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Evolution Of The Proton Pump


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#1 Air-run

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Posted 29 May 2017 - 07:15 PM

These are some thoughts swirling in my brain about materials from my cell bio course...

 

We talked about the evolution of the hydrogen ion pump - which would have been a precursor to ATP synthase - which we require to make sufficient ATP.

 

Our professor mentioned that the evolution of a hydrogen ion pump would have been necessary as early cells were becoming dangerously acidic inside.

 

I asked her why they were becoming acidic inside.

 

She said one of the reasons was that these early cells used hydrogen ions outside the cell to bring certain nutrients into the cell via a coupled symporter protein pump.

 

I don't think she really understood my responding critique of this notion.

 

If these early cells used the energy of hydrogen ions to pump nutrients inside, the increase in H+ ions would begin to acidify their internal pH from the very beginning - which would throw off their chemistry and ruin the cell.  

 

In short, if these cells were using hydrogen ions to power their intake pumps, they would also need pumps to expel the excess hydrogen ions at the same time.  If the cell didn't evolve both of these pumps at the same time, the cell would have been toast.

 

If anyone has a deeper understanding of this subject than I - feel free to correct me if I'm wrong.


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#2 what if

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Posted 30 May 2017 - 01:01 AM

it's my understanding that ATP synthase can run forward, or backward.
the ions can be pumped into mitocondria, or they can be pumped out.

the cell is apparently dealing with this sort of thing, or it wouldn't be alive.

The motor is reversible, and hydrolysis of ATP by the ?3?3-catalytic hexamer can supply the torque for the rotation in the opposite direction, catalyzing the active transport of protons from inside to outside the cell.

it's quite possible that an increase in PH activates the method that causes this reversal.

since PH is important to the cell, the cell could have methods of dealing with it besides ATP synthase.

my best guess it that an increase in PH activates a catalytic hexamer (mentioned earlier).

#3 mike the wiz

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Posted 30 May 2017 - 02:27 AM

 

 

What If: it's my understanding that ATP synthase can run forward, or backward.
the ions can be pumped into mitocondria, or they can be pumped out.

 

I think he's talking about a stage earlier than the ATP synthase. (and perhaps earlier than organelles but I'm not sure my guess is a good one on that)

 

It seems to me your explanation of how horse and buggies functioned is to say that they had a combustion engine.

 

:P



#4 what if

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Posted 30 May 2017 - 04:03 AM

there is no mystery here, the cell is dealing with this, or it would be dead.
we've already seen how these motors can run both ways, and in at least one scenario a chemical substance determines the direction according to the PH.
a chemically controlled chemical motor.
awesome.

#5 mike the wiz

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Posted 30 May 2017 - 11:42 AM

 

 

What If: there is no mystery here, the cell is dealing with this, or it would be dead.
we've already seen how these motors can run both ways, and in at least one scenario a chemical substance determines the direction according to the PH.
a chemically controlled chemical motor.
awesome. 

 

There is no mystery, because the real-life cell with an ATP synthase has as you say, a "motor", and motors are designed, and there was no precursor to it. 

 

The usual cause of intelligent design is an intelligent designer and evolution has no intelligence. The same "correct by design" chemical substances will also be found in our eyes, the rhodopsin. Notice we don't find anti-freeze in our eyes or curry sauce, but the exact correct fluid. Same for the Bombardier beetle;

 

 

German chemist Dr Schildknecht discovered that the beetle mixes two chemicals (hydrogen peroxide and hydroquinone) which would usually form a dirty ugly mixture. The well-designed beetle uses a special ‘inhibitor’ chemical to keep the mixture from reacting. How then can the explosion instantaneously occur when needed?

Dr Schildknecht discovered that in the beetle’s specially designed combustion tubes are two enzymes called catalase and peroxidase which make chemical reactions go millions of times faster. These chemicals catalyze the extremely rapid decomposition of hydrogen peroxide into water and oxygen and the oxidation of hydroquinone into quinone, causing them to violently react and explode—but not so soon as to blow up the beetle, of course!

Common sense tells us that this amazing little insect cannon which can fire four or five ‘bombs’ in succession could not have evolved piece by piece. Explosive chemicals, inhibitor, enzymes, glands, combustion tubes, sensory communication, muscles to direct the combustion tubes and reflex nervous systems—all had to work perfectly the very first time—or all hopes for ‘Bomby’ and his children would have exploded!

http://creation.com/...mbardier-beetle

 

The chances of this beetle designing itself are ZERO. The cause is right there and sits under your nose every day yet you waffle on about codswallopal epigenetics, and miss the real meal because your focus is on the bread and butter. :P

 

Wake up - it's obvious that only God could have created these miraculous little designs, all of those chemicals show teleological precision, it is like saying this; "see that painting on the sistine chapel ceiling, how the hand and fingers look like they are meant to be touching God's hand? That's a coinicidence, and see how they all look human, coincidence the paint just congealed that way."

 

 

:snapoutofit: I mean reading that about that beetle, anyone can see that all of those things are there on purpose so as to make the explosion. It's about the same as asking this; "do you think the brake pads being made of that material in a car's brakes, are that material by accident?"

 

Response; "Ermmm.........is 2 add 2, 4?"



#6 Air-run

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Posted 30 May 2017 - 11:43 AM

it's my understanding that ATP synthase can run forward, or backward.
the ions can be pumped into mitocondria, or they can be pumped out.

the cell is apparently dealing with this sort of thing, or it wouldn't be alive.

The motor is reversible, and hydrolysis of ATP by the ?3?3-catalytic hexamer can supply the torque for the rotation in the opposite direction, catalyzing the active transport of protons from inside to outside the cell.

it's quite possible that an increase in PH activates the method that causes this reversal.

since PH is important to the cell, the cell could have methods of dealing with it besides ATP synthase.

my best guess it that an increase in PH activates a catalytic hexamer (mentioned earlier).

As  mike mentioned - we're talking about a stage before ATP synthase.  The discussion is how ATP synthase evolved.  Yes it can run backward and forward depending upon the needs of the modern cell.  But, if the cell is using H+ ions to import nutrients, it also needs a mechanism to pump extra H+ out of the cell.  And if it doesn't have the mechanism to pump the extra H+ out, it can't continue to import nutrients.  So basically, the early cell would need to evolve both of these mechanisms at the same time for either of them to work.



#7 what if

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Posted 01 June 2017 - 04:17 PM

it's my understanding that ATP synthase can run forward, or backward.
the ions can be pumped into mitocondria, or they can be pumped out.

the cell is apparently dealing with this sort of thing, or it wouldn't be alive.

The motor is reversible, and hydrolysis of ATP by the ?3?3-catalytic hexamer can supply the torque for the rotation in the opposite direction, catalyzing the active transport of protons from inside to outside the cell.

it's quite possible that an increase in PH activates the method that causes this reversal.

since PH is important to the cell, the cell could have methods of dealing with it besides ATP synthase.

my best guess it that an increase in PH activates a catalytic hexamer (mentioned earlier).

As  mike mentioned - we're talking about a stage before ATP synthase.  The discussion is how ATP synthase evolved.  Yes it can run backward and forward depending upon the needs of the modern cell.  But, if the cell is using H+ ions to import nutrients, it also needs a mechanism to pump extra H+ out of the cell.  And if it doesn't have the mechanism to pump the extra H+ out, it can't continue to import nutrients.  So basically, the early cell would need to evolve both of these mechanisms at the same time for either of them to work.

well, like koonin said, animal phyla arrived here ready made.
science doesn't know how this stuff "evolved", except it was extremely rapid.
it certainly wasn't any kind of "gradual mutation" type of evolution.
koonin seems to think animal phyla arrived here radially from eukaryote super groups, not by any kind of bifurcated treelike pattern.
IOW, science doesn't know what the early stages were to ATP synthase, but it does seem that bacteria flagella uses a similar type of mechanism.

#8 what if

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Posted 01 June 2017 - 06:32 PM

The chances of this beetle designing itself are ZERO. The cause is right there and sits under your nose every day yet you waffle on about codswallopal epigenetics, and miss the real meal because your focus is on the bread and butter. :P

i don't think so in face of current knowledge.
the cell is indeed a designer.
and it's been that way since at least eukaryote super groups, possibly earlier, maybe even the first life, because epigenetics and the DNA strand HAD to co evolve.
if you thought abiogenesis was tough before . . .

Wake up - it's obvious that only God could have created these miraculous little designs, all of those chemicals show teleological precision, it is like saying this; "see that painting on the sistine chapel ceiling, how the hand and fingers look like they are meant to be touching God's hand? That's a coinicidence, and see how they all look human, coincidence the paint just congealed that way."

that's one interpretation i guess, but it does seem highly unlikely that it happened "by chance".

#9 Air-run

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Posted 01 June 2017 - 08:21 PM

 

 

it's my understanding that ATP synthase can run forward, or backward.
the ions can be pumped into mitocondria, or they can be pumped out.

the cell is apparently dealing with this sort of thing, or it wouldn't be alive.

The motor is reversible, and hydrolysis of ATP by the ?3?3-catalytic hexamer can supply the torque for the rotation in the opposite direction, catalyzing the active transport of protons from inside to outside the cell.

it's quite possible that an increase in PH activates the method that causes this reversal.

since PH is important to the cell, the cell could have methods of dealing with it besides ATP synthase.

my best guess it that an increase in PH activates a catalytic hexamer (mentioned earlier).

As  mike mentioned - we're talking about a stage before ATP synthase.  The discussion is how ATP synthase evolved.  Yes it can run backward and forward depending upon the needs of the modern cell.  But, if the cell is using H+ ions to import nutrients, it also needs a mechanism to pump extra H+ out of the cell.  And if it doesn't have the mechanism to pump the extra H+ out, it can't continue to import nutrients.  So basically, the early cell would need to evolve both of these mechanisms at the same time for either of them to work.

 

well, like koonin said, animal phyla arrived here ready made.
science doesn't know how this stuff "evolved", except it was extremely rapid.
it certainly wasn't any kind of "gradual mutation" type of evolution.
koonin seems to think animal phyla arrived here radially from eukaryote super groups, not by any kind of bifurcated treelike pattern.
IOW, science doesn't know what the early stages were to ATP synthase, but it does seem that bacteria flagella uses a similar type of mechanism.

 

 This would have been pre-eukaryotes, and probably pre-flagella.  At this point, the prokaryotes only source of ATP would have been fermentation.  I'm not sure if that would have provided enough ATP to power a flagella.  But, I don't know how these organisms could have survived if they needed to import H+ ions to get their nutrients, but didn't have a way to get rid of the excess H+.

 

As a side note, I love it how (don't really love it) the evolution story is always something like this:  "such and such organism needed this part to survive, and that pressure led to them evolving it."  You need a proton pump?  Boom!  Evolution got you covered.  No need to bother with trying to figure out HOW it happened or IF it could happen - just need to know WHY it happened.  If the need is there, the solution is magically there.



#10 mike the wiz

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Posted 02 June 2017 - 02:29 AM

 

 

Air-Run: As a side note, I love it how (don't really love it) the evolution story is always something like this:  "such and such organism needed this part to survive, and that pressure led to them evolving it."  You need a proton pump?  Boom!  Evolution got you covered.  No need to bother with trying to figure out HOW it happened or IF it could happen - just need to know WHY it happened.  If the need is there, the solution is magically there.

 

I've noticed that too. It's because, "evolution is a fact" and they just need to understand the details...type reasoning. (circular). It's also a tautologous argument because it can apply to any feature which means it's also an argument which can't be falsified. If anything can come about by selection pressure then I guess it wouldn't matter if they found robocop in the fossils, with a spaghetti monsters head, it would just mean there was a selection pressure to create a robocop to enforce termite-law. ;)

 

 

What If

i don't think so in face of current knowledge.
the cell is indeed a designer.
and it's been that way since at least eukaryote super groups, possibly earlier, maybe even the first life, because epigenetics and the DNA strand HAD to co evolve.

 

The cell isn't a designer, because the cell doesn't exist as an intelligence. Molecular parts aren't sentient. Even if the cell was a designer, my argument pertained to the anatomy of the Bombardier beetle, which can't be explained as being designed by cells any more than bricks could design cathedrals.

 

Basically you commit the pathetic fallacy, or some sort of personification, which is when you treat a "thing" as though it is an intelligence or can feel. The cell has no brains, everything in nature that has intelligence can be shown to have one, so why should I believe that the cell has intelligence? It's clear the intelligence in the cell is the same as the intelligence in the design of a car, the intelligence put into the cell/car, isn't tangibly there, but the cell/car merely represents the agent that created it.

 

"The phrase pathetic fallacy is a literary term for the attributing of human emotion and conduct to all aspects within nature. It is a kind of personification that is found in poetic writing when, for example, clouds seem sullen, when leaves dance, or when rocks seem indifferent."

 

Or; "the cell is indeed a designer."



#11 what if

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Posted 02 June 2017 - 07:10 AM

The cell isn't a designer, because the cell doesn't exist as an intelligence. Molecular parts aren't sentient. Even if the cell was a designer, my argument pertained to the anatomy of the Bombardier beetle, which can't be explained as being designed by cells any more than bricks could design cathedrals.

a seemingly valid and logical argument, but it's erroneous.
a computer without its programs are as smart and intelligent as that rock in your driveway.
add the programs, viola!, we have a system that can mimic intelligence and can design.

there can be little doubt that the cell itself is creating at least some of the genetic sequences needed to form new organs, and it does this while maintaining cell functionality.

i can't say the cell is intelligent, but i can, and certainly will, say the cell is a designer, there is no question about that.
something must explain how reptiles acquire new organs within a few generations.
how do you propose to explain that mike?
this is definitely NOT the slow, gradual accumulation of "random" genetic material.
how do you propose to explain cell differentiation during embryo development?
epigenetics and transposons are a proven reality, both were experimentally proven over 70 years ago, and both have been validated. 

Basically you commit the pathetic fallacy, or some sort of personification, which is when you treat a "thing" as though it is an intelligence or can feel. The cell has no brains, everything in nature that has intelligence can be shown to have one, so why should I believe that the cell has intelligence? It's clear the intelligence in the cell is the same as the intelligence in the design of a car, the intelligence put into the cell/car, isn't tangibly there, but the cell/car merely represents the agent that created it.

why are you insisting that i'm saying the cell is intelligent?
i have NEVER said that.
your thermostat isn't intelligent either, but it knows what the temperature is.
my computer isn't a designer, but i can write programs for it that can create truly unique, and complex, designs just by inputting simple numeric sequences such as 31,33,3,3 and 1,1,3,3 (an actual case).
 

"The phrase pathetic fallacy is a literary term for the attributing of human emotion and conduct to all aspects within nature. It is a kind of personification that is found in poetic writing when, for example, clouds seem sullen, when leaves dance, or when rocks seem indifferent."
 
Or; "the cell is indeed a designer."

fair enough, the onus is on you to SCIENTIFICALLY explain the arrival of new reptilian organs within a few generations.
have at it.

#12 mike the wiz

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Posted 02 June 2017 - 07:25 AM

 

 

What If: a seemingly valid and logical argument, but it's erroneous.
a computer without its programs are as smart and intelligent as that rock in your driveway.
add the programs, viola!, we have a system that can mimic intelligence and can design.

there can be little doubt that the cell itself is creating at least some of the genetic sequences needed to form new organs, and it does this while maintaining cell functionality.

 

The problem is you're forgetting that a computer also contains intelligent design, meaning the true reason and the true cause of the programs actions, are the intelligent designers of the computer. I can admit the cell, "does things" on it's own, but that's just a sign of a more sophisticated intelligent designer.

 

Can you show me a computer that invented itself? This is the problem - if the intelligence and design is coming from cells, then what created the cells and where does the intelligent design in the cells come from?

 

 

 

What If: i can't say the cell is intelligent, but i can, and certainly will, say the cell is a designer, there is no question about that.
something must explain how reptiles acquire new organs within a few generations.
how do you propose to explain that mike?

 

I'd say it's built in. I believe the epigenetics is dormant information God has put there in case of severe environmental changes. (contingency planning). I don't think the design in the cell is being designed by the cell because first the cell has to exist. If a cell doesn't exist to begin with then what created the cell? It seems you are saying a cell that did not yet exist, created the cell. Although I know you entertain the possibility that life itself is somehow eternal or some such thing, with no beginning?

 

I'm not saying these things to insult you, I know you're free to believe what you will and I don't mock people, I just think you're sacrificing the best explanation because you don't like the idea that God exists because of things like hell and judgement, which you have expressed disdain for.

 

 

 

What If: fair enough, the onus is on you to SCIENTIFICALLY explain the arrival of new reptilian organs within a few generations.
have at it. 

 

But don't we agree on this one? But it seems you tend to merge evolution and epigenetics. I just think it's inbuilt epigenetics.


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#13 what if

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Posted 02 June 2017 - 09:52 AM

The problem is you're forgetting that a computer also contains intelligent design, meaning the true reason and the true cause of the programs actions, are the intelligent designers of the computer. I can admit the cell, "does things" on it's own, but that's just a sign of a more sophisticated intelligent designer.

maybe, maybe not.
the concept you are describing above is the "information" that must be accounted for concerning abiogegesis.
the so called "control program".
i agree, it's highly unlikely such a thing happened haphazardly, but science must assume that it did.
how do you think we have come this far without assuming otherwise?
anyway, there are still things undiscovered with the cell, there must certainly be a "molecular language".
not only the basic atomic makeup, but the size and shapes of these things also play a role.

i have no idea how ATP synthase could have evolved, but i find it a remarkable design that man apparently never thought of.

kind of compares with the 2 pounds of e. coli DNA doesn't it?
 

Can you show me a computer that invented itself? This is the problem - if the intelligence and design is coming from cells, then what created the cells and where does the intelligent design in the cells come from?

like i mentioned before, this is the "information" that must be accounted for concerning abiogenesis, the "control program"
the cell isn't "intellgent", it's the control program that makes it appear so, just like the programs on your computer.

what matters (or should) to science is how this stuff works, and it's getting a pretty good handle on it.
but it pushes the question of origins straight into the stratosphere, there is simply no way this stuff co evolved, and it had to.
 

I'd say it's built in. I believe the epigenetics is dormant information God has put there in case of severe environmental changes. (contingency planning). I don't think the design in the cell is being designed by the cell because first the cell has to exist. If a cell doesn't exist to begin with then what created the cell? It seems you are saying a cell that did not yet exist, created the cell. Although I know you entertain the possibility that life itself is somehow eternal or some such thing, with no beginning?

yes, life could be "eternal" in the sense of some weird quantuum space warp time disturbance
but, let's stay a little closer to rationality

science has no answers for how life got here, don't forget, koonin said it would be a "seeming miracle"
 

I'm not saying these things to insult you, I know you're free to believe what you will and I don't mock people, I just think you're sacrificing the best explanation because you don't like the idea that God exists because of things like hell and judgement, which you have expressed disdain for.

wrong, very wrong.
i'm interested in how this stuff works, you know, evolution.
how it all came together in the first place is the question that needs answered, not evolution proper.
well, there are questions that still need answered but i believe science is well on its way to answering them.
and some of those answers are going to upset a few people.

#14 aelyn

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Posted 11 June 2017 - 05:24 AM


Our professor mentioned that the evolution of a hydrogen ion pump would have been necessary as early cells were becoming dangerously acidic inside.

 

I asked her why they were becoming acidic inside.

 

She said one of the reasons was that these early cells used hydrogen ions outside the cell to bring certain nutrients into the cell via a coupled symporter protein pump.

 

I don't think she really understood my responding critique of this notion.

 

If these early cells used the energy of hydrogen ions to pump nutrients inside, the increase in H+ ions would begin to acidify their internal pH from the very beginning - which would throw off their chemistry and ruin the cell.  

 

In short, if these cells were using hydrogen ions to power their intake pumps, they would also need pumps to expel the excess hydrogen ions at the same time.  If the cell didn't evolve both of these pumps at the same time, the cell would have been toast.

 

If anyone has a deeper understanding of this subject than I - feel free to correct me if I'm wrong.

 
I know of prominent researchers in the field of abiogenesis that would agree with you so I don't think you are off-base on this at all. I expect your professor is making speculative comments (as pretty much all comments on abiogenesis must be at this point of our knowledge on the question) and might not have put as much deep thought into them as someone whose core interest was the evolution of cells might have.
 
Here is an article describing the views of researchers who, like you, think the proton pump is an absolutely vital aspect of cell metabolism (and in fact think abiogenesis research should start with thermodynamics), and have gone further and looked at where such pumps occur naturally and whether this would have implications for the origin of life:
 
 
The article is a good overview of the question as a whole, but here are quotes on the research into proton gradients as the key to the origin of life:

 

For the last two decades, Russell has been the dynamic force behind the emerging paradigm shift in our understanding of the origin of life. Drawing on a background in ore geochemistry (many ores are precipitated by hydrothermal vent systems), Russell postulates that alkaline vents, akin to the modern Lost City vent system in the mid-Atlantic (Figure 3), were the ideal incubators for life, providing a steady supply of hydrogen gas, carbon dioxide, mineral catalysts, and a labyrinth of interconnected micropores (natural compartments similar to cells, with filmlike membranes; Lane et al. 2010).

Russell has long maintained that natural proton gradients played a central role in powering the origin of life.

 

But the centerpiece of Russell's conception lies in natural proton gradients. Four billion years ago, alkaline fluids bubbled into what would then have been mildly acidic oceans (CO2 levels were about a thousand times higher than they are today, and CO2 forms carbonic acid in solution, rendering the oceans mildly acidic). Acidity is just a measure of proton concentration, which was about four orders of magnitude (four pH units) higher in the oceans than in vent fluids. That difference gave rise to a natural proton gradient across the vent membranes that had the same polarity (outside positive) and a similar electrochemical potential (about 200 millivolts [mV] across the membrane) as modern cells have.
 
 
And a youtube video of a talk by one of the researchers pioneering this topic:
 

 

The article would be good to share with your professor I think.

 

EDIT: listening to the video as I'm typing this and I just got to the point where Dr. Lane points out that while the "intake pump" half of metabolism is the same in all living things, the proton pump isn't, suggesting they indeed didn't evolve in the same way or at the same time.






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