Novel Idea on the Origin of Life

[Feeble Wonk]

Eeek, don't say that. Gravitationally bound systems do not decrease in entropy. Even though they "clump up" so to speak, it does not mean that the overall entropy decreases. It doesn't.

I believe he was referring to the localized subsystem. The same would be true of the terrestrial biosphere. It was a general discussion about dynamical systems in "far from equilibrium" states.

 

[Feeble Wonk]

That is an intriguing principle. I have never heard it put that way before. Can you cite a reference?

Smolin refers to the idea as "the principle of driven self-organization", stating that "flows of energy through open systems tend to drive them to states of higher organization". Open systems were defined as "any bounded systems that can exchange energy with their surroundings".

 

[Feeble Wonk]

I think the principal has general application in virtually all fields, even including information theory.
http://www.igi-global.com/dictionary/self-organization-principle/26244
But the direct application in biological systems is apparently somewhat more controversial.
http://www.scholarpedia.org/article/Self-organization

 

[Buzz Bloom]

But the bottle necks simply impact the direction of evolutionary changes. The general process of self-organization should theoretically continue regardless of such events.

Hi @Feeble Wonk:
The bottle neck I was thinking of takes place before cells formed. I do not recall that de Duve discussed in detail how the process of RNA evolution took place. The process must involve four distinct activities in a repeated sequence.
1. An RNA double helix chain molecule separates into two single chain molecules.
2. An RNA linear single chain molecule forms a folded 3D shape that can act in the manner of an enzyme in expediting organic chemistry interactions.
3. An RNA folded single chain molecule unfolds and forms a linear shape.
4. An RNA linear single chain molecule maintains its linear shape while complementary RNA nucleotides attach to it to form a double helix chain.

Periodic changes in pH can influence steps 1,2, and 3. Section 3.5 of the article

http://www.intechopen.com/books/cla...-in-chemical-evolution-and-the-origin-of-life​

suggests a mechanism whereby apatite clay assists step 4.

What is missing is a mechanism to allow the 4 step process to repeat regularly a great many times. One possibility might be repetitive solar and lunar tidal patterns involving low and high, neap and spring tides.

(See http://oceanservice.noaa.gov/education/kits/tides/media/supp_tide06a.html .)​

If there were no moon, then such a four phase tidal pattern would not exist.

I understand that this suggested mechanism is only a speculative possibility. Its purpose is to illustrate one possibility for why luck may have played a critical role in biogenesis.

Regards,
Buzz

 

[mfb]

What is missing is a mechanism to allow the 4 step process to repeat regularly a great many times.

If the RNA is not bound to a specific place, anything that produces ocean currents would lead to periodic changes for (approximately) closed orbits in those currents. No moon necessary.

 

[Buzz Bloom]

If the RNA is not bound to a specific place, anything that produces ocean currents would lead to periodic changes for (approximately) closed orbits in those currents. No moon necessary.

Hi @mfb:

I think at the present time any discussion about the mechanism that drives the four-step cycle of RNA evolution is entirely speculative. Your speculation that ocean currents might be the mechanism is certainly a possibility. On the other hand, it seems plausible that before cell membranes established boundaries within which repetitive chemistry could occur, and evolutionary progress could thereby avoid destructive dispersion, the four-step cycle would have to be relatively confined to specific localized areas, possibly tidal basins. Can you suggest a plausible mechanism for the pH of the ocean to change periodically with a period as short as hours? A stream flowing through soluble minerals and then through a tidal basin at low tide could change the pH in the basin in one direction, and a high tide could bring ocean water into the basin changing the pH in the opposite direction.

Regards,
Buzz

 

[mfb]

A stream flowing through soluble minerals and then through a tidal basin at low tide could change the pH in the basin in one direction, and a high tide could bring ocean water into the basin changing the pH in the opposite direction.

Sure, but tides are there without moon as well. Just not as pronounced, and without the 2 week cycle in amplitude.

 

[Buzz Bloom]

Sure, but tides are there without moon as well. Just not as pronounced, and without the 2 week cycle in amplitude.

Hi @mfb:

The moon's role is to enable a four phase tidal pattern. With the Sun only, the tidal pattern will have only two phases. The following is a (speculative) example of how the four tidal phases might work.

The spring high tide will bring sea water into a higher basin which will then flow like a waterfall into the lower basin where the RNA activity takes place. The neap high tide does not do this. When the waterfall is active, the RNA basin will experience turbulence; when inactive, the RNA basin will be calm. An assumption is needed that the RNA lower basin has some kind of protection so that the high spring tide does not dilute the content of the RNA basin too much. A possibility might be sheets of semi-permeable organic material that will later evolve into cell membranes.

When the pH is low, hydrogen bonds are weak. When the pH is high, hydrogen bonds are strong. When the basin is calm, RNA molecules will sink. When the basin is turbulent, RNA molecules will not sink.
1. An RNA double helix chain molecule separates into two single chain molecules. This occurs when the RNA basin is turbulent, and the pH is low.
2. An RNA linear single chain molecule forms a folded 3D shape that can act in the manner of an enzyme in expediting organic chemistry interactions. This occurs when the RNA basin is turbulent, and the pH is high.
3. An RNA folded single chain molecule unfolds and forms a linear shape. This occurs when the RNA basin is calm, and the pH is low. The calmness allows the linear molecules to sink and its backbone to attach to apatite clay. BTW, the crystals in these clays have a periodicity close to that of the RNA backbone.
4. An RNA linear single chain molecule maintains its linear shape while complementary RNA nucleotides attach to it to form a double helix chain. This occurs when the RNA basin is calm, and the pH is high.

I hope you will find this scenario of some interest, if only for entertainment.

Regards,
Buzz

 

[1oldman2]

To be perfectly frank, I'm not sure what to do with that. Sorry.

My impression is your speaking of a body of humans, that works.

 

[Torbjorn_L]

Considering this is England's work from 2 years back, I'm not sure it merits "novel" any longer. I remember reading it as I am interested in astrobiology.

England's initial work on replicators is fairly solid what I know of, it nicely explains why RNA predates DNA as genetic material and not the other way around, and I cite it a lot.

The later work on his supplementing energetic constraint on evolution is way out there, and I have never had to go back for seconds. If he wants to test it, more the power to him. Until then I have put it in the round archive.

Yes, mostly crackpots.

But in the process I learned quite a bit more about entropy.

When most people think of entropy increase they think of well ordered, well organized states deteriorating into less ordered, less organized states. While many times (most of the time?) those ideas hold true, it's not the whole picture.

If we consider where the energy is initially and where it ultimately goes, and what form the energy takes and consider all the macrostates and microstates of the matter we started with and ended with, sometimes a lower higher entropy configuration (considering the entire system) is one that produces well organized and ordered structures (sometimes extremely well organized). Crystal formation, repeated vortecies in turbulent fluids and snowflake formation are three such examples of this.

Thanks! I have seen some of that material when I myself got around to junk the "order/disorder" myth. The video is an update on especially Glotzer's work. I learned two things:

- Someone else can be as enthusiastic about Glotzer's work.

- Physicists have balls.*

* OK, I confess I knew that from my own experience. =D

 

[Torbjorn_L]

As I understand what I have read about biogenesis

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

there are bottlenecks in the process. I have also read about several suggestions that our relatively over-sized moon may have played an important role in getting past such a bottleneck. It seem reasonable that if the moon played such a role, the fact that such a moon exists would be a bit of luck.

My take:

There are two main theories of life emergence, soup and vent. The soup theory is preferred by many chemists & biochemists as it looks into chemical pathways to replicating protocells, the vent theory is preferred by many geologists & biologists as it looks into phylogenetic pathways from geology to biology.

The main problem with soup theories is to drive some key steps. Therefore they tend to end up with many pot systems (i.e. different reactors for different reactions) and freeze/thaw or wet/dry cycles to drive steps that are non-spontaneous. That is why they can see the Moon, or Mars, as important.

Vent theories have the same problem, but they tend to stick with the observed reactors. E.g. for Orgel's theoretical problem with squandering in side reactions of non-enzymatic reaction chains, Keller et al showed that gluconeogenesis/glycolysis and the phosphate pentose pathway are as efficient without enzymes in the Hadean ocean. And for RNA replication it has been shown that vents doing PCR for replication are the only known reactors that naturally lengthen strands.

Instead you the problem to do it all without enzymes and other cycling than thermal. Since vents can produce the substrate pyruvate from H2 and CO2 with self-deposited greigite under Hadean conditions in the lab, and Keller et al just showed that there is a natural pH/FeII control of the pathways so that the inner vent would produce pentose and the outer a glucose buffer, we are halfway to RNA and an energy (polyphosphate) metabolism. (The requisite amino acids have glycolysis as starting pathway IIRC.)

Two reactions to get the purine base pairs are still outstanding... And of course no one has yet showed natural PCR akin to Keller's natural metabolisms. So make that 3 reaction steps out of some 30+ steps, depending on how you count them. The cells could be inorganic pores at the start.

TL;DR: With this rate we have a geological reactor making RNA cells quicker than the next blue moon.

The current fossil record indicates that the vent theory is likelier I find, because life may have emerged as soon as the ocean became habitable over 4.3 Ga [billion years ago]. There is a putative 4.1+ Ga fossil, and TimeTree phylogenetics prefer the first known split (bacteria/archaea) to happen 4.2+ Ga. Soup theory seems too complicated and fragile for all that. Admittedly I can't quantify the conclusion in any way.

Let me see what I can find. I know I've read about it again just recently in a book by Lee Smolin.
https://www.amazon.com/dp/0544245598/?tag=pfamazon01-20

He was discussing this concept during a section covering physical systems that tend to behave in ways that are anti-thermodynamic (with decreasing entropy)... such as gravitationally bound systems.

Yes, please do not say that! Thermodynamics in GR is complex since you have spacetime volumes that changes. However gravitationally bound systems on an approximately flat background can be completely understood to radiate away heat to the universe as they bind tighter, same as all systems with potential wells behave. [ http://math.ucr.edu/home/baez/entropy.html ]

 

[Feeble Wonk]

Yes, please do not say that! Thermodynamics in GR is complex since you have spacetime volumes that changes. However gravitationally bound systems on an approximately flat background can be completely understood to radiate away heat to the universe as they bind tighter, same as all systems with potential wells behave. [ http://math.ucr.edu/home/baez/entropy.html ]

Absolutely agreed. The "decrease" in entropy was specifically limited to the isolated subsystem of increasing order. But, definitely, entropy is correspondingly increased over the entire system as a whole.

 

[Feeble Wonk]

Hi @Feeble Wonk:
The bottle neck I was thinking of takes place before cells formed. I do not recall that de Duve discussed in detail how the process of RNA evolution took place.

For whatever it's worth, de Duve did address this issue in his earlier Vital Dust publication (1995), but he left it as an unsolved mystery... perhaps the key unsolved mystery of abiogenesis.

 

[Buzz Bloom]

And for RNA replication it has been shown that vents doing PCR for replication are the only known reactors that naturally lengthen strands.

Hi @Torbjorn_L:

I didn't know what PCR was, so I found the following:
From https://en.wikipedia.org/wiki/Polymerase_chain_reaction

The method relies on thermal cycling, consisting of cycles of repeated heating and cooling of the reaction for DNA melting and enzymatic replication of the DNA.
​

Can you cite any references about the PCR mechanism being used to demonstrate one or more of:
(1) RNA replication (rather than DNA)
(2) the use of RNA "enzymes" (rather than protein enzymes)
(3) evidence of PCR functiong in an open vent-like environment (rather than in test-tubes)?

Regards,
Buzz