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Author
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Topic: positive prediction of IC? (RE: the complement pathway)
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rafe gutman
Member
Member # 134
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posted 12. April 2002 03:57
it is my understanding, from reading mike gene's posts, that a prediction of IC is that the components of an IC "core" will either be entirely present, or entirely absent in an organism. this can be either a positive prediction or a negative prediction, depending on the case. by positive prediction, i mean a prediction of something we will find, and by negative, a prediction of what we won't. negative predictions are in my opinion, bad science (most of the time), not because it is hard to prove a negative (which it is), but rather because it takes more effort to falsify it than to promote it. if an IDist were to make a prediction that a specific flagullar gene would not be found in a certain group of bacteria (based on the fact that the bacteria had no flagella), then how would they go about studying this? what kind of research would this lead to? all they could do is try and sequence the bacteria's genome, look for the gene, and hope they fail. this wouldn't make for a very interesting paper. however, not all IC predictions are necessarily negative. let's say that we identified a species of bacteria, and found 8 of 9 flagellar proteins in it. then IC would lead to the prediction that the 9th would be found. this would lead to meaningful research, as now the IDist could go through the sequence and look for the 9th gene. mike has done this. while i might argue that this type of logic was around long before anyone had heard of IC, at least it's a start. the question is, how often would this prediction be confirmed?
there are around 30 proteins involved in the mammalian complement system. 9 of them are called C1, C2, C3,......C9. those 9 are mentioned in behe's "darwin's black box". behe doesn't specify what the "core" of what he considers the IC complement pathway to be, but since he mentions all 9 C proteins, let's assume for the time being that all 9 are part of the "core". according to the concept of IC, if we look in any organism, either we'll see all 9 components there, or all nine absent. at least, that's what IC would predict. for example, sharks have a complement system with "most" of the 9 components. IC would therefore predict that the remaining components will eventually be found. what about agnathans (jawless fish)? so far, only 1 C protein has been positively identified (C3), though there are putatively others. however, several proteins homologous to other Cs have been identified (these are also present in mammals). functionally, 2 of the 3 complement activation pathways are present, and at least 1 (maybe 2 or even 3) of the complement response pathways have been identified. so does IC predict that eventually we'll find the remaining C proteins? could this be a useful research project for a young IDist?
for IC to be a meaningful concept, regardless of its relation to ID, it must make positive predictions. additionally, those predictions must be confirmed. if they are wrong as often as they are right, then IC will not offer any meaningful perspective to the study of biochemical systems.
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Mike Gene
Member
Member # 149
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posted 12. April 2002 08:09
Hi Rafe,
But as I explained on my thread:
quote:
Two factors came into play in fine-tuning the concept of IC to make it a more effective research tool:
1)Understanding the logic of the IC system and why the parts are required and; 2) coupling IC to the concept of minimal function. Both factors stem from an approach that attempts to reverse engineer that which is hypothesized to have been engineered.
Let's say you are a "young IDist" submitting this as a proposal for funding. I would have to reject it since the "IC core" appears to have been chosen arbitrarily or myopically. I'd suggest that you refine the hypothesis by laying out the logic of the complement system, how the individual function of the different parts map to that logic, and why the logic of this system would entail something like nine parts. If your IC hypothesis leads to false predictions, it may simply be because the IC hypothesis has not formulated with enough rigor.
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charlie d.
Member
Member # 159
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posted 12. April 2002 09:54
You are right, Mike, but that's because you use structure/function reasoning in your definition of "IC", and therefore stick to molecular machines.
However, it seems to me that the "official" definitions of IC/CSI work irrespectively of how the components are organized, because they are either entirely probabilistic (Dembski) or refer to "unselected evolutionary steps" (Behe).
To them, a molecular machine made of 10 well-integrated, 100-aminoacid proteins, all indispensable, is pretty much equivalent to a cascade of 10 well-integrated, all indispensable, 100-aminoacid enzymes like complement. Obviously, it is not by chance that Behe listed complement and coagulation in DBB.
So, rafe, anyone like me, with a long (and often painful) grant application experience, would simply suggest you submit your grant to Dembski's study section, not Mike's. ![[Wink]](wink.gif)
[ 12 April 2002, 11:17: Message edited by: charlie d. ]
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rafe gutman
Member
Member # 134
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posted 17. April 2002 22:34
oops, forgot about this thread:
quote:
mike: Let's say you are a "young IDist" submitting this as a proposal for funding. I would have to reject it since the "IC core" appears to have been chosen arbitrarily or myopically.
i agree. i'm fairly confident in my understanding of the basics of the complement cascade, and i have no idea what the IC core would be. it does seem to be chosen arbitrarily. i couldn't tell you what the "function" of the system is, although behe makes it seem like its the formation of the membrane attack complex (MAC):
quote:
"like the blood-clotting pathway, the complement pathway is a cascade. inevitably, in both cases one encounteres the same problems trying to imagine their gradual production. it is not the final activity of a cascade that is the problem. the formation of a hole in a membrane does not necessarily require several different components... (DBB page 135)"
would you agree that that is a reasonable interpretation from his writings? if not, what do you think the function is?
i mention all 9 parts because behe does. again, he does not specify which parts are part of the "core", and does nothing to simplify it from the 9 parts he mentions. if i were to guess what the "core" would be, if the function is MAC formation, then i would say that it's C5b, C6, C7, C8, C9 (the components of the MAC), C3, Bf, and factor D. that would be the minimal set. if that is in fact the minimal set, then in every organism we find one component, we should find the others, right?
let me repeat the IC hypothesis in a more general way, so we can see how it can be used in a positive sense. if one component of an IC system is found in an organism, then IC would predict that the other components are also present. the only exception to this rule is when another system has co-opted one or more components from the original system. in that sense, we can say that the newer system evolved from the older system, as is therefore not involved in the origin of the older system.
if you do not agree with the above paragraph, what would you change to make IC a concept that yields positive predictions?
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