|
Author
|
Topic: Evolving Inventions
|
gedanken
Member
Member # 594
|
posted 14. March 2003 12:19
quote:
Nelson:
Why don't you discuss the one, now two, examples that I gave you that clearly absent of an IC core? The one membrane system, and now, hemoglobin. Of course, telling me that everything has an IC core wouldn't surprise me, as I suspect specificity in life through and through. So I don't really see the point your making if this goes either way.
Thanks, Alonso, I think this is a good idea.
First I want to clarify that I was focusing on “evolvability” when questioning the number of layers, and also on the notion of a stark contrast. I’m not sure that this means that we have any contradiction to the definition of “IC,” in fact I am asking to determine what objective criterion can be used. (Because so far the “objective” criterion seems to be that a potential evolutionary pathway was discovered, like adding one layer at a time.) (I may also have been focusing on the issue of lack of clarity of whether we have IC or not, as the degree is declared to have a threshold at a certain number of layers -- what is that “threshold”?)
Also I was questioning the claim was possible, that N+1 layers could starkly stop “photons” but N layers would not do so. My problem is that I see degrees of functionality in small change being possible in all cases and can’t quite see the point that is typically claimed of a stark change being required in biological change transitions (descent with modification changes) in the cases presented. This is an example where this is clear, the change in N to N+1 is possibly a ratio of (N+1)/N in effectiveness, but other examples may simply be more complex in understanding the variations that make for slight change.
In the case in question, Alonso was postulating that 45 membranes would stop photons, but 44 would not in an earlier post:
quote:
But in an IC system you don't have this direct pathway for the simple reason that if the 45 membranes were required to stop photons, 44 membranes wouldn't be less effective in stopping photons, it would be completely ineffective in stopping photons. That is an IC system and that is an abrupt precipice. That is the invention that it so hard to get in TRIZ. That is what makes both TRIZ and IC such powerful indicators of intelligent design.
But as Alonso is now pointing out that we pretty much showed that there won’t be a “precipice” in this case. The key is a physical impossibility of such a case meeting this description existing. Photons are absorbed in their entirety by something that can absorb the entire quanta of energy, and may possibly be reradiated at a different frequency/energy. But fraction of photons stopped depends on amount of stopping material, thus 45 has approximately 45/44 as much stopping power as 44 layers. The problem is that this example shows how degree comes into play clearly, while other examples may not be so clear in how issues of continuous or small step modification can occur. As soon as a small step modification can be identified, we have an issue of degree rather than the precipice. I also note the irony in Alonso’s use of the failure of his previous argument in favor of IC here as support for a different argument for IC. But this is precisely the problem -- the lack of ability to objectively describe a condition of such a “precipice” that actually has no stepwise resolution.
Rex discussed before the issue of degree of IC. Now the essence of IC is essentially the essence of TRIZ, that of a contradiction that cannot be overcome directly. So as soon as someone describes a step-wise sequence, apparently the “contradiction” has become overcome by a sifting of possibilities by the evolutionary process. (I wanted to clearly relate this issue to the subject of this thread.)
We have an apparent resolution of the TRIZ issue, by the sifting properties of a kind of optimization as N layers transition to N+1 layers. This has not cleared up the issue of why this is not IC, however, and these issues may be clarified better in the next example.
Quote of Behe:
quote:
The starting point, myoglobin, alraedy can bind oxygen. The behavior of hemoglobin can be achieved by a rather simple modifaction of the behavior of myoglobin, and the individual proteins of hemoglobin strongly resemble myoglobin. So although hemoglobin can be thought of as a system with interacting parts, the interaction does nothing much that is clearly beyond the individual components of the system.
Once again this discusses the evolutionary pathway to hemoglobin. Behe’s fragment “although hemoglobin can be thought of as a system with interacting parts…” is telling. What is the objective criterion here that makes hemoglobin not “IC”? I can’t tell in this case, except for two aspects:
1) The identification of a plausible evolutionary pathway. But this cannot be the definition of that aspect of IC, because if it is it is question begging. IC cannot be defined in part as an inability to find an evolutionary pathway (and thus there is believed to be no evolutionary pathway) without it clearly being an “argument from ignorance” in that part. It would be much more meaningful if IC retained the character of its earlier definition, e.g. “one cannot remove a part” which was objective without regard to the question of how it could have gotten that way (and thus begging the question). But the statement here of how it got that way is a statement of process, not an objective criterion of the system configuration itself as occurred in the original definition of IC.
2) I think I understand the “complexity” issue presented to some degree, but things are still not clear. Behe says that “the interaction does nothing much that is clearly beyond the individual components of the system.” I don’t see how that differs from all the other systems that are considered “IC”. Those systems individual parts only do what those individual parts do. Then as they interact, the function of the whole system does what the function of the whole system is. It is not sufficient that in one case one chooses to examine the individual parts as having their own functions as part of a larger system of interaction, then in other cases one chooses to examine the larger system as an assembly of interacting parts. The choice seems arbitrary here -- thus not objective. (The choice seems to be made depending on the desired outcome, not upon objective criterion.) Now I do understand that the notion of nested systems being considered, and how as the number decreases from say 20 down to 2 and finally to 1 part that we have a decreasing view of complexity. But this is strictly a matter of degree, where is the objective criterion? Is the “objective criterion” simply a judgment call of the degree, and everybody can call it as they see it? I think the main issue is that parts change in their function slightly as they are modified slightly. So to identify the removal is a change of focus that is irrelevant to evolutionary processes, which typically change things by degree.
This is where we can relate back to the N layer problem. In N layers, we have a simple way to understand the complexity of the system, and the “simplicity” of the pathway. Since we have a simple mathematical representation of the transition (N+1)/N, we have s a simple way to describe it. But how does the complexity or simplicity of the random bounces of the “modification” part of descent with modification make any difference in whether the system is evolvable, or of a criterion being objective in defining IC. (Because if each random “bounce” has selective advantage, there is no argument against the pathway being evolvable. Claims of low probability are irrelevant, as there would be some equally improbable but different outcome if the “tape” of evolution were replayed again, just as there would be some different outcome in a constrained or unconstrained coin toss sequence of 500 tosses. If they are constrained, then the probability of an individual outcome increases, if not, then the number of probable outcomes increases, and a ratio of density is maintained either way.)
Remember my previous quote of Behe, “Reply to My Critics,” Biology and Philosophy 16: 685–709, 2001:
quote:
However, commentary by Robert Pennock and others has made me realize that there is a weakness in that view of irreducible complexity. The current definition puts the focus on removing a part from an already-functioning system. Thus, seeking a counterexample to irreducible complexity, in Tower of Babel Pennock writes about a part in a sophisticated chronometer, whose origin is simply assumed, which breaks to give a system that he posits can nonetheless work in a simpler watch in a less demanding environment.5 The difficult task facing Darwinian evolution, however, would not be to remove parts from sophisticated pre-existing systems; it would be to bring together components to make a new system in the first place. Thus there is an asymmetry between my current definition of irreducible complexity and the task facing natural selection. I hope to repair this defect in future work.
So far in this discussion, I see no attempt to “repair this defect.” I have not seen how the definitions can be objectively applied to a given observable structure without recourse to an argument in the form of an “argument from ignorance” in which the contradiction is resolved when we know how it happened, but is claimed as difficult for evolutionary processes when we don’t yet know the processes. (And I note that often there is a claim of difficulty or not knowing the process when multiple possibilities are proposed -- which would seem to be the exact opposite of difficulty when multiple pathways have high probability. But when multiple pathways are considered possible, that is when science can have no distinguishing evidence of which of them was the actual pathway, and thus scientifically it is described as “unknown”, and ID promoters seem to then make claims of IC because of being “unknown” how the structure could arise.)
[ 14. March 2003, 15:10: Message edited by: gedanken ]
IP: Logged
|
|
ASCSCommanding
Member
Member # 682
|
posted 14. March 2003 16:51
Nelson,
quote:
Nelson:
I disagree because IC eliminates so many of these possibilities by its very own nature. As we see it eliminates all direct pathways. Direct pathways lies in a zone where the potential for probable pathways mostly exist.
ASCS:
I would expect that in trying to determine the likelihood of ending in final state F if starting in initial state A is the sum of the probabilities over all possible paths from A to F, not just a comparison of the probability of some direct path vs. the probability of some particular indirect path. To state it another way, if you divide possible paths into either direct or indirect, then even if the direct path is much more likely than any indirect path, if the probability over all indirect paths is high, one would expect some unlikely, indirect path to be taken.
Nelson:
This is why we have to take into account how natural selection works instead of getting into these abstract possibilities. For example, if A and B are conserved by natural selection, natural selection would be selecting for that particular function. The relationship between that system and natural selection is not random. To quote Dawkins again, what we have with IC is an abrupt precipice where any number below 20 is not inefficient, it does not work. Each step in a direct pathway confers a selective advantage all the way to the top of the mountain for the same function. Even if you were correct, that indirect routes would most likely be taken by a natural process to any particular function to does mean that the indirect route itself is more likely then a direct route, where you are just selecting parts that make the original function more efficient.
Well, I’m talking about abstract possibilities in part because I perceive that ID arguments are based upon a general inference that is wrong. Specifically that the argument depends upon saying that if the most likely, or direct, path from state A to state F has a very low probability and if all other paths (indirect) have much lower probabilities than the direct path, we can conclude that going from state A to state F is improbably. This inference is wrong. Inasmuch as I’m talking about a general inference I need to talk somewhat in the abstract. To actually determine the likelihood of transitioning from state A to F (or Y for a 20+ part system) one needs to consider the total probability over all possible paths. And it is perfectly reasonable to have a large number of possible paths, each with a very low probability, but the total probability is high (> 0.5) so that the transition is likely. In these circumstances one has the expectation that the transition will take place over some very improbable path.
Now the actual process by which natural selection operates is, of course relevant to the specific probability associated with each possible path and with the total number of possible paths. But my point is that both of these need to be determined (or at least given reasonable estimates) to say anything about the probability of getting state Y. However improbabable a particular path is, just doesn’t say much about the overall probability.
quote:
ASCS:
I have not seen an ID argument with regard to the total probability over all indirect paths. What I’ve seen are arguments to the effect that the direct path is proportionally more likely that whatever indirect path is proposed. This argument is irrelevant. Furthermore, given that the direct path has zero probability, it doesn’t make sense to claim that it has a higher probability than the indirect path. The ID argument seems to require that the probability of the direct path be both fairly high and zero.
Nelson:
I don't see this argument as irrelevant. For example, an indirect path looks something like this. A does some job which natural selection has locked on and conserved. B comes along and not only starts working interactively with A, but changes the function of the two part system to something other than what A was originally being pruned for by natural selection. The new function is now "irreducible", removing B changes the function of AB we cannot preserve it. Now skipping over the details of how one part can start interacting with and become well-matched to another, all the way spontaneously changing the original function that natural selection locked onto, is unimportant, what’s important here is for a 20 part system, you have to invoke these pure chance events multiple times. C comes along and starts working with ABC maybe making it more efficient but then another part, D comes along and starts interacting with ABC all the while changing the function of ABC. Then E comes along maybe making the ABCD function more efficient, so natural selection adds on ABCDEFG, but then antother part H comes along and starts acting interactively and becomes well-matched to ABCDEFG while spontaneously changing the function of the ABCDEFG system and on and on until you get the IC F function that requires 20 parts.
Yes, I agree entirely, whatever particular path is taken will have a low probability. Keep in mind though that conservation of characteristics by natural selection is to a degree. Some are highly conserved and some are not conserved. Other features are, due to change in environment or other changes in an organism becoming unnecessary. Also, the question is, how many pathways exist from A alone to state Y (with 25 parts to pick an easy round number near 20)? Do we have to start with A and add each part in a specific order or are there some variations in the order. How many different versions of each part will work (we have, after all, a wide variety of different flagella functioning today)? How many different environments can shape the course of changes in a lineage and in how many different ways? I realize that I’m not demonstrating that there are sufficient pathways. My point is just that the relevant question is what is the total probability over all pathways? In other words how many pathways are there and what is the probability of each.
quote:
ASCS:
I think the basic problem is that the ID “direct” pathway is a misnomer and has little to do with how biological systems actually change.
Nelson:
The term "direct path" are in the peer-reviewed literature and with respect to IC to boot. The most common pathways are Serial Direct Evolution, Parallel direct Evolution. These are the two pathways that Darwin inferred from looking at finch beaks, and antibiotic resistance to drugs. A gene duplication that causes a group of genes to produce more estersase is making the original function more efficient and therefore more able to resist large portions of pesticide and therefore selectively advantageous.
This last was my least significant problem and one that I was particularly unclear in presenting. Suffice it to say that if by direct pathway we mean any sequence of modifications in which the systems function does not change, then I’ll withdraw my claim that there is a problem and carry on with this meaning.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 14. March 2003 20:34
Nelson:
This is not to say that IC is irrelevant to evolutionary pathways, the consequence of IC is that it is a barrier to Darwinian pathways in that now pure chance events have to be added rather than a direct path up mount improbable, where each step confers a selective advantage by making the original function more efficient. Instead natural selection is blind to the function we are interested in, and is left to tumble around looking for different functions that have nothing to do with motility (protein secretion). This opens up the door to a design inference, in that a better explanation for complex systems that are also irreducible points to intelligent design.
GD:
It seems to me that your answer implies an affirmative to my question. Assuming that this is in fact the case, I would like to follow up then with the natural question: What additional evidence are you speaking of?
Nelson:
As I quite clearly stated, the best explanation for the IC molecular machines that are pointed out here and elsewhere is that they were intelligently designed.
GD:
You seem to hint at this in your reply, that "[IC] is a barrier to Darwinian pathways in that now pure chance events have to be added rather than a direct path up mount improbable." I do not find this thesis impressive for at least two reasons. The first is that "pure chance" events are already being employed "to climb Mt. Improbable," which I take to mean "to explain evolutionary relationships."
Nelson:
No, the only pure chance event in a direct Darwinian pathway is the first one, where a function, say binding oxygen, is selectively advantagous. Once natural selection "locks" onto this function, anything that comes along that makes it more efficient will be "locked" onto as well. Although the mutation that occurs itself is a random event, the relationship between natural selection and that particular function is not random. Natural selection then continuously selects for this function, where more and more efficiency comes from the "pruning" of this function by natural selection.
In an indirect pathway, there are too many pure chance events. While natural selection is selecting for protein secretion, a completely random event has to spontaneously change each of the interacting parts of the protein secretion machine in order to change it's function. This has to happen multiple times. Selection has very little to do with this.
GD:
Secondly, absent an accurate probabilistic and physical model, I find that there is no compelling evidence to support IC as a barrier. There is no measurable and quantifiable argument.
Nelson:
This is an assertion that can be batted away quite easily. The measurable and quantifiable argument has been a project that has been undergoing since 1996 by William Dembski in The Design Inference and No Free Lunch . These two books make IC a quantifiable and measurable argument.
GD:
Having said that, I applaud your effort to devise an experiment to test an interesting hypothesis. Let's take a look at what you wrote:
quote:
Nelson:
You can place the bacteria in the center of a "circle" or set up a perimeter. You can then put some food outside the "circle" (or set up a gradiant). Those that get to the outside of the circle are obviously the "fittest", but they need to do it by moving, and futhermore, motility is selected for, since the fittest are the ones who get to eat. Those who can't move and get to the food source, die. If you keep moving the "goal post" so that it takes more than just a wiggle to get to the food source we should see how bacteria evolve, step by step, a way to master the brownian storm and get to the prize. If you start them off with all the pieces that Darwinists say was used by natural selection to build a flagellum, an ion channel, then it is not completely crazy to think we will get something flagellum-like although not exactly the bacterial flagellum,(if we do, throw Darwinism away, there was nothing random about that). Anyone up for a grant proposal?
If we get something an IC structure as sophisticated as the bacterial flagellum I would certainly drop ID right after I read the peer reviewed paper about it.
GD:
In my opinion, this experimental set up would not pass most peer review. Your hypothesis is that a motility pressure would result in the generation of "something flagellum-like." But, your setup does not necessarily promote motility. A bacterial colony will "grow" on a petri dish regardless of motility structures. So setting up a nutrient gradient seems insufficient.
Nelson:
A bacterial colony will not grow if it does not have a source of nutrients. This is why the bacteria will be forced to move or die. Thus selecting for motility. If you continue to increase the gradient in subsequent iterations bacterial that get to the outside first are the ones who will be selected for, since they aquired mutations that gave them a bit of motility. Subsequent generations of bacteria will have this selectively advantageous trait, and since these bacteria are able to get to more and more sources of nutrients, the ones with more and more complex motility structures will be selected for.
GD:
Also, if you are overly restrictive in the medium growth, you will not promote growth at all (not to mention that the model is completely unrealistic/unnatural). [There is interesting research on the geometric pattern of colony growth of non-motile bacteria. Let me know if you're interested.]
Nelson:
There is no need to be overly restrictive in the medium growth, since the restriction is the getting-to-the-actual-food-source. There is nothing unrealistic or unnatural about this process even if I didn't allow the bacteria to grow beyond my perimeter as an initial condition, we are testing the viability of how a colony invented a machine to get them more food after their local food source has been depleted.
GD:
Of course, the other issue is that a petri dish is of a finite size. Do you know how many bacteria can grow on a restrictive agar medium? After they have used up their nutrients, the bacteria naturally have to be transplated to fresh medium, or otherwise they die (once again, creating an unnatural situation).
Nelson:
There is a restriction of growth here, again, with the fact that the nutrient gradiant is outside the circular growth area. There is no unrestricted growing here, since, again, the "goal posts" will continually be moved once they finally get to their food source. As far as transplants go, I don't seem them as unnatural. There is an experiment that is kind of like the one I am proposing that was done by Ben-Jacob.
quote:
We tried exposing bacterial colonies to conditions so novel that the creatures could never have encountered them before. Tough conditions, conditions of life and death. We wanted to know how inventive they could be in reworking their genetic code. For example, we took bacteria that can't move on agar but are able to roam freely in liquid. We put them on the wilderness of their worst nightmares, agar, and deprived them of food. The need to branch out in search of grazing land was a true creative challenge.
They were able to succeed in moving however by forming a "round rotating circular structures (dots at the end of the branches) which, like circular saws, cut their way through the recalcitrant medium." They are able to do this, however, because they already had a motility structure, they just found, as a group, a novel way of using it. What would happen if we removed that and reverted them to their supposed ancestral state? Thats what the experiment seeks to look for. If bacteria do this by reengineering their genome in a complex way, that still wouldn't be Darwinian evolution.
GD:
How many different colony transplants would you need?
Nelson:
I'm not sure, these are ad hoc details that can be worked out though. These are not no-go reasons.
GD:
How do you prevent the exponential growth in petri dishes?
Nelson:
By essentially limiting the food source to those bacteria that have figured out how to move and can get to the food source.
GD:
Of course, the better question is how you give a majority of the bacteria a "fair chance" at evolving? It seems to me that these are important logistical questions.
Nelson:
I don't understand this question.
GD:
But of course, the interpretation of the results matter as well. You require that "we will get something flagellum-like although not exactly the bacterial flagellum." This specification is a bit vague. As you are aware, flagellum is one of several motile structures. However, flagellar evolution is not the only strategy to increase the bacterium's reproductive fitness. Bacteria do in fact go dormant. How do you control for that event? Bacteria also form spores so that they can be transported physically across distances. How can you control for that phenomenon?
Nelson:
We can use E. coli and/or E. aerogenes.
GD:
Of course, the negative evidence is not necessarily interesting. Suppose, that we get lucky and in fact one bacterial colony develops a novel motility structure through some co-option event. I do not see how this controverts the notion that certain IC structures may in fact have been designed. After all, can one data point be sufficient to convince you of the IC argument, when similar evidence already exists (as I think you have admitted) that IC structures do in fact evolve?
Nelson:
Of course now you've begged the question, indeed, the mother of all question: What evidence exists that IC structures, like the bacterial flagellum, evolve?
[ 14. March 2003, 23:54: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Moderator
Administrator
Member # 1
|
posted 14. March 2003 20:42
Nelson, et. al.
This is a reminder that we do not like quote by quote rebuttals. Try to summarize positions in your own words. Remember, 90% of the content of a post should be original (not quotes).
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 14. March 2003 21:22
My apologies, moderator. I've been writing posts like that for 3 years, off and on, and it's hard to break the habit, I will be more careful not to quote like that in my posts.
Rex, the reason why I do not extrapolate from mutations but I do extrapolate from technology is because I don't see point mutations building motors. I see intelligent agents building motors, and motors that look extremely like the ones attached to bacteria.
quote:
"More so than other motors, the flagellum resembles a machine designed by a human"
David J. DeRosier, Cell 93, 17 (1998)
The reason why Darwinian evolution can't build IC systems through co-option like intelligent designers do is precisely the subject of this thread. Intelligent designers have foresight and don't need to rely so much on pure chance events like a non-intelligent co-option story tends to give. There is a lot of motility specific stuff to invent. There are a lot of design problems to solve. How do we build the flagellum from inside out?
I don't see how increasing the number of intermediates solves the problem of too much chance. Even one step in a co-option story involves a pure chance event, and you can see this in simpler systems. Extrapolating 1 pure chance event to 19 (the more complex an irreducible system is), you'll see what I mean. Invoking more intermediate steps, enhances this problem, it doesn't solve it.
As far as your proposed falsification criteria, your (1) looks promising. I would like to know the specifics of how to falsify that natural selection and random mutation built that recent molecular machine from a simpler system.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 14. March 2003 23:19
In my opinion your post comes down to equating
"removing parts to get to the IC core or lack thereof" with an evolutionary pathway.
This is an interesting way to look at the method of deteriming whether a system is IC. In that the
backward reengineering of an IC system is essentially telling it's evolutionary history. This is false however, since, as Darwinists love to point out, direct evolutionary pathways are not the only pathways that Darwinian mechanism can take. As Behe, Ussery, and Thornhill point out, there are indirect pathways.
As far as I can tell, this is no complaint at all. In fact, I kind of like looking it at this way. This mirros nicely why David Ussery and Thornhill are able to eliminate direct Darwinian pathways, because reducing the function to one part is essentially impossible for an IC system. Thus you are only reiterating what the peer
reviewed literature say about irreducible complexity.
Now, my membrane example shows how one can delineate between an IC system and a non-IC system, or in the words of Dawkins, how one can find an abrupt precipice. As you said yourself:
quote:
“44 membranes” surely reduces the frequency of photons doing whatever damage is envisioned, even one membrane would to that to a slight degree.
But although you can reduce the 99-membrane complex, which is very efficient at stopping photons, to a 1-membrane system (thus the function is not beyond the original components), you cannot do that with an IC system. Lets look at an 8-part IC system and apply to Dawkin's explanation of how evolution works:
quote:
"We would be dealing with an abrupt
precipice if, say, any number of membranes above forty five was very effective while any number below forty-five was totally ineffective.
Neither common sense nor the evidence leads us to suspect any such sudden discontinuities."
I like to do this little mountain drawing.
So 91 membranes
are more effective then 90
which in turn are more effective then 89
which in turn are more efffective then any lower number especially 0
We can't do that with an IC system like F-ATPase.
So 8 parts
are more effective then....nothing.
The reason why is if you remove any part from the ATP synthase you don't get a less efficient ATP synthesis machine, you don't get ATP synthesis at all. Going back full circle, of course this doesn't rule out an indirect route, nevertheless, it accentuates how many diversionary roads you have to go through to finally get at the function of ATP synthesis.
Now to my hemoglobin example. Remember that if the function is not beyond the individual components (another way to state IC) then it can be reduced to one component, ergo it is not IC by it's very definition. The funcion of binding oxygen is reducible to one component (myoglobin), and the various subunits of the hemoglobin do this. That it is interacting is irrelevant, since that just makes it able to bind more oxygen, again the path up Mount Improbable is straight and direct, applying this definition to Dawkins's scenario.
You cannot equate reducing the function to one component as eliminating a plausible evolutionary pathway, since it only eliminates, as a consequence of not being able to reduce it to one component, direct ones. Even if I can't reduce the function to one component, I can still envision a circutious route, again Behe, Ussery, and Thornhill all stated this. The only thing that we can get from this is if the evolutionary pathway imagined by the Darwinist when confronted with an IC system is exclusively a co-option story, then it's IC. However, one can completely forget that Darwinian theory even exists and still determine if the function of the system is either IC or non-IC. I can test this without even knowing that there is such a thing as an evolutionary pathway, shows that the delineation of IC systems is an objective, empirical test.
As far as your second objection, reducing the function of a system to one component is the antithesis of the very meaning of irreducible. This is not just an unobjective statement about "degree" this is showing that the function can be accomplished without all those interacting parts. Again, if the parts themselves interact but all they do is make the original function that it can do on it's own more efficient then of course removing one part will not get you an IC core, it is a non-IC system. This isn't a judgement call, either one component can do the job and adding components just makes it better, or you can't remove all the parts needed for function. This is not an argument from ignorance, it can be ascertained empirically and even experimentally:
quote:
"A fliD-deficient mutant becomes non-motile because it lacks flagellar filaments and leaks flagellin monomer out into the medium."
Ikeda T, Oosawa K, Hotani H. 1996. Self-assembly of the filament capping protein, FliD, of bacterial flagella into an annular structure. J Mol Biol 259(4):679-86.
As far as Behe's quote,
quote:
However, commentary by Robert Pennock and others has made me realize that there is a weakness in that view of irreducible complexity. The current definition puts the focus on removing a part from an already-functioning system. Thus, seeking a counterexample to irreducible complexity, in Tower of Babel Pennock writes about a part in a sophisticated chronometer, whose origin is simply assumed, which breaks to give a system that he posits can nonetheless work in a simpler watch in a less demanding environment.5 The difficult task facing Darwinian evolution, however, would not be to remove parts from sophisticated pre-existing systems; it would be to bring together components to make a new system in the first place. Thus there is an asymmetry between my current definition of irreducible complexity and the task facing natural selection. I hope to repair this defect in future work.
you seem to completely misunderstand what he is saying here. What Behe is saying here is that the focus on parts has lead to undetailed, vague, but pathways. However, because it is irreducibly complex you can be sure that all of them are indirect. This alone shows that it is not an argument from ignorance to tell that is IC, it is completely and objective statement. All Darwinists can really do is show indirect pathways, since, only as a consequence, the definition eliminates direct pathways.
However, back to the quote, notice what Behe says:
quote:
Thus there is an asymmetry between my current definition of irreducible complexity and the task facing natural selection.
This is the problem that Behe sees with the original definition, it gives too much imaginary leeway to the Darwinist. This has absolutely nothing to do with a problem of "argument from ignorance". Which is why, in other writings, Behe did is stepping closer to "repair this defect."
quote:
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.
Improbability is not irrelevant, since unselectable steps are essentially pure chance steps. Which is what got ID on the throne in Paley's day in the first place.
If we analyse this new definition you can see that this is still not requiring that an IC system have no evolutionary pathway. It can still have an indirect pathway, but the now the focus is on the pure chance event in delineating how complex the irreducible system really is.
[ 14. March 2003, 23:57: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Rex Kerr
Member
Member # 632
|
posted 14. March 2003 23:44
I don't see intelligent agents building things that from subunits that have essentially no function on their own or any simple relationship between their properties and the properties of the constructed system. In fact, when such tasks face us, one of the primary ways we solve it is--to use genetic algorithms!
Of course, if you postulate an omnipotent, omniscient intelligence it can by definition do anything. However, such an entity could equally well tweak a system to evolve as it could use a non-evolutionary mechanism, so that isn't a very useful hypothesis.
This leaves us with the observation that in some ways the functionality of protein complexes seem like devices built by intelligent agents, and in some ways like the output of genetic algorithms. Which way you extrapolate is a matter of preference and evidence; extrapolation ought to be valid either way, but to distinguish between the two requires more than just the initial observation and extrapolation. You need additional evidence that discriminates between the two.
-----------
You seem to have missed the point of the mathematics again. Extrapolating one pure chance event to 19 does reduce the probability. But that is not what I was calculating! Rather, I was noting that one really big jump, from nothing to flagellum, could be made easier if you subdivide the jumps into multiple functional intermediates. As I said before, there is presumably some penalty for needing a functional intermediate, as the path is no longer direct. But there is a benefit (that depends on the size of the population and number of generations available) for each additional step. The relative magnitude of functionalization penalties to population size bonuses hasn't, as far as I know, been addressed. (Especially since I just made up the formalization on the spot.) But something like that is necessary in order to understand whether adding intermediates helps or hurts.
If you want to see this in practice, take three dice and count how many times it takes you to roll (in order)
1 2 3
then, count how many times it takes you to roll
1 4 x
(where x is anything) and from there, preserving the functional 1, roll
(1) 2 3.
We would predict a functionalization penalty of (1/6) to get the 4 in there and no penalty to remove it (since it had to be removed anyway); we have N=1 organisms and so by my calculation before we would estimate that the indirect pathway would be of greater probability to the direct pathway for a number of generations M>12.
Give it a try, if you're curious. The direct pathway, which requires you to hit only three numbers will be obtained on average after about 216 rolls. The indirect pathway, which requires you to hit four numbers in two steps will be obtained on average after approximately 72 rolls.
-----------
Finally, we have a problem that mass extinctions are bad not only for the number of extant species, but for preserving intermediates that we'd need to assay simple->complex transitions. Ideally, the molecular system in question would be predicted to be less than 65 million years old, or found in an organism that wasn't much impacted by the KT event. The key here is that one could predict the rate of subfunctionalization and elaboration of the simple system, and then directly look at extant organisms to see if the distribution matched the expected values. If you had a massively complex system appear, with no intermediates to be found, that would be powerful evidence against the complex-system-as-elaborated-simple-system theory.
Unfortunately, I don't know of any molecular machines with such recent origins. Maybe some will be found. What could be used instead, perhaps, is regulatory cascades; for example, the adaptations for swimming in whales and seals and flight in bats are thought to have arisen more recently than 65 million years ago. Seals and otters might be particularly good choices since they have various other relatives who could be examined. If entire new regulatory cascades with many novel components are found in seals and walruses but not anywhere else in the order Carnivora, I suspect that the elaboration theory would be in deep trouble. I'm not sure--I haven't looked at the mathematics--but I think that some place like this would be the place to start.
Added in edit: another place to look might be to see if we could recapitulate a 2,4-DNT metabolism pathway in the lab. This wouldn't be good as evidence against co-option, since its hard to tell if you've done something stupid in your lab experiment (e.g. lack of diversity of habitats). But if one could get it--and given the recency of the development in the wild, one would expect so--then it would allow the intermediates, if any, to be analyzed in detail.
[ 14. March 2003, 23:54: Message edited by: Rex Kerr ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 15. March 2003 00:06
Rex,
I hope the moderator will forgive me for this short post, but I don't have time for a full reply tonight (i can barely keep my eyes open).
With respect to your middle argument (with the dice), I don't see how my post didn't address this. For example, with direct pathways the probability of getting function X is 1, since the function itself is reducible to one part, we already started with a mutation that all selection has to do now is tweak it and prune it.
With a co-option story, not only are we bringing in pure chance events, but now we have to assess how many steps are needed to get function X. It's no longer one, and the more complex the irreducible system is, the more pure chance events will be needed to assess this. In about 6 or 7 years, you will see pretty rigorous calculations comming from the ID camp that will , as Dembski says, "nail this down". I will take a closer look at your example and try to show what I mean in in direct relation to your math and dice example, but I think this was suffice for now. By the way, thanks a lot Rex, I'm enjoying our conversations.
[ 15. March 2003, 00:08: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
GP
Member
Member # 570
|
posted 15. March 2003 00:22
Nelson,
Once again, I applaud your zeal in defending your position. But let us slow down a bit and explore what I had actually asked you to consider. In your original reply to me, you made it quite clear that IC is by itself a non-indicator for evolutionary likelihood. That is to say, as a definitional argument, IC makes no explicit statement about whether the structure evolved. Logically, then, I am interested in the additional considerations that were necessary to make ICness a potent argument against evolutionary pathways. But, having asked that question, I am terribly confused by your reply: "As I quite clearly stated, the best explanation for the IC molecular machines that are pointed out here and elsewhere is that they were intelligently designed." Can you see how this response is non-responsive to my question?
As I await a reconsideration, let me then briefly address your other replies. Specifically, in my last post, I made two points that I personally found unimpressive about the IC argument. Your reply to my first point that pure chance events are already employed in evolutionary analysis is that "there are too many pure chance events." But, then that reply merely defers to my second point that "[t]here is no measurable and quantifiable argument." At this point, because the weight of the defense seems to fall on this latter observation, I was hoping for a convincing reply. Yet, what I receive is a deference to Dembski's arguments in his books. I suppose, then, a suitable response from me is to cite counterarguments that exist abundantly and, in my opinion, validly against Dembski's probabilistic models [see Wein, Orr, et al.]. In point of fact, I see no justification in Dembski's assumptions. The point, of course, is that a probabilistic model typically depends on a working knowledge of the system being modeled. If we do not have an adequate knowledge of the actual evolutionary pathways in making the flagellum, it seems absurd to base any strong conclusions on a priori assumptions.
However, I will leave a discussion about Dembski aside for the moment, because in this thread, there is my first glimpse of actual experimental science being developed. Experiments are far more interesting, in my opinion, than theoretical musings. In our previous discussion, I had asked you to devise an experiment that would implement a challenge originally issued by Behe. As I recall, your plan was to select for motility by establishing a nutrient gradient. The goal was to see if a non-motile bacterial species would develop "something like a flagellum" in a finite amount of time. My first criticism in pointing out to you that your experimental setup would not pass peer review (and hence the reason why I believe most scientists viewed Behe's request skeptically) was that establishing a nutrient gradient was insufficient as an external pressure. To this criticism you wrote,
quote:
A bacterial colony will not grow if it does not have a source of nutrients. This is why the bacteria will be forced to move or die. Thus selecting for motility.
While it is true that a colony will die if it does not have a source of nutrient, it does not therefore follow that a "bacteria will be forced to move or die." I mentioned briefly that there are many adaptive strategies that bacteria take to escape certain death. It seems to me that by providing a restrictive medium, you are pressuring for the evolution of a variety of solutions, not the least of which, is the positive selection of perhaps already existing methods to address starvation which do not involve motility. Of course, it is worth noting here that a selective pressure in nature does not imply a near absence of an essential. This brings us to the second, albeit minor point, that setting up the bacteria to starve to death is not necessarily the smartest way to get them to evolve. To this criticism, you wrote:
quote:
There is a restriction of growth here, again, with the fact that the nutrient gradiant is outside the circular growth area. There is no unrestricted growing here, since, again, the "goal posts" will continually be moved once they finally get to their food source. As far as transplants go, I don't seem them as unnatural. There is an experiment that is kind of like the one I am proposing that was done by Ben-Jacob.
quote:
--------------------------------------------------------------------------------
We tried exposing bacterial colonies to conditions so novel that the creatures could never have encountered them before. Tough conditions, conditions of life and death. We wanted to know how inventive they could be in reworking their genetic code. For example, we took bacteria that can't move on agar but are able to roam freely in liquid. We put them on the wilderness of their worst nightmares, agar, and deprived them of food. The need to branch out in search of grazing land was a true creative challenge.
--------------------------------------------------------------------------------
They were able to succeed in moving however by forming a "round rotating circular structures (dots at the end of the branches) which, like circular saws, cut their way through the recalcitrant medium." They are able to do this, however, because they already had a motility structure, they just found, as a group, a novel way of using it. What would happen if we removed that and reverted them to their supposed ancestral state? Thats what the experiment seeks to look for. If bacteria do this by reengineering their genome in a complex way, that still wouldn't be Darwinian evolution.
Yes, the bacteria, that I am aware of in Ben-Jacob's work, are motile. So I fail to see your point in response to my criticism [but please, Nelson, provide citations for your quotes -- Ben Jacob deserves that much]. Bacteria are fragile living creatures. We do not simply demand of them some evolutionary miracle, by depriving them of genetic resources and then ask them to form de novo within our lifetime. More to the point, we also do not place insurmountable goals -- we do not place bacteria in a finite amount of medium and order them to make flagellum in the amount of time it takes them to use up the nutrients. This is why I am interested in how you plan to ensure a continuing lineage for the duration of your experiment. Disappointingly, in rapid fire fashion, you dismissed many of my logistical concerns. For instance, you clearly imply that you are working in a controlled setting with a finite area for growth. Thus, in order to maintain a fresh concentration gradient of nutrient, you have to constantly transplant colonies from one fresh medium. How do you do this repeatedly in a sterile environment (especially away from all those other DNA carrying vectors)? How many colonies do you transplant to maintain sufficient evolutionary rates? If for each depleted petri dish, you just take a million bacteria to a fresh petri dish, I would say you are not even modeling the real life conditions a bacteria can have to evolve.
I will write a few brief remarks to the remaining points:
quote:
We can use E.Coli and/or E. aerogenes.
These are already motile species, Nelson.
quote:
Of course now you've begged the question, indeed, the mother of all question: What evidence exists that IC structures, like the bacterial flagellum, evolve?
Let me turn that question back around, Nelson, since it belongs to the context in which I started this discussion with you. If IC structures aren't by definition proof of the inability evolutionary pathways, then one requires additional information beyond ICness to make that argument. To address your concern, requires only one true negative (and I believe I will leave this point to the many others who are debating you on this very matter). To address my concern requires much more than a definition.
Thank you very much for your attention,
GP
[ 15. March 2003, 00:33: Message edited by: GP ]
IP: Logged
|
|
gedanken
Member
Member # 594
|
posted 15. March 2003 00:45
Alonso said:
quote:
This alone shows that it is not an argument from ignorance to tell that is IC, it is completely and objective statement. All Darwinists can really do is show indirect pathways, since, only as a consequence, the definition eliminates direct pathways.
I think this summarizes what Alonso had to say about my post. Mirrored in this was the claim that I was not actually making any argument against the IC argument.
First on the clarity of the definition of IC. I think that I fully recognize that we can have cases in which there is an irreducible core, but that irreducible core is not “complex”. But I don’t’ recognize that there is ever a case in which we cannot find an irreducible core -- the only issue is the “complexity” of that core. Since “complexity” is a matter of degree, I would ask if we can thus agree that the issue of finding a case of IC’ness, (which reduces to finding the “irreducible core”) is a question of degree in which the degree of complexity of that identified irreducible core is the only issue for an objective definition?
(Or does one have to also include the “directness” of an evolutionary pathway in the definition of “IC”?)
But the essence of my point can be found in examining this quote. Is there a difficulty for evolution if one has identified that the development pathway was indirect rather than direct?
(In fact, what does “indirect” actually mean?)
But even more important was the issue of “unselected pathways.” The N+1 membranes are a clear “direct” pathway because N-1 to N is the same “direct” pattern as N to N+1. It is simple to understand what was selected for, and a compressed natural language description encompases the entire sequence from 1 to N+1.
But what evidence is presented that an “indirect” pathway is also an “unselected” pathway? The fact that each step might have had a particular advantage in a particular environment, and yet each step was in a somewhat different direction has not been explored. And also a very important aspect, that changes in size or orientation or the like of a change that are not so easily described as the N to N+1 layer case have not been explored.
So a part, if it were completely removed, causes the function to stop operating. Clearly the intended implication is that there are no pathways from a working subsystem using all the parts but the one in its final form to the system in its final form. The description of “removal” of the part is visually descriptive.
Now suppose I said lets remove the 99 membranes -- considering the 99 membranes as a single “part”. This would also be a clearly visually descriptive change. Now it would be readily challenged as not a case of a single part according to the IC concept, since 99 membranes have a ready language description as separate “parts”.
But is it true that cases in which the system reduces to a “well matched” set of parts in a “core” system does not have ready explanations in terms of evolution. Clearly, as per Pennock’s description that Behe was commenting on there can be cases of co-option in which the steps are clearly selected, yet not of the smooth directionality as seen in “climbing mount improbable”. The N to N+1 is simply a simplifying example, and is not intended to represent the entirety of selected pathways.
quote:
What Behe is saying here is that the focus on parts has lead to undetailed, vague, but pathways. However, because it is irreducibly complex you can be sure that all of them are indirect.
This also gets to this same issue, that co-option can happen in irreducible cores. Indeed, a series of co-options of small changes could have a very irregular pathway -- and thus “indirect”. That does not mean that every step is not selected, however.
The issue of “vagueness” in describing what is known is very important, however. Vagueness is obviously used when we lack knowledge. But if this is a claim of a “gap” argument, that scientists have simply not filled in the gaps yet, we must recognize that the history of science is one of filling in gaps. One does not have a convincing argument that a sequence of steps is unselected when in fact one can describe possible intermediates (though vaguely).
The essence of an effective IC argument (or TRIZ argument of a contradiction that is difficult to assail) is that one must show that there are no pathways that can reasonably be constructed, and which have reasonable possibility of being “selected”.
Because we simply have an enormous grid of evidence that suggests descent with modification. And we have a tremendous history of observation of changes on “selected” pathways showing “microevolutionary” changes. We furthermore have evidence that the change rate of “microevolutionary” change would be sufficient to produce the large scale changes -- and a lack of evidence for actual difficulties therein.
The TRIZ and IC arguments are claims of just those difficulties. But they are still worded in the form of an “argument from ignorance,” as they only seem to be argued in terms of gaps in knowledge.
Now the discussion of unselected steps is refreshing in the later quote from Behe. But I want the reader to think back to all the quotes from Alonso about how ICness could be described as “scientific” or one of direct observability and which could be tied to relationships studied in peer-reviewed papers. Here we finally come to recognize the irrelevance of ICness itself in terms of any objective claim that a part being removed causes the system to cease function. This turns out to be irrelevant -- the only relevant issue is one of asking if there are necessary unselected steps.
Now having finally recognized that unselected steps are the essence, and irreducability or complexity alone is basically irrelevant (except with an additional demonstration of some sort of necessity for unselected steps) we can go to work on that issue.
What has been done to show that any definition of IC implies that there are unselected steps? What has been done to show that cases of claims of unselected steps to an “IC” system is not just another case of a gap argument? (And thus an argument from ignorance.) We still have not seen this -- where is the demonstration of this.
Very specifically, why are indirect pathways ones that we should expect are also unselected? We have simply shifted the burden from IC to indirectness! So far indirectness only has the characteristic of complexity of the zagged pathway going for it in terms of giving many more opportunities for lack of evidence from fossil record (or record from descendents) of the gap. Thus it is a prime play area for gap arguments again.
Can we please have some evidence that “indirect” pathways are “unselected” pathways?
(And I also note that Behe, in his quote that Alonso gave, clearly asks for “gap” evidence that cannot be developed because of the lack of information. Thus he sets up an unresolvable demand in which one can play with gap arguments and sound as though one was making scientifically valid arguments.)
IP: Logged
|
|
gedanken
Member
Member # 594
|
posted 15. March 2003 01:32
PS, I had not read GP’s post when I wrote mine immediately above. But this appears to support what I was thinking, though in a different way and different focus -- thanks.
GP says “you made it quite clear that IC is by itself a non-indicator for evolutionary likelihood.”
I wanted to return to my earlier point about the definitions and arguments of IC (and TRIZ) being placed carefully on a ‘fractal edge’ (back on page 8). If interpretation seems to move one way away from the ‘edge’, then something will be added to move the argument and interpretation back to that edge.
The essence is that what is being searched for is evidence of design from a designer that leaves no evidence beyond the designs themselves. (In essence the designer must have the characteristics of an “unembodied” designer -- if not actually unembodied, then performing such feats over millions or billions of years with technology indistinguishable from magic so as to leave no evidence whatsoever of the designer’s presence with these extremely regular and repeated incursions.)
As soon as it is seen that IC is by itself insufficient to directly show a difficulty for evolution having a high probability, then some additional issue must be added such as “indirectness” of the evolution. What is found must simultaneously have the properties of being found regularly in nature, and of not having an evolutionary explanation. Because the essence is to show problems for evolution that can only be resolved with this “unembodied” kind of designer (or one with the essence of that character as mentioned).
I predicted that arguments would spin in a chaotic fashion with a kind of “attractor” to that fractal edge -- but wherein the argument returns to similar points but does not stabilize to any resolution. I also predicted that definitions would be changed to accommodate this need to shift back to this “fractal edge.” Even though it is denied, we seem to observe this, as we see in the response of Behe to "repair this defect” by noting “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.” So contrary to assertions, we do see even Behe fine tuning the definitions to return to the fractal edge based on a gap in knowledge.
Now if there are clear and repeated cases of such unembodied (or unembodied-like) designers creating jumps across “contradictions” that cannot be crossed with understandable evolutionary processes, then we should be able to clearly detail the conditions and repeatedly show examples fitting the conditions.
But now if there are not any such cases of unembodied (or unembodied-like) designers creating such jumps across “contradictions,” can we expect the arguments to stabilize? No, we would not expect this, because the apparent objective has not been met. So we would see the continuing refinement of definitions and bringing in of different conditions when the last condition failed to be convincing. Thus we would see challenges that ICness has not demonstrated unevolvability met with some new variant that puts us back on the fractal edge.
But in each case, the only resolution seems to come from an argument in the form of an “argument from ignorance”. Previously I pointed out the “argument from ignorance” form, and this was met with claims that IC was demonstratable scientifically -- yet this demonstration did not tackle the prime issue of unevolvability. (In other words the failure of the IC argument was met with a claim that it did not fail and then showing a result that was irrelevant to unevolvability.) So the perception has fallen on one side of the fractal edge and needs to be brought back with the next argument. Now again if actual cases of unembodied design were regularly occurring, we could expect resolution when we finally characterize that design, but if not then we must expect a chaotic continuation of the argument with further refinements that always seem to come back to an argument from ignorance. The reason is that the only way to approach the fractal edge (and thus making that edge “fractal” rather than an actual gap with a point in the middle sufficiently far from both sides to be stable) is to pull the argument toward a diffierent side of that edge in some hyperspace of dimensions of discussion.
[ 15. March 2003, 01:49: Message edited by: gedanken ]
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 15. March 2003 02:25
Nelson writes,
quote:
The reason why is if you remove any part from the ATP synthase you don't get a less efficient ATP synthesis machine, you don't get ATP synthesis at all.
Who's to say the function is ATP synthesis? Couldn't we just as well say that the function of the ATPase is proton transfer? Certainly that is part of the function.
Looked at it that way, the function appears to be performable by the very simple (and apparently homologous) one-part PPase. The reaction in each case -- hydrolyzing a phosphate bond to drive proton transport -- is very similar.
E.g.:
quote:
http://www.abo.fi/isb/students/anssi.malinen.html
STRUCTURAL STUDIES OF PROTON TRANSLOCATING PYROPHOSPHATASE
Membrane-bound proton translocating pyrophosphatases (H+-PPase) use the energy of pyrophosphate (PPi) hydrolysis to drive proton transport across biological membranes. The formed proton gradient is subsequently used to energize many cellular processes e.g. solute transport and ATP synthesis. The active H+-PPase is a dimer of 60–82 kDa polypeptide monomers, which are predicted to contain 15 transmembrane a-helices. Transmembrane helices are connected by short extracellular turns and longer cytoplasmic loops, three of which are mainly thought to form the active site for PPi hydrolysis. Overall the predicted H+-PPase structure is pretty simple which makes it a good model system for structural and functional elucidation of the mechanism by which pyrophosphate hydrolysis is coupled to proton pumping.
3.A.10 The H+-translocating Pyrophosphatase (H+-PPase) Family
Proteins of the H+-PPase family are found in the vacuolar (tonoplast) membrane of higher plants, algae, and protozoa, and in both bacteria and archaea. They are therefore ancient enzymes. The plant enzymes probably pump one H+ upon hydrolysis of pyrophosphate, thereby generating a proton motive force, postive and acidic in the tonoplast lumen. They establish a pmf of similar magnitude to that generated by the H+-translocating ATPases in the same vacuolar membrane . The bacterial and archaeal proteins may catalyze fully reversible reactions. The enzyme from R.rubrum contributes to the pmf when light intensity is insufficient to generate a pmf sufficient in magnitude to support rapid ATP synthesis.
Eukaryotic members of the H+-PPase family are large proteins of about 770 amino acyl residues with fifteen putative transmembrane a-helical spanners (TMSs). The N-termini are predicted to be in the vacuolar lumen while the C-termini are thought to be in the cytoplasm. These proteins exhibit a region that shows convincing sequence similarity to the regions surrounding the DCCD-sensitive glutamate in the C-terminal regions of the c-subunits of F-type ATPases (TC #3.A.2).
And of course any reaction that runs one way can do the reverse just by changing the amounts of the reactants and products.
"Function" is a very squidgy thing in biology. This is yet another problem with IC-based arguments, which assume single, clear functions that are unchanging.
More stuff on ATPase origins from the AE resource thread on it
[ 15. March 2003, 03:12: Message edited by: yersinia ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 15. March 2003 17:38
GP:
IC simultaneously, as a consequence of the definition, points us to intelligent design and, as the complexity of the irreducible system increases, points to the unlikelyhood of an evolutionary pathway.
Now when I said, "As I quite clearly stated, the best explanation for the IC molecular machines that are pointed out here and elsewhere is that they were intelligently designed." this was not a non-responsive answer. We are both , after all, looking at the same data. It's in how we interpret this data according to our own hypothesis, where the data is an observation that is consistent with the ID hypothesis. With that said, it is clear that IC molecular machines themselves are evidence for the ID hypothesis, in that it looks designed and that it presents a problem for evolutionary accounts. These two consequences are not a coincidence, they are consistent with the ID hypothesis that the bacterial flagellum was designed. You might say that the design is apparent, I say it's actual. Indeed, this is the crux of the our disagreement.
I can reword my original reply like this. A lot of things are improbable (i.e. complex). However, those things that are both improbable(i.e. complex) and specified (i.e. irreducible) point to intelligent design. The bacterial flagellum in that it is both complex and specified is evidence for intelligent design. It is specified in that the function is beyond the components of the actual system. It is complex in that it requires many interacting, well-macthed parts, not just one or two.
We can see this in the very words we type. You're not talking to a natural process. If you were to see the word:
"to"
Although "irreducible" (the meaning is not reducible to the letters or the computer processes that brought the letters to your screen) it is not complex. If a book fell on the keyboard it is likely that along with a random stirng of letters, the word "to" can appear by chacne. However, the sentence:
"Hello my name is nelson alonso"
is not complex and "irreducible". The meaning is beyond the components of the system. If I remove a letter or a word I lost it's meaning (i.e. function). This is only an analogy, and it's an imperfect one. If you were chinese and had no idea the english language existed you would see this as random. But not so with machines, machines are complex and specified whether you are Chinese or Russian. And this is what makes the design inference exact.
With respect to Dembski's argument, you missed the point. In an earlier reply you stated:
"There is no measurable and quantifiable argument"
This was clearly false. There is a measurable and quantifiable argument. Of course, as you said, there are those that disagree that the measurable and quantifiable argument are valid. Thats irrelevant. Your claim was that the measurable and quantifiable argument does not exist, indeed it does exist. That there are those that disagree that the measurable and quantifiable arguments hold water is a different claim.
Besides, Dembski has replied to Orr:
http://www.designinference.com/documents/2002.12.Unfettered_Resp_to_Orr.htm
and has replied to Wein:
http://www.designinference.com/documents/05.02.resp_to_wein.htm
We can go two ways here now. You can begin defending Orr and Wein's critique and I can respond by pointing out Dembski's rebuttals. I suggest this isn't the thread for that, and I would advise participating in the various threads at ARN and here that are already discussing these (unless the moderator doesn't have a problem with
creating a thread discussing these critiques in case they don't already exist). There are no a priori assumptions here. We have the systems in question. Lets test our hypothesis.
Nonetheless, my interest in citing Dembski was simply to refute the claim that none exist. There are quantifiable , measurable ways of delineating IC systems through experimentation and mere genetics, molecular biology, and biochemistry, and there are quantifiable, measurable ways (through statisics) to measure the improbability of getting these systems. To say that they don't exist is blatantly false. Those who want to tell evolutionary stories about the Darwinian evolution of flagella should take Dembski's and Behe's arguments seriously, from now on. As Dembski says, do the calculation.
Dembski's and Behe's models are interesting in that they are not only useful to an ID theorist they are useful to the Darwinist who wants to construct an evolutionary pathway, one such pathway already exists , albeit not in any detailed way. Still, ID theorists can use these pathways to illustrate just how improbable such scenarios can get. One such illustration has already been done, and as Darwinists and ID theorists learn to cooperate as I see they are doing now, more illustrations, no matter which side of the fence the conclusions fall on, can advance this stagnant field in science. Thats just my opinion of course.
Now to your criticism of my experiment, I submit that I successfully discussed each of your objections. In fact, in this post, I simply need to reiterate my points. You say first that depriving a bacterial colony of nutrients would not getting them to move. Unfortunately, the experiment that I documented (Ben-Jacob's) shows otherwise. The bacteria, although motile, could not move, and therefore, they had no choice but to figure out how to move . This is a proof-of-concept experiment in that unless the bacteria found a way to move, they died. And move they did. When they moved they got to eat. This experiment illustrates how effective a selective pressure for motility can be.
As you correctly state, these bacteria were already motile and used this motility to get the job done. However, my experiment requires non-motile bacteria. There is no need to constantly transplant the medium. The need for this will only occur once bacteria learn to move.
As far as your transplant questions, I do not see this as either required nor as a reason to stop the experiment. Very long experiments have been done which did not require a transplant of the colony, but still was able to ascertain the evolutionary significance:
quote:
Our collaborative work builds on two previous studies. One examined genomic variation among cells recovered from populations of Escherichia coli that had been stored as a "stab" culture for 30 years without renewal of the medium and, hence, with little opportunity for growth (1, 2). A high level of diversity was found using restriction fragment length polymorphism (RFLP) analysis with eight insertion sequence (IS) elements as molecular probes. Clones differed from their putative ancestor by ~12 changes, on average. It was unclear, however, whether the prolonged starvation had an important role in promoting or maintaining this variability and whether the derived bacteria were any better adapted to the storage regime than was their ancestor.
Proc Natl Acad Sci U S A 1999 Mar 30;96(7):3807-12
Let me think about putting some concrete numbers here for this experiment, though, but I think that the concept itself, in principle, is tractable. Time is no big deal, here, this experiment ranged about 5 years.
Now earlier you claimed that bacteria when undergoing starvation either go dormant or send out spores. However, you failed to mention bacteria that do not. When I pointed these bacteria out, you mentioned that they were motile. However, since we are interested in gram-positive bacteria anyway, we can knock-out the genes that code for a bacterial flagellum, since we need to leave them with an ion channel anwyay.
As for your last point, I already address this above. However, I think that your reply was truly non-responsive. You stated:
"After all, can one data point be sufficient to convince you of the IC argument, when similar evidence already exists (as I think you have admitted) that IC structures do in fact evolve?"
Although I think that in principle, IC structures can evolve, I don't think that they do and I have never admitted this. So again I ask, what data are you referring to?
[ 15. March 2003, 17:57: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 15. March 2003 18:20
Yersinia,
First of all I want to thank you for your post as you nicely illustrate a function that has no IC core, so I don't have to repeat myself when it comes to Ged's post.
However, there is certainly good reason to say that the function of the 8 part ATP synthase is ATP synthesis. Function is the cornertone of Biology. In order to understand what the various parts of the ATP synthase machine does, you have to refer to the function of ATP synthesis and not to just proton transfer.
If I reinterpret the function of the mousetrap so that it is a weapon, well then heck, I don't even need the spring for that. I don't need the hammer. I don't even need the catch. I can just throw one of these parts at you, or gouge your eyes out with the spring. Or throw the base at your head. But I won't understand the parts of the mousetrap unless I invoke the function of all those interacting parts. And more importantly for the organism, unless I have all those parts, I won't get ATP synthesis. In fact, all those parts are so important for ATPase activity that one part, epsilon, inhibits it if F1 is not attached to Fo.
Dunn, S.D. and Heppel, L.A. (1981) Properties and functions of the subunits of the Escherichia colicoupling factor ATPase.Arch. Biochem. Biophys.210, 421436
[ 15. March 2003, 18:30: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
GP
Member
Member # 570
|
posted 15. March 2003 18:54
Nelson,
It may seem that we are at an impasse, if you are beginning to put forth arguments for me that I have not in fact put forth. You also seem unwilling to continue this dialogue in a patient, non-accusatory manner. So I think I shall write a summary of the discussion thus far, since you do not find the need to revisit it.
You wrote, "IC simultaneously, as a consequence of the definition, points us to intelligent design and, as the complexity of the irreducible system increases, points to the unlikelyhood of an evolutionary pathway." In other words, ICness is therefore not a definition of non-evolvability. The non-evolvability argument is derived from a structure that exhibits IC. Hence, you are now changing the argument that you originally put forth to me, when you wrote explicitly to gedanken, "No, finding a pathway to an IC system is finding a pathway to an IC system. You can surmise whether you can reduce the function to one component whether you know of any potential evolutionary pathways or not. Just remove a part from the IC core and see if it still functions. It's quite simple." I agree with the latter. IC is what IC is -- the inability of a function to be preserved under some test. However, you have not yet answered my question about how to conclude non-evolvability. No, instead you go off on a tangent telling me about my interpretation of "apparent" design, when I bring forth no such conceptions. What I am interested in knowing is the additional considerations required to make the inference that IC points to intelligent design.
A factor to this argument, I suspect, is that this inference requires a great deal of incredulity. You constantly refer to "too many pure chance events" as an obstacle for you. This, of course, is how Dembski came briefly into the picture. I argued two points. The first was that "pure chance events" were already employed to explain evolutionary pathways. The second was that the notion of "too many" suffers from a lack of a measurable and quantifiable argument. You argue that Dembski had provided such argumentation, as if I was unaware of his thesis. I responded that I did not find them convincing for several reasons, which coincide with many of his critics. Why? As I pointed out to you later in our discussion, Dembski's thesis relies on a priori assumptions, which by definition are neither measured or quantified. They are assumed. Of course, you are right to urge those in the scientific world, to "do the calculations." But it also seems fair to turn the exhortation right back at you. Evolutionary pathways exist independently of their probabilistic distribution. To discover them is to provide information about an accurate probabilistic model. To do the calculations before ascertaining the pathways is to put the cart before the horse. Now, we can continue to trade articles by critics and proponents, but in all honesty, I believe that in such a game, you are at a significant disadvantage. But, as I mentioned before, my real interest is in the experiment that you had proposed. You wrote,
quote:
Now to your criticism of my experiment, I submit that I successfully discussed each of your objections. In fact, in this post, I simply need to reiterate my points. You say first that depriving a bacterial colony of nutrients would not getting them to move. Unfortunately, the experiment that I documented (Ben-Jacob's) shows otherwise. The bacteria, although motile, could not move, and therefore, they had no choice but to figure out how to move . This is a proof-of-concept experiment in that unless the bacteria found a way to move, they died. And move they did. When they moved they got to eat. This experiment illustrates how effective a selective pressure for motility can be.
As you correctly state, these bacteria were already motile and used this motility to get the job done. However, my experiment requires non-motile bacteria. There is no need to constantly transplant the | | |
