Evidence for God from Science

Is the bacterial flagellum not a complex structure? There appears to be a consensus among certain scientists that it is not or that you could probably grow one from scratch in your own backyard.

Basically its an old argument revitalized by new data. Irreducible Complexity (IC) macromolecular machines have multiple inter-dependent parts. Loss of one component results in loss of function. Consequently, evolution must explain how the system arose to its present state. In other words, you don't have a functioning system until you have all the parts in place.

Operational parameters of the bacterial flagellum

1. Water-cooled rotary engine.
2. Driven by proton motive force.
3. Two gears: forward and reverse.
4. Operates at 6,000 to 17,000 rpm and can reverse direction within ¼ turn.
5. Hard-wired to signal transduction system with short term memory.
6. Rotary engine with 30 structural parts: the basal body-hook complex. 10 protein parts for the motor's sensor and control circuitry and 10 more protein parts to construct the motor.



It requires a precise timing sequence of assembly instructions in order to build it. It appears to be built inside out, one part before the other. The bacterial flagellum is an elegant efficient machine with all the elements of Design in its intrinsic function, genetic regulation, and chromosomal organization. This organelle is irreducibly complex and it is this very parameter that has made it amenable to molecular genetic dissection. Of the thousands of papers written on this organelle, none address its mechanism of emergence or evolution (although there may be ideas).

Furthermore complex structures such as the bacterial flagellum are not religious texts or objects. The flagellum is a biological machine that resembles an outboard motor. If someone were to examine the parts of an outboard motor they would conclude that it was intelligently designed. Let's look at a mousetrap as another example. According to Behe, "If any one of the five components of the mousetrap (the base, hammer, spring, catch, or holding bar) is removed, then the trap does not function. With even four of these parts, it's utterly useless as a trap. The mousetrap therefore is found to be irreducibly complex.” This same thinking can also be applied to the bacterial flagellum or any other complex biological machine found in nature.

More movies on the flagellum here:
http://www.arn.org/docs/mm/motorzoomuprotation-2.mov
http://www.arn.org/docs/mm/flagellarassembly-l.mov

I prefer to look at the basic central dogma. DNA replication or transcription requires hundreds of proteins and yet DNA replication and transcription are required to obtain proteins.

The Wikipedia article you linked in the first post gives good insight into a plausible path that may have led to the flagellum - it was a modification of a simpler mechanism having a very similar structure, lacking a few key parts (making it inoperative as a flagellum BUT performing another function. The links in the Wikipedia article describe this.

As to Behe's IC mousetrap - leaving out a few parts may give you a "mousetrap" that won't catch any mice, but it does give you a fully operational, if somewhat inelegant, tie clip (trap less catch and holding bar = tie clip).

Since this is a dedicated thread to discussion of IC, I thought I'd copy my response from the other thread here:

Most of the "irreducibly complex" structures have been shown to be not so irreducible after all. True, no one has shown that a bacterial flagellum actually did actually develop from a simpler structure having a different purpose and lacking certain key parts required for a workable flagellum. But the fact that such a simpler structure does exist (see http://en.wikipedia.org/wiki/Type_three ... 5D_.5B3.5D) makes this "irreducibly complex" structure considerably less "irreducible".

Waynepi:

You are right about one thing that since some systems are composed of simpler components irreducible complexity from that POV may not be so irreducible. To understand why irreducible complexity has not been falsified all it takes is to understand what a template is. A template is the blueprint for an object, it specifies what the object is composed of and what the object can perform (its function). Simpler systems play an entirely different role then the bacterial flagellum. When a system is said to be irreducibly complex that means that it has parts (properties) that if any of them were to be dismantled it would not perform the target function it is currently performing. Further going by this logic, if it is not irreducibly complex then life was not dependent on it at one point in time. However, irreducible complexity means that life was always dependent on it and thus it has always "been" from the beginning (of the design implementation). If you simply say that a system looks to be an ancestor of the bacterial flagellum then you are saying that the bacterial flagellum once did not exist because there was no need for it, as the system as a whole was not dependent on it.

But most attempts at "design detection" I know of have very plausible explanations. While some may not find the explanations compelling, they certainly call the specific method of "detection" of design into question.

Did you bother seeing the video I pointed too? The method Kirk Durston used had been published in the National Academy of Science and he applies it to biology while taking natural selection into account. Even if the numbers are offset by 20 or more orders of magnitude Design is still the best explanation hands down. I understand though if you don't bother seeing it.

Even if some "irreducibly complex" structures cannot be currently explained (ie if the similarity of the type three secretion system to the flagellum hadn't been recognized) does not mean that an explanation doesn't exist. The fact that many "irreduciibly complex" structures have been shown to be reducible after all significantly reduces the weight of the "irreducible complexity" as a problem for evolution.

Do you mean to say that once upon a time the bacterial flagellum needn't have existed and can you provide concrete facts supporting this why it wasn't needed and what took the role of the flagellum? Next up, what took the role of ATP syntheses, a far more complex structure? How about DNA, was a base 2 system implemented before by selection? Base 2 system works as far as I can tell and works pretty darn well, are you saying that selection skipped over 2 bases to 4 bases when it could have used 2? Why did it choose the more complex base 4 system, that sounds like a design decision.

All these components are essential to life. They are not only interdependent for said system (interaction of parts), but for the system as the whole. If you knock down a core pillar, a whole building can collapse, that is what I mean by interdependency as a whole (global wide)

You are right about one thing that since some systems are composed of simpler components irreducible complexity from that POV may not be so irreducible. To understand why irreducible complexity has not been falsified all it takes is to understand what a template is. A template is the blueprint for an object, it specifies what the object is composed of and what the object can perform (its function). Simpler systems play an entirely different role then the bacterial flagellum. When a system is said to be irreducibly complex that means that it has parts (properties) that if any of them were to be dismantled it would not perform the target function it is currently performing. Further going by this logic, if it is not irreducibly complex then life was not dependent on it at one point in time. However, irreducible complexity means that life was always dependent on it and thus it has always "been" from the beginning. If you simply say that a system looks to be an ancestor of the bacterial flagellum then you are saying that the bacterial flagellum once did not exist because there was no need for it, as the system as a whole was not dependent on it.

Do you mean to say that once upon a time the bacterial flagellum needn't have existed and can you provide concrete facts supporting this why it wasn't needed and what took the role of the flagellum?

The flagellum is used to actively propel the bacterium. Without a functioning flagellum, the bacteria is either unable to propel itself or must rely on other mechanisms for active propulsion. The flagellum is not necessary for life.

Did you bother seeing the video I pointed too? The method Kirk Durston used had been published in the National Academy of Science and he applies it to biology while taking natural selection into account. Even if the numbers are offset by 20 or more orders of magnitude Design is still the best explanation hands down. I understand though if you don't bother seeing it.

Not yet, although I intend to when I get a chance (I am doing this during breaks in a conference and don't think playing the video would be appreciated).

I'll respond to the rest when I get a chance.

The flagellum is not necessary for life.

I don't understand how you came to this conclusion given your own words, you say:

*the bacteria is unable to propel itself

You mean that it is indeed IC?

*must rely on other mechanisms for active propulsion

Since it relies on external mechanisms to perform the function then the external mechanism/s MUST be added to sustain irreducibility. The keyword here is outsourcing. In computer programming we call this modularity. For companies its called subcontracting, its more time and cost efficient to get other third-parties (who specialize in a particular set of things) to get the job done for you then you having to do all of it yourself. To you this seems like the complexity is reducible (has been reduced) and it is, but only to your company since you rely on external "mechanisms" to achieve the desired effect either way. Hence, it is still IC.

You say the flagellum is not necessary for life, so what is? Is DNA not necessary for life either? What is necessary for life in your opinion. How do you come to this conclusion exactly? I am wondering because it sounds as though you have an opinion on how things should work and therefore claiming it to be suboptimal, irreducible and possibly even vestigial.

In computer programming, most complex projects start off with a template; defining program objectives and goals, program interaction. The template (usually flow charts, diagrams etc...) is based off the "end" goal in mind, Thus we start off with a top-down approach before we ever begin to code. This is done because in complex projects it is quite hard to keep track of anything hence is it easy to lose track of what your doing. The point here is that given a system like the bacterial flagellum we have components that could easily lose track of where they are, where the previous one is, and where the next one should be. This is logical since a bottom-up, completely mindless approach through trial and error type manufacturing/orchestrating there is absolutely no certainty we will reach a functional state, never mind a beneficial or enhancing state. Given that, do you feel that bacterial flagellum is a "vestigial" system?

If you say any system can be reducible, you are admitting that all subsequent forms are merely vestigial, in that they are no more useful then the preceding one. This may not be what your implying directly, but indirectly it feels as though you are implying this. Its late here as well, I will clear many more things up if need be.

waynepii wrote:The Wikipedia article you linked in the first post gives good insight into a plausible path that may have led to the flagellum - it was a modification of a simpler mechanism having a very similar structure, lacking a few key parts (making it inoperative as a flagellum BUT performing another function. The links in the Wikipedia article describe this.

I'm familiar with the Type III secretion system (T3SS) by Ken Miller, but I don't think it's a good explanation of the function of the motor like godslanguage said. To understand Miller's "co-option" explanation does not necessarily refute irreducible complexity. As an example of a outboard motor, one must focus on the function of the engine itself, not on the possible function of some subpart that may operate elsewhere. Of course a bolt out of the motor could serve some other purpose in a motorcycle for example. His observation does not explain how many complex parts such as pistons, cylinders, valves, spark plugs, and wiring came together in the appropriate configuration to make a "functional" motorcycle engine. Even if all of these parts could perform some other function in the motorcycle, how were these parts assembled properly to construct an engine that runs? That is the question... Precision like this begs the works of an intelligent designer.

Question: If you looked at a car or motorcycle engine today, would you really say it came together by chance? I wouldn't think so...

waynepii wrote:As to Behe's IC mousetrap - leaving out a few parts may give you a "mousetrap" that won't catch any mice, but it does give you a fully operational, if somewhat inelegant, tie clip (trap less catch and holding bar = tie clip).

If you took the wire or spring out of the mouse trap, it's just a wire with no resistance unless you intentionally held it back with your fingers. You could probably use it for a tooth pick, but not really anything else.

godslanguage wrote:

The flagellum is not necessary for life.

I don't understand how you came to this conclusion given your own words, you say:

*the bacteria is unable to propel itself

You mean that it is indeed IC?

No, simply that the bacteria wouldn't be able to propel itself.

*must rely on other mechanisms for active propulsion

Since it relies on external mechanisms to perform the function then the external mechanism/s MUST be added to sustain irreducibility. The keyword here is outsourcing. In computer programming we call this modularity. For companies its called subcontracting, its more time and cost efficient to get other third-parties (who specialize in a particular set of things) to get the job done for you then you having to do all of it yourself. To you this seems like the complexity is reducible (has been reduced) and it is, but only to your company since you rely on external "mechanisms" to achieve the desired effect either way. Hence, it is still IC.

You say the flagellum is not necessary for life, so what is? Is DNA not necessary for life either? What is necessary for life in your opinion. How do you come to this conclusion exactly? I am wondering because it sounds as though you have an opinion on how things should work and therefore claiming it to be suboptimal, irreducible and possibly even vestigial.

It's been a long time since my biology courses, but AIR most single-cell organisms don't have flagella and many are "content" to drift passively in their environment. Single-celled plants obtain their nutrition directly from sunlight and thus have no need for active propulsion nor the source of sufficient energy to support active propulsion.

A single-cell organism that "discovers" how to "steal" energy from its neighbors would no longer be limited to the fairly meager energy it could make itself but could greatly increase the energy available to it. The type III transport system is an admittedly advanced structure that could be used in perpetrating the "theft" of energy (it injects toxin into the victim). With an adequate supply of fuel and an extra part or two, the toxin transport device becomes an early form of flaggelum, and the "robber bacteria" now has an "outboard motor" and thereby a much greater fuel supply (and also the need for it).

Listing the steps leading to a sophisticated toxin delivery system that then could become a flagellum is beyond my capabilities, but I have faith (yeah "faith" ) in the scientific community and the scientific method that plausible steps do exist. A progression such as ...

1. developing an enzyme that breaks down the victim's "skin" letting its insides leak out
2. developing "stalks" tipped with the enzyme
3. the stalks become active, "stabbing" the victim
4. the stalks become hollow, allowing more effective transfer of the insides
5. developing a suction device, food transfer is now active rather than passive
6. ...

... again, I stress this is just an off the top of my hypothesis, but it is one possible progression.

In computer programming, most complex projects start off with a template; defining program objectives and goals, program interaction. The template (usually flow charts, diagrams etc...) is based off the "end" goal in mind, Thus we start off with a top-down approach before we ever begin to code. This is done because in complex projects it is quite hard to keep track of anything hence is it easy to lose track of what your doing. The point here is that given a system like the bacterial flagellum we have components that could easily lose track of where they are, where the previous one is, and where the next one should be. This is logical since a bottom-up, completely mindless approach through trial and error type manufacturing/orchestrating there is absolutely no certainty we will reach a functional state, never mind a beneficial or enhancing state. Given that, do you feel that bacterial flagellum is a "vestigial" system?

This is true, but it presupposes both a goal and a design. Evolution involves neither. Several years ago, I saw a description of a computer simulation of a random collection of very simple "organisms". Each "organism" was a simple software module which had several distinct movable parts. The locations of the movable parts, the plane(s) of motion of each part, and the degree(s) of freedom of each were controlled by a "DNA" value that defined the "organism". The "reproduction" of the "organisms" were slightly imperfect - there was a very small possibility of random errors so the "child" sometimes wasn't identical to its parent. The "rules" for "survival were simple, the chance of an individual "organism" "surviving" to reproduce was determined by its "propulsion score", which was based on the ability of the "organism" to produce effective propulsion. The initial values of the "DNA" variables were set randomly and the simulation was let run.

At first, the researchers had a population of floppers, twitchers, and do-nothings. After a number generations, the population had evolved a number of quite effective (and in some cases, quite unusual) methods of propulsion.

You might say this experiment had a goal - propulsion, and that would be valid as the only criteria for survival was propulsion. But none of the resulting "organisms" were designed. In "real" world evolution, the only goal is survival, if propulsion increases chances of survival, so be it.

Unfortunately, I've forgotten the name of the experiment but if I can find it, I'll post a link to it.

If you say any system can be reducible, you are admitting that all subsequent forms are merely vestigial, in that they are no more useful then the preceding one. This may not be what your implying directly, but indirectly it feels as though you are implying this. Its late here as well, I will clear many more things up if need be.

Well, there is no reason that ALL the toxin transport sites on an individual have to become flagella, an individual could conceivably have both the "rev x" (toxin transport) and "rev y" (flagellum) versions of the structure. And future generations could continue to refine each structure.

And there are certainly plenty of examples of vestigial structures as well.

Listing the steps leading to a sophisticated toxin delivery system that then could become a flagellum is beyond my capabilities, but I have faith (yeah "faith" ) in the scientific community and the scientific method that plausible steps do exist. A progression such as ...

1. developing an enzyme that breaks down the victim's "skin" letting its insides leak out
2. developing "stalks" tipped with the enzyme
3. the stalks become active, "stabbing" the victim
4. the stalks become hollow, allowing more effective transfer of the insides
5. developing a suction device, food transfer is now active rather than passive
6. ...

... again, I stress this is just an off the top of my hypothesis, but it is one possible progression.

I have no issue with discussing POSSIBILITIES. I like to include in the list of possibilities, all the possibilities. Most discussions end up with each side claiming that they alone have found the one true answer. In fact, science ought to continue to study both the possibility that evolution occurred, and that perhaps life was designed by an outside designer.

Science ought to be objective enough to investigate the evidence wherever it leads - not embrace an unproven projection while ridiculing any alternative.

Did you bother seeing the video I pointed too? The method Kirk Durston used had been published in the National Academy of Science and he applies it to biology while taking natural selection into account. Even if the numbers are offset by 20 or more orders of magnitude Design is still the best explanation hands down. I understand though if you don't bother seeing it.

I have now watched the video. (http://www.seraphmedia.org.uk/ID.xml)

Some observations:

• He says there are two possible explanations for any given entity; it is the product of "mindless natural processes" OR it is the product of an "intelligent agent".
• He specifically rejects the concept that "nothing caused the effect" (the third possible explanation being that nothing caused the entity).
  
  So then where did the designer come from? (I know, it's a cheap shot , but he was presenting a scientific analysis.)
• Most of his presentation addresses the probabilities of reproducing a specific, predetermined result, namely what has already happened. That is only valid if the target result is the only possible result.
  
  Consider a specific make and model of an automobile (say a 1960 VW Beetle). How likely is it that an independent design team, working without access to or knowledge of the target model could produce essentially the same design? The same wheelbase, the same weight, the same drivetrain, the same horsepower, ... obviously the probability is negligible.
  
  To be a valid indicator of design in the way he is trying to do, he would need to use the number of possible workable "designs" and use that to calculate his probability of design. In the case of the automobile, the number of workable designs is nearly infinite, so the probability that our design team could produce a car is quite good. However, the probability they would reproduce a 1960 VW is virtually nil.
• He completely avoids the pertinent parameter, how many possible workable solutions are there? Biology isn't Grandfather's safe, there are many solutions to any problem (witness the diversity of life).
  
  Of course, determining the number of solutions in fairly difficult (spelled 'n', 'o', 't', ' ', 'a', ' ', 'c', 'h', 'a', 'n', 'c', 'e')

Net result - far from convincing.

Evolution has many different meanings, you have merely one, that is fine since when I discuss evolution with Darwinists I am discussing their view of evolution. When you say "evolution involves neither" you are making evolution to be absolute, as in the context of chance and randomness, the opposite of goal and direction. I only iterate this so that everyone knows what we are discussing, in which context and such.

A single-cell organism that "discovers" how to "steal" energy from its neighbors would no longer be limited to the fairly meager energy it could make itself but could greatly increase the energy available to it. The type III transport system is an admittedly advanced structure that could be used in perpetrating the "theft" of energy (it injects toxin into the victim). With an adequate supply of fuel and an extra part or two, the toxin transport device becomes an early form of flaggelum, and the "robber bacteria" now has an "outboard motor" and thereby a much greater fuel supply (and also the need for it).

Listing the steps leading to a sophisticated toxin delivery system that then could become a flagellum is beyond my capabilities, but I have faith (yeah "faith" ) in the scientific community and the scientific method that plausible steps do exist. A progression such as ...

1. developing an enzyme that breaks down the victim's "skin" letting its insides leak out
2. developing "stalks" tipped with the enzyme
3. the stalks become active, "stabbing" the victim
4. the stalks become hollow, allowing more effective transfer of the insides
5. developing a suction device, food transfer is now active rather than passive
6. ...

... again, I stress this is just an off the top of my hypothesis, but it is one possible progression.

This is true, but it presupposes both a goal and a design. Evolution involves neither.

This is a hypothetical scenario. Like all hypothesis, testing is required. Behe tested the IC hypothesis by reverse-engineering the bacterial flagellum. A part was removed causing the function as a whole to seize. What Behe has actually done is reversed evolution because at one point in time a "component" had not been part of the system. Since evolution was reversed to a prior state we must ask, what is a rotor without a propeller and vice versa? This must be taken into the equation since that is the core of the IC argument.

The components of a bacterial flagellum are interdependent, they function as a "whole" to achieve a desired effect. The components exhibit strong asymmetry which distinguish it from symmetrical objects such as repetitive and predictable patterns in snow flakes. Objects that function while exhibiting high asymmetry, low predictability relative to itself are strong cases for design.

Listing the steps leading to a sophisticated toxin delivery system that then could become a flagellum is beyond my capabilities, but I have faith (yeah "faith" ) in the scientific community and the scientific method that plausible steps do exist. A progression such as ...

No, the scientific method is including all possible scenarios, that includes design.

Several years ago, I saw a description of a computer simulation of a random collection of very simple "organisms". Each "organism" was a simple software module which had several distinct movable parts. The locations of the movable parts, the plane(s) of motion of each part, and the degree(s) of freedom of each were controlled by a "DNA" value that defined the "organism". The "reproduction" of the "organisms" were slightly imperfect - there was a very small possibility of random errors so the "child" sometimes wasn't identical to its parent. The "rules" for "survival were simple, the chance of an individual "organism" "surviving" to reproduce was determined by its "propulsion score", which was based on the ability of the "organism" to produce effective propulsion. The initial values of the "DNA" variables were set randomly and the simulation was let run.

Well, I don't think we should concentrate on simulation software written by intelligent designers. Not for this thread at least. Evolutionary simulations have proven to require a significant amounts of preloaded information, such as the expected end result which would be inevitably "latch" onto given the algorithms objective. Never mind that there is no such thing as true randomness within computing, consider that most computer software written the "random" numbers are seeded off the current time such that each subsequent execution a new "random" number is generated within a range of values. This is just to show that nothing within a computer is random, the most you will achieve is pseudo-randomness. Consider that the computer itself was created to run algorithms that can do more then one thing at a time as many times as desirable. These simulations take advantage of computing capabilities to make their own point, that is cheating. As a rule of thumb, you don't take a designed computer and use it to prove chance and randomness by rewarding the digital organism through conditional statements and doing it enough times using loop constructs to reach the desired outcome/s. They know quite well what they are doing ahead of time, (they can anticipate) what the program is attempting to produce etc... because after all, the simulation is designed to do just that.

At first, the researchers had a population of floppers, twitchers, and do-nothings. After a number generations, the population had evolved a number of quite effective (and in some cases, quite unusual) methods of propulsion.

NASA had "evolved" a weird looking antenna which the reception that was produced outperformed all human designed antennas. Rest assured that they knew exactly what they were looking for ahead of time, the qualities they wanted in a antenna, what the program attempts to search for (ie: a better signal). The fact is that evolutionary simulations are nothing more then search algorithms, as they attempt to search through, buffer in and search from the point of the last buffered in result. I have programmed a few of these in c. One is atypical in that I wouldn't say it models evolution correctly, what it does show (never mind it takes on average 80 thousand trials to reach the an insignificant "target") nevertheless is that significant amounts of information are required before hand which must be preloaded into the program.

But I think this discussion is beyond IC nevertheless so I don't think it should be discussed.

You might say this experiment had a goal - propulsion, and that would be valid as the only criteria for survival was propulsion. But none of the resulting "organisms" were designed. In "real" world evolution, the only goal is survival, if propulsion increases chances of survival, so be it.

If it has a goal, then it is directed by the program itself. Survival is nothing but conditional constructs within the code that say if propulsion, select faster propulsion while filter out the less propulsive. That is selection, and that is a search that selects for more propulsion. The problem is that you have not explained propulsion itself. You have not explained propulsion itself because that was already explained in the programs objective (by a governing intelligence, ie: the programmers), nothing was "evolved" from scratch at all, at best modifications (select faster propulsion) were selected, not select propulsion.

And there are certainly plenty of examples of vestigial structures as well.

Yup, and most have been proven not to be vestigial at all.

I will respond to your other comment when I find the time.

Godslanguage wrote:http://www.seraphmedia.org.uk/ID.xml

Godslanguage, this was a real insightful video on ID. Really long and really good. I wish I had the powerpoint slide of it.

I thought I would also add this video into the mix from Scott Minnich at UC Santa Barbara. The topic, "Bacterial Flagella: A Paradigm for Design" from the Veritas Forum. I took a lot of my information from it.

http://www.veritas.org/media/talks/92

(making it inoperative as a flagellum BUT performing another function

If you do show simpler systems these simpler (or I would call "different") systems still have a function of some sort, another function as you say. What needs to be laid out is all the intermediate forms going up to the flagellum that do and do not have a function, one component at a time. This isn't as simple as Ken Miller thinks, if he thought more deeply about it then perhaps he wouldn't be making his so called "refutation".

Not all biological parts are necessarily interchangeable either. Miller's explanation merely explains how proteins could become available to be borrowed. It's just his idea.. But in biology, "a system is not just an assembly of genes and proteins, its properties cannot be fully understood merely by drawing diagrams of their interconnections." Miller's explanation really does oversimplify the argument... A hunch at best.

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