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Author Topic:   The great basic question of science on origin of life
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 1 of 64 (776433)
01-13-2016 12:54 AM


The great basic question of science: Membrane compartment or non-membrane phase compartment (biophase) is a physical basis for origin of life?

Matveev V.V. 2016. Comparison of fundamental physical properties of the model cells (protocells) and the living cells reveals the need in protophysiology. International Journal of Astrobiology, Page 1-8.
Stable URL: http://journals.cambridge.org/abstract_S1473550415000476

Preview PDF with highlights: http://www.bioparadigma.spb.ru/...Preview.and.Highlights.pdf

The Biophase is the Physical Basis of Life
http://www.bioparadigma.spb.ru/...physical.basis.of.life.jpg

Comments and critisim are welcome.

Highlights
1. If life originated in seawater, the origin of the first cell inevitably comes down to the origin of the sodium pump and any structure supporting it – the lipid membrane – without which the work of any pump would make little sense.
2. Since the sodium-potassium pump (Na+/K+-ATPase) was discovered, no molecular model has been proposed for a predecessor of the modern sodium pump. Neither Miller’s electrical charges, nor Fox’s amino-acid condensation, nor building ready-made biomolecules into coacervates; none of this has managed to lead to the self-origination of the progenitor of the ion pump even in favourable lab conditions.
3. In 2007, we saw the simultaneous release of two articles, in which it was posited that life originated not in seawater as previously thought, but in smaller bodies of water with a K+/Na+ ratio necessary to sustain life. In this conditions sodium pump is not needed and the pump can originate later. But why the pump is needed if K+/Na+ ratio is good? The origin of the sodium pump in conditions where there is no natural need for it may require the agency of Providence.
4. Potassium Big Bang on Earth instead of potassium ponds.
5. Fox's microspheres do not need potassium ponds.
6. Despite the fact that Fox's microspheres have no fully functional membrane with sodium pumps and specific ion channels, they generate action potentials similar to that by nerve cells and in addition have ion channels which open and close spontaneously. This ability of the microspheres contradicts to the generally accepted ideas about the mechanism of generation of biological electrical potentials.
7. Hodgkin-Huxley model of action potentials is similarly well-compatible with both the nerve cell and Fox’s microsphere.
8. Biophase as the main subject of protophysiology. In the past they considered the living cell as a non-membrane phase compartment with different physical properties in comparison to the surrounding medium, and this physical difference plays a key role in cell function. According to a new take on an old phase, non-membrane phase compartments play an important role in the functioning of the cell nucleus, nuclear envelope and then of cytoplasm. Somebody sees the compartments even as temporary organelles. According to available data, the phase compartments can play a key role in cell signaling. In this historical context, studies in recent years dedicated to non-membrane phase compartments in the living cells sound sensational.
9. It is essentially a Protocell World which weaves known RNA World, DNA World and Protein World into unity.
10. In the view of non-membrane phase approach, the usage of liposomes and other membrane (non-biophase) cell models to solve the issue of the origin of life is a deadlock way of the investigation.

Edited by Vladimir Matveev, : No reason given.


Replies to this message:
 Message 2 by Admin, posted 01-13-2016 8:06 AM Vladimir Matveev has responded
 Message 5 by RAZD, posted 01-13-2016 1:22 PM Vladimir Matveev has responded
 Message 36 by Genomicus, posted 01-16-2016 1:10 PM Vladimir Matveev has not yet responded

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 3 of 64 (776435)
01-13-2016 9:00 AM
Reply to: Message 2 by Admin
01-13-2016 8:06 AM


Details
Are added details enough?

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 Message 2 by Admin, posted 01-13-2016 8:06 AM Admin has acknowledged this reply

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 6 of 64 (776479)
01-14-2016 8:02 AM
Reply to: Message 5 by RAZD
01-13-2016 1:22 PM


RAZD: "In the above scenario we could have evaporating ponds providing the concentrations, then the cell membranes to protect them, perhaps in a semi-dormant phase, and then the pump."
Matveev: Only one question: why membrane sodium pump is needed in the potassium pond? In the pond K+/Na+ ratio is the same as in the living cell.

This message is a reply to:
 Message 5 by RAZD, posted 01-13-2016 1:22 PM RAZD has responded

Replies to this message:
 Message 7 by Percy, posted 01-14-2016 8:42 AM Vladimir Matveev has responded
 Message 9 by AZPaul3, posted 01-14-2016 9:52 AM Vladimir Matveev has not yet responded
 Message 10 by RAZD, posted 01-14-2016 9:53 AM Vladimir Matveev has responded

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 8 of 64 (776484)
01-14-2016 8:53 AM
Reply to: Message 7 by Percy
01-14-2016 8:42 AM


quote:
See RAZD's Message 5 for an explanation of how to use quote codes

Thanks, Percy.

This message is a reply to:
 Message 7 by Percy, posted 01-14-2016 8:42 AM Percy has acknowledged this reply

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 11 of 64 (776488)
01-14-2016 10:02 AM
Reply to: Message 10 by RAZD
01-14-2016 9:53 AM


quote:
First, evolution does not work with a purpose. Is there some reason such a pump, even a most primitive one, could not develop absent a need? Second, does the ratio remain the same forever?

Sea tide floods potassium pond. And what happens after that?

This message is a reply to:
 Message 10 by RAZD, posted 01-14-2016 9:53 AM RAZD has responded

Replies to this message:
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 12 of 64 (776489)
01-14-2016 10:10 AM
Reply to: Message 11 by Vladimir Matveev
01-14-2016 10:02 AM


quote:
To contain the concentration when the pond is diluted (rains) and perhaps they get flushed out of the pond into a stream etc. So the proto-life is now capable of surviving drought with the membrane and flood with the pump.

We need physical mechanisms rather than general assumptions. Pump, pump, pump... Where is experimental evidence of its spontaneous origin? There is no evidences, no proofs! No pump, no life.

This message is a reply to:
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Replies to this message:
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 17 of 64 (776497)
01-14-2016 11:05 AM
Reply to: Message 15 by RAZD
01-14-2016 10:39 AM


quote:
But obviously there's life, so what does the absence of a sodium pump mean to you?

quote:
For the proto-life without a pump it has a problem maintaining it's optimum inner ecology, and osmosis would not help. Thus an "accident" that provided a pumping action would be beneficial, allowing it to survive and breed in the wider environment.

quote:
Indeed, so now we need to look at what the physical mechanism is and then see if we can hypothesis and test how it could develop.

From my point of view, this means that life has been made possible without the pump. Here are 4 steps of my argument.
(1) Since the sodium-potassium pump (Na+/K+-ATPase) was discovered, no molecular model has been proposed for a predecessor of the modern sodium pump. Neither Miller's electrical charges, nor Fox's amino-acid condensation, nor building ready-made biomolecules into coacervates; none of this has managed to lead to the self-origination of the progenitor of the ion pump even in favourable lab conditions.
(2) It is impossible to explain the properties of well-studied cellular model (Fox's microspheres) on the basis of fudamental ideas of membrane physiology (lipid membrane, ion channels, sodium pump).
(3) According to recent studies, non-membrane phase compartments play an important role in the functioning of the cell nucleus, nuclear envelope and then of cytoplasm. Somebody sees the compartments even as temporary organelles. According to available data, the phase compartments can play a key role in cell signaling.
(4) In the view of non-membrane phase approach, the usage of liposomes and other membrane (non-biophase) cell models to solve the issue of the origin of life is a deadlock way of the investigation.

With regard to the "accident", I can say the following: the conditions for life on Earth arose by chance, but the origin of life under suitable conditions is regularity.

RAZD, you're welcome in St.Petersburg.


This message is a reply to:
 Message 15 by RAZD, posted 01-14-2016 10:39 AM RAZD has responded

Replies to this message:
 Message 18 by Blue Jay, posted 01-14-2016 12:25 PM Vladimir Matveev has responded
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 19 of 64 (776513)
01-14-2016 10:49 PM
Reply to: Message 18 by Blue Jay
01-14-2016 12:25 PM


quote:
Let's see if I understand you correctly here. Basically, the sodium pump is irreducibly complex. There are no known progenitor molecules, and all experiments attempting to spontaneously form sodium pumps or insert them artificially into membranes have failed. This is therefore evidence that sodium pumps cannot have emerged spontaneously in nature. Is this a fair restatement of your claim?

Yes you are right. No experimental evidence of spontaneous emergence of the sodium pump in the literature. The scientific method requires experimental evidence.

quote:
I also don't know what you're saying here. Are you basically saying that protocells couldn't have functioned without both membranes and sodium pumps, so the membrane-and-pump system is irreducibly complex?

This statement relates to the ability of the microspheres to generate an action potential which is indistinguishable from action potential genereted by living nerve cell. The well-known mechanism of action potential of a living cell can not be applied to the microspheres (the microspheres have NO a lipid membrane, specific ion channels and sodium pump).

quote:
Here, you seem to be saying that phase compartments could have played a role in structuring proto-life processes, but do not help explain the origin if the sodium pump, because a sodium pump needs a membrane to be useful.

The phase state of matter has special properties and it does not need in the membrane as a prison needs in a fence. The phase properties are determined by adsorption processes. Selective adsorption-desorption and ion exchange properties create inside physical conditions necessary for life processes. With this understanding fully functional membrane is not necessary. Why should we give up such a mechanism of origin of life?

Edited by Vladimir Matveev, : No reason given.


This message is a reply to:
 Message 18 by Blue Jay, posted 01-14-2016 12:25 PM Blue Jay has responded

Replies to this message:
 Message 27 by Blue Jay, posted 01-15-2016 11:30 AM Vladimir Matveev has responded

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 21 of 64 (776527)
01-15-2016 7:51 AM
Reply to: Message 20 by Pressie
01-15-2016 7:38 AM


quote:
I'm wondering why you put this or these questions (not being a biologist of biochemist or anything like that at all) on evc and not in any scientific journal where he specialists would know what you're talking about? I'm smelling a dead rat.

Your advice, please.

This message is a reply to:
 Message 20 by Pressie, posted 01-15-2016 7:38 AM Pressie has responded

Replies to this message:
 Message 22 by Pressie, posted 01-15-2016 7:58 AM Vladimir Matveev has responded

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 23 of 64 (776529)
01-15-2016 8:00 AM
Reply to: Message 22 by Pressie
01-15-2016 7:58 AM


quote:
The first step is to publish your research in peer-reviewed scientific journals.

Done: http://journals.cambridge.org/abstract_S1473550415000476

Edited by Vladimir Matveev, : No reason given.


This message is a reply to:
 Message 22 by Pressie, posted 01-15-2016 7:58 AM Pressie has responded

Replies to this message:
 Message 24 by Pressie, posted 01-15-2016 8:10 AM Vladimir Matveev has responded
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 25 of 64 (776531)
01-15-2016 8:13 AM
Reply to: Message 24 by Pressie
01-15-2016 8:10 AM


quote:
So, why do you write here amongst the non-specialists? Something still smells like a dead rat.

Any discussion is useful if the problem is complicated.

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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 29 of 64 (776542)
01-15-2016 12:19 PM
Reply to: Message 27 by Blue Jay
01-15-2016 11:30 AM


quote:
My rebuttal is that a lack of evidence doesn't mean it didn't, or couldn't, happen. I think a lot more work needs to be done before we can reasonably draw that conclusion.

I believe that an abiotic synthesis of proteins, and properties of proteins are studied well enough. If the spontaneous formation of the pump would be possible in principle, it has already happened. Otherwise, waiting for the spontaneous formation of the pump turns into the expectation of the second coming of Christ.

quote:
But, if I extrapolate a bit, I think you are essentially arguing that a protocell requires a mechanism for generating an action potential relative to its surroundings. Do you think the protocell could not have survived without this mechanism?

Survival is not key point. Why the microspheres are able to generate an action potential without fully functional membrane, that is the question. Perhaps microspheres show us that our understanding of living cell physics is erroneous. The physics of the living cell is the key point. If we wrongly understand the physics, we never understand the origin of life.

quote:
RAZD proposed that a protocell might simply tolerate changes in turgor and ion gradients, until it evolved a mechanism to regulate ion flux. Do you think this tolerant "spore" state is impossible?

Ion gradients are impossible without pumps. If the pump we replaced by adsorption of ions by proteins the protocell structure is simplified and become understandable. We know nothing about the old pumps, but we know very well that the proteins had the ability to adsorb ions of several billion years ago as well as nowadays.

quote:
Do you think phase compartments eliminate the need for membranes? I don't agree. I imagine that the chemistry of phase compartments would be much more delicate than membrane-bound bodies, and would thus require a lot more complex molecular mechanisms to maintain them. Is my assumption wrong?

With regard to the operation of the pump, we have only this children's animation: https://youtu.be/8XD7FXufB5I?t=44s At the same time we are well aware physical principles of adsorption. I prefer the science of adsorption rather than children's drawings of ion pumps. The ability of proteins to spontaneous synthesis is proved by experiments. But with the pumps we have a problem: we are waiting for their second coming.

I go to sleep.

Edited by Vladimir Matveev, : No reason given.

Edited by Vladimir Matveev, : No reason given.


This message is a reply to:
 Message 27 by Blue Jay, posted 01-15-2016 11:30 AM Blue Jay has responded

Replies to this message:
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 34 of 64 (776569)
01-16-2016 1:31 AM
Reply to: Message 33 by AZPaul3
01-15-2016 7:39 PM


quote:
Consider the other options. The pump doesn't necessarily have to suddenly emerge, fully intact: it may begin as a simple protein that bonds to an ion, or a simple protein that intercalates into a membrane, and gradually gains the other functions of a sodium pump via later innovations. This is why RAZD and I proposed protocells that could survive without a sodium pump: because if they could survive without it, then it could have evolved gradually later, and wouldn't have to appear suddenly, spontaneously, fully intact.

The fundamental requirement: molecular evolution can take place only in the intracellular environment. No these conditions, no evolution. Biological evolution can not proceed in a non-biological conditions. [This also applies to RAZD's and AZPaul3's arguments.] It is an axiom. Fox microspheres can accumulate potassium without the pump and create needed intracellular environment. The microspheres are easy to study in a laboratory. Why nobody examines them? Instead, the literature is full of discussions about the possible evolution of the pump. Elephants have become a mammoth because the climate gets colder. Why do some protein molecule should evolve in the direction of the pump? Does this molecule "know" that pumps will be needed? May be agent of Providence gave it the direction to the pump?

quote:
The microspheres can generate an action potential without a membrane?

Yes, yes, and yes again! It is one of the key point of my paper. Nobody can explain this similarity.

quote:
That's not strictly true. Ion concentrations can change in the environment for various reasons, and those changes inevitably create temporary ion gradients. Imagine a protocell (lacking an ion pump) in a pond where the salinity changes. That protocell would need one of two things:

Evolution is a long process and it needs a long-term ion gradient. Temporary gradient? For a few minutes or a few hours? A diffusion equilibrium is established quickly.

quote:
This just seems like a restatement of the "tornado in a junkyard making an airplane" argument. I think you're being too quick to dismiss the possibilities based on far too little evidence.

Nobody knows what is to be done to create pump spontaneously in a tube. Is the following argument better: let us wait patiently? No one has a plan for the experiment. They were waiting for the Higgs boson 20 years. However, they had a theory that predicts the existence of it. This theory described specifically conditions under which one can observe the boson. Where is the theory describing specifically conditions of the spontaneous emergence of the pump? This theory does not exist! Hence we are not dealing with the science on the pump, we are dealing with a faith in the pump.

quote:
AZPaul3. Since you mentioned Sidney Fox in your OP I assume you to mean microspheres as created by Fox’s method or something similar. Sodium and potassium ions could then be extracted from/expelled to the surrounding medium by certain (unspecified) proteins thus achieving the charge imbalance, or action potential, required for further chemical reactions within the microsphere.
From here, through the usual processes of evolution, the cell wall (lipid bilayer) was evolved complete with ion pumps resulting in, albeit primitive, a functioning living cell.

My main question is: if Fox's microspheres can produce life without a fully functional membrane, then why such membrane is needed for life after it came? I want to say that living cells have inherited the key physical properties of the microspheres (based on sorption properties of proteins) while the membrane has played a supporting role only as border structure.
Thanks guys for the discussion. However, please read my paper for full intellectual contact!

Edited by Vladimir Matveev, : No reason given.

Edited by Vladimir Matveev, : No reason given.

Edited by Vladimir Matveev, : No reason given.


This message is a reply to:
 Message 33 by AZPaul3, posted 01-15-2016 7:39 PM AZPaul3 has responded

Replies to this message:
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Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 38 of 64 (776593)
01-16-2016 10:17 PM
Reply to: Message 37 by RAZD
01-16-2016 3:17 PM


quote:
RAZD: Evolution happens, that is all we need to know.
as soon as biological evolution occurs we have biological conditions.

What are these conditions in its physical nature? I think these conditions are inside non-membrane phase based on adsorption properties of proteins. Most people think that these conditions exist within the membrane compartment. These opposing views presented in my article.

Edited by Vladimir Matveev, : No reason given.

Edited by Vladimir Matveev, : No reason given.


This message is a reply to:
 Message 37 by RAZD, posted 01-16-2016 3:17 PM RAZD has responded

Replies to this message:
 Message 39 by RAZD, posted 01-17-2016 3:38 PM Vladimir Matveev has responded

  
Vladimir Matveev
Junior Member (Idle past 1403 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 40 of 64 (776653)
01-17-2016 11:46 PM
Reply to: Message 39 by RAZD
01-17-2016 3:38 PM


The physical basis of life
Thomas Huxley: Protoplasm is the physical basis of life. (http://aleph0.clarku.edu/huxley/CE1/PhysB.html)
Over the past 150 years, the concept of protoplasm has been perverted and lost. The development of science allows us to take the next step: biophase is the physical basis of life. When we understand the physical basis of life, then we will understand the phenomenon of life.

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