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Author
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Topic: Evolving Inventions
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Nel
Member
Member # 614
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posted 15. March 2003 20:00
GP,
If I sounded accusatory or impatient in any way I do apologize, that was not my intention. So if I sound terse don't take it personally. Take it as the fact that interpeting any kind of emotion from an emotionless grouping of words will likely be a wrong interpretation.
With that said, I must disagree with you when you say that I did not answer your question concerning the evolvability issue and it's relation to IC. My point in bringing up "apparent" design and "actual" design is with respect to your question about evidence. If you do not agree that the design we see is apparent then I do apologize, although this is a common argument from the ID critic that I usually encounter.
Here is what I said with respect to evolvability and IC:
quote:
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.
Now when you talked about what additional evidence I needed to make my case, I stated specificially that all the evidence I needed was the identification of an IC system. I thought we had already went over why an IC system excludes direct routes, and although does not exclude indirect routes, the more complex the IC system is, the less likely that an indirect route would accomplish it. Indeed, I have been writing about this subject in depth for quite some time now.
Now, in an evolutionary pathway to an IC system, I can count how many pure chance events need to occur in order to get to the final system. This is different from a direct pathway, in that you start with the function you need and it's selection all the way to the top of mountain. But with an IC system, it's multi-component machines being added spontaneously , all the while changing the function, of the origin multi-component machine.
Perhaps it is incredulity but incredulity has meaning in science. We invoke homology because we don't regard coincidence as a good explanation, especially when the sequence similarity is high. That is an argument from incredulity.
You claimed that there is no quantifiable way to assess these probabilities. I replied that Dembski has provided a way. You said people disagree with Dembski. I say they failed to show why he's wrong. Now you say that it relies on too many a priori assumptions. Which ones? You don't say in your reply.
Evolutionary pathways exist only in the imagination. If you are saying the only way to assess evolutionary pathways is if they are right before our eyes is ridiculous in my opinion. We are saying that there are no evolutionary pathways, scientists can only propose evolutionary pathways. Of course we could find evidence for each and every step in a pathway, but how likely is that? These are historical sciences and if we do find independant evidence of evolutionary pathways then the argument is over. However, as long as the evidence can go either way, we can assess just how probable and grounded in reality our evolutionary stories are. Thats where Behe and Dembski come in.
On to your critique of the experiment, I have no idea why you brought up the point about Behe and falsification. Indeed, if this experiment works, like I said before, it would falsify my ID hypothesis as well.
In my experiment I provided not only starvation but also a gradient where a "goal post" can be reached. Like the Ben-Jacob experiment, where a novel way to move was selected for, we should see something evolve especially if we start with an ion channel (i'll let you know what I mean by that below.) Now you keep talking about these other ways to get to the outside of the growth circle. But there are various ways to circumvent these strategies, for example, using bacteria that do not go dormant. I really explained all this. This should model the evolution of the flagellum nicely, since an evolutionary explanation would most definitely need to show how bacteria had need for a flagellum in the first place.
My point in bringing up the paper had nothing to do with monitoring motility but showed the fact that one didn't have to constantly renew the medium , and it was a very long experiment as well. That it had a selective pressure at all, is also what I am pointing to. Growth was limitied, there was selective pressure, it was a long multigenerational experiment and it had evolutionary significance. Couple this with the Ben-Jacob experiment, and you have a proof-of-concept experiment in the making.
As far as nutrient gradients, I don't really see how this is a "logistical nightmare". Nutrient gradients are added, removed, replaced, incresed, decreased in plenty of experiments involving chemotaxis in bacteria. So I don't see your point about that.
With respect to bacterial species, E. aerogenes is gram negative, but E. Coli is gram-positive. Since we are interested in the most ancient of bacteria anyway, we can use E. Coli, knock-out the genes for motility (in fact I think Behe wanted to do this as well) and see if we get a flagellum-like system. We don't need to keep deleting genes like a crazy person. You just need to delete the genes that encode the bacterial flagellum. This is easy, since the bacterial flagellum is IC we can do something like this:
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.
These deletions do indeed lead us to a picture of the ancestral species in that Darwinists themselves don't think that bacteria came with a flagella (otherwise they would be IDers). Bacteria that have lost their flagella can survive just fine.
As far as the issue about the ion channel, the reigning evolutionary story , at least here, is that the bacterial flagellum evolved from a T3SS, basically an export machine. Fine. I say , lets start with an export machine and see if the bacteria co-opt this secretion system in order to evolve a flagellum. Since the genes that are essential for secretion will still be present when we destroy motility in these critters, I think that this is a good conclusion to make.
Now the results of the experiment will be interesting. If the results show that mutational accidents and natural selection alone were responsible for the bacterial flagella evolution, I will drop ID. However, if the result of the evolution was directed mutation and a complex mix and matching (what Shapiro calls genetic engineering) then we are left with a complex, non-Darwinian mechanism (cf. Margulis) for which we need to account for. If the result was negative in that no flagella evolved , but instead the same rehashing of another solution over and over and over again, then I'm sorry, but Darwinism has no empirical basis. Thats just my opinion of course.
I thank you too for your conservation regarding this experiment. I hope there are no bad feelings between us. These are just ideas after all.
[ 18. March 2003, 19:12: Message edited by: Nelson_Alonso ]
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yersinia
Member
Member # 324
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posted 15. March 2003 20:08
Nelson, a brief request:
...could you use quote tags when you are quoting...it's quite hard to read many of your posts.
Thanks...
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gedanken
Member
Member # 594
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posted 16. March 2003 02:42
Alonso said to Yersinia:
quote:
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.
But as I read Yersinia’s post referred to, it simply showed how that there were other functions possible for a particular case (namely function of ATP synthes and near variants, Yersinia showed other functions).
Now this gets precisely to what I have been talking about in the lack of clarity of definitions, and precisely the issue of the “fractal edge” to which the arguments tend to be pulled as though by a fractal or chaotic attractor.
At an earlier point Alonso argued that ATP synthes had an irreducible core, in the sense:
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. 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.
Then Yersinia showed that there were other functions and near variants of ATP would be functional in part and thus have selectable evolutionary pathways. At that point Alonso made the comments first quoted.
This is precisely the type of argument jumping around the “fractal edge” that I have been describing. It is due to the lack of clarity of the definitions, a lack of clarity of now to determine if something is IC.
All that is really left to determine if something is “IC” is to determine if it has a selectable pathway to have evolved. But that is in essence itself a “argument from ignorance” because of the potential complexity of selectable pathways.
Note that selectable pathways have not been defined or shown to be contrary to “indirect pathways”. As far as I can tell, “indirect” route is only a term for not having a simple description of the evolutionary pathway (as in 1,2.3..N layers which is a simplistic explanation).
We still have distinctions being made, toward separate directions:
1) Directness in terms of simple explanation -- this case, like N to N+1 layers, is easily describable in terms of the single function (or a function that can be described as having some sort of semi-linear or monotonic property that is changing over the described change, such as N+1 has more of one thing and less of another). Now what is important about the “direct” pathway is that it is easy to see that there is a narrow focusing in that particular “direction”, such that the range of variances being considered is narrowed. This is an example of the tree branching probabilities being focused more toward a narrow range of options. Thus the probability of a particular option is high, while the number of options that could have occurred that contain increased complexity are low.. This will be important in next case.
2) Indrectness in terms of simple explanation -- and note most especially that we have not denied that the indirect pathway is selectable. The examples above (Yersinia’s post) is precisely the demonstration that these other options were selectable, that other functions for ATP synthesis-type variants were useful to the organism. This lead to indirect pathways that were not necessarily unselected, just complex in the “jagged” or complexly variable pathways of the evolution in question. Since each alternate function which gives a “selected” evolutionary pathway takes the system in a slightly different direction, there is no clear and simple description of the evolutionary pathway in the slightly larger picture. (The microscopic analysis of individual small changes may be simple, but the assembly of the various sub-paths becomes complex.
Now what is most important in this second case is that the number of options that could have occurred that contain increased complexity is now much larger than in case one. Since various aspects are selectable, the environmental situation plays a much greater role in making the situation complex to analyze, and less is immediately known about the potential evolutionary pathways precisely because the relative importance in the environment of various possible selective pressures is complex. Because of this, the number of options that could have occurred is larger, and the individual probability of a particular option occurring is smaller.
Because of this situation number two, Alonso is exactly correct to point out that there was a lower probability in the so-called “indirect” route. The problem is that this does not provide any evidence against a particular pathway having occurred by these natural processes. When there is a large density of possibilities, there is a lower probability of a particular possibility being taken -- this is simple to understand. The point is that the various options could each have been selectable, and lead to a different direction of change -- yet one particular one was the result of the complex set of environmental forces.
We have a situation just like the tossing of a sequence of coins. When the number of coins increases (representing the complexity of the possible selectable pathways) we see a lowering of the probability of any particular outcome -- just as described in the “indirect” route. But the likelihood of a development that maintains or increases complexity has not decreased. The particular end point (corresponding to the particular results of this large number of coin tosses) becomes less and less likely as the number of possible selectable destinations increases in this indirect route -- but the corresponding terms in numerator and denominator change together. There is no argument against the process occurring according to a pathway that is thus described. There are no teeth in an argument against “Darwinian evolution”.
And back to the “fractal edge”, the variation back and forth between these two cases are argued circularly, in each case appearing to make a convincing case for a problem for evolution, either a problem in the number one or the number two case, and shifting back and forth.
Remember that my argument about the “fractal edge” is that an unembodied-like designer who regularly leaves cases that can be detected by only this kind of information in “gaps” in evolutionary steps but no other evidence should at least leave steps that have a clear gap. There should be a way to define the “irreducible complexity” or “contradiction” so that it can be clearly identified as neither a case of high density of selectable alternatives, or a high probability of narrowly focused selectable alternatives. But if there actually are no regular occurrences of unembodied-like designers acting over millions or billions of years, then we will find that all “gap” arguments approach this “fractal edge” wherein one problem or another problem is found with the argument and it is continually needing to be “patched”. This is the behavior I seem to observe here in the presentations.
My request is for clear definitions to be given for IC.
I don’t mean that it is not reasonable for there to be different definitions, that have to be tested differently. In that case one can simply label the different definitions being tested at the particular time, and indicate by name which definition is being tested in the particular case. As it is the different definitions (or shades of definitions) lead to logic failures as the definitions seem to change as the argument progresses. This failure makes the IC argument less convincing. Breaking up and labeling the different IC definitions would help with clarity and lead to fewer logical inconsistencies of argument.
Now here is how this breaking up of the IC definitions and ways to test for evolutionary difficulty will be helpful and more “scientific”. We can simply go through the definitions or clearly objective tests in sequence, say by number. If the particular case fails #1, then go on to #2, etc. Then when the entire list is exhausted, then we have none of the IC definitions satisfied. In this manner we avoid the “fractal” attractor of the argument jumping around to aspects of the different definitions or tests for IC, such that it never settles on which version is being tested and the arguments spin out in circular loops wherein nothing gets settled because of lack of clarity of definitions.
[ 16. March 2003, 03:08: Message edited by: gedanken ]
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gedanken
Member
Member # 594
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posted 16. March 2003 13:32
I would like to point out the new thread:
A sequence of tests for IC. I am having trouble going from a definition of IC or a description of a test for IC and the cases that Alonso gives showing that ATP synthes was not “IC” as per Alonso’s post that Yersinia’s post supposedly demonstrated.
What I would like is that a sufficiently detailed definition or presentation of the test for IC be given in that thread. Then we can apply the definition or test here to understand how it applies.
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