Origin of life - a response

[TheLurch]

So proton pumps would seem to be widespread, in eukaryotes, and then in bacteria, some of these would apply:

Source: Wikipedia

The energy required for the proton pumping reaction may come from light (light energy; bacteriorhodopsins), electron transfer (electrical energy; electron transport complexes I, III and IV) or energy-rich metabolites (chemical energy) such as pyrophosphate (PPi; proton-pumping pyrophosphatase) or adenosine triphosphate (ATP; proton ATPases). … Complex III is present in the inner mitochondrial membrane of all aerobic eukaryotes and the inner membranes of most eubacteria.

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And what about that indicates the earliest cells needed them?

[lee_merrill]

Are you saying just because Miller made the claims, than that makes it true?

No, that opens the topic for discussion.

... I have provided references that say no energy is not an issue concerning abiogenesis.

No energy would indeed be an issue.

The development of the proton pump is not necessary for the energy required for the initial formation of life, when there is abundant energy from natural sources.

Well, proton pumps are common in cells, they provide energy for making ATP, for instance. Are you saying proton pumps developed after the first cells?

First this is an argument from ignorance, as usual, as you claiming that you believe the solution for abiogenesis is not achieved.

No, this is an observation.

"So far, we have hydrogen ions moving downhill through transporters and releasing energy. We also have these ions moving uphill, into areas of higher concentration, using a proton pump. Pumping against a gradient can be difficult, so the job of proton pumps is hard work. There is one pump that isn't as strong, and so acts a little out of the ordinary. It is called the Proton Pyrophosphatase Pump. "

Well, fine, but I'm not sure why you are pointing this out.

Source: Barge et. al.

In this paper, we discuss how prebiotic geo-electrochemical systems can be modeled as a fuel cell and how laboratory simulations of the origin of life in general can benefit from this systems-led approach. As a specific example, the components of what we have termed the “prebiotic fuel cell” (PFC) that operates at a putative Hadean hydrothermal vent are detailed, and we used electrochemical analysis techniques and proton exchange membrane (PEM) fuel cell components to test the properties of this PFC and other geo-electrochemical systems, the results of which are reported here. The modular nature of fuel cells makes them ideal for creating geo-electrochemical reactors with which to simulate hydrothermal systems on wet rocky planets and characterize the energetic properties of the seafloor/hydrothermal interface. That electrochemical techniques should be applied to simulating the origin of life follows from the recognition of the fuel cell–like properties of prebiotic chemical systems and the earliest metabolisms. Conducting this type of laboratory simulation of the emergence of bioenergetics will not only be informative in the context of the origin of life on Earth but may help in understanding whether life might emerge in similar environments on other worlds. Key Words: Astrobiology—Bioenergetics—Iron sulfides—Origin of life—Prebiotic chemistry. Astrobiology 14, 254–270.

© Copyright Original Source

And I can't look behind the paywall to read further, though it does seem odd to think of organisms starting with fuel cells first.

Blessings,
Lee

[lee_merrill]

And what about that indicates the earliest cells needed them?

Because they're so widespread in usage, across cell types and microorganisms and multicellular creatures.

Blessings,
Lee

[shunyadragon]

[QUOTE=lee_merrill;740246]No, that opens the topic for discussion.

No energy would indeed be an issue.

My references clearly indicate that no 'racecar' is needed in abiogenesis.

Source: https://www.livescience.com/26173-hydrothermal-vent-life-origins.html

A new theory proposes the primordial life-forms that gave rise to all life on Earth left deep-sea vents because of their "invention" of a tiny pump. These primitive cellular pumps would have powered life-giving chemical reactions.

The idea, detailed Dec. 20 in the journal Cell, could help explain two mysteries of life's early origin: How did the earliest proto-cells power chemical reactions to make the organic building blocks of life; and how did they leave hydrothermal vents to colonize early Earth's oceans?

Authors of the new theory argue the environmental conditions in porous hydrothermal vents — where heated, mineral-laden seawater spews from cracks in the ocean crust — created a gradient in positively charged protons that served as a "battery" to fuel the creation of organic molecules and proto-cells.

Later, primitive cellular pumps gradually evolved the ability to use a different type of gradient — the difference in sodium particles inside and outside the cell — as a battery to power the construction of complex molecules like proteins. And, voilŕ, the proto-cells could leave the deep-sea hydrothermal vents. [Image Gallery: Unique Life at Deep-Sea Vents.

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Well, proton pumps are common in cells, they provide energy for making ATP, for instance. Are you saying proton pumps developed after the first cells?

Yes, of course, that is the result of abiogenesis, based on the references cited. The proton pumps do not require significant energy, as cited.

I have cited references, you have cited nothing to support Miller's assertions, except a reference that agrees with me.

Still waiting

[TheLurch]

Because they're so widespread in usage, across cell types and microorganisms and multicellular creatures.

That just suggests an early cell had them, not every early cell needed them.

[shunyadragon]

Because they're so widespread in usage, across cell types and microorganisms and multicellular creatures.

Blessings,
Lee

You are making assumption that he earliest primitive cells did not depend on natural sources of energy to function. It does not require a 'racecar' as previously referenced for primitive life to exist. The theory of primitive life evolving around mid ocean ridge sea vents is a viable source of energy.

The problem of entropy remains a bogus Discovery Institute misunderstanding of basic physics.

Still waiting for peer reviewed research that supports Millers assertions. . .

[lee_merrill]

My references clearly indicate that no 'racecar' is needed in abiogenesis.

Source: https://www.livescience.com/26173-hydrothermal-vent-life-origins.html

A new theory proposes the primordial life-forms that gave rise to all life on Earth left deep-sea vents because of their "invention" of a tiny pump. These primitive cellular pumps would have powered life-giving chemical reactions.

© Copyright Original Source

This article concludes with:

Source: LiveScience

Testing the idea, however, will be tricky, Amend told LiveScience. "Mimicking natural conditions in the lab is a lot more difficult than it sounds."

© Copyright Original Source

So what we have here is an idea, not a tested procedure.

Yes, of course, that is the result of abiogenesis, based on the references cited. The proton pumps do not require significant energy, as cited.

As cited where?

I have cited references, you have cited nothing to support Miller's assertions, except a reference that agrees with me.

Here is a reference:

Source: Miller

Harold Morowitz estimated the probability that a bacterial cell might have originated through thermal fluctuations, and determined that the probability of spontaneously going from low to high, when every other system was spontaneously going from high to low, was on the order of one part in ten to the power of a hundred billion [Harold Morowitz, Energy Flow in Biology (Oxford: Ox Bow Books, 1979), 66.]. This number represents a least upper bound since it measures the smallest increase in free energy needed to form a bacterial cell. And, of course, the probability is essentially zero.

Source

© Copyright Original Source

Blessings,
Lee

[lee_merrill]

That just suggests an early cell had them, not every early cell needed them.

Well, it was apparently early in the history of life:

Source: Wikipedia

The evolution of ATP synthase is thought to have been modular whereby two functionally independent subunits became associated and gained new functionality. This association appears to have occurred early in evolutionary history, because essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life.

Source

© Copyright Original Source

So why not put it at the very start?

Blessings,
Lee

[TheLurch]

Well, it was apparently early in the history of life:

Source: Wikipedia

The evolution of ATP synthase is thought to have been modular whereby two functionally independent subunits became associated and gained new functionality. This association appears to have occurred early in evolutionary history, because essentially the same structure and activity of ATP synthase enzymes are present in all kingdoms of life.

Source

© Copyright Original Source

So why not put it at the very start?

Blessings,
Lee

Because there's almost certainly a very big difference between the first primitive cells and the last universal common ancestor. The ATP synthase/proton gradient was almost certainly present at the latter stage, explaining its omnipresence today. But it was almost certainly not present at the stage of the first primitive cells, which were very likely to drive their metabolisms by directly incorporating chemicals found in their environments, rather than by burning through ATP.

The inability to recognize those sorts of differences is exactly what i'd fear happening when a bunch of physicists start talking about the origin of life.

[lee_merrill]

Because there's almost certainly a very big difference between the first primitive cells and the last universal common ancestor. The ATP synthase/proton gradient was almost certainly present at the latter stage, explaining its omnipresence today. But it was almost certainly not present at the stage of the first primitive cells, which were very likely to drive their metabolisms by directly incorporating chemicals found in their environments, rather than by burning through ATP.

Well, that may be, but see the quote by Harold Morowitz the biophysicist above.

The inability to recognize those sorts of differences is exactly what i'd fear happening when a bunch of physicists start talking about the origin of life.

I believe England could be characterized as a biophysicist:

Source: Wikipedia

England earned a bachelor's degree in biochemistry from Harvard in 2003.

Source

© Copyright Original Source

Blessings,
Lee

[TheLurch]

Well, that may be, but see the quote by Harold Morowitz the biophysicist above.

Why don't, for a change, you pay attention to your own quotes. It's for a bacterial cell, which is irrelevant to the discussion of pre-LUCA life forms.

[TheLurch]

I realize, that for people who aren't Lee, it's probably worth elaborating what's going on here.

All indications are that the last universal common ancestor (LUCA) of life on earth existed over 3 billion years ago. That means current organisms have had billions of years to:
Evolve extremely efficient ways of extracting energy from their environment.
Evolve an elaborate metabolism to match their energy input.

I don't think i'm going out on a limb to say that, if you kept the modern metabolism, but swapped in the energy harvesting abilities of LUCA, the resulting cells would die. They would be completely unable to produce the levels of energy that the whole rest of the cell needs to function. Billions of years of evolution will do that.

But LUCA likely came hundreds of millions of years after the first primitive cells. And the difference here is likely to be even more striking. The first primitive cells likely had a series of unconnected metabolisms sharing a membrane with something that could replicate RNAs. They were almost certainly entirely dependent upon their environment for both energy and key molecules that were central to their metabolism. You likely couldn't do the same experiment of swapping their energy-harvesting portion of metabolism into LUCA, simply because they didn't have a unified energy harvesting system.

How could something like this constantly harvest fresh, energy-rich molecules from its environment? Probably one or both of two ways. In some cases, like geothermal vents, environmental processes provide a constant flow of energy rich molecules. In other cases, cyclical processes can drive the formation of molecules that won't form under average conditions. For example, ATP won't form spontaneously from a watery solution of AMP and phosphate. But if you dehydrate the solution, then it can form, since the addition of phosphates liberates a water molecule.

It's because of these issues that the apparent argument here, to the extent that Lee has elaborated anything at all, becomes standard creationist fare. If you take a bunch of average conditions, many energy rich molecules won't form. And if you try to power a full LUCA-like metabolism - or even worse, a modern metabolism - with the sorts of molecules that likely did form, they'll fail. And the creationist argument is that, therefore, it's impossible for life to have formed. But the reality is that the conditions they're trying to limit consideration to - nothing but average conditions, a relatively high-powered metabolism - are pretty much irrelevant to what the first cells were actually doing. And they were doing much less than more modern organisms like LUCA.

It's the standard creationist approach of taking a start and end point that are very distant, ignoring all the possible transition states in between them, and then declaring that the full leap between the two is impossible.

[shunyadragon]

No, that opens the topic for discussion.


No energy would indeed be an issue.


Well, proton pumps are common in cells, they provide energy for making ATP, for instance. Are you saying proton pumps developed after the first cells?


No, this is an observation.


Well, fine, but I'm not sure why you are pointing this out.

Source: Barge et. al.

In this paper, we discuss how prebiotic geo-electrochemical systems can be modeled as a fuel cell and how laboratory simulations of the origin of life in general can benefit from this systems-led approach. As a specific example, the components of what we have termed the “prebiotic fuel cell” (PFC) that operates at a putative Hadean hydrothermal vent are detailed, and we used electrochemical analysis techniques and proton exchange membrane (PEM) fuel cell components to test the properties of this PFC and other geo-electrochemical systems, the results of which are reported here. The modular nature of fuel cells makes them ideal for creating geo-electrochemical reactors with which to simulate hydrothermal systems on wet rocky planets and characterize the energetic properties of the seafloor/hydrothermal interface. That electrochemical techniques should be applied to simulating the origin of life follows from the recognition of the fuel cell–like properties of prebiotic chemical systems and the earliest metabolisms. Conducting this type of laboratory simulation of the emergence of bioenergetics will not only be informative in the context of the origin of life on Earth but may help in understanding whether life might emerge in similar environments on other worlds. Key Words: Astrobiology—Bioenergetics—Iron sulfides—Origin of life—Prebiotic chemistry. Astrobiology 14, 254–270.

© Copyright Original Source

And I can't look behind the paywall to read further, though it does seem odd to think of organisms starting with fuel cells first.

Blessings,
Lee

By the source the proton pump does not need a 'racecar' of energy to function. The original simple early life forms likely did not use the proton pump for an energy source, as The Lurch noted. There is abundant energy in the form of volcanic sources for pre-life forms to thrive.

LUCA did not suddenly appear with the wave of a wand. It evolved from more primitive organic forms as the sources describe.

[shunyadragon]

This article concludes with:

Source: LiveScience

Testing the idea, however, will be tricky, Amend told LiveScience. "Mimicking natural conditions in the lab is a lot more difficult than it sounds."

© Copyright Original Source

So what we have here is an idea, not a tested procedure.


As cited where?


Here is a reference:

Source: Miller

Harold Morowitz estimated the probability that a bacterial cell might have originated through thermal fluctuations, and determined that the probability of spontaneously going from low to high, when every other system was spontaneously going from high to low, was on the order of one part in ten to the power of a hundred billion [Harold Morowitz, Energy Flow in Biology (Oxford: Ox Bow Books, 1979), 66.]. This number represents a least upper bound since it measures the smallest increase in free energy needed to form a bacterial cell. And, of course, the probability is essentially zero.

Source

© Copyright Original Source

Blessings,
Lee

Miller alone is not a reliable evidence, because no research on his part and his religious Creationist agenda. Need peer reviewd indepenednt sources. Also it is not a good idead to selectively cite Harold J. Morowitz

Source: https://en.wikipedia.org/wiki/Harold_J._Morowitz

The origin of life

Morowitz's book Energy Flow in Biology laid out his central thesis that "the energy that flows through a system acts to organize that system,"[12] an insight later quoted on the inside front cover of The Last Whole Earth Catalog. He was a vigorous proponent of the view that life on earth emerged deterministically from the laws of chemistry and physics,[13] and so believed it highly probable that life exists widely in the universe.[5][14]

In 1983, he testified at "McLean v. Arkansas" (nicknamed "Scopes II") that creationism has no scientific basis and so should not be taught as science in public schools.[15]

His work is sometimes associated with the Gard model of evolutionary biology

© Copyright Original Source

[lee_merrill]

If you take a bunch of average conditions, many energy rich molecules won't form. And if you try to power a full LUCA-like metabolism - or even worse, a modern metabolism - with the sorts of molecules that likely did form, they'll fail. And the creationist argument is that, therefore, it's impossible for life to have formed.

But I was taking Miller's starting point, in hydrothermal vents.

Blessings,
Lee