Self Organization

[Bishadi]

http://staff.science.nus.edu.sg/~parwani/c1/node2.html


Current view

Self-Organisation

In the last chapter we understood that biological diversity and complexity does not contradict the Second Law of thermodynamics because living organisms are structures that maintain themselves far from equilibrium: They use an inflow of energy to create "order from disorder" within themselves, but dissipate heat and other waste products to increase the net entropy and disorder of the universe. The remarkable self-organisation exhibited by living organisms is also illustrated in simpler non-living systems such as that of Benard cells and the BZ cemical reaction. In this chapter we will look at further examples of self-organisation, that is, macroscopic order or pattern formation in a complex system.


this share few items but I will add in a few to the thread

 

[Bishadi]

….

State VariablesWe are all familiar with the concept of temperature. The Zeroth Law of Thermodynamics formalizes our intuition and experience as follows:
“If a system A is in equilibrium with system B (that is, has no exchange of heat with it), and if system B is in equilibrium with system C, then A is in equilibrium with C”.
This law allows us to associate a quantity called temperature to each system in thermal equilibrium, so that two systems in equilibrium have the same temperature. The thermometer is a device that uses the Zeroth Law in a quantitative and practical way.In addition to the temperature, one may need more thermodynamic parameters, called state variables, to completely characterize the state of the system. For example, for a gas these are the pressure P and volume V. Variables such as temperature and pressure that are independent of the size of the system are called intensive, while those such as the volume are called extensive. The parameters that can be used to describe a system are not all independent but related by an equation of state. For an ideal gas one has the equation

PV=NkT​

(4.1)​

​

where k=1.38 * 10-23 Joules/K is called Boltzmann’s constant, and N is the number of molecules. As you must have learnt in school, an ideal gas is the universal limiting description of real gases when their density is very low and the temperature high. In general, the equation of state of a real substance is more complicated. It is usual to plot the equation of state as a function of its parameters. One useful curve follows by keeping V constant and representing the equation of state on a P -T plot as shown in the figure for a generic substance. The lines mark boundaries between the different phases of the substance, where changes occur in the physical properties of the substance

these Phase differences are what creates the hydrophilic and hydrophoic descriptions of the properties known as the 'water and oil' effect.....

to note how H3 and H4 can resonant and associate to like, based on their resonance/structure; this is how phospholipid bilayers form...for the assembly of the cell walls....

a phenomenon left unaswered.... who wants the nobel?

 

[Bishadi]

so the idea is not unique as a nobel winner suggested in his autobiography that he had the same idea

My adult scientific career began with graduate study in chemical physics with Harden McConnell at Stanford. I had the idea of elucidating the mechanism of ion transport across biological membranes by nuclear resonance. I thought ion transport must involve rotation of the transport protein in the membrane. Struggling to prove this wrong idea, it occurred to me to study the rotation in the membrane of a lipid molecule, about 1,000 molecular weight, rather than a protein fifty times larger. This led to my discoveries, by nuclear and paramagnetic resonance methods, of phospholipid flip-flop, an exceedingly slow process, and lateral diffusion, exceedingly fast (Kornberg and McConnell, 1971a ; Kornberg and McConnell, 1971b)

Roger D. Kornberg - Autobiography

So the idea is good but the math is what their missing

what is funny is to realize not only has Kornberg shared quite the same model but not only is the idea not shared in schools as to how lipid combine to be phospholipids but that it is the math that has kept it from being described properly.

So who wants to call this guy and get the ball rolling.....?

I have a bunch of evidence on 'free energy' convey in biology... and above has a form to observe the energy. All that is left is identifying the wavelength and combine the simple 'f' with a batch of cold lipids and do an experiment combined with the math and bingo.... you get your name in the news, the million bucks and then unknowlingly open up a huge can of worms in the intellectual community about how mass and energy 'actually work'

 

[China Cat Sunflower]

Hey Bish,

Is it possible to translate what you're saying here into anecdotal terms? Because I'm trying to follow along and understand, but it isn't immediately obvious to me what is meant by "self organizational." I'm a carpenter, not a physicist. I hadn't encountered the term "hydrophobic" before.

Chris

 

[Bishadi]

Hey Bish,

Is it possible to translate what you're saying here into anecdotal terms? Because I'm trying to follow along and understand, but it isn't immediately obvious to me what is meant by "self organizational." I'm a carpenter, not a physicist. I hadn't encountered the term "hydrophobic" before.

Chris

In chemistry, hydrophobicity (from the combining form of water in Attic Greek hydro- and for fear phobos) refers to the physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water


like water on the leaves of a plant

caused by opposing resonances upon the mass

as often the combining or pattern disipations can be changed by temperature

 

[lunamoth]

Hydrophobic, repels water. Fats and oils are hydrophobic, they don't mix with water.

The membranes of cells are made of proteins and lipids (fats). That's what the Kornberg reference is talking about.

 

[China Cat Sunflower]

Yeah, I read the wiki entries on hydrophobia and hydrophilia. I read the Kornberg stuff, and I'm working my way through the Parwani material. I understand about state variables. What I want to know, in layman's terms, is what is "self-organizational"? DNA?

I'll keep reading.

Chris

 

[lunamoth]

Phospholipids, lipid-protein membranes and membrane transport are all taught in intro bio courses. I'm not sure why you (Bishadi) think it's not shared in schools. Kornberg's work is also presented.

By self-organizational in the OP, that probably refers to the fact that if you have polar molecules (imagine little bar magnets) and you put a bunch of them together, you don't get a random pile but one organized with opposite poles attracting.

In a liquid medium non-polar molecules (like fats) will be attracted to each other, and repelled by polar molecules (like water), so they form spheres. Like when you drip oil into water. That's a form of self-organizing.

If you have phospholipids (more complex because they have both polar and non-polar ends) you get the formation of bilayers that can form hollow spheres.

I don't understand though how Bishadi's various references in this thread go together.

 

[China Cat Sunflower]

Thanks Luna! That makes sense. I'm going to have to find time to read the Parwani material from Bishadi's link in the OP. Thanks for taking the time to explain that to me.

Chris

 

[Bishadi]

Hydrophobic, repels water. Fats and oils are hydrophobic, they don't mix with water.

But to increase temp, often breaks down these barriers

ie.... put creamer in a cold cup of coffee versus a hot cup

 

[Bishadi]

Phospholipids, lipid-protein membranes and membrane transport are all taught in intro bio courses. I'm not sure why you (Bishadi) think it's not shared in schools. Kornberg's work is also presented.

Can you forward something to the effect on his 71' representation of how resonance conveys (gibbs free energy) across a membrane.

But specifically it was the 'idea' mentioned about how the bilayer assemble by resonance that is the first choice; please I would like to read this material and the math behind his work.

By self-organizational in the OP, that probably refers to the fact that if you have polar molecules (imagine little bar magnets) and you put a bunch of them together, you don't get a random pile but one organized with opposite poles attracting.

This is a chemically based rendition when the choice is observing in a quantum form in which the properties of the energy (em/resonance) can be furthered. as well please take a peak on this http://departments.colgate.edu/physics/research/Photon/root/P120/Entanglech20.pdf

The probability is a maximum when​

​

µ1 = µ2. This means that the entangled state of Eq. 20.6 is much more that what it seems. The HH+VV entangled state is not jut the superposition of photons polarized horizontally with photons polarized vertically. It is a state of photons that are parallel to each other regardless of the orientation.

​

One final remark about polarization-entangled states. The state HH+VV
that we considered is only one of several possibilities. Another one is the state HV-VH, in which the photons are in a state where their polarizations are always perpendicular to each other, regardless of the orientation.​

​

the idea to observe is the energy upon the mass 'polarizes'​

In a liquid medium non-polar molecules (like fats) will be attracted to each other, and repelled by polar molecules (like water), so they form spheres. Like when you drip oil into water. That's a form of self-organizing.

Yet temperature or the energy state, without breaking down the structure, but the 'state' of the relation is as important as the structure itself. So a new dimension is being observed

If you have phospholipids (more complex because they have both polar and non-polar ends) you get the formation of bilayers that can form hollow spheres.

Good stuff

I don't understand though how Bishadi's various references in this thread go together.

please be patient.... at least you all read and enjoying the participation

What this is going is in addressing the energy upon the mass as well the structures themselves. Then the observed evolutionary pattern can be defined in both logical and mathematical frame at the molecular level.

 

[Dondi]

This is fascinating stuff here. Is the goal here to eventually get to abiosynthesis through self-organization?

 

[lunamoth]

I'm not sure where B. is headed.

While I doubt anyone has done all the equations that describe life physiology, there's nothing mysterious, secret, or non-logical about the mathmatical approach to describing biomechanics, metabolism, evolution, or the way thermodynamics affect biology.

As for abiogenesis, I'm as sure as I am that I'm sitting here at my computer typing that abiogenesis occurred and that the parameters of the universe support that event.

 

[Dondi]

I'm not sure where B. is headed.

While I doubt anyone has done all the equations that describe life physiology, there's nothing mysterious, secret, or non-logical about the mathmatical approach to describing biomechanics, metabolism, evolution, or the way thermodynamics affect biology.

As for abiogenesis, I'm as sure as I am that I'm sitting here at my computer typing that abiogenesis occurred and that the parameters of the universe support that event.

I'm not interested in if abiogenesis happened, I'm interested in how it happened, specifically. That is a barrier that if broken, and can be proven theoretically either biologically or mathmatically, it would go far in advancing acceptance to the whole sphere of evolutionary thought.

 

[lunamoth]

I'm not interested in if abiogenesis happened, I'm interested in how it happened, specifically. That is a barrier that if broken, and can be proven theoretically either biologically or mathmatically, it would go far in advancing acceptance to the whole sphere of evolutionary thought.

Would a workable, mathmatically supportable model for abiogenesis affect your belief in a Creator God?

Added: What holds you (or anyone) back from accepting the model of evolution of species as it currently stands? The evidence is overwhelming.

 

[Bishadi]

I'm not interested in if abiogenesis happened, I'm interested in how it happened, specifically.

Mass and energy associate in a pattern that progresses; completely opposite to the macro observance of chaos.

That is a barrier that if broken, and can be proven theoretically either biologically or mathmatically, it would go far in advancing acceptance to the whole sphere of evolutionary thought.

and it was in observing biological processes that revealed that the energy upon mass is what causes the 'intent' of life... rather than the current ideas of 'potential differences' in a chemical rendition of todays biology.

So the perfection starts with observing how atoms and energy 'evolved' in to structures versus from adam and eve.

and the change that enables the comprehension to unfold is to identify energy as light (em upon mass) rather than an electical potential between bodies (mass).

 

[Dondi]

Would a workable, mathmatically supportable model for abiogenesis affect your belief in a Creator God?

Added: What holds you (or anyone) back from accepting the model of evolution of species as it currently stands? The evidence is overwhelming.

I'm open to the idea of evolution. But I haven't sifted though all that overwhelming evidence enough to allow me to decide to fully buy into it. I will tell you that I'm old earth/old universe. Nor am I afraid of what I might find. And I do not think it will affect my relationship with God. It's His game, not mine. And despite the evidence, as it were, there are still problems of both sides of the fence. I'm equally annoyed at athiests who became athiests because of evolution. There are plenty of thiests who hold to it.

FWIW, I have been reading and interesting book called "The Language of God" by Francis Collins that as gone a long way is leaning me more toward evolutionary biology. But Collins is a theist, so I'm curious about what his findings are.

Naturally, most of those in my church hold to a young earth/young universe/six day creation view. As does my immediate family. For the most part, I keep quiet about my views. I don't see any reason to jeopardize my position and service in the church or cause agnst for my family because I believe differently than they. Life has been good to me and I'm serving the Lord, why spoil a good thing.

At any rate, the fear for most Christians is that if evolution is true, then the biblical account cannot be. The idea of the Fall would make no sense, and thus the concept of sin would be invalid. And to follow further, it would stand to reason that Christ's redemptive work would be unnecessary. It would also make Christ's statements concerning Adam and Eve invalid as well.

And while that is a concern for me as well, I cannot ignore scientific evidence. When I first began reading creationist literature, it seemed to satisfy my inquiries for a time. But the deeper I got into it, I couldn't help ask myself why God would allow the 'appearance' of evolution to be so prevelent? Is He trying to test us? Or if it was a 'lie' from Satan, as some would insist, why on earth (pun intended) does it seem so convincing? I thought the idea was to get people to believe in God? So it seemed to me that, gee, God sure is making it hard for people.

I am comforted in my spiritual journey to learn that much what I've read in Jewish thought doesn't seem to mind that the six day account in Genesis is not necessarily literal. That there is some allowance to believe in an alternate interpretation whist still allowing certain core beliefs to remain intact. But I'm still trying to hash out what that all means. Suffice to say, my inquiry has been stimulating so far.

 

[Dondi]

Mass and energy associate in a pattern that progresses; completely opposite to the macro observance of chaos.

and it was in observing biological processes that revealed that the energy upon mass is what causes the 'intent' of life... rather than the current ideas of 'potential differences' in a chemical rendition of todays biology.

So the perfection starts with observing how atoms and energy 'evolved' in to structures versus from adam and eve.

and the change that enables the comprehension to unfold is to identify energy as light (em upon mass) rather than an electical potential between bodies (mass).

Would this have something to do with the formation of the left-handed amino acids that are predominately found in life? Did light have a polarizing effect in how these molecules were formed?

 

[path_of_one]

At any rate, the fear for most Christians is that if evolution is true, then the biblical account cannot be. The idea of the Fall would make no sense, and thus the concept of sin would be invalid. And to follow further, it would stand to reason that Christ's redemptive work would be unnecessary. It would also make Christ's statements concerning Adam and Eve invalid as well.

If it helps any, Dondi- I am an evolutionist. I've held the early hominid and early human skulls in my own hands; I've seen the progression with my own eyes. I can't get away from that data and I refuse to believe in a God that would allow Satan to plant things that are so appealing to our God-given logic only to deceive us.

That said, it doesn't detract from the relevance, authenticity, truthfulness, or meaning of Genesis in the least for me. With the Spirit, I am able to still embrace the meaning of Genesis, of sin, of Christ's work, and Adam and Eve without thinking it is a literal story of the details of creation. The first couple chapters of Genesis alone are crammed full of meaning and relevance for life today. I do not believe in the concept of original sin, but I do believe people sin, and I do believe people are saved through Christ. I do not believe in a fallen world or earth, but I do believe people have consistently chosen, since the origins of human thought, to alienate themselves from God and the earth, and we live with the consequences. The earth could be the Kingdom of Heaven- the Kingdom is among/within us. But if we do not bring it forth and embrace what God gave us out of grace, well- things continue as they are.

 

[Dondi]

If it helps any, Dondi- I am an evolutionist. I've held the early hominid and early human skulls in my own hands; I've seen the progression with my own eyes. I can't get away from that data and I refuse to believe in a God that would allow Satan to plant things that are so appealing to our God-given logic only to deceive us.

That said, it doesn't detract from the relevance, authenticity, truthfulness, or meaning of Genesis in the least for me. With the Spirit, I am able to still embrace the meaning of Genesis, of sin, of Christ's work, and Adam and Eve without thinking it is a literal story of the details of creation. The first couple chapters of Genesis alone are crammed full of meaning and relevance for life today. I do not believe in the concept of original sin, but I do believe people sin, and I do believe people are saved through Christ. I do not believe in a fallen world or earth, but I do believe people have consistently chosen, since the origins of human thought, to alienate themselves from God and the earth, and we live with the consequences. The earth could be the Kingdom of Heaven- the Kingdom is among/within us. But if we do not bring it forth and embrace what God gave us out of grace, well- things continue as they are.

"And the LORD God formed man of the dust of the ground, and breathed into his nostrils the breath of life; and man became a living soul." - Genesis 2:7

In guess God forgot to tell us there are some intermediary steps here, huh?

But I agree that there are deeper meanings in the text of the Torah than what we see at the surface, as BB can attest. A Jewish astrophysicist by the name of Gerald Schroeder has some interesting theories from which he draws heavily from Nachmanides and Maimonides interpretations of the Genesis account. Samples from his website:

The Age of the Universe

Evolution: Rationality vs. Randomness

Existence: What the meaning of the word "is" is

The caution here is that some of his ideas have naturally been scrutinized by critics, so take them with a grain of salt. But it has led me to search deeper into the matter. I'm learning.

But I appreciate your view, path. And your firm faith in light of your scientific leanings. I hope that I can find firm ground of my own.