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Old 22-October-2009, 11:35 PM
DrWho DrWho is offline
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Default The Origin of Life: Descent of Protons

Some interesting info in a New Scientist article: Was our oldest ancestor a proton-powered rock?

Quote:
The last common ancestor of all life was not a free-living cell at all, but a porous rock riddled with bubbly iron-sulphur membranes that catalysed primordial biochemical reactions. Powered by hydrogen and proton gradients, this natural flow reactor filled up with organic chemicals, giving rise to proto-life that eventually broke out as the first living cells - not once but twice, giving rise to the bacteria and the archaea.
10 easy steps to life evolving in alkaline hydrothermal vents:

1. Water percolated down into newly formed rock under the sea floor, where it reacted with minerals such as olivine, producing a warm alkaline fluid rich in hydrogen, sulphides and other chemicals - a process called serpentinisation.

This hot fluid welled up at alkaline hydrothermal vents like those at the Lost City, a vent system discovered near the Mid-Atlantic Ridge in 2000.

2. Unlike today's seas, the early ocean was acidic and rich in dissolved iron. When upwelling hydrothermal fluids reacted with this primordial seawater, they produced carbonate rocks riddled with tiny pores and a "foam" of iron-sulphur bubbles.

3. Inside the iron-sulphur bubbles, hydrogen reacted with carbon dioxide, forming simple organic molecules such as methane, formate and acetate. Some of these reactions were catalysed by the iron-sulphur minerals. Similar iron-sulphur catalysts are still found at the heart of many proteins today.

4. The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that powers living cells.

These molecules drove the formation of amino acids – the building blocks of proteins – and nucleotides, the building blocks for RNA and DNA.

5. Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA – and providing an ideal setting for their evolution into the world of DNA and proteins. Evolution got under way, with sets of molecules capable of producing more of themselves starting to dominate.

6. Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules – the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated within the vents.

7. The evolution of an enzyme called pyrophosphatase, which catalyses the production of pyrophosphate, allowed the protocells to extract more energy from the gradient between the alkaline vent fluid and the acidic ocean. This ancient enzyme is still found in many bacteria and archaea, the first two branches on the tree of life.

8. Some protocells started using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthase, found within all life today.

9. Protocells further from the main vent axis, where the natural electrochemical gradient is weaker, started to generate their own gradient by pumping protons across their membranes, using the energy released when carbon dioxide reacts with hydrogen.

This reaction yields only a small amount of energy, not enough to make ATP. By repeating the reaction and storing the energy in the form of an electrochemical gradient, however, protocells "saved up" enough energy for ATP production.

10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.
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Old 25-October-2009, 08:20 AM
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I'm particularly interested in no.6 on that list:
Quote:
6. Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules – the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated within the vents.
I mentioned this possibility on another thread; life might not need to organise itself into permanent cells in order to persist. Given enough locations wth alkaline vents, non-cellular life could exist as a frothy or slimy layer with self-replicating molecules of several sorts working together.

I don't know how long such a situation could persist, however; living, evolving cells can adapt to a wide variety of environments, but cell-less life would be limited to one environment and would die out as soon as that environment dissapeared.

From this I would expect that life without permanent cells might have arisen and died out many times before the emergence of cells.

If we ever get the chance to explore many extrasolar worlds, we might find a certain number of them support such primitive pre-cellular biologies. By examining any such discoveries we could estimate how persistent and robust such biologies are, and maybe draw some conclusions about the origin of life on Earth.

This might be the only way we can ever investigate the process of abiogenesis directly, as the process (whether it happened as described in the way described in this article or not) will probably not be detectable in the fossil record.

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Old 26-October-2009, 12:43 AM
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Originally Posted by eburacum45 View Post
If we ever get the chance to explore many extrasolar worlds, we might find a certain number of them support such primitive pre-cellular biologies. By examining any such discoveries we could estimate how persistent and robust such biologies are, and maybe draw some conclusions about the origin of life on Earth.

This might be the only way we can ever investigate the process of abiogenesis directly, as the process (whether it happened as described in the way described in this article or not) will probably not be detectable in the fossil record.
It will be a long, long time before we get to the stage of being able to directly explore extrasolar worlds. It would be much quicker to simulate early Earth environments that we think led to abiogenesis here on Earth, but do it super realistically and over months or even years.
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Old 29-October-2009, 02:34 AM
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Laboratory experiments and computer simulations have come a long way from when Profs. Urey and Miller performed their landmark experiments in the early 1950's and with cutting edge "data mining" techniques I dare say that there is currently (?) more work than most researchers can "shake" a stick at... when it comes to pre-biotic chemistry.

As a former mentor said to me: "There are alot of people with plenty ideas... but there are too few that can see it through to fruition."
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Old 29-October-2009, 01:23 PM
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A limitation of lab experiments and computer simulations is that they're limited by our scientific preconceptions about what to try simulating.

We could try simulating "chemical soup" for millenia without realizing that the critical factor is the scaffolding of alkaline hydrothermal vents. If we start with the assumption that it's all about the chemistry, then our experiments will be limited by that assumption.

So it could be that we still need to "go out there and look" rather than just simulate things to learn.
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Old 31-October-2009, 06:47 AM
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Quote:
Originally Posted by DrWho View Post
10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.

I find this one the most intriguing. It gives credence to the notion that there may very well be alien life that is based on DNA.


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Old 01-November-2009, 12:14 PM
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Quote:
Originally Posted by "DrWho"
10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.
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Originally Posted by m74z00219 View Post
I find this one the most intriguing.
I find it interesting, but rather controversial. There may have been two separate 'cellular exodus' events, or just one, which then split up into bacteria and archaea. I don't think there is enough evidence to say one way or another, and there may never be.
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Old 02-November-2009, 12:55 PM
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Originally Posted by m74z00219 View Post
I find this one the most intriguing. It gives credence to the notion that there may very well be alien life that is based on DNA.
Why?

There's nothing in the theory which suggests DNA would be developed by alien life.
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Old 02-November-2009, 01:11 PM
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Quote:
Originally Posted by eburacum45 View Post
I don't know how long such a situation could persist, however; living, evolving cells can adapt to a wide variety of environments, but cell-less life would be limited to one environment and would die out as soon as that environment dissapeared.
I'm not sure about that. If the change was reasonably slow, the chemical system could move to a new stable equilibrium under the new conditions. In fact it could have been changes to the environment that drove the required chemical changes.
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Old 02-November-2009, 01:14 PM
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I find it interesting, but rather controversial. There may have been two separate 'cellular exodus' events, or just one, which then split up into bacteria and archaea. I don't think there is enough evidence to say one way or another, and there may never be.
I haven't read the article again, but I thought the point was that some differences between bacteria and archaea suggested they didn't have a common ancestor. But could be explained if they emerged at different times (or locations). Hardly conclusive though, I agree.
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Old 02-November-2009, 01:36 PM
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Quote:
Originally Posted by Henna Oji-san View Post
I haven't read the article again, but I thought the point was that some differences between bacteria and archaea suggested they didn't have a common ancestor. But could be explained if they emerged at different times (or locations). Hardly conclusive though, I agree.
I don't think there is any evidence for them having different ancestors, and far too many similarities (i.e. all life forms have enough genes in common to suggest anything other than a single ancestor, or a least a small group of ancestors that could exchange genetic material).

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Old 02-November-2009, 01:53 PM
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I haven't read the article again, but I thought the point was that some differences between bacteria and archaea suggested they didn't have a common ancestor.
No. You can read the summary in the first post.

The idea is that they did have a common ancestor, but this common ancestor did NOT have cellular walls. Instead, the common ancestor lived within porous rocks where the numerous small channels within the rock formed the protocell's borders instead of cell walls.
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Old 02-November-2009, 02:23 PM
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Isaac,

I think we agree. My point was just about whether there was any evidence to support the "two separate 'cellular exodus' events". The article points out a number of areas where there are differences that are hard to account for by divergent evolution:
Quote:
the detailed mechanics of DNA replication would have been quite different. It looks as if DNA replication evolved independently in bacteria and archaea
Quote:
many biochemical pathways are catalysed by quite different enzymes. The most surprising and most significant of these is fermentation
Quote:
Even more baffling, says Martin, neither the cell membranes nor the cell walls have any details in common. "At face value, the defining boundaries of cells evolved independently in bacteria and archaea," he says.
And so they suggest that a possible explanation is that these things evolved independently after the the exoduses (exodi?).
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Old 02-November-2009, 05:20 PM
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Sounds fairly convincing now that you have highlighted the relevant parts of this article. There are genes in common, but the cell walls are different. Intriguing.
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Old 02-November-2009, 05:48 PM
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Quote:
Originally Posted by DrWho View Post
Some interesting info in a New Scientist article: Was our oldest ancestor a proton-powered rock?


10 easy steps to life evolving in alkaline hydrothermal vents:

1. Water percolated down into newly formed rock under the sea floor, where it reacted with minerals such as olivine, producing a warm alkaline fluid rich in hydrogen, sulphides and other chemicals - a process called serpentinisation.

This hot fluid welled up at alkaline hydrothermal vents like those at the Lost City, a vent system discovered near the Mid-Atlantic Ridge in 2000.

2. Unlike today's seas, the early ocean was acidic and rich in dissolved iron. When upwelling hydrothermal fluids reacted with this primordial seawater, they produced carbonate rocks riddled with tiny pores and a "foam" of iron-sulphur bubbles.

3. Inside the iron-sulphur bubbles, hydrogen reacted with carbon dioxide, forming simple organic molecules such as methane, formate and acetate. Some of these reactions were catalysed by the iron-sulphur minerals. Similar iron-sulphur catalysts are still found at the heart of many proteins today.

4. The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophospate, which act just like adenosine triphosphate or ATP, the chemical that powers living cells.

These molecules drove the formation of amino acids – the building blocks of proteins – and nucleotides, the building blocks for RNA and DNA.

5. Thermal currents and diffusion within the vent pores concentrated larger molecules like nucleotides, driving the formation of RNA and DNA – and providing an ideal setting for their evolution into the world of DNA and proteins. Evolution got under way, with sets of molecules capable of producing more of themselves starting to dominate.

6. Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules – the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated within the vents.

7. The evolution of an enzyme called pyrophosphatase, which catalyses the production of pyrophosphate, allowed the protocells to extract more energy from the gradient between the alkaline vent fluid and the acidic ocean. This ancient enzyme is still found in many bacteria and archaea, the first two branches on the tree of life.

8. Some protocells started using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthase, found within all life today.

9. Protocells further from the main vent axis, where the natural electrochemical gradient is weaker, started to generate their own gradient by pumping protons across their membranes, using the energy released when carbon dioxide reacts with hydrogen.

This reaction yields only a small amount of energy, not enough to make ATP. By repeating the reaction and storing the energy in the form of an electrochemical gradient, however, protocells "saved up" enough energy for ATP production.

10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.
Chemotrophs are very interesting organisms.
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Old 12-November-2009, 08:31 PM
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