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Author Topic:   The great basic question of science on origin of life
NoNukes
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Message 31 of 64 (776551)
01-15-2016 4:33 PM
Reply to: Message 24 by Pressie
01-15-2016 8:10 AM


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

I am a bit confused by your objection. Don't we want serious discussion here? I for one want to understand Vlad's claims and examine them for what they reveal. Even if they simply point to gaps in our knowledge, that discussion is useful.

No irreducibly complex argument that I've seen so far long survives serious examination, but at a minimum such arguments are entertaining, and in some cases we learn some biology along the way.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

History will have to record that the greatest tragedy of this period of social transition was not the strident clamor of the bad people, but the appalling silence of the good people. Martin Luther King

If there are no stupid questions, then what kind of questions do stupid people ask? Do they get smart just in time to ask questions? Scott Adams


This message is a reply to:
 Message 24 by Pressie, posted 01-15-2016 8:10 AM Pressie has responded

Replies to this message:
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RAZD
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(2)
Message 32 of 64 (776556)
01-15-2016 6:15 PM
Reply to: Message 17 by Vladimir Matveev
01-14-2016 11:05 AM


RAZD, you're welcome in St.Petersburg.

Well I was there on a tour so I'm sure we saw the best side of it. I did get a chance to get out and walk around for a bit, and see the parks and canals, as well as the tour high spots.

From my point of view, this means that life has been made possible without the pump. Here are 4 steps of my argument.

Well I do think that the modern cell is the product of billions of years of evolution, so it is a bit difficult to extrapolate back to the first working models. But we can attempt that by breaking it down into steps along the way.

(1) self-replicating molecules arise, many varieties, and they interact and compete for materials, so there is selection of those best able to consistently reproduce their basic pattern.

(2) a semi-permeable lipid membrane is developed - see Szostak Proto-Cell.

(3) the semi-permeable membrane allows ions and other atoms or molecules to migrate and balance the inside with the outside environment via openings like ion channels, or what develops into ion channels.

(4) the proto-cell develops the ability to close the ion channel\openings when the outside environment is not compatible with the inside "work environment" and go into a dormant stage or low energy state until the outside environment becomes compatible again.

(5) an ion channel evolves into a ion pump -- see Ion channels versus ion pumps: the principal difference, in principle

quote:
Nat Rev Mol Cell Biol. Author manuscript; available in PMC 2010 May 1.
Published in final edited form as:
Nat Rev Mol Cell Biol. 2009 May; 10(5): 344–352.
Published online 2009 Apr 2. doi: 10.1038/nrm2668

Abstract

Two kinds of border guards control the incessant traffic of ions across cell membranes: ion channels and ion pumps. When open, channels let selected ions diffuse rapidly down electrical and concentration gradients, whereas ion pumps labour tirelessly to maintain the gradients, by consuming energy to slowly move ions against them. Because of their diametrically opposed tasks and their divergent speeds, channels and pumps have traditionally been viewed as completely different entities, as alike as chalk and cheese. But new structural and mechanistic information about both classes of these molecular machines challenges this comfortable separation, forcing its reevaluation.

The very different behaviours of ion channels and ion pumps – passive, thermodynamically downhill, and high speed ion movement through channels, versus active, thermodynamically uphill transport, frequent incorporation of enzyme-like reaction mechanisms, and low speed of ion movement through pumps – led to a separation of the efforts to understand them. And only recently have atomic-resolution X-ray crystal structures and high-resolution functional measurements of examples from both classes begun to suggest that ion channels and ion pumps are not as different as once thought and, in fact, have much in common. So now seems an appropriate time to reconsider their similarities and differences ...

One gate versus two gates

The principal difference, in principle, between channels and pumps is that a channel needs no more than a single gate whereas a pump needs at least two gates that should never be open at once. So what is a gate? A gate can be considered to be the part of the protein that precludes ion movement along the translocation pathway in the prohibitive conformation but not in the permissive conformation. ...

(image with text)


Full paper available on-line free. There are also references to similar papers and papers that cite this paper.

Seems like the similarities point to the pump evolving from the channel by the addition of a second gate.

Enjoy.

Edited by RAZD, : added at end


we are limited in our ability to understand
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This message is a reply to:
 Message 17 by Vladimir Matveev, posted 01-14-2016 11:05 AM Vladimir Matveev has not yet responded

  
AZPaul3
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Posts: 3427
From: Phoenix
Joined: 11-06-2006
Member Rating: 7.4


Message 33 of 64 (776561)
01-15-2016 7:39 PM
Reply to: Message 29 by Vladimir Matveev
01-15-2016 12:19 PM


I’ll summarize my understanding (or misunderstanding) of what you are proposing here. Please correct me if I err.

In the beginning the precursors to living cells may have been microspheres of RNAs, DNAs and proteins without any covering, shell or pseudo-cell wall. 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.

I read your contention is that in the discipline of abiogenic research this microsphere possibility is not being given due appreciation and study over the more popular spontaneously self-organizing lipid sphere as the vessel of the first precursor cells since, in the lipid sphere, there appears to be no mechanism to shunt ions through a primitive lipid membrane to maintain the charge imbalance, action potential, as necessary.

Let me press you further in that you are NOT saying that the cell, the lipid bilayer cell wall or the sodium-potassium adenosine triphosphatase enzyme were created ex nihilo but were the products of natural evolution stemming from developments within the microspheres.

Is my understanding correct?


This message is a reply to:
 Message 29 by Vladimir Matveev, posted 01-15-2016 12:19 PM Vladimir Matveev has responded

Replies to this message:
 Message 34 by Vladimir Matveev, posted 01-16-2016 1:31 AM AZPaul3 has responded

  
Vladimir Matveev
Junior Member (Idle past 187 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:
 Message 35 by AZPaul3, posted 01-16-2016 6:48 AM Vladimir Matveev has not yet responded
 Message 37 by RAZD, posted 01-16-2016 3:17 PM Vladimir Matveev has responded

    
AZPaul3
Member
Posts: 3427
From: Phoenix
Joined: 11-06-2006
Member Rating: 7.4


Message 35 of 64 (776572)
01-16-2016 6:48 AM
Reply to: Message 34 by Vladimir Matveev
01-16-2016 1:31 AM


Thanks guys for the discussion. However, please read my paper for full intellectual contact!

Your paper is behind a pay wall. I will not buy your paper for this discussion. If there is an open access copy of your paper available I may read that and try to understand your view. Absent that, Vladimir, you will have to present your ideas to us here as best you can if you wish us to discuss them in any intelligent way.

Except at a very cursory level I am not skilled in this area and probably shouldn't try to discuss this at the level you seem to need. You have peaked my interest, however, and I will follow the discussion as it unfolds.

I am pleased to meet you, Vladimir. Welcome to EvC.


This message is a reply to:
 Message 34 by Vladimir Matveev, posted 01-16-2016 1:31 AM Vladimir Matveev has not yet responded

  
Genomicus
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Posts: 815
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(1)
Message 36 of 64 (776587)
01-16-2016 1:10 PM
Reply to: Message 1 by Vladimir Matveev
01-13-2016 12:54 AM


Hey Vladimir,

Hmm. I'm trying to understand your argument. Is there any way you could send me the PDF of your paper? Most journals AFAIK do not prohibit this; they only prohibit dissemination of your paper to the broader public. Let me know.

Having said that, I've briefly outlined my understanding of your thesis:

1. Proto-life forms cannot easily survive in an environment rich in Na+. This puts the origin of life in K+ ponds ("potassium big bang").

2. But if life originated in potassium-rich ponds, why is an ATPase needed? This raises the possibility that the origin of the ur-ATPase required the intervention of agency.

3. To understand the origin of life, we must understand non-membrane phase compartments.

I'm still a little confused. Maybe you can expand further on how your points are linked together in a logical sequence. Thanks.


This message is a reply to:
 Message 1 by Vladimir Matveev, posted 01-13-2016 12:54 AM Vladimir Matveev has not yet responded

  
RAZD
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Posts: 18471
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


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Message 37 of 64 (776590)
01-16-2016 3:17 PM
Reply to: Message 34 by Vladimir Matveev
01-16-2016 1:31 AM


The fundamental requirement: molecular evolution can take place only in the intracellular environment. No these conditions, no evolution.

Evolution happens, that is all we need to know.

Biological evolution can not proceed in a non-biological conditions. [This also applies to RAZD's and AZPaul3's arguments.] It is an axiom.

No, it is a tautology begging the question -- as soon as biological evolution occurs we have biological conditions.

Enjoy.

Edited by RAZD, : sp


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 34 by Vladimir Matveev, posted 01-16-2016 1:31 AM Vladimir Matveev has responded

Replies to this message:
 Message 38 by Vladimir Matveev, posted 01-16-2016 10:17 PM RAZD has responded

  
Vladimir Matveev
Junior Member (Idle past 187 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

    
RAZD
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Posts: 18471
From: the other end of the sidewalk
Joined: 03-14-2004
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Message 39 of 64 (776630)
01-17-2016 3:38 PM
Reply to: Message 38 by Vladimir Matveev
01-16-2016 10:17 PM


Message 34, Vladimir Matveev: Biological evolution can not proceed in a non-biological conditions.

Message 37' RAZD: as soon as biological evolution occurs we have biological conditions.

What are these conditions in its physical nature? ...

Part of the issue here is when does 'life' begin (and built into that is the question of what is 'life').

To my mind 'life' begins when (biological) evolution begins, but that is still pretty muddy (how many processes of evolution are involved).

But I don't thinks there are significantly differences between just prior to and just post this OOL (origin of life) event. And since that point 'life' has become more and more complex.

There was a discussion about this definition issue on Definition of Life.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
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This message is a reply to:
 Message 38 by Vladimir Matveev, posted 01-16-2016 10:17 PM Vladimir Matveev has responded

Replies to this message:
 Message 40 by Vladimir Matveev, posted 01-17-2016 11:46 PM RAZD has not yet responded

  
Vladimir Matveev
Junior Member (Idle past 187 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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Pressie
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Posts: 1605
From: Pretoria, SA
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Message 41 of 64 (776719)
01-19-2016 6:37 AM
Reply to: Message 31 by NoNukes
01-15-2016 4:33 PM


NoNukes writes:

I am a bit confused by your objection. Don't we want serious discussion here? I for one want to understand Vlad's claims and examine them for what they reveal. Even if they simply point to gaps in our knowledge, that discussion is useful.

Actually, what would be more useful to me, personally, would be objections to his article from the specialists on the subject. I can learn from the specific objections given by them.

To me it seems as if Vlad is trying to bypass all those thousands of specialists on the subject and then wants to shout "victory".


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 Message 31 by NoNukes, posted 01-15-2016 4:33 PM NoNukes has acknowledged this reply

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RAZD
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Posts: 18471
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 3.9


Message 42 of 64 (776748)
01-19-2016 1:50 PM
Reply to: Message 41 by Pressie
01-19-2016 6:37 AM


To me it seems as if Vlad is trying to bypass all those thousands of specialists on the subject and then wants to shout "victory".

Well, I get the impression that he is concerned about something that he feels is being ignored by the specialists, and that he is looking for answers more than saying he has them.

Enjoy


we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


• • • Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click) • • •

This message is a reply to:
 Message 41 by Pressie, posted 01-19-2016 6:37 AM Pressie has not yet responded

Replies to this message:
 Message 43 by Vladimir Matveev, posted 01-20-2016 12:24 AM RAZD has not yet responded

  
Vladimir Matveev
Junior Member (Idle past 187 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


Message 43 of 64 (776773)
01-20-2016 12:24 AM
Reply to: Message 42 by RAZD
01-19-2016 1:50 PM


Silence
quote:
I get the impression that he is concerned about something that he feels is being ignored by the specialists, and that he is looking for answers more than saying he has them.

All the experts are trying to solve the problem of the origin of life only through protocells as the membrane compartments. For this they need in self-generation of sodium pump. Nobody watched such self-generation. Nobody knows what is to be done for that. Prior to the publication, I asked for 60-70 specialists in the West: in which point I'm wrong? All (all!) of them chose to remain silent.

Edited by Vladimir Matveev, : No reason given.


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 Message 42 by RAZD, posted 01-19-2016 1:50 PM RAZD has not yet responded

Replies to this message:
 Message 44 by Percy, posted 01-20-2016 7:50 AM Vladimir Matveev has responded
 Message 46 by Pressie, posted 01-20-2016 8:30 AM Vladimir Matveev has responded

    
Percy
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Posts: 15625
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


(1)
Message 44 of 64 (776787)
01-20-2016 7:50 AM
Reply to: Message 43 by Vladimir Matveev
01-20-2016 12:24 AM


Re: Silence
Vladimir Matveev writes:

Prior to the publication, I asked for 60-70 specialists in the West: in which point I'm wrong? All (all!) of them chose to remain silent.

Pick yourself up, dust yourself off, and get back to work researching and developing more effectively persuasive evidence and arguments. Wegener didn't begin letter writing campaigns with laypeople after rejection of his continental drift ideas, he just kept working. He died during a data gathering expedition in Greenland. Don't let the bitterness of rejection cause you to waste your time on Internet discussion boards. Stiff upper lip, old boy, and all that. Keep on pluggin'.

--Percy


This message is a reply to:
 Message 43 by Vladimir Matveev, posted 01-20-2016 12:24 AM Vladimir Matveev has responded

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 Message 45 by Vladimir Matveev, posted 01-20-2016 7:55 AM Percy has acknowledged this reply

    
Vladimir Matveev
Junior Member (Idle past 187 days)
Posts: 25
From: St.Petersburg, Russia
Joined: 11-08-2015


(1)
Message 45 of 64 (776788)
01-20-2016 7:55 AM
Reply to: Message 44 by Percy
01-20-2016 7:50 AM


Re: Silence
quote:
Pick yourself up, dust yourself off, and get back to work researching and developing more effectively persuasive evidence and arguments.

Of course, I continue to work. Thank you!
This message is a reply to:
 Message 44 by Percy, posted 01-20-2016 7:50 AM Percy has acknowledged this reply

    
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