|
Author
|
Topic: Evolving Inventions
|
Nel
Member
Member # 614
|
posted 12. March 2003 20:20
Ged:
But this simply confirms what I already thought. The basic claim of IC is that if one can figure out the potential pathway, then it must not have been IC after all.
Nelsn:
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.
Ged:
Thus IC is based on gaps in scientific knowledge. As soon as the gap is filled, it is inherently no longer IC. Thus unfalsifiable.
Nelson:
This is completely false. IC is based on knowledge of what removing a component would do to the system, not on gaps on scientific knowledge. What is unfalsifiable is the hypothesis that flagella evolved from the T3SS, I'm seeing so much resistance to the idea of testing this hypothesis experimentally, and I find this resistance telling.
[ 12. March 2003, 20:46: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Argon
Member
Member # 276
|
posted 12. March 2003 20:29
Nelson write:
quote:
The 9+2 pattern of MTs in cilia are not IC, it's just more efficient than the 3+0 pattern.
One can knock out or mutate components of the "9+2 patterned" cilia and kill function (mobility). It is therefore IC. That other arrangements (e.g. "3+0 patterns") are possible in other organisms is irrelevant to the determination of ICness. Presumably the "3+0" systems are likewise IC. If we accept the claim that IC systems cannot arise via evolution then we would conclude that the various types of cilia are unrelated and represent separate design "events". And that's despite the substantial protein and functional homologies observed.
Classification of a system as IC is independent of that system's historical origins, the relatedness of organisms carrying similar but different arrangements of components, and the likelihood of evolutionary paths. Remember, ICness is assigned based on a pattern of interactions between extant components, irrespective of the history of the parts or the system.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 12. March 2003 20:46
Ok this is my last post, I promise.
Argon:
One can knock out or mutate components of the "9+2 patterned" cilia and kill function (mobility). It is therefore IC. That other arrangements (e.g. "3+0 patterns") are possible in other organisms is irrelevant to the determination of ICness. Presumably the "3+0" systems are likewise IC.
Nelson:
The 9+2 pattern of MTs are not IC. The fact that 3+0 pattern exists alone shows that the same function can be done with a simpler pattern. Mike Gene made this point a while back, if we remove doublet 6, then doublets 5 and 7 can simply link up, that is an 8+2 pattern.
Argon:
If we accept the claim that IC systems cannot arise via evolution then we would conclude that the various types of cilia are unrelated and represent separate design "events". And that's despite the substantial protein and functional homologies observed.
Nelson:
If the data leads us in this direction, I don't see why we shouldn't follow it. But I don't think it is.
Argon:
Classification of a system as IC is independent of that system's historical origins, the relatedness of organisms carrying similar but different arrangements of components, and the likelihood of evolutionary paths. Remember, ICness is assigned based on a pattern of interactions between extant components, irrespective of the history of the parts or the system.
Nelson:
Right, but the consequence of the definition is that it is a barrier for Darwinian pathways. Even eliminating two of the four proposed in the peer reviewed literature.
IP: Logged
|
|
GP
Member
Member # 570
|
posted 12. March 2003 20:59
Nelson,
Thank you for complying with my request to provide a citation to J. Thomas' writing. It is unfortunate, however, that the quote you offered was part of another article by J. Thomas that I could not find on Google. I hope this exercise demonstrates the futility of using Internet discussions as primary sources for academic purposes. Having said that, I was hoping you could indulge me further on this thread. You wrote:
quote:
You can surmise whether you can reduce the function to one component whether you know of any potential evolutionary pathways or not.
If the property of ICness exists independently of whether there are in fact any potential evolutionary pathways, then would it be fair to say that ICness must be used in addition with other evidence to promote a design argument? That is to say, I find your claim above to indicate to me that ICness by itself has no explanatory power with regards to establishing a timeline of origins.
quote:
What is unfalsifiable is the hypothesis that flagella evolved from the T3SS, I'm seeing so much resistance to the idea of testing this hypothesis experimentally, and I find this resistance telling.
I have followed this thread, and I am confused about what experimental testing you are putting forth. Perhaps you are referring to the following? quote:
I don't agree that the experiment is not tractable due to timescales. An experiment involving thousands of generations of selective pressure for motility, involving something like this:
Papadopoulos D et. al. Genomic evolution during a 10,000-generation experiment with bacteria.
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3807-12.
and we can increase the mutation rate. This should (theoretically) produce a flagellum-like IC motile structure that is at least beneficial, if we start with a structure that, as Darwinists say,the flagellum was co-opted from -- an ion channel. I don't see anything particularly difficult about this experiment. Except that the stakes are pretty high here for Darwinian accounts of evolution. Even thinking about how this would work boggles my mind.
I vaguely recall that Behe also offered a similar experimental setup as a challenge to scientists. But, I also remember that the challenge was offered as a rhetorical gesture, because no scientist would find the experiemntal results indicative. I guess it is your right to interpret this finding as "resistance."
However, because you find no difficulties with the experiment, permit me to ask you a few questions. How would you setup a selective pressure with respect to motility? Why would you expect motility pressure to result necessarily in motility structures that are IC (as opposed to non-IC structures)? Why must the structure be flagella-like?
Thanks in advance for helping me with my difficulties,
GP
IP: Logged
|
|
yersinia
Member
Member # 324
|
posted 12. March 2003 21:31
quote:
Nelson:
The 9+2 pattern of MTs are not IC. The fact that 3+0 pattern exists alone shows that the same function can be done with a simpler pattern. Mike Gene made this point a while back, if we remove doublet 6, then doublets 5 and 7 can simply link up, that is an 8+2 pattern.
Similarly, the proteins of the bacterial flagellum rod are all very similar to each other, and if we removed one, more copies of another rod protein could conceivably suffice. Therefore, having 3 or 4 rod proteins is not part of the IC flagellum, only 1 rod protein is really required in the minimal IC "core".
Right?
nic
PS: We should also subtract multiple flagellin proteins and the outer two rings of the flagellum as some bacteria lack these.
PPS: We might even get by without hook proteins, just have a single stop-start helical flagellum sticking straight out of a spherical bacterium, no "universal joint" required. (And in archaea it appears that the hook protein vs. flagellin protein is not always distinct anyway)
Just knocked 6 or so proteins out of the "required parts" list right there. And of course a type III secretion system gets you up to 8-10, and MotAB homologs get you another 2.
PPPS: Just trying to show how dangerous Nelson's ad hoc defenses can be for the argument from IC...
[ 12. March 2003, 21:33: Message edited by: yersinia ]
IP: Logged
|
|
Argon
Member
Member # 276
|
posted 12. March 2003 21:46
Nelson wrote:
quote:
The 9+2 pattern of MTs are not IC. The fact that 3+0 pattern exists alone shows that the same function can be done with a simpler pattern. Mike Gene made this point a while back, if we remove doublet 6, then doublets 5 and 7 can simply link up, that is an 8+2 pattern.
Terminology drift, I think. Patterns cannot be classified as IC. Neither can functions or transitions. Instead, it's actual, physical systems that are.
I understand your idea however, that the IC, 9+2 systems might have evolved from earlier IC systems with other patterns (3+0, 8+2, whatever). But we shouldn't label a transition/pattern as "IC" or "not-IC" when what we are really talking about is evolvability. Let's rephrase is this way:
"The 9+2 pattern of MTs is likely to have evolved from a simpler, functional pattern out of roughly the identical components, possibly under conditions where there was less stringency".
![[Roll Eyes]](rolleyes.gif) Ok, so I added that last clause...
[ 12. March 2003, 21:49: Message edited by: Argon ]
IP: Logged
|
|
gedanken
Member
Member # 594
|
posted 12. March 2003 22:04
quote:
Ged:
Thus IC is based on gaps in scientific knowledge. As soon as the gap is filled, it is inherently no longer IC. Thus unfalsifiable.
Nelson:
This is completely false. IC is based on knowledge of what removing a component would do to the system, not on gaps on scientific knowledge. What is unfalsifiable is the hypothesis that flagella evolved from the T3SS, I'm seeing so much resistance to the idea of testing this hypothesis experimentally, and I find this resistance telling.
That is what I thought earlier, but then Alonso argued with respect to the non-IC’ness of “ADP synthesis (I think)” that:
quote:
Nelson:
I don't have time to get into the details of the system I mentioned but you can see how this is possible with some functions that we already discussed, for example, the membranes that Dawkins talked about, the function can be reduced to one membrane. Here you see that the addition of additional membranes just makes the function more efficient. The 9+2 pattern of MTs in cilia are not IC, it's just more efficient than the 3+0 pattern.
I appreciate the time issue. But what I am interested in is not so much the details of ADP, but with what aspect of the definition of IC and “IC Core” shows that there is no IC “core” here. Thus this answer (that it appears to be evolvable) does not answer the question of what part of the definition of “IC Core” is not objectively present.
Rex has suggested that there are cases such that the “complexity” part (rather than the “irreducible” part) is at issue. But how can any single protein or single part whatsoever function independent of other parts. I don’t see how that can happen, they must function in context of the rest of the organism -- and as such the other parts that they interact with are also parts of the system in question. The fact that scientists make one particular identification in one way is irrelevant -- because the idea of the “IC Core” is clearly to look for a different identification until one fines the core. One has not found the “core” if one has not cut enough out. But also one has not found the “core” if one has already cut out of consideration parts of the system that are essential for the function to proceed (and thus having “removed” too many parts, at least from consideration of the issue).
So far I can see nothing that shows my point to be incorrect that every possible function has an irreducible core. So far I can see nothing that gives an objective way to know why one case of IC is supposed to give difficulty to evolution, when another does not.
[ 12. March 2003, 22:08: Message edited by: gedanken ]
IP: Logged
|
|
Rex Kerr
Member
Member # 632
|
posted 12. March 2003 22:34
Nelson wrote:
quote:
I don't agree that the experiment is not tractable due to timescales. An experiment involving thousands of generations of selective pressure for motility, involving something like this (reference to a paper)
Except we only know of a handful of motility systems in bacteria; they seem to be conserved. Thus the best guess would be that motility systems have only evolved a handful of times throughout the history of the earth. There are about 10^30 bacteria on the earth, and they have had on the order of 10^12 generations. Even if motility systems have arisen hundreds of times with only a billionth of bacteria being under positive selection for motility, and we can increase mutation rates a thousandfold, we still would expect to need on the order of 10^27 bacteria. If multiple advantageous steps are needed,
A common lab experiment has maybe a few trillion bacteria. We're off by factors of a 10^12 or more from where we might expect to see a motility system arise.
Of course, it may be that it is fantastically more probable to get a motility structure than one might guess based on the number of extant motility structures. But there is a very wide probability range in between that is not experimentally accessible, but was evolutionarily accessible.
How do you propose that we resolve this difficulty?
quote:
I think that studies in AL, nanotechnology, and the fact that we invented the motor before we found one attached to bacteria is effectively an experiment that supports the ID inference here.
Those are about as sophisticated as point mutations compared to assembling a living cell from scratch. I am unimpressed.
quote:
As I have repeatedly said, the indirect pathways were seriously considered, in my opinion, here:
http://www.idthink.net/biot/flag1/index.html
And taking the T3SS into account, the calculation is still way below the probability bound.
This considers one indirect pathway, and focuses too much on the T3SS. The T3SS just alerted us to the possibility of starting with an export system; it is not necessarily the precursor to the flagellum. Mike Gene extensively considers the T3SS, but does not consider any other possible intermediate, nor does he consider other possible export systems. He certainly doesn't estimate the functionality penalties I mentioned above for all relevant numbers of intermediates.
quote:
Any number below 20 is not a less efficient motility structure, it is a non-functional motility structure.
This may be true of the flagellum as seen now, but why must it have evolved that way? My car is a gas-electric hybrid; if either the gas motor or the electric motor breaks, it is nonfunctional for motility. However, it does not follow that all cars must contain both components!
quote:
I don't think the existence of possible intermediate steps or how good we are at imagining intermediate steps is what makes these indirect routes so unlikely, what makes them unlikely is the number of pure chance, unselectable steps along the way to the flagellum.
If you can't imagine intermediate steps, you will think that there have to be a lot of chance, unselectable steps, won't you?
What is relevant to the probability is how many intermediate steps there are. What is relevant to our estimation of the probability is how well we can imagine these steps and compute their probability. If we have severe defects in our ability to do such imagining (and the history of biology is replete with examples of said inability), we can't be very confident of our probability predictions.
quote:
I don't see how grouping all the subfunctions of the filament or the motor to one part really reduces the complexity of the flagellum.
The current flagellum isn't specified. Something rotory-motor-like may be, but my four-component "flagellum" fits that specification. And you don't need to have all the subfunctions to be functional. You need something to provide energy, something with which to push the water, a way to couple your pusher with your energy source, and a way to couple your pusher with the structural supports of the cell. Everything else is elaborations.
Early versions of IC (and your apparent interpretation of it) seems to make a mistake in not accounting for subfunctionalization. For example, a crude fork can be used to cut, scoop, and stab. Duplication and degeneration of this utensil into something sharp, something bowl-shaped, and something with a point allows the same trinity of functions, and allows you to eat your meal. Lose any one of these and you have lost the ability to eat your meal. However, this type of subfunctionalization is not evolutionarily inaccessible, as demonstrated by this thought-experiment (given a fork, you can generate a three-component system where each part is needed in order for the system to function as well as a fork does), and by the eng/eng1b example.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 13. March 2003 15:38
GP:
Having said that, I was hoping you could indulge me further on this thread. You wrote:
quote:
You can surmise whether you can reduce the function to one component whether you know of any potential evolutionary pathways or not.
If the property of ICness exists independently of whether there are in fact any potential evolutionary pathways, then would it be fair to say that ICness must be used in addition with other evidence to promote a design argument? That is to say, I find your claim above to indicate to me that ICness by itself has no explanatory power with regards to establishing a timeline of origins.
Nelson:
My point about establishing the irreducible complexity of a system independantly of whether people can think up a co-option story about it is precisely that. Whenever an IDer proposes an IC system, someone replies with an evolutionary story about it, and it's always a co-option story. The original function is never preserved. But then they say "it's not IC because this part can do this different function" or "this part looks like that part". A system doesn't become non-IC just because you can imagine a co-option story about it. A system is IC because you can't reduce the function to a single component.
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.
Let me try to bring this back to TRIZ and it's connection to IC systems. It is ironic that co-option stories are closer to the way an intelligent designer would build a system rather than a blind watchmaker, something I mean to explore with the various machines of the immune system. In co-option stories, you can see how each step is in need of a solution that overcomes a technical contradiction, but where a blind trial and error process would have trouble opening up the ion channel in order to glom it onto a proto-rotor, an intelligent designer with foresight would have no problem with it. Let me try to illustrate this with a simpler example.
This reminds me of a story I was told, of a woman fed up with her Microsoft software so she decided to install Linux and made some interesting discoveries, which inspired me to strip down my computer layer by layer. I had a problem with installing Microsoft Streets and Trips on my desktop computer. Everytime I installed it the software would hang, and sometimes give me the much feared "blue screen of death". I began deleting as much extraneous software as I possibily could, thinking it was a space problem. The problem persisted. I added memory, the problem persisted. Fed up, I decided to rebuild the software on my computer component by component, starting from scratch. Stripping down each Microsoft component, I realized just how many layers there are in the operating system, from Windows NT to Windows 95 to DOS.
As it did with the woman in the story attempting to install Linux on her machine, stripping a computer down to it's most basic function lead me to a Basic interpreter which is obvious when in large print the computer spewed "NO ROM BASIC". This was IBM's fault, they built the PC by installing a Basic interpreter in the bios ROM. In order for the code to access files from a computer operating system, they had pc dos which is dependant on the basic intepreter. Microsoft came along and created MS Dos which is not dependant on the Basic intepreter, therefore it could be run on almost any machine not just IBM, this hurt IBM, whose version of PC Dos was platform dependant. Eventually this software "evolved" to the Microsoft Behemoth operating system we see today.
This is a co-option story. In some cases, the new software was built on a previous function, in other cases, it came up with a completely new invention (platform independant Basic). One that I think may apply to some of the IC systems we discuss (not necessarily all of them).
Nelson:
I don't agree that the experiment is not tractable due to timescales. An experiment involving thousands of generations of selective pressure for motility, involving something like this:
Papadopoulos D et. al. Genomic evolution during a 10,000-generation experiment with bacteria.
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3807-12.
and we can increase the mutation rate. This should (theoretically) produce a flagellum-like IC motile structure that is at least beneficial, if we start with a structure that, as Darwinists say,the flagellum was co-opted from -- an ion channel. I don't see anything particularly difficult about this experiment. Except that the stakes are pretty high here for Darwinian accounts of evolution. Even thinking about how this would work boggles my mind.
GP:
I vaguely recall that Behe also offered a similar experimental setup as a challenge to scientists.
Nelson:
Yes this is the experiment I am referring to.
GP:
But, I also remember that the challenge was offered as a rhetorical gesture, because no scientist would find the experiemntal results indicative. I guess it is your right to interpret this finding as "resistance."
Nelson:
I don't see it as a rhetorical gesture. I simply find it astonishing that no Darwinist feels comfortable with testing their hypothesis experimentally. I hear all about how Darwinian evolution is a testable scientific fact amenable to the scientific method and rigorously vindicated by observation. So when I say "lets test it" all I get is mumbling and nay saying and it wouldn't prove anything. It's almost as if Darwinists know the experiment wouldn't work. I say it wouldn't work precisely because the flagellum is IC and it shows exactly how difficult it is for natural selection to build it. It is exactly what Bracht says a trial and error process would not be able to accomplish. If there is no way to test the hypothesis that the bacterial flagellum evolved from a T3SS, then I say the hypothesis that the bacterial flagelum evolved from a T3SS is unfalsifiable, untestable, and by definition, unscientific.
GP:
However, because you find no difficulties with the experiment, permit me to ask you a few questions. How would you setup a selective pressure with respect to motility? Why would you expect motility pressure to result necessarily in motility structures that are IC (as opposed to non-IC structures)? Why must the structure be flagella-like?
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.
[ 13. March 2003, 15:53: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 13. March 2003 16:49
Yer:
Similarly, the proteins of the bacterial flagellum rod are all very similar to each other, and if we removed one, more copies of another rod protein could conceivably suffice. Therefore, having 3 or 4 rod proteins is not part of the IC flagellum, only 1 rod protein is really required in the minimal IC "core".
Nelson:
Nope. Fortunately, Mike Gene already addressed this:
quote:
It would seem there is no reason why the rod should be built around three proteins instead of simply one. Yet these three gene products are found in all flagella, dating back to the putative ancestral flagellum. This suggests one protein is not sufficient to form a functioning flagellar rod. Furthermore, the size of these proteins among these five distantly related bacteria has been held relatively constant (Fig 2), despite billions of years of experiencing very different selective pressures. It would seem some form of constraint or specification is at work, as natural selection will not tolerate too much deviation. And these size constraints map back to the last common ancestral flagellum, indistinguishable from the first flagellum.
and
quote:
Recall that flgB, flgC, and flgG are found in all bacterial flagella. Apparently, loss of one gene product cannot be compensated by the presence of the other structurally similar gene products. And recall the way they are laid down: six copies of flgB form one turn of the helical lattice, then six copies of flgC form the next turn, then twelve copies of flgG form two more turns. Is this crucial? Recall also that all subunits are needed to form a rod that can span the length of the periplasm. If a hypothetical ancestral rod was homogenous, being composed of only one gene product, it is difficult to envision the selectable nature of turning it into such a highly ordered, heterogenous structure. Without such a demonstration, there is no need to go beyond the default position that such similarities reflect functional constraints only.
If we turn to the sequence similarities themselves, the functional hypothesis is strengthened. The rod proteins tend to be most conserved at the N-terminal and C-terminal ends. This makes sense in light of their assumed assembly, where the C-terminal end of one protein interacts with the N-terminal end of the next protein. We can imagine that the C-terminal end of flgB must interact with the N-terminal end of flgC to form the helical lattice (where the transition from flgB to flgC occurs). However, the C-terminal end of flgB must also be able to interact with the N-terminal end of an adjacent flgB to form the first turn of the lattice. Thus, it is not surprising from an engineering perspective that similarities in structure and sequence would be found. Nevertheless, the sequence similarities are not that convincing.
http://www.idthink.net/biot/flag5/
In other words, there is a functional reason why we need all those rod subunits, and this strengths the IC nature of the bacterial flagellum, there is simply no reason to think that one rod protein would do the job.
Again, this type of data follows nicely from Bracht's TRIZ paper. Here we find a solution to the problem of how to build a stable, fine-tuned rod that contributes to mastering the brownian storm.
Yer:
PS: We should also subtract multiple flagellin proteins and the outer two rings of the flagellum as some bacteria lack these.
Nelson:
This was not a part of the IC scoring of the bacterial flagellum, so you aren't saying anything I didn't already know:
quote:
The L and P rings are not needed in gram-positive bacteria, since such bacteria lack outer cell membranes, thus we can eliminate this from the prototype (although it raises an interesting question about the origin of gram-positives and gram-negatives to be explored at a later date).
http://www.idthink.net/biot/flag4/index.html
Yer:
PPS: We might even get by without hook proteins, just have a single stop-start helical flagellum sticking straight out of a spherical bacterium, no "universal joint" required. (And in archaea it appears that the hook protein vs. flagellin protein is not always distinct anyway)Just knocked 6 or so proteins out of the "required parts" list right there.
Nelson:
The hook is needed for the flagellum to rotate. It generates torque. The "universal joint" is essential for producing "thrust". So, no, you havn't knocked out any parts from the required list.
Yer:
And of course a type III secretion system gets you up to 8-10, and MotAB homologs get you another 2.
Nelson:
These are just similarities. You keep failing to mention that the T3SS post-dates the flagellum. Showing me similarities is not a delimeter of redundant parts. In order to show that it doesn't need the export machine or MotAB you need to remove it and still preserve motility. MotA MotB and FlgG is absolutely required for motility in the bacterial flagellum, and the export machine is absolutely required to assemble it.
Yer:
PPPS: Just trying to show how dangerous Nelson's ad hoc defenses can be for the argument from IC...
Nelson:
You failed. Try again.
[ 13. March 2003, 17:04: Message edited by: Nelson_Alonso ]
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 13. March 2003 17:02
Nelson:
The 9+2 pattern of MTs are not IC. The fact that 3+0 pattern exists alone shows that the same function can be done with a simpler pattern. Mike Gene made this point a while back, if we remove doublet 6, then doublets 5 and 7 can simply link up, that is an 8+2 pattern.
Argon:
Terminology drift, I think. Patterns cannot be classified as IC. Neither can functions or transitions. Instead, it's actual, physical systems that are.
Nelson:
Patterns and functions can be applied to the IC definition, especially when we are talking about well-matched interacting linkers.
Argon:
I understand your idea however, that the IC, 9+2 systems might have evolved from earlier IC systems with other patterns (3+0, 8+2, whatever). But we shouldn't label a transition/pattern as "IC" or "not-IC" when what we are really talking about is evolvability.
Nelson:
Again, if you can show that the function of the 9+2 pattern can be accomplished by a simpler pattern, the 3+0 pattern then you have reduced the function, the 9+2 pattern is not IC. So of course the efficiency can be increased by more linkers. I even showed you how removing a component of the supposed IC candidate did not destroy function, it simply made it less efficient. Organisms with the 3+0 pattern beat very slowly. What is important is the presence of these components for motility. As Behe said:
quote:
"Just as a mousetrap does not work unless all of its constituent parts are present, ciliary motion simply does not exist in the absence of microtubules, connectors, and motors. Therefore we can conclude that the cilium is irreducibly complex" (Behe p.65).
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 13. March 2003 17:14
Nelson:
I don't have time to get into the details of the system I mentioned but you can see how this is possible with some functions that we already discussed, for example, the membranes that Dawkins talked about, the function can be reduced to one membrane. Here you see that the addition of additional membranes just makes the function more efficient. The 9+2 pattern of MTs in cilia are not IC, it's just more efficient than the 3+0 pattern.
Ged:
I appreciate the time issue. But what I am interested in is not so much the details of ADP, but with what aspect of the definition of IC and “IC Core” shows that there is no IC “core” here. Thus this answer (that it appears to be evolvable) does not answer the question of what part of the definition of “IC Core” is not objectively present.
Nelson:
Actually, I never said that it appears to be evolvable. Secondly, like I said, I don't have time to get into the details of each process of ADP synthesis, and I think I'm wrong about it anyway (which is why I said "I think"), so I replaced them with two examples that can be reduced to one part. You yourself admitted this in a recent posting with regard to "stopping photons" and membranes. That one is right up your alley since you claim to be a physics guy. Why ignore that?
There's another example that is in Behe's book. Hemoglobin.
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 hte system.
Rex has suggested that there are cases such that the “complexity” part (rather than the “irreducible” part) is at issue. But how can any single protein or single part whatsoever function independent of other parts. I don’t see how that can happen, they must function in context of the rest of the organism -- and as such the other parts that they interact with are also parts of the system in question. The fact that scientists make one particular identification in one way is irrelevant -- because the idea of the “IC Core” is clearly to look for a different identification until one fines the core. One has not found the “core” if one has not cut enough out. But also one has not found the “core” if one has already cut out of consideration parts of the system that are essential for the function to proceed (and thus having “removed” too many parts, at least from consideration of the issue).
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.
Ged:
So far I can see nothing that shows my point to be incorrect that every possible function has an irreducible core.
Nelson:
I gave you two examples where one function can be reduced to one component.
Ged:
So far I can see nothing that gives an objective way to know why one case of IC is supposed to give difficulty to evolution, when another does not.
Nelson:
It's simple. The larger the IC core, the more of a problem it is for indirect pathways to access the IC system. As opposed to the membrane example that Dawkins gives, where stopping photons can be reduced to one part, where addition of parts simply makes the function more efficient.
IP: Logged
|
|
Nel
Member
Member # 614
|
posted 13. March 2003 17:45
Nelson
I don't agree that the experiment is not tractable due to timescales. An experiment involving thousands of generations of selective pressure for motility, involving something like this (reference to a paper)
Rex:
Except we only know of a handful of motility systems in bacteria; they seem to be conserved. Thus the best guess would be that motility systems have only evolved a handful of times throughout the history of the earth. There are about 10^30 bacteria on the earth, and they have had on the order of 10^12 generations. Even if motility systems have arisen hundreds of times with only a billionth of bacteria being under positive selection for motility, and we can increase mutation rates a thousandfold, we still would expect to need on the order of 10^27 bacteria. If multiple advantageous steps are needed,
A common lab experiment has maybe a few trillion bacteria. We're off by factors of a 10^12 or more from where we might expect to see a motility system arise.
Of course, it may be that it is fantastically more probable to get a motility structure than one might guess based on the number of extant motility structures. But there is a very wide probability range in between that is not experimentally accessible, but was evolutionarily accessible.
How do you propose that we resolve this difficulty?
Nelson:
Actually we should constrain the number from the origin of the earth, to the appearance of the first bacterial flagellum. And even if we needed 10^27 bacteria you can just grab a few hundred thousand mliters of sea water and you got it. There is no reason to count all extant bacteria into the equation as if they had just recently received flagellum. Also, RM&NS is a stochastic process. There is absolutely no reason to think that you need 10^27 bacteria as an ingredient to get flagellum, as if it was some kind of magic number,in fact,you may get it a few thousand generations after, but if you directly apply selective pressure and increase the mutation rate, then you should get it. Especially if you kick start the process by giving them an ion channel. Heck, isn't that what Nic has been preaching all throughout ID boards? All you need is a wiggly thing sticking out.
As we can see from Rex's statement, the assertion that evolution had something probabilistically accessible that we cannot never possibly test for
in the lab stengenths the idea that ID hypothesis are not only needed to provide alternative explanations, but perhaps even necessary.
Nelson:
I think that studies in AL, nanotechnology, and the fact that we invented the motor before we found one attached to bacteria is effectively an experiment that supports the ID inference here.
Rex:
Those are about as sophisticated as point mutations compared to assembling a living cell from scratch. I am unimpressed.
Nelson:
Well, gee Rex, we don't see point mutations building motors that look like the outboard motors on flagellum. We only see intelligent agents doing that. I think that if you are unimpressed by what humans can do that would cause a scientist to compare human motors to bacterial motors, you should be even more unimpressed with what we have been able to do with RM&NS. Why aren't you an ID proponent? All we need to make the extrapolation exact is advancement in technology and thats inevitable.
Nelson:
As I have repeatedly said, the indirect pathways were seriously considered, in my opinion, here:
http://www.idthink.net/biot/flag1/index.html
And taking the T3SS into account, the calculation is still way below the probability bound.
Rex:
This considers one indirect pathway, and focuses too much on the T3SS. The T3SS just alerted us to the possibility of starting with an export system; it is not necessarily the precursor to the flagellum. Mike Gene extensively considers the T3SS, but does not consider any other possible intermediate, nor does he consider other possible export systems. He certainly doesn't estimate the functionality penalties I mentioned above for all relevant numbers of intermediates.
Nelson:
Rex, how do you falsify the hypothesis that the bacterial flagellum evolved from a simpler system?
Nelson:
Any number below 20 is not a less efficient motility structure, it is a non-functional motility structure.
Rex:
This may be true of the flagellum as seen now, but why must it have evolved that way?
Nelson:
Actually no, what I have done here is used Mike Gene's Ur-IC, where each component is mapped to all bacterial genomes, thus giving us a view of the ancestral state. Since we don't see any bacteria without these core components there is no reason to think they didn't consist of this IC core, much less evolved.
Rex;
My car is a gas-electric hybrid; if either the gas motor or the electric motor breaks, it is nonfunctional for motility. However, it does not follow that all cars must contain both components!
Nelson:
But if follows that that car must contain those components. And we are concerned with the origin of that car.
Nelson:
I don't think the existence of possible intermediate steps or how good we are at imagining intermediate steps is what makes these indirect routes so unlikely, what makes them unlikely is the number of pure chance, unselectable steps along the way to the flagellum.
Rex:
If you can't imagine intermediate steps, you will think that there have to be a lot of chance, unselectable steps, won't you?
Nelson:
I see the chance and unselectable steps in the story that has been imagined. Since all stories will inevitably be co-option stories (because of IC), I infer that most imagined stories will be cursed with the same fate. Too much chance.
Rex:
What is relevant to the probability is how many intermediate steps there are. What is relevant to our estimation of the probability is how well we can imagine these steps and compute their probability. If we have severe defects in our ability to do such imagining (and the history of biology is replete with examples of said inability), we can't be very confident of our probability predictions.
Nelson:
We can view the components, the structure of the flagellum, and it's function and apply Darwinian thinking to the system we are interested in. If too many unselectable steps are invoked in any of these stories, well gee thats what lead us to put Paley on the throne in the first place. What Darwinian theorists need is the existence of physical precursors, not some abstract number of fantasy intermediates.
I will respond to the rest of Rex post, and Charlie's post in the other thread a bit later tonight or tomorrow, I just ran out of time for the moment.
IP: Logged
|
|
GP
Member
Member # 570
|
posted 13. March 2003 17:56
Nelson,
Thank you for your thoughts. I would like to address quickly several issues. You write: quote:
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.
in response to my question about whether additional information is required to make ICness a problem for the current evolutionary synthesis. 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? 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." 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. 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:
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.
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. 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.] 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). How many different colony transplants would you need? How do you prevent the exponential growth in petri dishes? 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.
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? 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?
But, I think we got ahead of ourselves. There are severe flaws with the experiment you are proposing. Nevertheless, I am encouraged that you are proposing some sort of empirical test.
GP
IP: Logged
|
|
Rex Kerr
Member
Member # 632
|
posted 14. March 2003 08:59
Nelson, why is it fine to extrapolate from technology but not extrapolate from mutations? I think both are fine. I could understand thinking that neither was fine; that one is fine and the other is not seems peculiar.
Also, you are right that my car will not work without both the gasoline and electric motors. However, one did not have to design the whole car from scratch--rather, one could re-use the design for a conventional car and make a few modifications to yield a supposedly "IC" system. However, re-use with a few modifications is exactly what evolution has to work with. Why can't evolution produce IC systems if this is the case?
You apparently didn't take much note of my mathematics when you inferred that there would be "too much chance" in co-option stories. My whole point was that if you had enough intermediates, the factors that originally made the chance very low would be overcome, and would be replaced by functional intermediate penalties, which one would also expect to diminish with the number of steps. You are welcome to infer "too much chance", but I will happily do the opposite in the absence of any quantitative argument to the contrary. Better still, I have extrapolation on my side--since we know about co-option of very simple systems in the laboratory.
I'll let other people comment in more detail on directly doing the experiments. For now, I'll just reiterate my claim that experiments can't generate enough numbers for a negative result to be conclusive (or even instructive).
Finally, how would one falsify the hypothesis that the bacterial flagellum evolved from a simpler system? It's rather tricky to do directly right now; probably the best two approaches would be (1) falsify the hypothesis that a recently appearing complex molecular machine evolved from a simpler system, and extrapolate to the flagellum; or (2) sequence enough bacterial genomes so that one could estimate the rate of retention of intermediates, and if intermediates were retained but flagellar intermediates were not found, it would be good evidence against flagellum-from-a-simpler-system.
The problem with taking things like the flagellum is that they are so incredibly ancient that it is difficult to investigate directly. You are almost forced to extrapolate from more experimentally and historically accessible systems.
IP: Logged
|
|
|
Printer-friendly view of this topic
