[_ Old Earth _] How It's Made.

[Vaccine]

There's a show called "How it's Made", a documentary series about how stuff's made. I like that show and thought I'd post a quick rundown on how ATP Synthase is made inside a cell. ATP Synthase is one of the "tiniest and most powerful motors ever made" weighing in at almost 400,000 atomic mass units, millions of these would fit into 1 drop of blood. They function similar to a generator to provide the energy in every cell. The production begins by copying a peice of DNA (a library of blueprints), with the instructions to build a strand of protein. Here is a video of that operation, even though it is making a hemoglobin protein the process is the same:

http://www.hhmi.org/biointeractive/translation-basic-detail


This raw strand of protein by itself is not very useful, it has to be folded and shaped. Within the cell are various other proteins to assist in making the tertiary shape. All of this folding and shaping is accomplished by other proteins bumping into it and either allowing or blocking specific chemical reactions. These other proteins "press" it into a specific shape.

View attachment 3478


Once a useful shape is accomplished, we have a building block necessary to assemble a structure. Throughout the cell various other building blocks are made the same way. They have to be made in certain parts of the cell otherwise undesired chemical bonding would occur.

View attachment 3479
Depending on the desired function, the structure is assembled from these building blocks, by means of blocking or allowing a chemical bonds at specific points. Here is the final product ready for use:


View attachment 3477

 

[Vaccine]

View attachment 3482

This generator exists in every form of life on the planet. My question is: which came first, the tiniest and most powerful motor ever made, the machinery that makes it, or the blueprints to make both?


Take a look at these pictures, the images on the left are the products of natural causes, the ones on the right are products of intelligent causes:


View attachment 3480



Look at these molecules:
View attachment 3481

The one on the left is H2O, the one on the right is C10H16N5O13P3. The water molecule is the product of natural causes, scientists are now beginning to see the the ATP Synthase molecule is not the product of natural causes, but requires intelligence to make. This is just my opinion, but looking at that microscopic generator is like seeing the mysteries of God revealed.

 

[Barbarian]

This generator exists in every form of life on the planet. My question is: which came first, the tiniest and most powerful motor ever made, the machinery that makes it, or the blueprints to make both?

The evidence is that they co-evolved, little at a time. The two subunits are remarkably similar to two other, simpler molecules found in cells. So the most likely of several possible ways such a molecule could evolve would be for them to form a polymer, which, in one particular orientation, would drive a bacterial helicase in reverse (because of the H+ motor activity of the other moeity, which his quite similar to things like the Type III secretory apparatus and the motor unit of the bacterial flagellum.

 

[Vaccine]

The evidence is that they co-evolved, little at a time. The two subunits are remarkably similar to two other, simpler molecules found in cells. So the most likely of several possible ways such a molecule could evolve would be for them to form a polymer, which, in one particular orientation, would drive a bacterial helicase in reverse (because of the H+ motor activity of the other moeity, which his quite similar to things like the Type III secretory apparatus and the motor unit of the bacterial flagellum.

I wonder where cells got their energy while all this co-evolving was going on?

 

[Barbarian]

Possibly from that phosphorylating rhodopsin we talked about earlier. Some bacteria still use it for energy. Or maybe something even more primitive.

So no question that the evolution of this molecule was a doable process for primitive cells. This one, from the evidence, involved the polymerization of two pre-existing molecules, which had other functions. Exaption, again.

 

[Vaccine]

Good evening [MENTION=30546]Barbarian[/MENTION]! There's no sarcasm intended, but I can't see anything in your posts which could be considered evidence it evolved. To me this is an origin issue. We see how a cell makes it, what outside a cell could make it?

-At the molecular level things are going to appear similar. Methane, carbon dioxide, or ammonia molecules probably look similar, the differences are in their chemical properties.
-helicases get their energy from ATP, there aren't any "other simpler molecules" which could do that.
-Comparing the H+ motor activity in ATP synthase with the H+ motor activity in flagellum is similar to a lawm mower motor (ATP) and a rotary airplane engine (flagellum). They both have pistons and work by conbustion, but where did either come from?
-phosphorylating rhodopsins are pumps making kinetic energy, which doesn't power a cell. ATP Synthase IS a source of energy, it catalyzes other reactions in the cell.
-"involved the polymerization of two pre-existing molecules, which had other functions" isn't evidence. Even as an argument, because motors have many uses in the cell, it doesn't address where the motor came from or how the cell had all the fittings there ready to use it.

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.
ATP Synthase rotates several times per second and performs 3 operations with each rotation. Without this recycling, Pedersen says, "people would have to produce more than half their body weight in ATP every day to meet their energy needs."
Where did all these microscopic machines come from? To me these are the hidden things of God being revealed.

 

[Barbarian]

Good evening @Barbarian ! There's no sarcasm intended, but I can't see anything in your posts which could be considered evidence it evolved.

It merely shows that there's no reason that it couldn't.

To me this is an origin issue.

That's not much of an objection, either.

We see how a cell makes it, what outside a cell could make it?

Makes what?

At the molecular level things are going to appear similar. Methane, carbon dioxide, or ammonia molecules probably look similar

To you, maybe. You never suffered through P-chem. To a biologist with all that chemistry, they don't look very much the same.

the differences are in their chemical properties.

Huge differences, even in gross orientation and number of atoms. The activity of these are very different.

-helicases get their energy from ATP, there aren't any "other simpler molecules" which could do that.

fig. 1
ATP generation via bacteriorhodopsin

Chemiosmotic coupling between sun energy, bacteriorhodopsin and phosphorylation by ATP synthase (chemical energy) during photosynthesis in Halobacterium salinarum (syn. H. halobium).

-phosphorylating rhodopsins are pumps making kinetic energy, which doesn't power a cell. ATP Synthase IS a source of energy, it catalyzes other reactions in the cell.

No, that's wrong. ATP is the source of energy.

"involved the polymerization of two pre-existing molecules, which had other functions" isn't evidence.

It just shows that the molecule could easily form as a polymer of two existing molecules. Which is more than enough evidence.

Even as an argument, because motors have many uses in the cell, it doesn't address where the motor came from or how the cell had all the fittings there ready to use it.

Turns out the rotor for many of these is present (but not as a rotor) in the Type III secretory system. So there you are.

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.

Not today. But then there are no longer any vendian organisms today. Obviously, the fact that only one sort of metazoan exists now, does not mean that there were not others. It is very risky to try to base God on what we don't yet know.

ATP Synthase rotates several times per second and performs 3 operations with each rotation.

If it was faster would you think it was more unlikely? Or less? Don't see the point.

Without this recycling, Pedersen says, "people would have to produce more than half their body weight in ATP every day to meet their energy needs."

Actually, we don't. Mitochondria do it for us. They are tiny endosymbionts, genetically unrelated to us, living in our cells. They have their own DNA, and reproduce independently from the cell. And we can't live without them.

But there's a very telling admission there. Human have a highly-stoked metabolism, that demands huge amounts of energy. Outside of birds, mammals are the most highly dependent on a constant high flow of energy. Bacteria can tolerate much, much lower levels. Which is consistent with other evidence that ATP synthase evolved in prokaryotes. I wonder if your guy knew he was giving away the farm on that one.

Where did all these microscopic machines come from?

As you learned, the evidence shows this one came about from the polymerization of two existing molecules.

To me these are the hidden things of God being revealed.

Yes, much to the dismay of creationists.

 

[Vaccine]

At the molecular level things are going to appear similar. Methane, carbon dioxide, or ammonia molecules probably look similar

To you, maybe. You never suffered through P-chem. To a biologist with all that chemistry, they don't look very much the same.

Ok. What "other, simpler" molecules did you mean when you said this: "The two subunits are remarkably similar to two other, simpler molecules found in cells."

-helicases get their energy from ATP, there aren't any "other simpler molecules" which could do that.

fig. 1
ATP generation via bacteriorhodopsin

Chemiosmotic coupling between sun energy, bacteriorhodopsin and phosphorylation by ATP synthase (chemical energy) during photosynthesis in Halobacterium salinarum (syn. H. halobium).

I don't see any correlation between my quote and your reply.

-phosphorylating rhodopsins are pumps making kinetic energy, which doesn't power a cell. ATP Synthase IS a source of energy, it catalyzes other reactions in the cell.

No, that's wrong. ATP is the source of energy.

Read my quote, the part in bold.
In post 4 I asked: I wonder where cells got their energy while all this co-evolving was going on?
Your reply in post 5: Possibly from that phosphorylating rhodopsin we talked about earlier.
Which doesn't make any sense. It's like saying, while ATP synthase was evolving, energy was provided by phosphorylating rhodopsin, which uses ATP synthase.

Even as an argument, because motors have many uses in the cell, it doesn't address where the motor came from or how the cell had all the fittings there ready to use it.

Turns out the rotor for many of these is present (but not as a rotor) in the Type III secretory system. So there you are.

The rotor is present, but not as a rotor? Read my quote, the part in bold.

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.

Not today. But then there are no longer any vendian organisms today. Obviously, the fact that only one sort of metazoan exists now, does not mean that there were not others.

Or just maybe Jesus created life. I hope you see what I mean now by Darwin's theory breaks down explaining the origin of all these microscopic machines, especially when it has to invoke some unknown organism with some unknown metabolism.

ATP Synthase rotates several times per second and performs 3 operations with each rotation.

If it was faster would you think it was more unlikely? Or less? Don't see the point.

Just pointing out how efficient the design is.

Without this recycling, Pedersen says, "people would have to produce more than half their body weight in ATP every day to meet their energy needs."

Actually, we don't. Mitochondria do it for us. They are tiny endosymbionts, genetically unrelated to us, living in our cells. They have their own DNA, and reproduce independently from the cell. And we can't live without them.

Click on the 1st small picture in post #2. Mitochondria have tons of ATP Synthase.

But there's a very telling admission there. Human have a highly-stoked metabolism, that demands huge amounts of energy. Outside of birds, mammals are the most highly dependent on a constant high flow of energy. Bacteria can tolerate much, much lower levels. Which is consistent with other evidence that ATP synthase evolved in prokaryotes. I wonder if your guy knew he was giving away the farm on that one.

I wonder if you realize without ATP prokaryotes don't have any energy. No evidence again, just another baseless assertion.

Where did all these microscopic machines come from?

As you learned, the evidence shows this one came about from the polymerization of two existing molecules.

Nobody else is saying that.

 

[Barbarian]

Ok. What "other, simpler" molecules did you mean when you said this: "The two subunits are remarkably similar to two other, simpler molecules found in cells."

Barbarian Earlier:
The evidence is that they co-evolved, little at a time. The two subunits are remarkably similar to two other, simpler molecules found in cells. So the most likely of several possible ways such a molecule could evolve would be for them to form a polymer, which, in one particular orientation, would drive a bacterial helicase in reverse (because of the H+ motor activity of the other moeity, which his quite similar to things like the Type III secretory apparatus and the motor unit of the bacterial flagellum.

Quote Originally Posted by Barbarian View Post
-helicases get their energy from ATP, there aren't any "other simpler molecules" which could do that.

The production of energy by the bacterium via bacteriorhodopsin isn't locked into ATP synthase. It just happens to be the current use. I cite one such system below.

-phosphorylating rhodopsins are pumps making kinetic energy, which doesn't power a cell.

No. At the molecular level, kinetic energy is merely thermal energy. This is chemical energy, in which a H+ ion is produced. Useful energy.

ATP Synthase IS a source of energy

In fact, the most useful source. But it would be saying that because we don't have any dinosaurs living today, there couldn't be any dinosaurs in the past.

Even as an argument, because motors have many uses in the cell, it doesn't address where the motor came from or how the cell had all the fittings there ready to use it.

Barbarian observes:
Turns out the rotor for many of these is present (but not as a rotor) in the Type III secretory system. So there you are.

The rotor is present, but not as a rotor?

Yep. Almost identical, but it serves a different purpose. Exaption, again.

Read my quote, the part in bold.

See below.

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.

Not as the primary means, today. But then there are no longer any vendian organisms today. Obviously, the fact that only one sort of metazoan exists now, does not mean that there were not others. We know of at least one alternative energy system, still in existence. (see below) A known stand-in. A clear precursor, and evidence that ATP synthase evolved. Pretty good.

Or just maybe Jesus created life.

He did. You're just uncomfortable with the way He did.

I hope you see what I mean now by Darwin's theory breaks down explaining the origin of all these microscopic machines,

Notice that exaption works, even at the molecular level. So that's a bad assumption for you to make.

specially when it has to invoke some unknown organism with some unknown metabolism.

As I pointed out, it's a bad idea to support God by things we don't yet know. I had conversations like this with people who made the same argument about no whale fossils with functional legs. If ID hopes to recover their momentum by talking about the things science hasn't yet conclusively demonstrated, they are doomed.

ATP Synthase rotates several times per second and performs 3 operations with each rotation.

If it was faster would you think it was more unlikely? Or less? Don't see the point.

Just pointing out how efficient the design is.

Since Hall demonstrated that to be a function of Darwinian processes, it would appear that you're undercutting your own argument. Natural selection, as even many creationists now admit, can do that.

Without this recycling, Pedersen says, "people would have to produce more than half their body weight in ATP every day to meet their energy needs."

Actually, we don't. Mitochondria do it for us. They are tiny endosymbionts, genetically unrelated to us, living in our cells. They have their own DNA, and reproduce independently from the cell. And we can't live without them.

But there's a very telling admission there. Human have a highly-stoked metabolism, that demands huge amounts of energy. Outside of birds, mammals are the most highly dependent on a constant high flow of energy. Bacteria can tolerate much, much lower levels. Which is consistent with other evidence that ATP synthase evolved in prokaryotes. I wonder if your guy knew he was giving away the farm on that one.

I wonder if you realize without ATP prokaryotes don't have any energy.

And I showed you how ATP could form by a simple polymerization from two existing molecules. We only exist now, because we have mitochondria. But that wasn't always so. Do you think mitochondria were poofed into place by supernatural means?

The evidence suggests otherwise. Is there evidence for evolution of endosymbiosis? There is. Would you like to learn about it? You see, the lower metabolic needs of early organisms could be meet by less energetic molecules, but the evolution of a more effective ATP generator would be highly advantageous. Eventually, the old mechanisms could be lost entirely. We see this happening in clotting mechanisms, today.

In fact, at least one alternative pathway still exists for energy transfer:

An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate
Scientific Reports 3, Article number: 1071

In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (Δp) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.

No evidence again, just another baseless assertion.

See above. I didn't know of this one, beforehand; but it's quite common for the scaffold system to continue in a minor role, long after another process has evolved to replace it. So I was pretty confident that I could find one. And there you are. In a small way, another verified prediction of evolutionary theory.

Where did all these microscopic machines come from?

As you learned, the evidence shows this one came about from the polymerization of two existing molecules.

Nobody else is saying that.

Nobody in ID wants you to know about it. I was surprised at the large number of slickly-produced articles by IDers denying the fact. But here you are:

The evolution of ATP synthase is thought to be an example of modular evolution, where two subunits with their own functions have become associated and gained new functionality. The FO particle shows significant similarity to hexameric DNA helicases and the F1 particle shows some similarity to H+ powered flagellar motor complexes.

The α3β3 hexamer of the FO particle shows significant structural similarity to hexameric DNA helicases; both form a ring with 3 fold rotational symmetry with a central pore. Both also have roles dependent on the relative rotation of a macromolecule within the pore; the DNA helicases use the helical shape of DNA to drive their motion along the DNA molecule and to detect supercoiling whilst the α3β3 hexamer uses the conformational changes due rotation of the γ subunit to drive an enzymatic reaction.

The H+ motor of the F1 particle shows great functional similarity to the H+ motors seen in flagellar motors. Both feature a ring of many small alpha helical proteins which rotate relative to nearby stationary proteins using a H+ potential gradient as an energy source. This is, however, a fairly tenuous link - the overall structure of flagellar motors is far more complex than the F1 particle and the ring of rotating proteins is far larger, with around 30 compared to the 10, 11 or 14 known in the F1 complex.

The modular evolution theory for the origin of ATP synthase suggests that two subunits with independent function, a DNA helicase with ATPase activity and a H+ motor, were able to bind, and the rotation of the motor drive the ATPase activity of the helicase in reverse. This would then evolve to become more efficient, and eventually develop into the complex ATP synthases seen today. Alternatively the DNA helicase/H+ motor complex may have had H+ pump activity, the ATPase activity of the helicase driving the H+ motor in reverse. This could later evolve to carry out the reverse reaction and act as an ATP synthase.
http://human.freescience.org/htmx/ATP_synthase.php

 

[Vaccine]

Barbarian Earlier:
The evidence is that they co-evolved, little at a time.

Seems there isn't any evidence (apart from wiki). This was said of a bunch of articles recently about ATP Synthase.
"All of them speak in machine terms (nanomachine, rotation, motor, mechanism, architecture) but none of them have much to say about evolution. They are indications of a major scientific revolution in our time that is transforming the nature of the origins debate."

http://www.evolutionnews.org/2012/07/the_other_rotar061761.html


The intent of my OP was to point out the conundrum, like the age old question: which came first the chicken or the egg? Which came first, the tiniest and most powerful motor ever made, the machinery that makes it, or the blueprints to make both? The answer is all of these things had to arise simultaneously.

The two subunits are remarkably similar to two other, simpler molecules found in cells. So the most likely of several possible ways such a molecule could evolve would be for them to form a polymer, which, in one particular orientation, would drive a bacterial helicase in reverse (because of the H+ motor activity of the other moeity, which his quite similar to things like the Type III secretory apparatus and the motor unit of the bacterial flagellum.

Another example of why wiki is unreliable when it comes to controversial subjects. Speaking of the rotary motor for flagellum, I wonder if wiki realizes it is several times bigger and more complex than ATP Synthase. The design is similar, both are ion driven rotary motors. ATP Synthase is just the most basic version if the ion motor with a rotor, stator and shaft. What a simple lawn mower motor is to a combustion engine. The rotary motor for flagellum on the other hand is much bigger and sturdier rotor, full stator, drive shaft, bushing, rings, rotation switch regulator, and has ~1.3 x 10-18 horsepower. If it were to scale it would have the about the same output as a turboprop airplane engine, except the flagellur rotary motor has near 100% efficiency. Wiki is saying a simpler form evolved from a complex one. Guessing some unspecified simpler molecules could form a polymer, which would drive a helicase, which has quite similar things to a bacterial flagellum motor is just nonsense.

-phosphorylating rhodopsins are pumps making kinetic energy, which doesn't power a cell.

No. At the molecular level, kinetic energy is merely thermal energy. This is chemical energy, in which a H+ ion is produced. Useful energy.

Light-driven pumps are just moving ions, not producing them.

ATP Synthase IS a source of energy

In fact, the most useful source. But it would be saying that because we don't have any dinosaurs living today, there couldn't be any dinosaurs in the past.

This thread was to show how ATP synthase is made, that's playing some shell game with an unknown energy source. ATP Synthase is highly conserved, which means is it present in all life and it doesn't change over time. Although, I'm beginning to see why evolutionists resist design so much. If ATP synthase exists in all known life there are two explanations, a common ancestor or a common designer. Seems the common designer is gaining momentum with Dembski's CSI theory being accepted.

Barbarian observes:
Turns out the rotor for many of these is present (but not as a rotor) in the Type III secretory system. So there you are.

The rotor is present, but not as a rotor?

Yep. Almost identical, but it serves a different purpose. Exaption, again.

You must be thinking of the failed exaptation argument for the flagellum rotary motor. We're discussing the "esquisite design" of ATP synthase, which seems some evolutionists are even admitting design.

http://www.evolutionnews.org/2012/07/the_other_rotar061761.html

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.

Not as the primary means, today. But then there are no longer any vendian organisms today. Obviously, the fact that only one sort of metazoan exists now, does not mean that there were not others. We know of at least one alternative energy system, still in existence. (see below) A known stand-in. A clear precursor, and evidence that ATP synthase evolved. Pretty good.

ATP synthase is highly conserved, the only alternative energy source is one we have to imagination.
I'm sure you're not trying to mislead anyone but you are willing to make assertions where other evolutionists are not. The theory just breaks down explaining origins.

In fact, at least one alternative pathway still exists for energy transfer:

An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate
Scientific Reports 3, Article number: 1071

In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (?p) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.

That article is about a link they found between ATP synthase and thiamine triphosphate production (ThTP is thought to be a signaling molecule).
It says nothing whatever about an "alternative pathway" for energy transfer.

See above. I didn't know of this one, beforehand; but it's quite common for the scaffold system to continue in a minor role, long after another process has evolved to replace it. So I was pretty confident that I could find one. And there you are. In a small way, another verified prediction of evolutionary theory.

It wasn't even remotely about evolution or energy transfer. ThTP is associated with signaling, not energy.

But here you are:

The evolution of ATP synthase is thought to be an example of modular evolution, where two subunits with their own functions have become associated and gained new functionality. The FO particle shows significant similarity to hexameric DNA helicases and the F1 particle shows some similarity to H+ powered flagellar motor complexes.

"is thought to" is not evidence. Modular evolution is just a fancy way of saying: presto-chango there it is. Again, the flagellar motor is much bigger and complex than ATP synthase, it might have been more convincing to start with a simpler design. More people are accepting design theory nowadays.

Nobody else is saying that.

Nobody in ID wants you to know about it. I was surprised at the large number of slickly-produced articles by IDers denying the fact.

The scientific community isn't easily fooled. IDers just took a big step by getting CSI published in the scientific journals. That gives the complex-specified biological information a lot of credibility.

 

[Barbarian]

Barbarian Earlier:
The evidence is that they co-evolved, little at a time.

An intermediate step in the evolution of ATPases: a hybrid F(0)-V(0) rotor in a bacterial Na(+) F(1)F(0) ATP synthase.
Fritz M, Klyszejko AL, Morgner N, Vonck J, Brutschy B, Muller DJ, Meier T, Müller V.
Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt/Main, Germany.
Abstract
1. Furthermore, this stoichiometry was independent of the carbon source of the growth medium. These analyses clearly demonstrate, for the first time, an F(0)-V(0) hybrid motor in an ATP synthase.

And...

An intermediate step in the evolution of ATPases--the F1F0-ATPase from Acetobacterium woodii contains F-type and V-type rotor subunits and is capable of ATP synthesis.
Fritz M, Müller V.
Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
Abstract
Previous preparations of the Na(+) F(1)F(0)-ATP synthase solubilized by Triton X-100 lacked some of the membrane-embedded motor subunits [Reidlinger J & Müller V (1994) Eur J Biochem233, 275-283]. To improve the subunit recovery, we revised our purification protocol. The ATP synthase was solubilized with dodecylmaltoside and further purified to apparent homogeneity by chromatographic techniques. The preparation contained, along with the F(1) subunits, the entire membrane-embedded motor with the stator subunits a and b, and the heterooligomeric c ring, which contained the V(1)V(0)-like subunit c(1) and the F(1)F(0)-like subunits c(2) and c(3). After incorporation into liposomes, ATP synthesis could be driven by an electrochemical sodium ion potential or a potassium ion diffusion potential, but not by a sodium ion potential. This is the first demonstration that an ATPase with a V(0)-F(0) hybrid motor is capable of ATP synthesis.

This was said of a bunch of articles recently about ATP Synthase...

Show us something from the literature.

As you see, there are numerous other ATP producing mechanisms, (albeit less efficient) And even more alternative energy-producing mechanisms. And as you see, the fact that there are different levels of complexity even in existing ATP synthases, make it clear that it can and did evolve. The point is that more primitive forms can provide scaffolding to allow the evolution of a more sophisticated system.

Barbarian observes:
The two subunits are remarkably similar to two other, simpler molecules found in cells. So the most likely of several possible ways such a molecule could evolve would be for them to form a polymer, which, in one particular orientation, would drive a bacterial helicase in reverse (because of the H+ motor activity of the other moeity, which his quite similar to things like the Type III secretory apparatus and the motor unit of the bacterial flagellum.

As you see, Wiki merely cites the professional literature, which documents the fact.

Speaking of the rotary motor for flagellum, I wonder if wiki realizes it is several times bigger and more complex than ATP Synthase.

Which one? There are several versions, and a smaller and simpler version isn't even a rotary motor (Type III secretory apparatus)

The design is similar, both are ion driven rotary motors. ATP Synthase is just the most basic version if the ion motor with a rotor, stator and shaft.

As you see, there are several versions of varying complexity. So obviously, it's not 'most basic.'

Wiki is saying a simpler form evolved from a complex one.

You've been misled on that one, too. Because there are a number of different levels of complexity, we don't know what the simplest possible version is.

ATP Synthase IS a source of energy

This thread was to show how ATP synthase is made, that's playing some shell game with an unknown energy source.

As you know, the fact that there are simpler energy sources, make it possible for more complex forms to evolve. Our ancestors once did our own energy production. Then we got symbionts, which produced an excess of chemical energy, which we could use. Eventually, metazoan cells lost the ability to make a sufficient amount of ATP, and our symbiont mitochondria took it completely over.

ATP Synthase is highly conserved, which means is it present in all life and it doesn't change over time.

It's rather simple. So it can't change without a loss of function.

Seems the common designer is gaining momentum with Dembski's CSI theory being accepted.

As ID inventor Philip Johnson admitted, the last few years have seen a "train wreck" for ID. It is now officially recycled creationism, and illegal to preach in public schools. IDer Michael Behe admitted, under oath, that ID is science in the same sense that astrology is science. ID is practically non-existent in scientific literature.

And IDer Michael Denton now (in Life's Destiny) concludes that:
Contrary to the creationist position, the whole argument presented here is critically dependent on the presumption of the unbroken continuity of the organic world--that is, on the reality of organic evolution and on the presumption that all living organisms on earth are natural forms in the profoundest sense of the word, no less natural than salt crystals, atoms, waterfalls, or galaxies.

If that's momentum, the Great Depression was an economic boom.

You must be thinking of the failed exaptation argument for the flagellum rotary motor.

Comes down to evidence. Exaption has it. Deniers don't. Woiuld you like to see that?

We're discussing the "esquisite design" of ATP synthase

Which one? As you see, they aren't all the same. So the argument that it had to be made in one leap collapses thereby.

All life uses ATP for it's energy needs, there is no known stand-in, there is no known precursors, no evidence whatsoever it evolved.

Not as the primary means, today. But then there are no longer any vendian organisms today. Obviously, the fact that only one sort of metazoan exists now, does not mean that there were not others. We know of at least one alternative energy system, still in existence. (see below) A known stand-in. A clear precursor, and evidence that ATP synthase evolved. Pretty good.
An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate
Scientific Reports 3, Article number: 1071

In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (Δp) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.

ATP synthase is highly conserved

Not so highly, or there wouldn't be various versions.

, the only alternative energy source is one we have to imagination.

See above. You've been misled on that.

I'm sure you're not trying to mislead anyone but you are willing to make assertions where other evolutionists are not.

See above. I didn't do that research. You've been misled about that, too.

The theory just breaks down explaining origins.

I know you want us to believe you, but there's all that evidence...

Quote Originally Posted by Barbarian View Post
In fact, at least one alternative pathway still exists for energy transfer:

An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate
Scientific Reports 3, Article number: 1071

In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (?p) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.
J Biol Chem. 2010 January 1; 285(1): 583–594.
That article is about a link they found between ATP synthase and thiamine triphosphate production (ThTP is thought to be a signaling molecule).

It says nothing whatever about an "alternative pathway" for energy transfer.

See above. The Respiratory chain normally involves ATP. But it turns out that a less efficient pathway still exists. Surprised me, too.

I didn't know of this one, beforehand; but it's quite common for the scaffold system to continue in a minor role, long after another process has evolved to replace it. So I was pretty confident that I could find one. And there you are. In a small way, another verified prediction of evolutionary theory.

It wasn't even remotely about evolution or energy transfer.

Read it again. It's about energy transfer.

but here you are:

The evolution of ATP synthase is thought to be an example of modular evolution, where two subunits with their own functions have become associated and gained new functionality. The FO particle shows significant similarity to hexameric DNA helicases and the F1 particle shows some similarity to H+ powered flagellar motor complexes.[/quote]

"is thought to" is not evidence.

More precisely, it's the result of evidence. We have a good deal of evidence for the the evolution of ATP synthase. Quite a bit about it in the biochemical literature. So there you are.

Modular evolution is just a fancy way of saying: presto-chango there it is.

Nope. As you see from the paper, there's quite a bit of evidence supporting the conclusion.

Again, the flagellar motor is much bigger and complex than ATP synthase,

So your argument is that a smaller rotor is impossible? Doesn't seem like a very good argument to me.

it might have been more convincing to start with a simpler design. More people are accepting design theory nowadays.

More creationists. Scientists have pretty much concluded that it's a religion. Which is what the courts have found in lawsuits. It is as the judge concluded, an attempt to put a scientific gloss on creationism.

Nobody else is saying that.

Nobody in ID wants you to know about it. I was surprised at the large number of slickly-produced articles by IDers denying the fact.

The scientific community isn't easily fooled.

True. It's why ID is almost nonexistence in the biochemical or biological literature. It's most prominent (as it should be) in religious journals.

IDers just took a big step by getting CSI published in the scientific journals.

A quick look at PubMed shows seven thousand, six hundred seventy-three articles from a search "natural selection."

"Complex Specified Information" had one. This one:
Annu Rev Genomics Hum Genet. 2003;4:143-63.
Creationism and intelligent design.
Pennock RT.
Source

Lyman Briggs School and Department of Philosophy, Michigan State University, East Lansing, Michigan 48825, USA. pennock5@msu.edu
Erratum in

Annu Rev Genomics Hum Genet. 2004;5:x.

Abstract

Creationism, the rejection of evolution in favor of supernatural design, comes in many varieties besides the common young-earth Genesis version. Creationist attacks on science education have been evolving in the last few years through the alliance of different varieties. Instead of calls to teach "creation science," one now finds lobbying for "intelligent design" (ID). Guided by the Discovery Institute's "Wedge strategy," the ID movement aims to overturn evolution and what it sees as a pernicious materialist worldview and to renew a theistic foundation to Western culture, in which human beings are recognized as being created in the image of God. Common ID arguments involving scientific naturalism, "irreducible complexity," "complex specified information," and "icons of evolution," have been thoroughly examined and refuted. Nevertheless, from Kansas to Ohio to the U.S. Congress, ID continues lobbying to teach the controversy, and scientists need to be ready to defend good evolution education.

Pub Med is operated by NIH.

That gives the complex-specified biological information a lot of credibility.

If that's "credibility", the flat Earth doctrine has a lot of credibility.

 

[Vaccine]

Barbarian Earlier:
The evidence is that they co-evolved, little at a time.
An intermediate step in the evolution of ATPases: a hybrid F(0)-V(0) rotor in a bacterial Na(+) F(1)F(0) ATP synthase.
Fritz M, Klyszejko AL, Morgner N, Vonck J, Brutschy B, Muller DJ, Meier T, Müller V.
Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt/Main, Germany.
Abstract
1. Furthermore, this stoichiometry was independent of the carbon source of the growth medium. These analyses clearly demonstrate, for the first time, an F(0)-V(0) hybrid motor in an ATP synthase.
And...
An intermediate step in the evolution of ATPases--the F1F0-ATPase from Acetobacterium woodii contains F-type and V-type rotor subunits and is capable of ATP synthesis.
Fritz M, Müller V.
Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University, Frankfurt am Main, Germany.
Abstract
Previous preparations of the Na(+) F(1)F(0)-ATP synthase solubilized by Triton X-100 lacked some of the membrane-embedded motor subunits [Reidlinger J & Müller V (1994) Eur J Biochem233, 275-283]. To improve the subunit recovery, we revised our purification protocol. The ATP synthase was solubilized with dodecylmaltoside and further purified to apparent homogeneity by chromatographic techniques. The preparation contained, along with the F(1) subunits, the entire membrane-embedded motor with the stator subunits a and b, and the heterooligomeric c ring, which contained the V(1)V(0)-like subunit c(1) and the F(1)F(0)-like subunits c(2) and c(3). After incorporation into liposomes, ATP synthesis could be driven by an electrochemical sodium ion potential or a potassium ion diffusion potential, but not by a sodium ion potential. This is the first demonstration that an ATPase with a V(0)-F(0) hybrid motor is capable of ATP synthesis.
As you see, there are numerous other ATP producing mechanisms, (albeit less efficient) And even more alternative energy-producing mechanisms. And as you see, the fact that there are different levels of complexity even in existing ATP synthases, make it clear that it can and did evolve. The point is that more primitive forms can provide scaffolding to allow the evolution of a more sophisticated system.

Barbarian, you clearly don't understand the articles you are posting. The article is about scientists discovered a one of a kind hybrid motor with both V0 and F0 C-subunits in the same c-ring of an ATP synthase motor. In case you didn't know F-type and V-type ATPases are structurally the same, the difference is in the c-ring function. There was no scaffolding, no primitive form, no more sophistication, no alternative energy production, and not numerous other ATP producing mechanisms. ATP synthase made ATP, albeit less efficient since both V0- and F0- c-subunits were in the same the c-ring. Just another loss of function mutation.
This is an origin issue. All life has ATP Synthase. It's a common design.

You must be thinking of the failed exaptation argument for the flagellum rotary motor.

Comes down to evidence. Exaption has it. Deniers don't. Woiuld you like to see that?

View attachment 3488

The Bacteria flagellum motor is a near 100% efficient ion driven rotary motor, with bushing, rings, rotation switch regulator, and has ~1.3 x 10-18 horsepower.
"For a working flagellum to be built by exaptation, the five following conditions would all have to be met: "C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function. "C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time. "C3: Localization. The selected parts must all be made available at the same 'construction site,' perhaps not simultaneously but certainly at the time they are needed. "C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant. "C5: Interface compatibility. The parts must be mutually compatible, that is, 'well-matched' and capable of properly 'interacting': even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly."
Those conditions still haven't been met.

In fact, at least one alternative pathway still exists for energy transfer:

An alternative role of FoF1-ATP synthase in Escherichia coli: synthesis of thiamine triphosphate
Scientific Reports 3, Article number: 1071
In E. coli, thiamine triphosphate (ThTP), a putative signaling molecule, transiently accumulates in response to amino acid starvation. This accumulation requires the presence of an energy substrate yielding pyruvate. Here we show that in intact bacteria ThTP is synthesized from free thiamine diphosphate (ThDP) and Pi, the reaction being energized by the proton-motive force (?p) generated by the respiratory chain. ThTP production is suppressed in strains carrying mutations in F1 or a deletion of the atp operon. Transformation with a plasmid encoding the whole atp operon fully restored ThTP production, highlighting the requirement for FoF1-ATP synthase in ThTP synthesis. Our results show that, under specific conditions of nutritional downshift, FoF1-ATP synthase catalyzes the synthesis of ThTP, rather than ATP, through a highly regulated process requiring pyruvate oxidation. Moreover, this chemiosmotic mechanism for ThTP production is conserved from E. coli to mammalian brain mitochondria.
J Biol Chem. 2010 January 1; 285(1): 583–594.

That article is about a link they found between ATP synthase and thiamine triphosphate production (ThTP is thought to be a signaling molecule). It says nothing whatever about an "alternative pathway" for energy transfer.

See above. The Respiratory chain normally involves ATP. But it turns out that a less efficient pathway still exists. Surprised me, too.
I didn't know of this one, beforehand; but it's quite common for the scaffold system to continue in a minor role, long after another process has evolved to replace it. So I was pretty confident that I could find one. And there you are. In a small way, another verified prediction of evolutionary theory.

It wasn't even remotely about evolution or energy transfer.

Read it again. It's about energy transfer.

I pointed out what the article was about hoping I wouldn't have to do it again. There isn't a nice way to say this but it's clear you haven't the slightest idea what that article is about and made that stuff about evolution up. The title says it all: An Alternative role for f0f1 ATP synthase. They discovered ATP synthase is also linked to production of a signaling enzyme. No alternative energy, no evolution, they just discovered in addition to making ATP, ATP synthase has something to do with ThTP production.

 

[Barbarian]

You must be thinking of the failed exaptation argument for the flagellum rotary motor.

Barbarian observes:
Comes down to evidence. Exaption has it. Deniers don't. Woiuld you like to see that?

(Series of excuses)

Actually, flagella vary widely from one species to another, and some of the components can perform useful functions by themselves. They are anything but irreducibly complex

It is a highly complex molecular machine. Protruding from many bacteria are long spiral propellers attached to motors that drive their rotation. The only way the flagellum could have arisen, some claim, is by design.

Each flagellum is made of around 40 different protein components. The proponents of an offshoot of creationism known as intelligent design argue that a flagellum is useless without every single one of these components, so such a structure could not have emerged gradually via mutation and selection. It must have been created instead.

In reality, the term "the bacterial flagellum" is misleading. While much remains to be discovered, we now know there are thousands of different flagella in bacteria, which vary considerably in form and even function...The best studied flagellum, of the E. coli bacterium, contains around 40 different kinds of proteins. Only 23 of these proteins, however, are common to all the other bacterial flagella studied so far. Either a "designer" created thousands of variants on the flagellum or, contrary to creationist claims, it is possible to make considerable changes to the machinery without mucking it up.

What's more, of these 23 proteins, it turns out that just two are unique to flagella. The others all closely resemble proteins that carry out other functions in the cell. This means that the vast majority of the components needed to make a flagellum might already have been present in bacteria before this structure appeared.

It has also been shown that some of the components that make up a typical flagellum - the motor, the machinery for extruding the "propeller" and a primitive directional control system - can perform other useful functions in the cell, such as exporting proteins.
http://www.newscientist.com/article...llum-is-irreducibly-complex.html#.UinEBT934Zw

So the notion that it is irreducibly complex goes out the window. If there are numerous variations, each a bit different from the next, none of them can be irreducibly complex. And you missed the point about the transitional form of ATPase; F0 forms are found in bacteria, and in eukaryotic mitochondria (which are endosymbiotic bacteria in our cells). VO forms are found in the cytoplasm of eukaryotes. A transitional form merely shows a divergence in the evolution of the two.

Just another loss of function mutation.

If that were true, then the loss of one form would result in an ATPase that did not work. But as you just learned, that's not what happened. It's a common theme in biology for complex systems to become simpler and more efficient.

Likewise, the transitional form of a rotor shown in the paper I cited, makes it clear that the rotor cannot be irreducibly complex. It's why you don't see Behe talking about it much any more. There's just too much data showing how it evolved.

 

[Vaccine]

Hi all! Instead of presenting an argument for my view on "how it's made", I thought I'd take a second an examine the thing we are talking about. Nobody can prove how this was made since we can't go back in time and observe it in the making, we are both presenting how we think it was made. Even if we disagree how this was made, I think we both agree, God made this:
View attachment 3495

View attachment 3496






It works the same as an electric motor, except it uses static electricity (ions) and no wires.


View attachment 3494





It has a stationary housing (stator), a center shaft which rotates (rotor), a bearing to support the shaft, and in the case of an ecoli flagellum a clutch to engage and disengage drive. With an electric motor a gear, grinding wheel, or even a propeller can be put on the end of the shaft, in the case of ecoli a whiplike string which functions as a propeller is attached. Some "whips" also has a sensory function (IntraFlagellur Transport) built in. This tiny, near 100% efficient, electric motor capable of only a fraction (~1.3 x 10-18) of horsepower, still produces enough torc to spin the whip at 6000-15000 RPM's. My 11 year old daughter saw these pictures said it looks like something out of a car. I brought up a microscopic picture of ecoli and pointed out thousands of those flagellums would fit into a crumb of bread. We didn't even address how it's made, we were just amazed at how it works. Even if we disagree how God did this, it's still one amazing piece of biology.

 

[Barbarian]

Yep. God made all things. It's just that He used nature to make most of it. BTW, the various evolved forms of rotor/secretory mechanism are not electrical; they are chemical. Chemistry is about the electron transfer/sharing in atoms. Electricity is about the flow of electrons through wires. Related phenomena, but not the same.

We can, however, use the transformation of chemical energy to effect a flow of electrons apart from atoms. The formation of complex organic moleclues is due to a relatively simple process; the SP3 orbital. Given four tetrahedral bonds from the hybridized orbitals, everything else forms. The truly amazing thing about nature is that God made something in which such marvelous mechanisms can evolve.

 

[Vaccine]

So we agree God made all things. I would even agree God used nature to make things too. The way I mean it though, is that he didn't violate the laws of physics or gravity to make things, just that he spoke and existing atoms assembled into fully formed creatures in the sea, or fully formed creatures on the earth. I believe from there evolution happens. Its the jump from non-living matter to living matter that I believe God is directly involved with.

Definition of life:

"the condition that distinguishes animals and plants from inorganic matter."

Isn't that such a vague definition? Of course it's all the same matter (atoms), life is just based on carbon with complex enzymes and reactions to speed things up. Does anyone know of a biblical definition of life?

 

[Barbarian]

So we agree God made all things. I would even agree God used nature to make things too. The way I mean it though, is that he didn't violate the laws of physics or gravity to make things, just that he spoke and existing atoms assembled into fully formed creatures in the sea, or fully formed creatures on the earth.

That's not what He says in Genesis.

I believe from there evolution happens.

But that's contrary to what He shows us in the world. Genetic analysis shows that all organisms on Earth have a common ancestor.

Its the jump from non-living matter to living matter that I believe God is directly involved with.

He's directly involved with every electron. Why is that so distrurbing?

Definition of life:

"the condition that distinguishes animals and plants from inorganic matter."

No. That would make fungi, protists, eubacteria and archaea, non-living.

Isn't that such a vague definition?

Incorrect.

Defining life is tough because there's very little that's common to all living things that can't be observed in non-living things. One of the best is "composed of organic reaction systems inside a phospholipid membrane."

 

[Vaccine]

I thought about explaining how its made, but here's a video that does just that. Really worth watching the whole thing, but skip to 2:37 if you just want to watch how its made. The first part explains how the motor works and a general overview.

http://www.youtube.com/watch?feature=player_embedded&v=Ey7Emmddf7Y

http://www.uncommondescent.com/inte...on-of-flagellar-motor-mechanics-and-assembly/

 

[Barbarian]

Tell us what it says about the fact of intermediate stages in the motor that have been documented here.

 

[Vaccine]

Since nobody can go back in time to observe the first bacteria flagellur motor, the term "fact" doesn't apply. I also think it's a bit hasty to call other bacteria flagellum "intermediates", these are organelles not species.
I would also add because other proteins in the bacteria flagellur system exist is no challenge to irreducible complexity. All life is based on carbon and built from just a limited amount of proteins.

In order to catch a mouse, a mousetrap needs a platform, spring, hammer, holding bar, and catch. Now, suppose you wanted to make a mousetrap. In your garage you might have a piece of wood from an old Popsicle stick (for the platform), a spring from an old wind-up clock, a piece of metal (for the hammer) in the form of a crowbar, a darning needle for the holding bar, and a bottle cap that you fancy to use as a catch. But these pieces, even though they have some vague similarity to the pieces of a working mousetrap, in fact are not matched to each other and couldn't form a functioning mousetrap without extensive modification. All the while the modification was going on, they would be unable to work as a mousetrap. The fact that they were used in other roles (as a crowbar, in a clock, etc.) does not help them to be part of a mousetrap. As a matter of fact, their previous functions make them ill-suited for virtually any new role as part of a complex system.
Darwin's Black Box, page 66.
​

Dr. Behe makes a good point, producing (not hypothesizing) a bacteria flagellur motor by Darwinian process would disprove irreducible complexity.

"To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved".- Dr Behe in 1997