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Author
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Topic: Dembski on functional subsystems in "Uncommon Dissent"
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yersinia
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Member # 324
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posted 23. July 2003 23:10
Nelson writes,
quote:
But, Nelson, this is mere assertion on Behe's part. His book is all about how direct pathways can't produce IC. He doesn't, say, spend a chapter somewhere documenting that indirect pathways are unlikely, he just asserts it in that one quote.
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This is not an assertion, it's actually quite intuitive. If you don't have many intermediates to reward in an evolutionary pathway, then most of the pathway is likely to be just pure chance, and pure chance drops the probability. Thats why natural selection was proposed in the first place.
Please show me where Behe discusses the existence of functional intermediates in that quote, Nelson. It's not here:
quote:
Even if a system is ireducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circutious route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows.
Nothing there about the presence or absence of functional subsystems. Just an assertion that pathways are unlikely.
However, are you saying that *because* functional subsystems in complex IC systems are rare, *therefore* Behe's assertion about indirect pathways is valid? That would at least be coherant.
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Pim van Meurs
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posted 23. July 2003 23:26
Nelson constructs a red herring when he asks "Since there are so many ways, and you are comparing this with flagellum, show me 10 such pathways for the bacterial flagellum."
I hope that Nelson understand how silly his request is. But he should also realize that without the necessary historical pathways Behe and Dembski's hopes of eliminating natural pathways for the flagellum to be able to infer design seems hopelessly frustrated by the lack of relevant data.
Instead of resorting to strawman calculations as found in NFL for the probability of the flagellum to arise in an almost random fashion, Lenski et al have shown some powerful arguments that contradict much of the claims made about complexity, complex systems, CSI and IC. Now I would agree that Lenski et al are not the only strong claims against CSI and IC but they show once and for all that such pathways are not 'just so stories'.
In fact I would argue that Lenski et al have advanced our knowledge of IC systems and the possible (in)direct evolutionary pathways more than ID has advanced its negative claims about evolution as it applies to such systems.
How many years ago was the flagellum proposed as an example of ICness and how close have its proponents gotten to showing reasonable probability estimates? ID had a great opportunity on expanding our knowledge of IC-like systems but it seems that the momentum has shifted to non-ID scientists who are engaged in very fruitful research.
I guess in some way one could consider this an example of fruitful research related to ID?
Thus when Nelson states "Complex systems like flagella are harder, because of what Dembski calls the "sea of non-functionality"." he lacks any supporting data about this 'sea of non-functionality' in fact this sea seems to be more like a dessert to me ![[Wink]](wink.gif)
Yersinia: However, are you saying that *because* functional subsystems in complex IC systems are rare, *therefore* Behe's assertion about indirect pathways is valid? That would at least be coherant
Coherent perhaps but begging the question as well.
Nelson suggests that "However, the reason why it is hard to envision the stepwise evolution of things like flagella is because it is so complex with very little, if any, simpler alternative functions. "
Hard to envision perhaps but how is that evidence of the absence or presence of such pathways? How is ICness going to help us establish the probabilities involved in these pathways if they are so hard to imagine? Would the ICness of the flagellum thus be linked to our ability to formulate such pathways and in fact would ICness be nothing more than a "ICness of the gaps" in this aspect?
But let's not get sidetracked from the astute observations by Yersinia as to the evolving arguments of Dembski. Perhaps the death of (darwinian) evolution has been severely exaggerated ![[Big Grin]](biggrin.gif)
[ 23. July 2003, 23:42: Message edited by: Pim van Meurs ]
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RBH
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posted 24. July 2003 00:07
Nelson Alonso wrote quote:
Then you are not saying anything differently from what Behe said in the very first printed version of the IC thesis as applied to modern ID theory. IC systems that have many simpler functions can evolve (and is thus simple itself). Complex systems like flagella are harder, because of what Dembski calls the "sea of non-functionality".
Behe made some brief remarks, qualitative but nonetheless probabilistic, about that, as yersinia has noted. Nowhere in Behe's remarks have I seen explicit reference to a relationship between varying numbers of simpler structures and the probability of indirect pathways. Further, as I said, I'm interested (in this context, at any rate) in the conditions under which IC objects, etc., can (or perhaps cannot) evolve. Behe has done nothing visible along those lines since that first appearance in print. I'm saying something quite different from his brief remarks about the (subjective) improbability of indirect pathways. I'm saying it is amenable to research, and am setting up the facilities to do that research. Why hasn't he, given that it's apparently an important variable in determining whether ID structures can evolve? It's his concept, after all.
Quoting me, Nelson then wrote quote:
RBH : quote:
As analyses of the Lenski, et al., lineages show, and as analyses of the devices evolved in the hardware evolution research literature show, it is very very difficult to reconstruct an evolutionary pathway looking at just the end product.
Not true. In fact, Lenski et. al. had written their own version of EQU which is much simpler than most that actually evolved.
Um, the observation that Lenski, et al., wrote an assembly language program that performed EQU is a non sequitur: it says nothing whatsoever about the problem of inferring the evolutionary history of a product by looking at that product. And at least one lineage evolved a program that performed the mapping corresponding to EQU in fewer (knockout-defined) instructions than that they wrote by hand. But the point that histories are difficult to infer from end-points is unaffected by observing that one can write such a program. That's irrelevant.
Nelson further wrote quote:
It is simple to envision the stepwise evolution of hemoglobin because it has so many functional intermediates, even simpler to envision the evolution of a two-part protein system that is IC.
Relative difficulty of envisioning depends on how much one knows, how good one's tutored, informed imagination is, and what cognitive set one begins with. Don't mistake the ability (or lack thereof) to envision something for what's the case in the world.
Nelson further wrote quote:
Really your reply here is just one big fat promisory note, which is nothing different from all the other promisory notes we get with other complex biological systems.
Like the immune system? and here? Or the blood clotting cascade? Or even the flagellum? It looks to me like whatever promissory notes that might have been given are in the process of being paid off.
By the way, when does Nelson envision that "ID theory" will present a plausible and perhaps even testable historical narrative of the origin of the flagellum?
RBH
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Pim van Meurs
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Member # 541
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posted 24. July 2003 00:11
RBH: Behe has done nothing visible along those lines since that first appearance in print.
Indeed this is my argument, intelligent design proponents had the momentum to propose and direct its contribution to our understanding of IC systems, instead we had to wait for Lenski et al to help us understand the limitations and usefulness of ICness.
Thus RBH's question to Nelson is an important one
"By the way, when does Nelson envision that "ID theory" will present a plausible and perhaps even testable historical narrative of the origin of the flagellum?"
[ 24. July 2003, 00:12: Message edited by: Pim van Meurs ]
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Nel
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posted 24. July 2003 18:42
Nic writes:
quote:
Please show me where Behe discusses the existence of functional intermediates in that quote, Nelson.
Nic, Behe mentions it when he quoted Darwin a page earlier with regard to small steps guided by natural selection.
Nic writes:
quote:
Just an assertion that pathways are unlikely.
Again, it's not an assertion. Co-option is ultimately pure chance, and co-option is an indirect pathway. Thats the probability for very complex systems "drops precipitiously".
Nic writes:
quote:
However, are you saying that *because* functional subsystems in complex IC systems are rare, *therefore* Behe's assertion about indirect pathways is valid? That would at least be coherant.
Thats what I've been saying. ![[Confused]](confused.gif)
[ 24. July 2003, 18:42: Message edited by: Nelson-Alonso ]
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Nel
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posted 24. July 2003 18:44
PvM writes:
quote:
Thus when Nelson states "Complex systems like flagella are harder, because of what Dembski calls the "sea of non-functionality"." he lacks any supporting data about this 'sea of non-functionality' in fact this sea seems to be more like a dessert to me
Ok. Show me all the simpler alternative functions of flagella. If it's a desert as you say, then this should be simple.
[ 24. July 2003, 18:44: Message edited by: Nelson-Alonso ]
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Pim van Meurs
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Member # 541
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posted 24. July 2003 19:06
Nelson after stating
"Complex systems like flagella are harder, because of what Dembski calls the "sea of non-functionality"." and asked for supporting data, all Nelson can do is point to absence of our understanding one way or another of the history of the flagellum.
Should our ignorance now count as a design inference? Are we now using "ICness of the gaps" ?
You quoted Dembski approvingly and thus I was wondering if there was some data suggesting the sea of non-functionality. I doubted that there was and I seem to have been correct.
Nelson additionally comments "Co-option is ultimately pure chance, and co-option is an indirect pathway".
Perhaps Nelson could show why co-option is an indirect pathway? What if evolution preferentially moves through co-option of existing function? Why is co-option a pure chance pathway.
Details would be helpful here Nelson.
In the mean time
quote:
Co-option occurs when natural selection finds new uses for existing traits, including genes, organs, and other body structures. Genes can be co-opted to generate developmental and physiological novelties by changing their patterns of regulation, by changing the functions of the proteins they encode, or both. This often involves gene duplication followed by specialization of the resulting paralogous genes into particular functions. A major role for gene co-option in the evolution of development has long been assumed, and many recent comparative developmental and genomic studies have lent support to this idea. Although there is relatively less known about the molecular basis of co-option events involving developmental pathways, much can be drawn from well-studied examples of the co-option of structural proteins. Here, we summarize several case studies of both structural gene and developmental genetic circuit co-option and discuss how co-option may underlie major episodes of adaptive change in multicellular organisms. We also examine the phenomenon of intraspecific variability in gene expression patterns, which we propose to be one form of material for the co-option process. We integrate this information with recent models of gene family evolution to provide a framework for understanding the origin of co-optive evolution and the mechanisms by which natural selection promotes evolutionary novelty by inventing new uses for the genetic toolkit
Gene co-option in physiological and morphological evolution. True JR, Carroll SB.Annu Rev Cell Dev Biol. 2002;18:53-80.
quote:
For example, it is becoming clear that co-option has played a critical role in evolution and the homeotic genes are not exempt in this regard. To demonstrate this point we can point to the expression pattern of the homeotic gene Ubx in various arthropod groups and the most basic morphology of the segments within its expression domains.
Understanding the genetic basis of morphological evolution: the role of homeotic genes in the diversification of the arthropod bauplan. ALEKSANDAR POPADIC, ARHAT ABZHANOV, DOUGLAS RUSCH and THOMAS C. KAUFMAN Int. J. Dev. Biol. 42: 453-461 (1998)
[ 24. July 2003, 20:39: Message edited by: Pim van Meurs ]
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yersinia
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posted 24. July 2003 20:49
Nelson writes,
quote:
Nic, Behe mentions it when he quoted Darwin a page earlier with regard to small steps guided by natural selection.
No, on the previous page he is discussing simpler systems *with the same function*. He is discussing *direct* pathways on the previous page.
quote:
Nic writes:
quote:
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However, are you saying that *because* functional subsystems in complex IC systems are rare, *therefore* Behe's assertion about indirect pathways is valid? That would at least be coherant.
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Thats what I've been saying.
Good, that's what I thought. Too bad for you, though, because Dembski says (or said, before Lenski's paper came up) that functional subsystems in complex IC systems are *common*, not *rare*. I documented this in opening post, you may recall.
So, Nelson, either you or pre-Lenski-Dembski is wrong. You just sided with post-Lenski-Dembski.
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Nel
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posted 24. July 2003 21:24
Well, still havn't finished my reply to RBH so I'll reply quickly to Nic,
Nic writes:
quote:
Good, that's what I thought. Too bad for you, though, because Dembski says (or said, before Lenski's paper came up) that functional subsystems in complex IC systems are *common*, not *rare*. I documented this in opening post, you may recall.
Where does Dembski say that they are common? That is a very important distinction. No, you didn't document any such thing. Common in the sense that every subsystem can be further broken down to even simpler subsystems, until eventually you have a very simple pre-cursor. This is true with EQU, it is not true with very complex machines like flagella.
[ 24. July 2003, 21:30: Message edited by: Nelson-Alonso ]
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Nel
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posted 24. July 2003 21:31
PvM,
I couldn't find any support for this statement:
quote:
'sea of non-functionality' in fact this sea seems to be more like a dessert to me
with regard to flagella in your post. Can you please support this statement?
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yersinia
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posted 25. July 2003 10:06
Nelson, Dembski says that subsystems "always" exist! What more do you want?
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Pim van Meurs
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Member # 541
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posted 25. July 2003 16:41
Nelson: Exactly my point, the absence of any evidence of a "sea of non-functionality" surely seems like a dessert to me.
I was hoping to get some clarification on your part as to the evidence. May we expect some?
Also, you may have missed my question to you
quote:
Nelson additionally comments "Co-option is ultimately pure chance, and co-option is an indirect pathway".
Perhaps Nelson could show why co-option is an indirect pathway? What if evolution preferentially moves through co-option of existing function? Why is co-option a pure chance pathway.
[ 25. July 2003, 16:48: Message edited by: Pim van Meurs ]
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Pim van Meurs
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posted 25. July 2003 16:47
An organism is a functional system comprising many functional subsystems
Dembski
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Nel
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posted 25. July 2003 22:13
There was some weird bandwidth problem yesterday and couldn't respond.
RBH writes:
quote:
Nowhere in Behe's remarks have I seen explicit reference to a relationship between varying numbers of simpler structures and the probability of indirect pathways.
He does so explicitily here:
quote:
Even if a system is ireducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circutious route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. And as the number of unexplained, irreducibly complex biological systems increases, our confidence that Darwin's criterion of failure has been met skyrockets toward the maximum that science allows.
and here:
quote:
"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."
Note that in both quotes he directly associates selectable steps with the degree of irreducible complexity. The second quote is much more explicitly referring to any function, even alternative functions.
Behe here is referring to co-option. An "indirect" pathway has different functions all the way leading up to the function we want (i.e. flagella). Since direct pathways are the same function, what we would need for flagella is many different functions (and thus indirect). Like EQU, we see this, many different functions lead up to EQU (although the comparison with flagella is ridiculous but it illustrates my point well).
RBH writes:
quote:
I'm saying it is amenable to research, and am setting up the facilities to do that research. Why hasn't he, given that it's apparently an important variable in determining whether ID structures can evolve? It's his concept, after all.
Actually what you are saying is nothing different from what Behe said. Also, Behe has in fact, both in print and in public debates in conferences (such as ID and it's Critics) discussed very extensively how T3SS, although it is a sub-function of flagella, do not make the indirect pathway required for flagella probable. I'm sure if the Baylor situation was better, you would see a lot more research on this subject. Unfortunately that turned into a circus.
RBH writes:
quote:
Um, the observation that Lenski, et al., wrote an assembly language program that performed EQU is a non sequitur: it says nothing whatsoever about the problem of inferring the evolutionary history of a product by looking at that product.
Actually it says everything about it. Wouldn't you be impressed, if I wrote out by hand, many simpler subfunctions that could lead to a functioning bacterial flagella that doesn't require all the 20 parts scored by IDers? Adding this to the fact that by looking at the end product (i.e. hemoglobin) we can very easily show functions that are selectable. Looking at the end-product has much value.
RBH writes:
quote:
And at least one lineage evolved a program that performed the mapping corresponding to EQU in fewer (knockout-defined) instructions than that they wrote by hand.
If you are referring to the 17 instruction EQU, it is unclear whether they underestimated the value because of redundancy.
RBH writes:
quote:
Relative difficulty of envisioning depends on how much one knows, how good one's tutored, informed imagination is, and what cognitive set one begins with. Don't mistake the ability (or lack thereof) to envision something for what's the case in the world.
Well I really don't share your faith. The trend in scientific discovery is that things usually turn out to be much more complex then they really are, for example, with regard to the Hebbosome, Dr. Seth Grant, a researcher on the subject, states:
quote:
Instead of floating in a sea of cytoplasm within the postsynaptic dendritic spine...many of the downstream signaling molecules involved in
NMDAR signaling are actually physically coupled to
NMDAR through a variety of protein–protein interactions and adaptor proteins.
NMDAR is part of a large multiprotein signaling machine.
The problem with flagella might just be that many of the parts do not have a non-flagellar function. That increases the unlikelihood of actually getting flagella through an evolutionary pathway. The situation is different with hemoglobin. We see the parts, we note the function, and we can reduce the function quite simply. We see EQU, we see the function, and we can reduce it to quite a few simpler functions, like Lenski et. al. did. We see flagella, we it's function and we can't seem to reduce it further than the T3SS.
RBH wrote:
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Like the Immune System ?
There is a big boo boo in that essay. Innate receptors with single specificities do not likely exist.
RBH writes:
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and here ?
Or the blood clotting cascade ? Or even the flagellum
None of these links currently work. However, I have a feeling that you are linking to Nic's various references which he rarely bothers discussing and that usually just speculate on genome duplications and simlarity.
RBH
quote:
By the way, when does Nelson envision that "ID theory" will present a plausible and perhaps even testable historical narrative of the origin of the flagellum?
When will you reply to the many responses you've been given to this question?
[ 25. July 2003, 22:14: Message edited by: Nelson-Alonso ]
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Nel
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posted 25. July 2003 22:16
Nic writes:
quote:
Nelson, Dembski says that subsystems "always" exist! What more do you want?
Of course subsystems always exist. As I already discussed, thats not what matters. What matters is how much of a gap there is between subsystems, such that a series of parts is unselectable. If a system can be decomposed to simpler functions, it can likely evolve. If only one (as in the case of flagella), then I'm afraid the sea of nonfunctionality needs to be dealt with.
[ 25. July 2003, 22:20: Message edited by: Nelson-Alonso ]
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