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Author Topic:   The great basic question of science on origin of life
AZPaul3
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Posts: 3422
From: Phoenix
Joined: 11-06-2006
Member Rating: 5.0


Message 16 of 64 (776494)
01-14-2016 10:41 AM
Reply to: Message 12 by Vladimir Matveev
01-14-2016 10:10 AM


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

I don't know. Reasonable speculation may be that those cells that had evolved such a pump would survive. Those that hadn't would probably not fare so well.

Where is experimental evidence of its spontaneous origin?

Spontaneous? Is that the only option available? Taking a page from Behe?

There is no evidences, no proofs! No pump, no life.

There is evidence. Such a pump exists. It came about somehow.

We may not know the exact steps taken for its evolution, what precursors may have developed first, but that doesn't mean there were none.

What is your explanation for the sodium pumps existence?


This message is a reply to:
 Message 12 by Vladimir Matveev, posted 01-14-2016 10:10 AM Vladimir Matveev has not yet responded

  
Vladimir Matveev
Junior Member (Idle past 124 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
 Message 32 by RAZD, posted 01-15-2016 6:15 PM Vladimir Matveev has not yet responded

    
Blue Jay
Member (Idle past 47 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


(2)
Message 18 of 64 (776499)
01-14-2016 12:25 PM
Reply to: Message 17 by Vladimir Matveev
01-14-2016 11:05 AM


Hi, Vladimir.

Welcome to EvC!

Vladimir Matveev writes:

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.

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?

Vladimir Matveev writes:

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).

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?

Vladimir Matveev writes:

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.

So, phase compartments are basically bubbles of liquids that are separated from one another, but aren't divided by membranes, kind of like a drop of oil floating in water?

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.

-----

Have I represented you fairly in my restatements? If not, can you please explain where I have misunderstood you?


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 17 by Vladimir Matveev, posted 01-14-2016 11:05 AM Vladimir Matveev has responded

Replies to this message:
 Message 19 by Vladimir Matveev, posted 01-14-2016 10:49 PM Blue Jay has responded

  
Vladimir Matveev
Junior Member (Idle past 124 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

    
Pressie
Member
Posts: 1479
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 1.8


Message 20 of 64 (776526)
01-15-2016 7:38 AM


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.

Edited by Pressie, : No reason given.


Replies to this message:
 Message 21 by Vladimir Matveev, posted 01-15-2016 7:51 AM Pressie has responded

    
Vladimir Matveev
Junior Member (Idle past 124 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

    
Pressie
Member
Posts: 1479
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 1.8


Message 22 of 64 (776528)
01-15-2016 7:58 AM
Reply to: Message 21 by Vladimir Matveev
01-15-2016 7:51 AM


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

Edited by Pressie, : No reason given.


This message is a reply to:
 Message 21 by Vladimir Matveev, posted 01-15-2016 7:51 AM Vladimir Matveev has responded

Replies to this message:
 Message 23 by Vladimir Matveev, posted 01-15-2016 8:00 AM Pressie has responded

    
Vladimir Matveev
Junior Member (Idle past 124 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
 Message 26 by Pressie, posted 01-15-2016 8:19 AM Vladimir Matveev has not yet responded

    
Pressie
Member
Posts: 1479
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 1.8


Message 24 of 64 (776530)
01-15-2016 8:10 AM
Reply to: Message 23 by Vladimir Matveev
01-15-2016 8:00 AM


Vladimir Matveev writes:

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

So, why do you write here amongst the non-specialists? Something still smells like a dead rat.
This message is a reply to:
 Message 23 by Vladimir Matveev, posted 01-15-2016 8:00 AM Vladimir Matveev has responded

Replies to this message:
 Message 25 by Vladimir Matveev, posted 01-15-2016 8:13 AM Pressie has not yet responded
 Message 31 by NoNukes, posted 01-15-2016 4:33 PM Pressie has responded

    
Vladimir Matveev
Junior Member (Idle past 124 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.
This message is a reply to:
 Message 24 by Pressie, posted 01-15-2016 8:10 AM Pressie has not yet responded

    
Pressie
Member
Posts: 1479
From: Pretoria, SA
Joined: 06-18-2010
Member Rating: 1.8


Message 26 of 64 (776532)
01-15-2016 8:19 AM
Reply to: Message 23 by Vladimir Matveev
01-15-2016 8:00 AM


Vladimeer Matveev writes:

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

So, I take it that your paper was deemed as being pretty horrendous amongst your peers and now you are trying to cry on non-peer shoulders?
This message is a reply to:
 Message 23 by Vladimir Matveev, posted 01-15-2016 8:00 AM Vladimir Matveev has not yet responded

Replies to this message:
 Message 28 by Blue Jay, posted 01-15-2016 11:58 AM Pressie has not yet responded

    
Blue Jay
Member (Idle past 47 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 27 of 64 (776540)
01-15-2016 11:30 AM
Reply to: Message 19 by Vladimir Matveev
01-14-2016 10:49 PM


Hi, Vladimir.

Vladimir Matveev writes:

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

Good. At least I got one of your points right.

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.

Vladimir writes:

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).

Okay, apparently I was wrong about what a "microsphere" is. I thought it was just another name for a protocell with a lipid bilayer membrane. I found the Wikipedia page for Sidney W. Fox, which clarifies that his concept of a "protocell" was a spherical arrangement of protein-like molecules.

Thanks for clarifying that for me. I don't understand how Fox's microspheres fit into the Origin-of-Life process, so I will assume that you're right. Let's ignore "proteinoid microspheres" in this discussion.

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?

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?

-----

Vladimir Matveev writes:

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?

Okay, I understand that the boundary between different phase compartments can act somewhat like a membrane.

I don't understand your last question, though. 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?


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 19 by Vladimir Matveev, posted 01-14-2016 10:49 PM Vladimir Matveev has responded

Replies to this message:
 Message 29 by Vladimir Matveev, posted 01-15-2016 12:19 PM Blue Jay has responded

  
Blue Jay
Member (Idle past 47 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 28 of 64 (776541)
01-15-2016 11:58 AM
Reply to: Message 26 by Pressie
01-15-2016 8:19 AM


Hi, Pressie.

Pressie writes:

So, I take it that your paper was deemed as being pretty horrendous amongst your peers and now you are trying to cry on non-peer shoulders?

Actually, no. He linked to a FirstView article, which means it's been peer-reviewed and accepted for publication, and it will appear in an upcoming issue of the journal. It's a small, young journal, but it seems legitimate; and Vladimir himself seems to have a legitimate scientific pedigree.

I haven't read the paper yet (paywall), but based on the abstract, it seems that he is simply arguing that most hypothetical models of "protocells" are too dissimilar from living cells to be plausible. He seems to be doing a lot of cut-n-paste from a "highlights" document he posted on his personal website (here). I wonder if the actual manuscript will include his little reference to "Providence"?

So far in this thread, it seems like he is a supporter of Intelligent Design, which means I ultimately think he's wrong in some way. But, since he's an actual researcher in the field, and he seems to know more about cell physiology than I do, I think it would be worthwhile to try to engage him constructively. I've already learned a couple new things.

Edited by Blue Jay, : No reason given.


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 26 by Pressie, posted 01-15-2016 8:19 AM Pressie has not yet responded

  
Vladimir Matveev
Junior Member (Idle past 124 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:
 Message 30 by Blue Jay, posted 01-15-2016 1:19 PM Vladimir Matveev has not yet responded
 Message 33 by AZPaul3, posted 01-15-2016 7:39 PM Vladimir Matveev has responded

    
Blue Jay
Member (Idle past 47 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 30 of 64 (776546)
01-15-2016 1:19 PM
Reply to: Message 29 by Vladimir Matveev
01-15-2016 12:19 PM


Hi, Vladimir.

Vladimir writes:

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.

This is a very bold claim, Vladimir. There is just too much we don't know.

Consider the scale. How many experiments have attempted to spontaneously produce proteins under hypothetical prebiotic conditions? Hundreds, maybe? Well, how many "experiments" might have been conducted by Mother Nature on the prebiotic Earth before She succeeded in producing a viable protein? Possibly trillions. It's like rolling the dice 10 times and concluding that '3' is impossible because we haven't seen one yet.

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.

These are very real possibilities that you are just dismissing because we believe "proteins are understood well enough." That seems very narrow-minded to me.

Vladimir Matveev writes:

Why the microspheres are able to generate an action potential without fully functional membrane, that is the question.

The microspheres can generate an action potential without a membrane?

Vladimir Matveev writes:

Blue Jay writes:

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

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:

  1. A mechanism to preserve its internal chemistry against changes in the salinity of the outside environment
  2. An ability to simply tolerate the change in its internal chemistry as the environment changes.

Is there any evidence that a protocell without an ion pump would perish?

If not, it seems that there is still a perfectly valid and reasonable hypothesis for the evolution of ion pumps in protocells that originally lacked them.

Vladimir Matveev writes:

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.

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.

Vladimir Matveev writes:

I go to sleep.

Have a good night! It's lunchtime for me!


-Blue Jay, Ph.D.*

*Yeah, it's real

Darwin loves you.


This message is a reply to:
 Message 29 by Vladimir Matveev, posted 01-15-2016 12:19 PM Vladimir Matveev has not yet responded

  
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