Brian Miller: Co-option and Irreducible Complexity

Design

#101

are you aware that humans designed genomes too? if so all your traits above arent necessary to conclude design. if for instance we will find a watch that made from organic components and has many living traits- we can still detect design. not because all traits you mentioned above but because a wacth cant evolve naturally. this is the main reason.

so an artificial flagellum is a motor by definition. right?


(Timothy Horton) #102

If humans design an object which mimics the function of something found in nature that isn’t evidence the natural feature was designed.

Seriously, is your understanding of logic so bad you can’t see the fatal fallacy in your argument?


(Mikkel R.) #103

Sure, an artificially created flagellum is a motor, and it was designed. But that doesn’t prove, nor even indicate, that all motors, nor the bacterial flagellum, were designed.

Look, how is it so difficult for you to understand that just because someone could in principle create a flagellum, that doesn’t mean the actual bacterial flagellum was also designed?

Human beings can create rocks. That doesn’t mean rocks in general were all designed. You understand this right? Can you please confirm that you undestand that much?

And you don’t establish that something was designed by labeling it with a word that is defined as a designed entity. That just assumes your conclusion.

Suppose I invented a new category for molecular machines that evolved. Evochines I call them. And by definition, an evochine is an evolved machine. A machine that evolved and was not designed or created.
I now say that the flagellum is an evochine. Have I now demonstrated that the flagellum evolved?


#104

but its like saying that not all cars requires design. you dont think its a problemamtic?

of course. but a rock isnt a motor.


(Timothy Horton) #105

That depends on how you define “car”. You’re going to get nowhere with these silly equivocating word games.

Not all rocks are designed. Not all motors are designed.


#106

so some kinds of cars dont need design?


(Timothy Horton) #107

What part of "that depends on how you define “car” don’t you understand?


#108

This cloud looks like a duck.

image

Does this mean it is a duck?


(Mikkel R.) #109

No.

And the label “motor” does not establish how the entity came to exist. I can just call it an evochine. Does that mean it evolved?


(Brian Miller) #110

The human designed rotary motor and the bacterial rotary motor share the same top-down design logic including many of same components in the same functional and spatial relationships. This connection is far stronger than the superficial similarities between human and natural bridges, pillars, or crosses. A major difference is that the latter are the result of natural processes creating configurations of matter directly driven by natural laws, and they do not need to meet tight constraints.

In contrast, human and biological engines represent configurations of materials which transcend their physical and chemical properties, and they must meet tight functional requirements in accordance with a top-down design logic in order to function. In addition, the configurations of atoms in both classes of motors require assembly processes which force pieces to form and fit together in ways which would never happen through purely natural processes.

Many biologists fully acknowledge the strong connection between the motors. For instance, Howard Berg described the flagellum as not simply similar to a human rotary motor, but he said it is a “rotary electric motor.” He even laid out the piece by piece comparisons:

Bacterial flagellar motor
The flagellar motor is a remarkably small rotary electric motor that drives a proximal hook ( flexible coupling ) and helical filament ( rigid propeller ). The motor components include a rod ( drive shaft ), L- and P-rings ( bushing ), MS-ring ( mounting plate ), and FliG, M, and N (circular arrays of subunits attached to the MS-ring that make up the cytoplasmic, or C-ring, also called the switch complex ). MotA and B act as force-generating elements ( pistons ), linked via MotB to the rigid framework of the cell wall. MotA engages FliG. Each force-generating element comprises four copies of MotA and two copies of MotB, which together constitute two transmembrane ion channels. The motors are powered by protons or sodium ions that flow through these channels from the outside to the inside of the cell, which, depending upon the configuration of the C-ring, drive the rod, hook, and filament CW or CCW. The chemotaxis signaling protein CheY–P (not shown) binds to FliM and N, enhancing CW rotation. At high loads, eight or more force-generating elements are active, each generating the same torque. The transport apparatus pumps rod, hook, and filament sub­units into an axial pore, upon transfer from cytoplasmic chaperones via the ATPase complex. Other components (not shown) include FlgJ (rod cap, discarded upon rod completion), FlgD (hook cap, discarded upon hook completion), FliK (hook-length control protein), and FlgM (factor that blocks late-gene expression). It is commonly assumed that the MS- and C-rings rotate as a unit (as the rotor ), but this has yet to be shown experimentally. The MotA and MotB force-generating elements comprise the stator.


The Flagellum is Not a Motor?
The Flagellum is Not a Motor?
(Timothy Horton) #111

Another post where you rote repeat ID-Creationist talking points while still avoiding all the tough questions about your earlier claims.

Who didn’t see that coming? :slightly_smiling_face:


(Brian Miller) #112

What other functions do you believe any of the flagellar proteins perform outside of a flagellum or T3SS? What might the “crossover” look like?

Focusing back on the addition of a filament, the challenge is that this structure can only form properly if the two junction proteins, the cap assembly tool, and the filament proteins are produced at the right time, and they enter the transport gate in the right order, immediately after the hook is finished. And, the proteins require the right recognition signal in their N-terminal region, so they can enter the gate. In addition, they must bind to specially assigned chaperone proteins (at least in Salmonella typhimurium) which protect them from degrading or interacting with other proteins until they reach the gate.

Even if the four proteins formed and found some other roles to play in the cell, the number of required, coordinated mutations would be enormous to properly code the required precision of regulation, generate the right binding sites and recognition sequences, and properly match them to the right chaperone molecules. Well before the right mutations appeared, some mutation would have disabled or degraded the FliC gene in order to conserve resources, preventing filament formation.

You make a good point in general, but it does not apply well to the flagellar filament. Genes experience greater selection when they are highly expressed. And, the flagellar filament (FliC) must be very highly expressed to make up a sufficiently long filament which comprises in some bacteria 8% of the proteins.

Adaptation in bacterial flagellar and motility systems: from regulon members to ‘foraging’-like behavior in E. coli
Also the ability to efficiently utilize cellular resources to conserve energy for individual self-protection, such as hibernation, would provide a significant survival advantage. We show that motile bacteria carry out tactical responses to a variety of carbon sources by increasing flagellar operation but restricting costly additional flagellar synthesis.

If the filament did not assemble properly, the cell would waist significant resources simply transporting thousands of FliC proteins into the environment. If bacteria restrict filament production to gain a “significant survival advantage,” then mutations which disabled or at least dramatically degrade FliC’s production capacity would experience strong positive selection.


(Timothy Horton) #113

This “it kinda looks like a human design so it must BE designed!!” argument for the flagellum was examined and rejected by science well over a decade ago when Behe first trotted it out. What makes you think it got any less worthless with age?

Some day ID-Creationists will realize arguments by analogy and arguments from personal incredulity just don’t work in science. But not today it seems.


(S. Joshua Swamidass) #114

Great questions! How would you go about finding the answers to them?


(T J Runyon) #115

You only listed one. Care to list more? Could be informative


(Timothy Horton) #116

This was included in the Berg article cited above

"Is the flagellar motor unique?

Yes and no. As a device that powers flagellar rotation, yes. As a device composed of rings, rods, and external filaments, no. There is a homologous structure, called the needle structure, assembled by the same kind of transport apparatus, used by pathogenic species (such as Salmonella) to inject virulence factors into eukaryotic cells. Some argue that the flagellar rotary motor evolved from the needle structure, but it was probably the other way around, since flagellated bacteria existed long before their eukaryotic targets. Perhaps they evolved from a common ancestor. What was the rotary motor doing before the helical propeller was invented, if indeed that was the order of events? Serving as a secretory apparatus that acquired the ability to spin? Packaging polynucleic acids into virus heads? Food for thought."

Those thoughts were written by Berg some 15 years ago but even then science had ideas about how flagellum evolved


(S. Joshua Swamidass) #117

I know, but I"m asking how Brian would go about answering those answerable questions.


(Timothy Horton) #118

OK, sorry to interrupt your question.


(Neil Rickert) #119

I’ll ignore the contentious questions of whether the flagellum is a rotary motor and whether it was designed. Is there any basis for the claim that the human designed motor and the flagellum “share the same top-down design logic”? I don’t see how there could be a basis.

In order to determine the design logic, you would first need to locate the designer and look for evidence of the planning and design that might have been left behind.

If you are looking only at the product, you cannot determine the design logic. At best, you can give your interpretive logic (the logic of your interpretation). But your interpretive logic might be very different from any actual design logic.


(John Mercer) #120

You produce nothing but words, many of them false. Point me to the evidence. ALL the evidence.

Evidence, not just empty words, please.

You’ve presented zero evidence to support your claim that genes experience greater selection when they are highly expressed.

Cells waste (not “waist”) significant resources all the time. You’ve presented no evidence to the contrary.

Evidence, please, not speculation.