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Author Topic:   The great basic question of science on origin of life
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 5 of 64 (776441)
01-13-2016 1:22 PM
Reply to: Message 1 by Vladimir Matveev
01-13-2016 12:54 AM


Welcome to the fray, Vladimir Matveev,

Interesting article

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.

I have previously thought of the cell membrane as a means to preserve an environment where the replicating molecules survive and thus make them more viable than the molecules alone.

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.

Enjoy

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This message is a reply to:
 Message 1 by Vladimir Matveev, posted 01-13-2016 12:54 AM Vladimir Matveev has responded

Replies to this message:
 Message 6 by Vladimir Matveev, posted 01-14-2016 8:02 AM RAZD has responded

  
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 10 of 64 (776487)
01-14-2016 9:53 AM
Reply to: Message 6 by Vladimir Matveev
01-14-2016 8:02 AM


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.

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.

It is surviving to reproduce, it is evolving. I see "life" beginning when evolution begins - beneficial traits are passed down from generation to generation.

See Definition of Life for discussion and Message 69 and Message 75 for more of my comments.

Enjoy

ps you can use the "peek" function to see how things are coded

Edited by RAZD, : .


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This message is a reply to:
 Message 6 by Vladimir Matveev, posted 01-14-2016 8:02 AM Vladimir Matveev has responded

Replies to this message:
 Message 11 by Vladimir Matveev, posted 01-14-2016 10:02 AM RAZD has responded

  
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 14 of 64 (776492)
01-14-2016 10:33 AM
Reply to: Message 11 by Vladimir Matveev
01-14-2016 10:02 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?

That was AZPaul3 in Message 9. The correct [reply] button is at the bottom of a post rather than at the top.

Indeed, I like to think of it as a series of accidents, some happy some not so happy.

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

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.

Enjoy

Edited by RAZD, : .


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RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 15 of 64 (776493)
01-14-2016 10:39 AM
Reply to: Message 12 by Vladimir Matveev
01-14-2016 10:10 AM


We need physical mechanisms rather than general assumptions. ...

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.

Enjoy

ps -- visited your lovely city in the 70's and rode on one of the hydrofoil boats.


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This message is a reply to:
 Message 12 by Vladimir Matveev, posted 01-14-2016 10:10 AM Vladimir Matveev has responded

Replies to this message:
 Message 17 by Vladimir Matveev, posted 01-14-2016 11:05 AM RAZD has responded

  
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(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


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This message is a reply to:
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RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
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


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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

  
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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


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RebelAmerican☆Zen☯Deist
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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

  
RAZD
Member (Idle past 33 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


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
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RebelAmerican☆Zen☯Deist
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This message is a reply to:
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Replies to this message:
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