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Author
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Topic: Joshua A. Smart: On the Application of Irreducible Complexity
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RBH
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Member # 380
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posted 12. June 2003 22:36
Nelson wrote quote:
However, with 26 possibilities, many individual organisms going through replication and mutation will likely hit upon all of them, seperate organisms of course, that is likely and quite probable, especially when there are 26 possibilities and the function isn't all that complex.
Again an ambiguous pronoun: What is the "them" that is likely and quite probable? And how "likely and quite probable" is it that "many individual organisms will hit upon them" (whatever "them" is)? That's the question I asked John when he first broached this chance explanation and he didn't answer. Rex Kerr's estimate above (12. June 2003 12:05) takes into account "many individual organisms" - 10^8 of them. I ask Nelson to provide an estimate showing it's "likely and quite probable" that at least one organism (or many, if he prefers) will hit upon "all of them," telling us in the process what "them" is.
RBH
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Nel
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posted 12. June 2003 22:38
RBH,
The problem with the minimal estimate is exactly related to the problem of defining the parts as instructions, we are already in murky waters. Also the fact that there is only one kind of EQU supports my contention about flagella, and again, how we can't really remove a part like we can with flagella.
A lot of this holds true for genetic programs as well, where distrupting quite a few "instructions" doesn't really do diddly squat to the phenotype, makes this program a bit outdated.
Shastry, BS (1995) Genetic knockouts in mice: An update.
I mention more examples in Davison's thread. This code exists inside computers. So they don't have any "real" parts. Biological organisms have both a genome (the DNA) and the materials (such as the flagella) that are being produced from instructions in the genome. That is, they have both a genotype and a phenotype. Genes can be considered the parts of a genotype, while something like a flagellum is a part of the phenotype of a bacterium. Genetic algorithms often only have a genotype so they don't really have phenotypic parts. I've always read Mike Gene's material concerning IC, and it has always been about the machine nature of phenotypic parts which is very different from what we may be discussing here.
With respect to my discussion on flagella of bacteria, you write about eukaryotic flagella. Wasn't really talking about them, as they are completely seperate and different from bidirectional motors (the way bacteria do it). But thats ok, my point still stands even with eukaryotic flagella.
RBH writes:
quote:
Well, now we actually do see all sorts of flagella attached to motile single-celled entities, ranging from the 'standard' 9+2 to the 3+0 of Diplauxis hatti. See p. 142 of Finding Darwin's God for examples of a number of variants.
What you are referring to with respect to the 9+2 and 3+0 is the pattern of microtubules . The components of the eukaryotic cilia are linkers, motor, and MTs. It is not surprising to me to see such small variation in non-essential components, it's the MTs themselves that need to be present and this part is universal in all eukaryotic cilia, you will never find cilia without MTs. However, the 9+2 pattern is not essential so variation is expected here, and it's not much. As Mike has mentioned, in the 9+2 pattern, if we remove doublet 6, then doublets 5 and 7 can simply link up, that is an 8+2 pattern.
Most likely, it is the 3+0 pattern that is essential (and therefore IC). If thats true, one would expect to see no variation with the 3+0 pattern, (i.e. lower than 3+0). However, all the parts are conserved, much like the intelligently designed replication program, whenver you see cilia, you will always see linker, a motor, and MTs (regardless of what pattern they are in).
This is a far cry from the 17 to 43 instructions required for EQU, to say the least.
On to your next points, the fact that my illustration is high level is irrelevant since I can make the same point with Assembly language. The reason I can do this is because I was not pointing to the syntax of the language I was using, but simply the fact that instructions are spread out unlike machine parts.
set a, %r1
ld [%r1], %r2
set b, %r1
ld [%r1], %r3
sub %r4, %r5, %r3
add %r2, %r3, %r2
As far as your second objection, I have to disagree. They had to reward specific intermediate steps leading up to the EQU. And yet, with the flagellum, there are unselectable steps which give absolutely no reward, for example, what are the alternative, or subfunctions, within the export machinery of flagella? There are none. It presupposes exactly what the concept of IC questions.
So, in reality, one cannot accurately say we see so much plasticity from eukaryotic flagella by simply looking at the pattern of their MTs. Indeed, such statements make no sense in light of Biology, since what is conserved is the MTs themselves, and they are universal regardless of the pattern they are in. Biology reuses design principles, it doesn't re-use the same components in different configurations and permutations as if it was derived from simplistic co-option events. We see radically different structures that remain in statis within their kingdom and universal, no derivation, very little variation within essential components, but also, sometimes, with very little difference in the genetic code across kingdoms. And that of course is the problem.
[ 12. June 2003, 22:50: Message edited by: Nelson_Alonso ]
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Nel
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posted 12. June 2003 22:40
RBH wrote:
quote:
I ask Nelson to provide an estimate showing it's "likely and quite probable" that at least one organism (or many, if he prefers) will hit upon "all of them," telling us in the process what "them" is.
That is exactly what Rex calculated (it was something like 10^-620), and exactly why it is incorrect. One organism did not evolve all of the possibilities of the program. A bunch of organisms hit upon at least one of the possibilities (which is why it was a probable event, and it occured, no calculation needed).
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Mike Gene
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posted 12. June 2003 22:48
Okay, at least I got some of what I wanted. It looks like we can go back and define the EQU parts as the primitive instructions. Keep in mind that I consider gene products to be the parts of the IC molecular machines.
It has become clear to me that the parts of the EQU are quite unlike the parts of the mousetrap or flagellum. This can be easily seen by surveying RBH’s listing of Run 130 (which he kindly provided). Consider part “t”. It is found in nine different positions/contexts – instruction # 14, 21, 24, 36, 40, 50, 56-58. In five positions, it is essential and in four positions is not. Thus, the same part, in the same assembly has both function and non-function, depending on the context. In a sense, the parts are smeared throughout the assembly.
The theme is repeated when we survey the various other ways to arrange the same parts to generate the same function (the 23 runs). What I see is permutations. Different ways to get the same function by shuffling around the same parts.
But if this were to map to the flagellum, it would be like saying flgC (part of the drive shaft) is part of the basal body, the drive shaft, the rotor, the motor, and the filament, but it is only essential in the basal body and drive shaft. The flagellar parts are not smeared across the assembly, where some just happen to be in positions that elicit function, while others are not. They are clustered as a function of their assembly.
We could isolate the individual flagellar parts and store them all in separate pools. If we tried to mix them together in different orders, to construct different flagellar assemblies with the same function as the natural assembly, the experiment would fail. You’re not going to make flagella where protein secretion components were from the filament and hook and the filament proteins were from the motor.
That the EQU parts can be smeared across the program, yet still remain functional, indicates the EQU parts are much more plastic than flagellar parts. That the EQU parts can be arranged in various permutations, yet still elicit the same function, indicates the EQU parts are much more plastic than flagellar parts.
Molecular machine parts are three-dimensional entities that interface with each other often through complementary conformations. I quote from a paper concerning one example on my web page exploring the flagellum:
quote:
The axial proteins form a long, continuous, hollow cylindrical structure consisting of the rod, hook, hook-filament junction proteins, filament, and filament cap. Not only is this structure important for the function of the flagellum as a motor organelle but its central channel or lumen is the physical pathway by which axial protein subunits reach their assembly destination, the tip of the growing flagellum. The component substructures are all built with the following common theme. The subunits lie on the so-called basic helix of a cylindrical lattice. This underlying local helical symmetry (not to be confused with the macroscopic helicity of the flagellar filament) means that, in principle, subunits could be added indefinitely like the steps of a helical staircase. This is in contrast to the substructures of the basal body such as the MS ring, which have closed annular symmetry and thus a fixed number of subunits (thought to be about 26 in the case of the MS ring protein, FliF).
The rod and MS ring appear to abut each other closely. How do substructures with fundamentally different symmetries join together? A specialized zone might facilitate the junction. FliE seems a possible candidate for construction of such a junction zone....We propose that the primary role of FliE may be as a structural adapter between the annular symmetry of the MS ring and the helical symmetry of the rod and all subsequent axial structures.
The three-dimensional interfaces are crucial not only because they physically link the parts (without need for separate molecular “nuts and bolts”), but because they often conduct a specific cascade of coordinated movements until the final interface is reached, where the final output (the function) is elicited. As fuzzy as the term “well-matched” may be, it is part of Behe’s definition and it aims for the essence of these structural, moving interfaces.
The EQU parts, on the other hand, do not have complex, three-dimensional surfaces that must structurally interface to function. This is what makes them more plastic. This is what allows the same function to emerge from a variety of different contexts. Thus, in a way, we can envision the EQU parts as “low information” parts. So it is not surprising that of all the parts that make up a hair dryer, RBH picks out the “low information” part – the screw (perhaps the reason Behe omits the staples from his list of mousetrap parts is because he intuitively recognized their “low information” nature).
The only question that matters is whether the plasticity of the EQU parts is in the same ballpark as gene products. But here, things become ambiguous. On one hand, proteins are not rigid particles like cardboard puzzle pieces. But on the other hand, they are not so floppy that one gene product can easily be replaced by another (if they were , genetics would be a useless ally for the biochemist) and you don’t make functioning bacterial flagella by getting its components to trade places.
This leads me to Rex’s points:
quote:
So here's the critical question: if circuity works so well for Avida, why doesn't it work for biological organisms?
Part of the answer is supplied above – Avida does not map to the 3-D reality of biology. It reminds me of those who want to replace classroom lab dissections with computer simulations. The latter only partially captures the former.
quote:
This is a question about the structure of the underlying space that's being searched. We often come across problems where the easiest solution is also one of the best: for example, if you are trying to boil water, you get a container, and some flame, and put the container over the flame. If you do a bunch of other stuff, almost none of it will yield boiling water for you. This is the type of problem where the "circuitous route" can be neglected.
Yes, and when it comes to the bacterial flagellum, if we fill our bins with its components, there is only one solution.
Of course, there is no intuitive reason why it should be that the only way to make a functioning flagellum is to use those parts. Thus….
quote:
However, there are other problems that have a very different structure. For example, in the Traveling Salesman Problem, you have a bunch of cities that you want to visit, and the goal is to choose the shortest route to visit them all. Typically, there are extremely few "best" solutions. However, there are ridiculously many solutions--you could visit cities by alphabetical order, or even at random, and you would end up visiting them all. It just would be inefficient. Here, a (literally) circuitous route gets you the answer almost all the time, simply because there are so many workable circuitous routes.
Interestingly, evolutionary algorithms work very well on the Traveling Salesman problem--to find a solution, they generate a circuitous route and then optimize it over succeeding generations until an efficient route remains.
Sure, but there is an important distinction between the flagellum and EQU. The multiple runs that RBH cites all use the same set of parts, yet arrive at different ways to hook them together to generate the same function. With the flagellar parts, there is only one assembly pattern that works (or at the very least, it’s not nearly as pliable as the EQU). Ironically, it’s the multiple functional contexts of the EQU that actually undermine its relevance.
quote:
Which type of search-space do complex macromolecular structures inhabit? Behe seems to assume that they're in the boiling-water class. But this seems like a dangerously unsafe assumption, for a number of reasons.
Avida is one, showing a prevalence of cooption in a system where one would otherwise be tempted to predict a direct route (since we know the "right" answer--when I sat down to come up with an EQU algorithm on my own, I picked the direct route as the "most obvious").
If we all agree that the “parts” are the primitive instructions, then how would this prevalence be shown only from a survey of the assembly? Clues come from the way the parts are smeared across the assembly, giving one the distinct impression of bricolage. What nails it is the various permutations and the way the same parts can be used in different contexts, yet still arrive at the same function. And this takes us to a point RBH made earlier:
quote:
But just as various kinds of bacteria evolved different sorts of flagella to perform the same principal function, motility, so the various Avida evolutionary runs evolved different programs to perform EQU.
There’s one big problem. Bacteria did not evolve different sorts of flagella to perform the same principal function. There is only one type of flagellum per domain (as indicated by an IC core). One for eubacteria. One for archaebacteria. And one for eukaryotes. And one can make a decent circumstantial case that each flagellar appearance coincides with the origin of the domain itself.
In other words, we see a non-Avida-like pattern with the flagella. Apart from the difference in assembly logic (as a consequence of the plasticity of the Avida parts), we also don’t see 23 different eubacterial flagella. We don’t see 23 different ways to rearrange the same IC core nor do we see 23 different IC cores. Ironically, the Avida runs themselves give us reason to think Avida-like processes did not generate the flagellum.
Of course, one can broaden the functional concept to “motility.” But here things don’t work so well either. First, and as a tangent, it entails a type of fuzzy thinking that would have us cite the origin of bipedalism as evidence for the origin of the flagellum. In a world where design and evolution may co-exist, pointing to the existence of evolution doesn’t mean anything. Expecting design to be tied to “one and only one solution” is unjustified. Secondly, and more to the point, the parts used by the independently generated EQUs are all the same. Remember, it’s drawing from the same bins. Even though there are many different motility methods in bacteria (actually a small number compared to the incredibly large number of different types of bacteria), these different motility systems don’t represent a reshuffling of flagellar parts. Thus, different motility methods don’t give us reason to think the flagellum was composed by an Avida-like process.
quote:
Another is the prevalence of components in a complex that aren't essential for function. One of the hallmarks of a circuitous route--clearly seen in Avida--is that you end up with a bunch of non-essential components that are largely historical artifacts in addition to the irreducible core. A good fraction of flagellum components are in this category.
Clearly, designed things can evolve. In fact, one of the sensational concerns among the nanotechnology and/or AI community is that we might design something that evolves into a threat. All you are citing here is that an IC core can be tweaked by RM&NS in different lineages. This gives us no reason to think a circuitous route is likewise behind the origin of the flagellum itself.
But this leads us to another problem with Avida. To consider the origin of the bacterial flagellum, we must account for the twenty gene products that form the IC core. That only happens to be the central issue – did these twenty gene products come into existence in a flagellum-independent fashion? The Avida program does not help as it begins with its fully formed parts and focuses on their assembly into a higher order structure. Well, if you could show that the 20 flagellar gene products existed in a global bacterial genome prior to the existence of the flagellum, you wouldn’t need to waste time with virtual experiments to convince me.
So perhaps the Avida program would be more useful in explaining the origin of the gene products. After all, whether we’re dealing with nucleotides, amino acids, or codons, the analogy is stronger since it represents the “same set” of “primitive parts” that don’t entail the 3-D interface problem. But if we go this route, we explode the permutation problem. For now each gene product comes with its own set of independently arrived at permutations. This means the very existence of a complex, uniform Ur-IC core speaks against an Avida-like construction.
The Avida simulation is either relevant or irrelevant to the origin of molecular machines. It may be irrelevant due to the serious differences entailed in the “parts.” But if relevant, it does add support to the hypothesis of design (at least concerning the flagellum) given that the flagellum lacks the hallmarks we see with the Avida program.
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Mike Gene
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posted 12. June 2003 23:04
Nelson: quote:
I've mentioned this before, we see so much plasticity, from a 35 instruction EQU, to a 19 instruction EQU, to a 17 instruction EQU, and different kinds of EQU (not from radically different "components" but using the (sic) the same set of instructions. What is the equivalent of this with the bacterial flagellum? (Emphasis original)
RBH: One could equally accurately say "we see so much plasticity, from a 9+2 flagellum to a 6+0 flagellum to a 3+0 flagellum, all using the same parts (microtubules)." Biology really does re-use stuff in various combinations and permutations.
It’s pretty obvious that the 6+0 and 3+0 flagella are derived from an ancestral 9+2 state. The latter is nearly universal and the former are restricted to recently evolved lineages. Furthermore, this is mostly a difference in the number of MTs and not really a core difference. In stark contrast, the different EQUs were arrived at independently . Clearly, the EQU parts are far more plastic that biological machinery.
But if there ever was an aspect of biology that should roughly share the plasticity of the EQU, it is the genetic code. Of course, the code is universal. The Avida work thus adds to the growing list of data that support the code as positive evidence for ID.
[ 12. June 2003, 23:05: Message edited by: Mike Gene ]
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GP
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posted 12. June 2003 23:14
quote:
The EQU parts, on the other hand, do not have complex, three-dimensional surfaces that must structurally interface to function. This is what makes them more plastic.
As I was reading through Mike's post, I tried putting aside the fact that he once told me he was not an engineer. But, finally this point (which comprised the bulk of his thesis) screamed for a response, because frankly, it was pretty lame.
Mike seems to suggest that Avida cannot manifest three-dimensional behavior in terms of "structural interfaces to function." One has to wonder then, how computers deal with 3D mathematics all the time? There are three registers in Avida. For any given program, it has to load the proper values in each for the EQU function to manifest. This is the mathematical essence of 3D interactions. If Mike demands only physical instantiations for experimental models, then I am afraid he throws away one of the most powerful modern tools in studying nature. Computer science is all about virtual realities.
But, let's grant Mike that only 3D spatial features are relevant to IC structures. Once again, we have an IDist who is extremely critical of current experimental protocols, who fails to supply alternative protocols. So, I am going to ask the question I have asked many of the IDists -- how would you do it instead? How would you set up a controlled experiment that deals with analogous three-dimensional spatial models that evolve?
postscript: Avida is not "plastic" because of the lack of "3D." It is plastic because its instruction sets comprise a universal Turing machine. But perhaps you have a different meaning for plasticity?
[ 12. June 2003, 23:16: Message edited by: GP ]
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RBH
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posted 12. June 2003 23:18
Having a little more time than I anticipated tonight, I read the 'Survival of the Flattest' paper Nelson mentioned as being relevant. It's here.
About it, Nelson wrote quote:
Actually they [Lenski, et al.] don't say specifically whether the 17 instructions were required or if they underestimated this, they simply point out that careful examination of the genome yielded a lot of redunancy. It looks like for this paper, they wanted to make sure to err on the side of claiming too few instructions rather than too many. Nonetheless, 17 instructions alone is what they found. There is another paper that goes a lot more into this type of analysis here:
Wilke CO, Wang J, Ofria C, Adami C, and Lenski RE, Evolution of
Digital Organisms at High Mutation Rate Leads To Survival of the Flattest Nature 412, 331-333 (2001)
where less is more so to speak.
I have to say I'm having trouble connecting the test of the 'quasi-species' hypothesis in the 'Flattest' paper with the knockout procedure that provided the estimate of 17 IC instructions in the Lenski, et al., paper. As far as I can tell, the 'Flattest' paper says nothing whatsoever about the "type of analysis" in the Lenski, et al., paper.
The 'Flattest' paper looks at the effect of robustness with respect to mutations on the outcome of competition between two genotypes with different mutation rates. They found that organisms that occupy high narrow-peaked optima (less supportive "mutational neighborhood") on a fitness landscape, being less robust with respect to mutations, were less competitive than slower replicators that occupied flatter but lower optima on the landscape, a more supportive "mutational neighborhood." Replicators that occupy domains on a landscape that render them mutationally robust can outcompete organisms on a narrow peak that renders most mutations very harmful, as opposed to a bit harmful. They also showed that there is a tradeoff between replication rate and mutation rate.
The 'Flattest' paper has nothing to say about the knockout procedure and nothing to say about redundancy analysis. I can't figure out why Nelson thinks it is relevant. I therefore ask what it has to do with the Lenski, et al., study. I can't even think of a more specific question than that.
RBH
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Mike Gene
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posted 12. June 2003 23:20
GP,
If the point is too lame, you need another explanation for the fact that you can rearrange the 26 EQU parts into different combinations and get the same function, while you are not going to get a variety of different flagella (or motility devices) by rearranging the 20 flagellar parts. What say you?
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GP
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posted 12. June 2003 23:21
RBH,
I have only managed to go through a few of the evolved programs to see just how the algorithms compute EQU.
Do you know if the authors have determined whether or not the EQU algorithms all essentially perform the 5 NANDs?
GP
Postscript: I need to clarify -- do the algorithms perform the "essential" 5 NANDS as described by the authors' hand-written code, in some set order. If you have trouble parsing what I mean, please give a personal message.
Thanks
[ 12. June 2003, 23:25: Message edited by: GP ]
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Nel
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posted 12. June 2003 23:22
RBH,
Read the paper. Lenski et. al. used knockout mutations in the functional genomic analysis in order to determine how many instructions were essential for EQU. Some of the organisms actually evolved redundancies in their
traits so that they would be more robust to mutations. That paper I referenced goes into that aspect a lot more, which is why I referenced it.
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Pim van Meurs
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posted 12. June 2003 23:48
Nelson: I don't think that co-option does the trick when it comes to complex machines.
Why not? Co-option seems like a very likely candidate for evolution to me.
Nelson: Also, I think you completely misunderstood Bracht's reply, he's basically saying that your calculation treats the event as if one organism was able to evolve all 26 possiblities of EQU, that would certainly be improbable.
Nope the probabilities calculated were for 23 evolutions of EQU.
Nelson:
However, with 26 possibilities, many individual organisms going through replication and mutation will likely hit upon all of them, seperate organisms of course, that is likely and quite probable, especially when there are 26 possibilities and the function isn't all that complex.
Not all that complex? According to what measure? Certainly the fact that organisms will 'hit upon' such functions shows the power of selection which is basically a probability amplifier.
Nelson: With the flagellum the situation is different, there is only 1 way to get bi-directional motor propeller etc, which is why it is IC.
That of course remains unsupported. Is there really one way to get a flagellum(like) structure? How did you reach such a conclusion?
Nelson: Instead, we see completely new innovations that are universal among the respective kingdom.
Hence common descent...
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RBH
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posted 13. June 2003 00:02
Well, I didn't want to sleep tonight anyway!
As an ex-aircraft modeler (in the 1960s) where computer simulations of the aerodynamics of various aircraft were used to drive physical displays and accept physical control inputs from a poor suffering pilot locked in a mockup cockpit, I second GP's remarks about "interfaces." The insistence that 3-D entities are somehow special; that a simulation in silico cannot represent the relevant properties of 3-D objects and processes is, as GP remarks, at considerable variance with a whole lot of practice in engineering. That's a pseudo-problem.
I think a greater problem with Mike Gene's 12. June 2003 22:48 posting above is that it is chasing a rabbit down a garden path so far as the central question is concerned. That question, as it has been raised in this thread from the beginning, is whether the Lenski, et al., study shows the evolution of the irreducible complexity that is held to be a hallmark of designed objects, an indicator of intellilgent design. It is not "Does this simulation map onto a specific biological phenomenon?" but is "Did objects - programs - that meet the criteria for being classified as irreducibly complex evolve?"
Mike Gene's criticism is that the Avida instructions are too "plastic," that the same parts can be used multiple times: "Thus, the same part, in the same assembly has both function and non-function, depending on the context. In a sense, the parts are smeared throughout the assembly." "Smeared throughout" is, I think, a misinterpretation - are the bricks that comprise an arch "smeared throughout" the arch?
The "plasticity" argument, though, is interesting. One could argue that very plasticity works against the Avida simulation. It places a much heavier load on the evolutionary process to arrange the instructions appropriately, since there are no physical or chemical laws operating to constrain the range of possible sequences in the AVida simulation.
Nevertheless, there are indications from the hardware evolution literature (see this ARN thread) that suggest that even when the evolution occurs in hardware, the outcomes can be both wholly unexpected from a human design point of view, and in some cases inexplicable by the very designers who ran the simulation. With 'rigid' components - transistors and wires - the evolutionary process produced (I'm real tempted to say "created"!) circuits that defied analysis yet performed the desired function. Even given the physical constraints on the operation of the components (their lack of "plasticity"), novel and unexpected circuits evolved. Interestingly, IIRC they also did knockout tests and found what amount to irreducible cores in the evolved hardware circuits. (I am too tired to reread that tonight.)
I infer from those results that the "plasticity" of the Avida simulation is not a serious problem. Whether evolved in hardware or in assembly language instructions, IC structures appear in simulations that employ only the operators of plain old evolution.
RBH
PS to Nelson added in latish edit Ah. I see. And you're right, it is at least marginally relevant since at least one Lenski program (run #109) shows considerable redundancy. It has 9 "nand" instructions in its genome, but only 3 are IC for performing EQU. Since performing EQU requires a minimum of 5 nand operations, there's considerable redundancy in that genome. I'm not sure what relevance that has for the applicability of the Avida simulation to the question of evolving IC structures, though.
PPS even later: GP: I PM'ed you.
[ 13. June 2003, 00:41: Message edited by: RBH ]
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Mike Gene
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posted 13. June 2003 01:35
RBH,
I have long made it clear that I do not think IC in of itself is a sufficient indicator of design. My interest in this goes beyond whether or not IC systems can evolve. The concept of IC remains quite helpful to these disputes, even if it does not represent a insurmountable barrier to evolution. I illustrate this above, as the flagellum does not exhibit the hallmarks of an IC system constructed by evolution.
As for 3-D entities, perhaps you ought to consider what the 3-D entities known as proteins look like. Because the fact remains that while you can take the EQU parts and rearrange them into 23 different assemblies to get the same function, you can’t do that with the flagellum. This clearly indicates a fundamental difference that strongly suggests the EQU fails to model molecular machinery.
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GP
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posted 13. June 2003 01:48
quote:
If the point is too lame, you need another explanation for the fact that you can rearrange the 26 EQU parts into different combinations and get the same function, while you are not going to get a variety of different flagella (or motility devices) by rearranging the 20 flagellar parts. What say you?
Sorry, I don't follow. "If [your] point is too lame," then you need a better criticsm, Mike, not a better explanation from me. Still your ending question misses the entire point. If one wants to talk about "rearrangements" and exchanging "parts," one needs all the possible parts to work with -- not just those he sees in front of him. Thus, to ask how the flagellum is specified by an arrangement of its 20 components is to assume a priori that the flagellum comprises of those specific, non-evolvable components. I can have no substantial answer to such question-begging requests. On the other hand, if you are demanding of me an evolutionary pathway for the flagellum, I admit quite freely that I do not yet know. But, for that matter, if you gave me any final Avida program with sparse data on the intermediates, I probably cannot successfully reconstruct its evolutionary pathway either.
Anyway, one has to realize that Avida instructions represent the set of sufficient instructions to implement all other Turing machines -- it is a universal Turing machine. So, in a sense, Avida is already endowed with all the "parts" to evolve other digital functions. This is not the case, as I mentioned above, with the flagellum. How many "parts" are necessary to build all, if not the majority, of biological structures, beyond the flagellum? How many different proteins? How many different domains? To me, that is the relevant analogous question -- whether the flagella can only be physically instantiated by certain parts (given any necessary arrangements). Not whether the flagella can only be made by certain arrangement of its current observed "parts." I have no reason to suspect that the former is true.
Remember, Avida was "designed" so that multiple observations/outcomes are possible. It is this crucial feature that allowed us to observe multiple evolutions of EQU. In biology, we unfortunately have only one set of observations/one outcome. There is simply no telling how many kinds of flagella (or motility structures) could have evolved -- or using how many different parts. How could one explore such possibilities experimentally?
Nevertheless, Darwinian mechanisms seem not to be confined to biology alone. Avida demonstrates quite clearly that Darwinian principles are applicable to digital entities. On the other hand, if one wants to continue to refine and constrain IC conditions, then so be it. I have conceded in previous posts that Avida quite possibly does not speak to IC, if not because the IC definition itself is often in reformulation (not surprisingly, quite ofetn after a Darwinian posits challenges to it). If one wants to limit IC to biology -- Fine. If one wants to limit IC to 3D spatial structures -- Fine. We can keep constraining the definition, until only perhaps the bacterial flagellum is IC. That's fine, too.
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Mike Gene
Member
Member # 149
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posted 13. June 2003 02:08
GP: quote:
Sorry, I don't follow. "If [your] point is too lame," then you need a better criticsm, Mike, not a better explanation from me. Still your ending question misses the entire point. If one wants to talk about "rearrangements" and exchanging "parts," one needs all the possible parts to work with -- not just those he sees in front of him. Thus, to ask how the flagellum is specified by an arrangement of its 20 components is to assume a priori that the flagellum comprises of those specific, non-evolvable components. I can have no substantial answer to such question-begging requests.
No, I think you are missing the entire point. With the EQU, we have 26 different parts sitting in front of us. You can arrange them into at least 23 different assemblies to get the same function. With the flagellum, we have 20 different parts sitting in front of us. Can we rearrange those parts into a few dozen different assemblies to get the same function? No.
The point?.......
Why this fundamental difference?
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