The great basic question of science on origin of life

[Vladimir Matveev]

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/files/Matveev-2016-Protophysiology.Preview.and.Highlights.pdf

The Biophase is the Physical Basis of Life
http://www.bioparadigma.spb.ru/files/Matveev-2016-Biophase.is.physical.basis.of.life.jpg

Comments and critisim are welcome.

HIGHLIGHTS OF THE PAPER (short list):
(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.

 

[Buzz Bloom]

Membrane compartment or non-membrane phase compartment (biophase) is a physical basis for origin of life?

Hi Vladimir:

I took a brief look at

http://www.bioparadigma.spb.ru/files/Matveev-2016-Protophysiology.Preview.and.Highlights.pdf ,​

and I was surprised that no mention was made of the Christian de Duve book

Vital Dust: Life as a Cosmic Imperative (1996) ISBN 0-465-09045-1 .​

The article discussed Sidney Fox's work at length, but ignored the later Vital Dust, which seems to me to be the most detailed plausible construction of a sequence of necessary pre-biological steps leading to life I have ever read. I am not saying that Matveev's ideas are not an improvement on de Duve, but he fails to explain how that might be so.

Regards,
Buzz

 

[Vladimir Matveev]

Hi Buzz,
Thanks you drew my attention to the work of de Duvall. I did not know about them.
I watched his articles:
De Duve, C. (1995). The beginnings of life on earth. American Scientist, 428-437.
De Duve, C. (1996). The birth of complex cells. Scientific American, 274(4), 50-57. http://sun.menloschool.org/~dspence/biology/pdfs/cell_evol.pdf
It is obvious that de Duve is a supporter of the membrane approach to the origin of life. In contrast, I believe that the phase approach (non-membrane phase compartments) undeservedly forgotten. I tried to show in my article illogic membrane approach in the context of the Hodgkin-Huxley model. de Duve took into consideration membrane priori and does not consider the physics of membrane processes.
Best wishes,
Vladimir

 

[Buzz Bloom]

Hi Vladimir:

I think you might find the discussion in the following thread of some interest.

https://www.physicsforums.com/threads/novel-idea-on-the-origin-of-life.851106​

I would particularly appreciate your thoughts about my posts there #45, #54, #56, and #58.

Regards,
Buzz

 

[Torbjorn_L]

The paper is paywalled. Why? Now I am forced to do a summary judgment from little detail!

Quite frankly it doesn't seem interesting in competition with my huge to-read-pile from the highlight. Hints of Koonin's misunderstanding of anthropic selection ("Big Bang"), hints of religion/Monod's chance/necessity misunderstanding of dynamic systems ("providence"), a claim that despite molecular phylogenies there is no "molecular model", claiming that cells with lipid membranes would make little sense (?).

And quite frankly I have no interest to waste time in all encompassing theories that try to explain everything and so explain nothing. (Too weak constraints - "too many assumptions", too few predictions - "too little detail". We call them "air castles" - castles magically flying in the air - locally.)

Here is my take as interested in astrobiology:

- Keller et al gluconeogenesis/glycolysis and PP nonenzymatic pathways under Hadean conditions provides a clear pathway to a pyrophosphate/ATP metabolism without a Na+/K+ -ATPase.

After it was shown that the substrate pyruvate would be produced by alkaline hydrothermal vents (that first produced the catalyst greigite), and now just the other week by Keller et al again that pH/FeII control naturally partitions the vent into a core of PPP (which can go on to produce RNA) and an outer glucose buffer (which can go on to couple to PPi/ATP), there is no reason to believe that first inorganic, later lipid cells would not evolve.

That would answer the lipid membrane and early ATP production.

- Sojo et al showed that the only environment where chemiosmosis, including a Na+/K+ -ATPase, could evolve was at the surface of an alkaline hydrothermal vent. [ http://www.nick-lane.net/Sojo%20et%20al%20PLOS%20Biology.pdf ] I don't think that has changed, but I (and I guess Sojo et al) would gladly be proven wrong.

That would answer the "molecular model" and the uncoupling from the vent towards free living cells that could evolve remaining autotroph pathways.

To be clear, there are outstanding questions and little agreement on details. However, that is the beauty with divide and conquer, not everything must be answered at once!

 

[Vladimir Matveev]

Thank you, Torbjorn_L, for your reply. My main point is that life and evolution are possible only in the (proto)cell. There were millions of different chemical reactions on early Earth. Our planet at that time can be called a global chemical plant, but it can not be called life. We can not consider chemical evolution on a sea beach as the biological evolution. For biological evolution we need a (proto)cell.

If so, then we have to decide what was the physical nature of the first cell, the membrane compartment or nonmembrane compartment. The first is a commonly accepted idea, but this view has no decisive experimental proof: no one has demonstrated that the sodium pump is able to spontaneous appearance in the primitive conditions of the early Earth. Why membrane model accepted without the key evidence? No the pump, no life! Non-membrane phase approach has all evidences for its reality.

According to the rule, you can get the full text of my article by personal request.

 

[Vladimir Matveev]

Buzz Bloom wrote:
https://www.physicsforums.com/threads/novel-idea-on-the-origin-of-life.851106?
I would particularly appreciate your thoughts about my posts there #45, #54, #56, and #58.

#45. You declares too general physical principles. Our knowledge of biological structures and physical properties of living cells require more specific physics solutions. Currently, it is proved the ability of proteins and synthetic hydrophilic polymers absorb much water (multilayer adsorption). Water molecules are the largest component of every biological system. Adsorption of large amounts of water leads to a decrease in entropy of the system. I would like physicists to decide the following issue: why water adsorption reduces the entropy without energy costs as required by the theory of Prigogine?

#54. I think that to talk about the evolution of RNA at out-cells conditions is the wrong and anacceptable way. Every biological evolution can take place only in the physical condition we find inside of living (proto)cell.

#56. It is obvious that you adhere to the membrane paradigm. While this paradigm resembles the castle in the air, it is possible any suggestion.

#58. The only obvious Moon's role is stabilization of Earth's axis of rotation, which gave a stable physical conditions on our planet during several billion years.

Unfortunately, many authores of theories of the life origin reminiscent of witnesses in court who tell how God before their eyes has beeing created the world and life. I am pleased that you share this feeling as a whole.

Thank you, Buzz Bloom, for your questions.

All the best,
Vladimir

 

[Drakkith]

My main point is that life and evolution are possible only in the (proto)cell. There were millions of different chemical reactions on early Earth. Our planet at that time can be called a global chemical plant, but it can not be called life. We can not consider chemical evolution on a sea beach as the biological evolution. For biological evolution we need a (proto)cell.

This seems to be a matter of categories and names more than anything else. One could simply extend biological evolution backwards past the first cells to their precursor chemicals, reactions, etc, right?

 

[Vladimir Matveev]

This seems to be a matter of categories and names more than anything else. One could simply extend biological evolution backwards past the first cells to their precursor chemicals, reactions, etc, right?

Replication on a rock? Mitosis on a sand?

It is proved that the life processes proceed in the cell only. One of the physical conditions of life: [K+]>[Na+]. It is possible to extend something but what it gives us? We can expand a fire in a steam locomotive into a forest near the road. Such kind of extending is useless.

We have no evidence that biological evolution is possible outside the cell. For this reason, this form of evolution is called chemical evolution.

Thanks for your participation.

All the best,
Vladimir

 

[Buzz Bloom]

Every biological evolution can take place only in the physical condition we find inside of living (proto)cell.

Hi Vladimir:

I much appreciate your responding to my posts in the other thread.

Do you know of any detailed description of a plausible process that leads to the first cell that does not involve what Cristian de Duve calls "the RNA world"?

Whether or not you agree that such a pre-cell process involves an RNA world, I am interpreting the above quote to voicing your preference to characterize such a process as "chemical evolution" rather than just "evolution". Is this correct?

#56. It is obvious that you adhere to the membrane paradigm. While this paradigm resembles the castle in the air, it is possible any suggestion.

I tend to "adhere" to a tidal basin paradigm. I suggested (#58) a role for a membrane as one plausible way to prevent destructive flooding in the RNA basin scenario.

#45. You declares too general physical principles.

Post #45 was intended to "paraphrase" England's text in a form I could understand, rather than putting forth my own thoughts.

BTW, I do not understand how the attached file got into this post, or how I might get rid of it.

Regards,
Buzz

 

[mfb]

You can define categories, no problem, but then you cannot use those categories to make claims about what happened. "Everything without a cell is not called life, therefore without cells nothing relevant for life could have happened" is not a valid argument.

#54. I think that to talk about the evolution of RNA at out-cells conditions is the wrong and anacceptable way. Every biological evolution can take place only in the physical condition we find inside of living (proto)cell.

So what about a non-biological evolution?

#58. The only obvious Moon's role is stabilization of Earth's axis of rotation, which gave a stable physical conditions on our planet during several billion years.

What about non-obvious roles? How life formed in general is certainly not obvious.

For this reason, this form of evolution is called chemical evolution.

Fine. So what did we gain, apart from introducing arbitrary category names?

Replication on a rock? Mitosis on a sand?

Bacteria building rockets? "Object X cannot do Y, therefore no object of the same category cannot do it" is a logical fallacy.

 

[Vladimir Matveev]

Hi Buzz:

According to my approach I discribed in my paper on protophysiology, first protocell was non-membrane phase---biophase. For such kind of protocell is quite enough to get polypeptide (self-synthesis of amino acids and polipeptides are prooved). Biophase are based on well known physical phenomenon---adsorption. I think protocell as biophase is compartment which able to give place to RNA- and DNA Worlds (or both). Protein adsorption ability must include adsorption of nucleotides and their further transformation and evolution. This ability of biophase is not studied but should be studied. Biophase with its specific physical environment is the best place to start life processes. What we know about adsorption properties of polypeptides in the context of origin of life? Nothing!Vladimir

 

[Vladimir Matveev]

Hi mfb:

I'm just saying that the existence of a "living pond", "living lake" or "living solution" in some flask in Texas University (for example) are not proven. One proves only that the carrier of life is the living cell. For this reason, it is logical to think that life is only possible in a cell, and originated in protocell. We do not have sufficient grounds to look for other forms of life.

They call non-biological evolution as chemical evolution or prebiotical one. No problem. Last terms are generally accepted. Users can add new categories. Bad category die eventually.

I agree with you, Moon may play multiple role for life on Earth.
http://link.springer.com/chapter/10.1007/978-94-010-0800-6_6

Our logic is dependent on our ideas. That is logical for a Muslim is not logical for the Christian.

Thanks for the discussion. Vladimir

 

[Drakkith]

They call non-biological evolution as chemical evolution or prebiotical one. No problem. Last terms are generally accepted.

Okay, that makes sense given a relatively accepted definition of "life". I thought you were somehow saying that life didn't arise from non-living chemicals.

 

[Vladimir Matveev]

Thanks, Drakkith. The illustartion for my paper is attached.

Vladimir

 

[mfb]

One proves only that the carrier of life is the living cell. For this reason, it is logical to think that life is only possible in a cell, and originated in protocell.

I don't see the logic. "We did not observe it yet, so we should expect that it is impossible"? With that approach, you cannot make any scientific progress at all.

 

[Vladimir Matveev]

I don't see the logic. "We did not observe it yet, so we should expect that it is impossible"? With that approach, you cannot make any scientific progress at all.

The Higgs' boson has been a hypothesis for over 20 years. The existence of the boson has only recently been proven. Higgs was based on the theory for boson prediction. On what theory is based the assumption that life is possible outside the cell? For unlimited speculation exists sci-fi literature. Fantasy is a good thing, but in science it should be based on the scientific method. Your proposal is very interesting if there is evidence for it anywhere.

Vladimir

 

[mfb]

It is not my proposal, but you cannot rule it out just because we didn't see it yet, that is my point.

 

[Fervent Freyja]

Neither. This is a strange(but highly creative) schema. What use is this information that you are trying to communicate? It is ambiguous enough that some people would find this obvious and therefore redundant- others have concepts as well. It doesn't make any sense for you to claim to be investigating this with Physics(where?) but yet deny the value of the Standard Model. I can appreciate your boldness to try and work between disciplines for sure though.

 

[Vladimir Matveev]

It doesn't make any sense for you to claim to be investigating this with Physics(where?) but yet deny the value of the Standard Model. I can appreciate your boldness to try and work between disciplines for sure though.

According to Standard Model (SM), life must begin from origin of membrane which works in accordant with SM principles. We have no any experimental support for self-origination of such membrane. In contrast, Fox's microspheres (biophase) easy demostrate ability to accumulate K+ without membrane and Na,K-pump. In this situation I have no boldness to spend my life with wrong SM. My goal is quite modest: To draw people's attention to biophase as alternative model. Why not?

 

[Buzz Bloom]

To draw people's attention to biophase as alternative model.

Hi @Vladimir Matveev:

I have scanned the articles cited in post #1, and I confess I don't understand the nature of the biophase model as a model for the origin of life except that it has something to do with a sodium-potassium pump. Does the biophase model include a discussion of the role of RNA, e.g., whether RNA preceded proteins, or whether RNA preceded a chemical boundary which separated RNA reproduction from a soup of organic molecules?

Regards,
Buzz

 

[Vladimir Matveev]

I have scanned the articles cited in post #1, and I confess I don't understand the nature of the biophase model as a model for the origin of life except that it has something to do with a sodium-potassium pump.

Hi Buzz:
Biophase is spontaneously formed due to protein adsorption properties. Physical conditions emerging inside biophase are necessary for life process. One of these conditions is [K+]>[Na+]. The literature does not know any spontaneous membrane model which is capable to do the same. Do you understand the role of RNA in the dead membrane compartment investigated for decades?

On the other hand, adsorption properties of proteins have not been investigated. It is possible that adsorption of nucleotides by proteins creates conditions for synthesis of polynucleotides. No one tried to investigate this. Vladimir

 

[Vladimir Matveev]

Vladimir Matveev. The great basic question of science: Membrane compartment or non-membrane phase compartment is a physical basis for origin of life?
Oral presentation at The 2nd All-Russian Conference on Astrobiology. Moscow, Pushchino, 5-9 June 2016.
Video in English:

Presentation slides in English as pdf:
http://www.bioparadigma.spb.ru/conf/Matveev-2016-The.great.basic.question.of.science_Eng_Slides.pdf

Comments for slides in English:
http://www.bioparadigma.spb.ru/conf...at.basic.question.of.science_Comments_Eng.pdf

 

[Fervent Freyja]

Vladimir Matveev. The great basic question of science: Membrane compartment or non-membrane phase compartment is a physical basis for origin of life?

How can you be comfortable with publishing something claiming that life began on the account of spontaneous mechanisms? I would at least try to work away from using the term...

Are you using an equivalent definition in your russian publications? It's a very dirty english word (reminiscent of spontaneous generation theory). Unknown or undiscovered mechanisms would work better. It could make people cry!

 

[Vladimir Matveev]

How can you be comfortable with publishing something claiming that life began on the account of spontaneous mechanisms?

Dear Fervent, "spontaneous mechanisms" is just the opposite of the idea of creationism.
"Spontaneous mechanisms" means "according to the laws of nature". Сan you offer other correct term?
Thanks for your reply.

 

[Buzz Bloom]

Biophase is spontaneously formed due to protein adsorption properties.

Hi Vladimir:

If I understand this correctly, you are saying that the biophase requires the pre-existance of proteins. Is this correct?

If so, are you also saying that the biophase preceded the (1) existence of RNA, (2) ribosomes, and (3) the mechanism that manufactures a protein based on the genetic code applied to a partiular RNA sequence?

Regards,
Buzz

 

[Buzz Bloom]

Do you understand the role of RNA in the dead membrane compartment investigated for decades?

Hi Vladimir:

I do not understand what this "role of RNA" refers to. Can you cite a paper that explains this? I also do not know what "the dead membrane compartment" is?

Regards,
Buzz

 

[Vladimir Matveev]

If I understand this correctly, you are saying that the biophase requires the pre-existance of proteins. Is this correct?
If so, are you also saying that the biophase preceded the (1) existence of RNA, (2) ribosomes, and (3) the mechanism that manufactures a protein based on the genetic code applied to a partiular RNA sequence?

Yes, Buzz. My idea: the biophase creates the physical conditions necessary for the origin of life. In other words, life (with RNA, ribosomes, etc) can only originates in cell-like conditions. Evolution is possible in the cell-like conditions too. No protocell, no life.

Literature on the "RNA World" or "DNA World" is large, but I can not accept them as a realistic model. It is needed firstly certain physical conditions for origin of life. They are available in the protocell only. Please see my paper for details:

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.
DOI: http://dx.doi.org/10.1017/S1473550415000476
Stable URL: http://journals.cambridge.org/abstract_S1473550415000476
Preview PDF with highlights: http://www.bioparadigma.spb.ru/files/Matveev-2016-Protophysiology.Preview.and.Highlights.pdf

 

[Buzz Bloom]

My idea: the biophase creates the physical conditions necessary for the origin of life. In other words, life (with RNA, ribosomes, etc) can only originates in cell-like conditions.

I understand that there are many proposed plausible scenarios regarding the sequence of events leading to the first living cells, and there is at the present time no evidence strong enough to gather a consensus about which scenario is the "right" one (if any). My understanding (admittedly limited) of the strong proposition that RNA preceded proteins is that there has been no plausible scenario proposed for how useful proteins came into existence without the aid of the genetic code, and without mutations of RNA variations that produced more useful proteins (in a non-cell environment) which would out reproduce RNA sequences that produced less useful proteins.

Would you please comment on this? Do you have a proposed mechanism about how useful proteins first came to exist?

Regards,
Buzz

 

[Vladimir Matveev]

Hi Buzz.
It is proved that first polypeptides can be formed from amino acids in the prebiotic conditions. Fox found out an interesting fact that the polycondensation of amino acids is defined by some rule: the sequence of amino acid residues is not totally random in a final polypeptide. Some physical law defines joining amino acids from a mixture of many amino acids. This Fox's discovery needs in experimental and theoretical investigation, but this discovery is forgotten.

The next step: The protein matrix of a protocell similar to Fox's microspheres can adsorb amino acids from the environment non-randomly again. We can discover a next rule, like the Fox's rule above-mentioned. The matrix may have properties of primitive ribosome. The adsorption properties of proteins are a black spot in biology. We need to move in this direction, however, the membrane style of thinking leads us to the other wrong side.

 

[Buzz Bloom]

The protein matrix of a protocell similar to Fox's microspheres can adsorb amino acids from the environment non-randomly again.

Hi Vladimir:

The Wikipedia summary of Sydney Fox's experiment says that proteins were never produced.

https://en.wikipedia.org/wiki/Sidney_W._Fox
One of the first experiments by Dr. Fox and Kaoru Harada that had to do with the formation of proteinoids was called Thermal Copolymerization of Amino Acids to a Product Resembling Protein. It was performed in February 1958.
The experiment did not prove that proteins were formed on primordial Earth using primarily heat, but Fox and Kaoru Harada believed it suggested that if proteinoids could be synthesized using just heat and the amino acids formed from the Miller–Urey experiment, then more research could lead to an answer to how anabolic reactions, enzymatic proteins, and nucleic acids were first formed and in turn, how the earliest forms of life originated.​

AFAIK, proteinoids have never been demonstrated to have any useful enzymatic properties.
Also AFAIK no scenario has ever been proposed for how hypothetical proteinoids with enzymatic properties could improve by mutation. In contrast, RNA sequences do mutate when reproducing, and RNA ribozymes have been demonstrated to have enzymatic properties.

https://en.wikipedia.org/wiki/Ribozyme
​

Regards,
Buzz

 

[berkeman]

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