Abiogenesis and the evolution of complex life

[Thunderbird]

 

I believe the cycle came first. Then the gradual encapsulation of the cycle(s) within membranes, then the development of a memory system (DNA.RNA) to aid in reproduction. Then the merger of prokaryotic cells to form cooperative, self-contained cells.

Indeed, you're right, but we are still left with a few organizational gaps.

Autocatalysis

Catalysts are chemical substances that modify reaction rates without themselves being changed in the process. Their kinetics are characterized by threshold and amplification phenomena. Enzymes are the major class of biological catalysts.

 

The molecules of an autocatalytic system speed up the very reactions by which they are formed. Autocatalytic loops are like feedback loops in that the presence of a substance stimulates production of the same element and that the kinetic equations describing them are non-linear . (Eg. the rate of variation of the concentration of X is proportional to the square of its concentration)

 

Cross-Catalysis is a similar loop involving several elements. The first element triggers the production of the second, which in turn produces the first. A hypercycle is a system of autocatalytic reactions arranged in a circle so each reaction's product catalyzes production of its clockwise neighbor.

 

The gene was described by H.J. Muller in 1926 as possessing the property of "specific autocatalysis," meaning self-replication. "Still more remarkable," he wrote, the gene can mutate without losing its specific autocatalytic power.

 

Stuart Kauffman studied auto-catalytic sets as a possible explanation of the origin of life, for they tend to grow as long as the materials for their synthesis are available. For Kaufman, at its heart, a living organism is a system of chemicals that has the capacity to catalyze its own reproduction. (See At Home in the Universe, p. 49) Different auto-catalytic sets might compete for the same raw materials and life could indeed have bootstraped itself into existence through this process rather than have waited for some ridiculously improbable random events. But is the occurence of auto-catalysis a simply fortuitous event? Kauffman studied systems to find out when auto-catalysis might occur and found that this tended to happen "at the edge of chaos" This state corresponded to the " phase transition" behaviour studied by Chris Langton and the students of Artificial life. For Langton, Life is eternally trying to keep its balance on the edge of chaos, always in danger of falling off into too much order on the one side, and too much chaos on the other.

 

For Kauffman, life, instead of being improbable, is an expected, emergent, collective property of complex systems of polymer catalysts when a system acheives catalytic closure. "As the complexity of a collection of polymer catalysts increases, a critical complexity threshold is reached. Beyond this threshold, the probability that a subsystem of polymers exists in which formation of each member is catalyzed by other members of the subsystem becomes very high" (p.289)

 

(See Prigogine Order Out of Chaos, pp. 133-135, Waldrop Complexity pp 124 - 125

[Pyrotex]

Indeed, you're right, but we are still left with a few organizational gaps.

If I read you right, you are proposing that the quotes from Prigogene help to "fill in" the afore-mentioned gaps.

 

If that is so, then I fully agree and concur.

 

The Wikipedia reference I gave on Krebs Cycle said a lot about how the various chemicals produced by one part of the cycle inhibited, enabled or self-catalyzed other parts of the cycle.

 

And did you know that enzymes and many proteins have an on-off switch? Yup. They have an "active site" which performs the molecule's "primary task", and a secondary site which prevents the protein from doing that task, unless there is an enabling molecule (such as an amino acid, or an ATP molecule) temporarily attached at that secondary site.

 

Fascinating.

[Thunderbird]

If I read you right, you are proposing that the quotes from Prigogene help to "fill in" the afore-mentioned gaps.

 

If that is so, then I fully agree and concur.

 

The Wikipedia reference I gave on Krebs Cycle said a lot about how the various chemicals produced by one part of the cycle inhibited, enabled or self-catalyzed other parts of the cycle.

 

And did you know that enzymes and many proteins have an on-off switch? Yup. They have an "active site" which performs the molecule's "primary task", and a secondary site which prevents the protein from doing that task, unless there is an enabling molecule (such as an amino acid, or an ATP molecule) temporarily attached at that secondary site.

 

Fascinating.

On the chemical cellular level I believe the above references we have given would suffice as the best evidence we have for how life emerged from non life. fascinating indeed. I still think there are quantum coherent molecular structures involved that form around incoming information outside these loops, sunlight-chlorophyll for example, and also geometric principles involved, The chemical factory needs to have an architecture. Environmental cycles would play the first simple rhythms of adaptation. This would signal the start of the evolutionary process.

 

To me these types of evolutionary constraints are also fascinating aspects of life. The forms. After all consider I am a sculptor. I take gemstones and form them into animals. Form and function develop hand in hand. The form is not addressed in evolution theory as much as I would like.

[Moontanman]

On the chemical cellular level I believe the above references we have given would suffice as the best evidence we have for how life emerged from non life. fascinating indeed. I still think there are quantum coherent molecular structures involved that form around incoming information outside these loops, sunlight-chlorophyll for example, and also geometric principles involved, The chemical factory needs to have an architecture. Environmental cycles would play the first simple rhythms of adaptation. This would signal the start of the evolutionary process.

 

To me these types of evolutionary constraints are also fascinating aspects of life. The forms. After all consider I am a sculptor. I take gemstones and form them into animals. Form and function develop hand in hand. The form is not addressed in evolution theory as much as I would like.

 

I agree, all these chemical reactions do indeed form under the right conditions but where did the form of a cell come from? shake up olive oil and vinegar and see the form! Yes oil when mixed with water or fluids containing mostly water form very tiny but stable bubbles. these bubbles are very complex, semipermeable, and consist of a bubble of water surrounded by a membrane of hydrocarbon molecules. these tiny containers could be the first times chemical reactions were isolated from the general "broth" of chemical reactions and this concentration suggests how chemical reactions become cells. they even split into new cells when the proteans dissolved in the water inside get to be numerous enough. free floating RNA formed by the same reactions that form both eh replicating proteans and the chemical cycles could have invaded these cells and brought about synthesis of More RNA. eventually these two mechanisms would have been the basis of evolution and real life as we think of it.

[Pyrotex]

Whattsa "quantum coherent molecular structure"? :shrug: :) :shrug: :hihi: :shrug: :P :shrug:

[Thunderbird]

Whattsa "quantum coherent molecular structure"? :shrug: :) :shrug: :hihi: :shrug: :P :shrug:

DNA for one, the double helix. cones in the eyes, , microtubules in the nerurons of the brain, to name a few.

[Thunderbird]

Whattsa "quantum coherent molecular structure"? :shrug: :) :shrug: :hihi: :shrug: :P

 

 

Simply put; A persistent complex structure that can conduct information in a quantum wave form that also has its origins from that wave form, therefore only persist because of it. This definition is mine, but it is descriptive one.

[freeztar]

Simply put; A persistent complex structure that can conduct information in a quantum wave form that also has its origins from that wave form, therefore only persist because of it.

 

This went right over my head. Can you elaborate?

 

This definition is mine, but it is descriptive one.

 

It seems that the phrase is yours as well since a google search turned up zero results for the phrase.

[Thunderbird]

This went right over my head. Can you elaborate?

 

 

 

It seems that the phrase is yours as well since a google search turned up zero results for the phrase.

 

To give a good explanation I would need to broaden the definition of quantum mechanics. A living organism is not only circular chemical functions that are collapsed to a finite point, but life also exhibits forms, movements and functions that were, as were the simple chemical reactive cycles, cycles of the environment.

Cycles of energy and rhythms of energy, These elements were the dynamical aspects. A creative tension between dualities, on both the micro-level and macro-level.

 

"Morphology is not only a study of material things and of the forms of material things, but has its dynamical aspect ... in terms of force, of the operations of energy. This is a great theme. Boltzmann, writing in 1886 on the second law of thermodynamics, declared that available energy was the main object at stake in the struggle for existence and the evolution of the world" D'Arcy Thompson, On Growth and Form, 1917

..to (in)form buildings with thematic meaning, they must convey a gestalt, the whole must be more than the sum of the parts, and there must also be an ambiguity and paradox immanent within that gestalt, as a tension. (And quoting Heckscher on composition...) It is the taut composition which contains contrapuntal relationships, equal combinations, inflected fragments, and acknowledged duality's. It is the unity which maintains, but only just maintains, a control over the clashing elements which compose it. Chaos is very near, its nearness, but its avoidance, gives ...force" Robert Venturi, Complexity and Contradiction in Architecture, 1966

[InfiniteNow]

Ah. Yes. Why use actual physics when you can change the existing and accepted definitions to meet your own personal fluffy non-measurable metaphysics.

 

An explanation which must redefine the words used in said explanation is not a good explanation at all. ;)

 

 

 

Let me tell you what I'm talking about when I mention the ground state of an electron. I am actually talking about rainbows and how they touch the ground in two places, where a pot of gold resides at each connection point. Don't you see! It's quite simple, really. :)

[Thunderbird]

Ah. Yes. Why use actual physics when you can change the existing and accepted definitions to meet your own personal fluffy non-measurable metaphysics.

 

An explanation which must redefine the words used in said explanation is not a good explanation at all. ;)

 

 

 

Let me tell you what I'm talking about when I mention the ground state of an electron. I am actually talking about rainbows and how they touch the ground in two places, where a pot of gold resides at each connection point. Don't you see! It's quite simple, really. :)

 

I said “broaden” to include it in life functions, as not purely chemical. I did not say change.

[Thunderbird]

When you start to observe and measure calculate a new aspect of life functions you need to acknowledge the fact that other system exist. System that are defined with other terms, detected and measured in other ways, however before that you need to perceive this systems as a quality, then you can move to the reducing these systems into specific aspect of measuring quantities and variables.

 

This is why it would be useless for me to try to breach the subject of biology and how it relates quantum mechanics, without first giving a broad description that can be perceived and understood. QM is not metaphysics, and it has aspects that can be observed on the biological level.

[freeztar]

QM is not metaphysics, and it has aspects that can be observed on the biological level.

 

It sounds like you are talking about Quantum Biology. Is this correct?

[Thunderbird]

It sounds like you are talking about Quantum Biology. Is this correct?

Yea, here's another link .... Quantum Biology

[freeztar]

Yea, here's another link .... Quantum Biology

 

Interesting. I must admit that I have zero knowledge on this subject. I'll have to do some reading and come back to this. It definitely seems appropriate for a discussion of abiogenesis.

[Thunderbird]

Interesting. I must admit that I have zero knowledge on this subject. I'll have to do some reading and come back to this. It definitely seems appropriate for a discussion of abiogenesis.

 

Great ! I'll look forward to it. :phones:

[freeztar]

This is rather interesting stuff.

 

Unfortunately, I can't interpret the results from studies, but the "laymans" version does a good job of describing why Quantum Biology (Biophysics) is valuable.

 

"Typically, quantum mechanics has been applied to solid-state problems because the symmetry makes the calculation smaller and easier, but there's really nothing different physically between a carbon atom in a protein and a carbon atom in a nanotube," he said. "Even though a protein is such an asymmetric, complex system, when you really zoom into the quantum mechanical level, they are just atoms. It doesn't matter if strange things are happening; it's still just carbon, nitrogen, hydrogen, and oxygen."

 

Quantum mechanics allows researchers to do things that can't be done with classical physics, such as modeling the way chemical bonds break and form, or including the effect of proton "tunneling" -- allowing protons to move through energy barriers that normal logic would deem impossible.

 

http://www.rpi.edu/news/PRpdfs/quantum011607.pdf

 

So, it seems that the challenge is to understand abiogenesis within the context of biophysics. It's quite a challenge!