreted MP-1.
quote:
A single system composed of several well-matched, interacting parts that contribute to any function of the system, wherein the removal of any one of the parts causes the system to be completely non-functional.
This is a structural definition that can be tested without knowing that Darwinian theory exists.
Here we have a system A, B, C, D with function F*. Removal of D causes the system to become functionless (no function at all and 1 degree of irreducible complexity). But removal of C causes the system to have a different function. But removal of B causes the system to be functionless (2 degrees of irreducible complexity). We now have a functionless 1 component system.
Note that this overlaps with MP-2 in that the original function cannot be reduced to 1 component.
EP-1 = 2 degrees
I'll call my definition MP-3. But I digress.
Back to EP-1.
This definition EP-1 requires that we be specific with the proposed pathway. The more specific we are, the more penalties will likely need to get worked into the details of the evolutionary pathway (such as gene silencing for a gene duplication event or complete loss of function of the particular part).
One can falsify EP-1 by showing that each step is functional and selectively advantageous. Consider evolutionary precursor with alternate function F1 and the system we are interested in , system Y with function F2. We have parts A, B, C, D, E, G, H for system Y and parts A,B,C for system Y.
If A has function F3 we have a selectable step.
If AB has function F4 we have a selectable step.
If ABC has function F2 we have a selectable step.
If ABCD has function F5 we have a selectable step.
Adding ABCDE gives us F6 , a selectable step.
If ABCDEG has function F1...DONE.
If there is even one step in the above where I was wrong, and in fact we had no F (no function) then the proposed evolutionary pathway is IC.
Of course, all of this displays a naive, oversimplistic way of looking at biological systems in that components of biological systems are very different from putting alphabetical letters together, but as a simplistic way of understanding IC, it should suffice. For a discussion of this, see:
John Bracht’s response to Matt Young, “Knotty Pine and Corroding Coins
and
Ursula Goodenough’s response to Bracht, “Of Flagella and Outboard Motors”:
and
John's response
And Part II
[ 18. March 2003, 22:45: Message edited by: Nelson_Alonso ]
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Nel
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posted 18. March 2003 23:12
Yersinia,
I think your point 1) maps to what Julie Thomas called "thematic IC" and when IDists point to U~21 parts of the flagellum they are pointing to what Julie Thomas called "Ur-IC". I think both are useful to ID/TOE in studying these systems and their origins.
2) Might be systematic IC. In a sense 2) is indistinguishable from 1) in that we can map the thematic parts to the schematic parts thus obtaining the same result in both cases.
3) is essentially indistinguishable from 2) (i.e. we get the same result) in that components A and B are not needed by all organisms (i.e. L and P rings in gram-negative bacteria) therefore they can be removed from the required list.
4) is interesting in that we can increase an IC system from 20 parts to 1000 parts. But I don't think we have the technology for this yet. But you still get the same result as 1) through 3).
Let us not forget molecular IC where the focus is on sequences such as the 9bp of OriC.
So in a sense they are all right. Function and system although not precise, is not, in my opinion, ambiguous either. But I'll stop there before I get zapped by the "mini-mod". Thats all I have time for tonight.
[ 19. March 2003, 00:04: Message edited by: Nelson_Alonso ]
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