Knowledge and subjectivity. Origin of life

[wellwisher]

The topic is the knowledge and subjectivity of the origin of life. Unique protein folding, is an example of well documented knowledge that is not fully addressed, since it might stimulate thinking. Instead the traditions stick to the blind use of statistics in light of this evidence making this approach subjective for many applications within life and evolution.

Statistics is a powerful tool, with its many useful predictions. The wide scale utility of this powerful tool, has biased the mind to think life and evolution is based on random events. As an analogy, a screwdriver is a useful tool designed for setting and removing screws. However, if you didn't have all the correct tools for a given job, the screwdriver can also be used as a pry bar or even a small hammer. If someone gets used to all these extra extrapolated applications for the screwdriver, a real hammer or a real pry bar do not seem necessary. In the case of proteins folds, the screwdriver is not the right tool to hit the nail yet the traditions have always done it this way. If the machine is not broken don't fix it. But it is broken and needs fixing. It is important to define the limits of the statistical screwdriver since it is still useful for setting and removing screws. But we need to ween away the screwdriver hammer.

To understand the how proteins can acquire and maintain unique folds, even with weak binding energy, you need to take onto consideration the impact of water. Water acts like a girdle or a nylon stocking to help shape the leg. To understand how this girdle works, you need to go back to the basics of hydrogen bonding in water. But in general terms, the oil-water analogy is useful, with the unique fold of the protein, forming a unique phase within the water relative to the folding.

 

[wellwisher]

The origin of life on earth occurred within water, due to unique properties of water. I am staying on topic since this knowledge will dispel some of the subjectivity lumped into blind random assumptions. The unique properties of water are all connected to the hydrogen bonding within water. Hydrogen bonding, in turn, displays both van der Waals and covalent bonding characteristics; as defined below.

Van der Waals forces include attractions and repulsions between atoms, molecules, and surfaces, as well as other intermolecular forces. They differ from covalent and ionic bonding in that they are caused by correlations in the fluctuating polarizations of nearby particles (a consequence of quantum dynamics[3])

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding.[1] For many molecules, the sharing of electrons allows each atom to attain the equivalent of a full outer shell, corresponding to a stable electronic configuration.

Without getting too technical, the hydrogen bonding between water molecules, can act like a binary switch, able to switch between these two distinct bonding states of hydrogen bonding, since these are very similar in energy with the covalent state slightly more stable. The van der Waals bonding causes the water to get denser for better dipole interaction (water molecules get closer) while the covalent state causes the water to expand, analogous to ice expanding, so the orbital wave functions can align better.

The result is both high and low density domaines within water, as the aqueous hydrogen bonding switches locally or in concert via clusters. Below is a qualitative energy diagram between the binary nature of hydrogen bonding, with A van der Waals and the B more associated with the covalent. The slight energy hill or potential energy barrier, between, allows the switch to remain either way. But with the barrier small and the states being so close in energy ,the switch can go either way under a wide range of situations.

Relative to entropy, the van der Waals is higher since it has more freedom of movement and position since it wants to get closer, while the covalent has less entropy since sharing electrons between atoms in orbitals require precise alignment, which in the case of water, involves expanding. The binary switch of hydrogen bonding within water can switch between the higher energy and entropy state (a) and the lower energy lower entropy state (b). The binary switch allows the water to add to take away from the net entropy, in the cell, thereby making the protein complete the entropy balance.

If you need an exact protein fold, which defines lower entropy, the water can help by taking up the entropy slack. Statistics is handed off to the water. If you need the exact fold to change to it can react, water can help by switching to the lowered entropy state so the protein can pick up the slack and gain the needed entropy. What makes this easier is the high and low density water takes up different amounts of volume, like water and ice, making or taking away room while exerting or not exerting pressure.

Below is an important water cluster, composed of 280 water molecules, hydrogen together, switching between the high and low density cluster configuration, putting on the squeeze via expanded volume/pressure or easing the volume/pressure, so the protein can expand. Along with the volume and local pressure change it also offers local changes in energy and entropy. If you need a protein train to coordinate, all you need a wave in the water with crests and troughs alternating between high and low water density. The protein get the squeeze and energy/entropy to alternate. Because the water clusters are precise, so is the protein change.

 

[mjs]

1) People didn't always know that the earth was not flat. It was found at some point of time in the ancient years. But human civilization existed before that. For instance, Neardertals definitely didn't know. (I am sure that was a provocative and controversial idea at the beginning).
2) I see that most of you either misunderstood, or didn't read all the OP until the end. I am definitely not preaching anything and when i use words like "amazing", "extraordinary",
i do it mostly ironically, to emphasize that something must be wrong with our current interpretation of things, because life cannot be spontaneously generated in a world that favors low energy states and increasing entropy. I am not arguing that there is an external force that does it instead, but rather i argue that actually the reactions that compose life are possibly not amazing or extraordinary at all. On the contrary, they might as well be random and spontaneously occuring. For an outside the living system observer they can even be meaningless. As been previously explained, it is our specific place inside the system of reactions that can "deceive" us to perceive even random reactions to be "pure magic". The causes judged by the result.
3) I think that it is wrong to interpret entropy of living systems the way you do it for other things. Again the subjectivity of the observer assumes that something with a greater surviving capacity has a lower entropy. Why? Maybe only because of our perspective?
After all, towards what are we comparing the entropy state of a living being? Answer: Toward the entropy of the rest of the living system (as a whole). It is therefore logical to assume that in this case entropy can exist only relatively to something else. Ones entropy can be constantly increasing (with every single reaction), but if you are a part of a system with increasing entropy and your own entropy is increasing with slower rates, you can perceive that actually your entropy is lowering. Once again, our specific point of view makes it difficult to interpret even simple phenomena if we ourselves are inside it.

 

[Yazata]

I see that most of you either misunderstood, or didn't read all the OP until the end.

I read it, but apparently I didn't understand it.

I am definitely not preaching anything and when i use words like "amazing", "extraordinary",
i do it mostly ironically, to emphasize that something must be wrong with our current interpretation of things, because life cannot be spontaneously generated in a world that favors low energy states and increasing entropy.

Why can't the entropy of a subsystem decrease, while the entropy of the larger system of which the subsystem is a part increases? I think that happens all the time.

I am not arguing that there is an external force that does it instead, but rather i argue that actually the reactions that compose life are possibly not amazing or extraordinary at all. On the contrary, they might as well be random and spontaneously occuring. For an outside the living system observer they can even be meaningless. As been previously explained, it is our specific place inside the system of reactions that can "deceive" us to perceive even random reactions to be "pure magic". The causes judged by the result.

I don't understand that. How is subjectivity relevant to questions about entropy?

3) I think that it is wrong to interpret entropy of living systems the way you do it for other things.

I don't believe that biological chemistry embodies special principles that apply only to life. (That was a widespread idea in the 19th century.)

Again the subjectivity of the observer assumes that something with a greater surviving capacity has a lower entropy. Why? Maybe only because of our perspective?
After all, towards what are we comparing the entropy state of a living being? Answer: Toward the entropy of the rest of the living system (as a whole). It is therefore logical to assume that in this case entropy can exist only relatively to something else. Ones entropy can be constantly increasing (with every single reaction), but if you are a part of a system with increasing entropy and your own entropy is increasing with slower rates, you can perceive that actually your entropy is lowering. Once again, our specific point of view makes it difficult to interpret even simple phenomena if we ourselves are inside it.

If I understood that correctly, I'm inclined to agree with it.

While living organisms do seem to be negentropic, they seem to accomplish that at the cost of the entropy of their surroundings increasing. It's easy to see that occurring with animals, since they have to eat to survive. I'm less sure how it would work with plants.

But I'm a layman with regards to chemistry and biology, and all this talk about entropy is out of my depth.

 

[Rav]

because life cannot be spontaneously generated in a world that favors low energy states and increasing entropy.

"The heat death of the universe is a historically suggested ultimate fate of the universe in which the universe has diminished to a state of no thermodynamic free energy and therefore can no longer sustain processes that consume energy (including computation and life). Heat death does not imply any particular absolute temperature; it only requires that temperature differences or other processes may no longer be exploited to perform work. In the language of physics, this is when the universe reaches thermodynamic equilibrium (maximum entropy)." - http://en.wikipedia.org/wiki/Heat_death_of_the_universe

Consider the phrase "exploit to perform work". One day the universe will be a place where nothing happens anymore; where nothing (certainly not biological processes or their precursors) can happen anymore (except, perhaps, another big bang if you can take Penrose seriously). But until then there will be countless stars radiating an abundance of energy into their surrounding space which in a very real sense forces things to continue happening. Very interesting things in fact. For example, it is a demonstrable scientific fact that certain dynamic environmental conditions such as those that might exist (or might have existed) on an innumerable number of planets (including Earth) can conspire to create molecules of gradually increasing complexity.

See: "Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions" by Matthew W. Powner, Beatrice Gerland & John D. Sutherland

Full text, in PDF format, is here: http://hoffman.cm.utexas.edu/courses/nature_prebiotic_rna.pdf
A summary can be found here: http://www.wired.com/wiredscience/2009/05/ribonucleotides/

Regardless of whatever else you might believe, or not, this is simply a feature of the incredible universe we live in. And now you know it

 

[wellwisher]

Why can't the entropy of a subsystem decrease, while the entropy of the larger system of which the subsystem is a part increases? I think that happens all the time.

This happens all the time, with life a prime example. The easiest way to prove this is with a simple experiment. We will start with one bacterium in a beaker. To the beaker we will add only small food and nutrient molecules and ions. Next, we let the bacteria grow and divide, collecting gases that might be expelled. Once we get enough mass as bacteria, we will chill the beaker to stop all chemical reaction activity.

What we will do is compare the entropy of the initial one bacteria in the beaker state and the final state. The metabolism would have broke down the food molecules for energy releasing CO2 and H20. There will be a large increase in metabolic based entropy from beginning to end.

Next, we will compare all the small molecules originally in the beaker (amino acids, etc.) to all the polymer structures into which these have been incorporated. This layer of the total entropy will decrease. If we add these two layers the net shows an entropy increase. The overall entropy is higher ,but it leaves behind all these stable lower entropy structures.

This is not a mystery of life, but fundamentally stems from the basic observational connection between water and oil (organics). Mixing water and oil will increase the system entropy. The observed phase separation, back into two layers, will lower system entropy. Life is composed of many phases that will separate within water. The reason this is possible is defined by the thermodynamic equation called the Gibbs free energy equation; G= H-TS, where G is the free energy, H is enthalpy, T is temperature and S is entropy.

Enthalpy is a measure of the total energy of a thermodynamic system.

Locally, entropy S can increase or decrease as long as the free energy G decrease. In the case of water and oil, the enthalpy change will dominate the entropy, locally. In some cases, the entropy can dominate the enthalpy. For example, when sweat evaporates from our skin, we feel cooler. The system energy is being absorbed by the increasing entropy of the water, as the water evaporates. Both ways are allowed, as long as the system free energy G goes down. In life, enthalpy and entropy can pull back and forth. They can also pull together, like in the case of metabolism.

Water is important to the free energy equation of life, since hydration creates a different G or free energy, than assuming the organics are self standing. When you see the DNA in text books, it is self standing with the G or Gibbs free energy being expressed wrong by such representation. In reality, the free energy balance includes water.

If you had pure lipids they look like a cup of oil. If we add water, there molecules form a bilayer and the bilayers curve into shells. The free energy needed is due to water, which allows new order that will not show up with only organics. We need water's contribution to the free energy equation to help shape the free energy curves of the organics of life.

 

[wellwisher]

When water and many organic surfaces meet, there is surface tension between the two surfaces. The tension implicit of surface tension, relative to water, implies the water molecules are stretched and pulled tight like a chain that is under tension. Relative to the hydrogen bonding binary (van der Waals and covalent) tension implies more of the lower energy covalent bonding configuration; expands to overlap the orbitals.

Picture a chain that is pulled tight. Under this state of tension, the chain will act almost solid if we pull hard enough. Without tension, the chain acts more like a fluid that can flow through your hands, but under tension one can walk on it like a tight rope. In the tension situation, the entropy is very low due to the order that the tensile force is creating on all the links of the chain; they align with the force.

Say we took a bolt cutter and cut any link in the chain. The result will be a recoil of the entire chain. Each link will lose its directional orientation, that made it align and feel solid, and all the links will become free floating. It is loosely similar to a solid to liquid transition. The increase in entropy, but cutting only one link in the chain, is amplified beyond that one link, since all the links will gain entropy not just one.

When water forms hydrogen bonds, near organic surfaces, it does so in a cooperative manner, where each additional hydrogen bond added makes all the rest of the bonds stronger. The covalent aspects shared electrons with cooperation a wider form of sharing. It is like a chain, with each link adding more and more tensile force, so all are under more tension (more covalent) with the bonds become stronger.

But like any chain under tension, if you cut any link, the strength falls rapidly for all. Water, via cooperative hydrogen bonding, creates a chain under tension analogy, with ATP, acting like a bolt cutter. Part of the ATP reaction is to absorb water, which is taken from local water chains under surface tension. ATP may take one water molecule, but the entire chain recoils due to the cooperative bonding.

If we plug this entropy amplification, within the water, into the free energy equation G=H-TS, cutting the chain adds a large local S increase than may propagate like a run in a nylon stocking. Entropy needs to absorb energy to increase, drawing in local free energy like a siphon. It is like of you swing open a door quickly, all the paper on the desk may go flying to balance the free energy.

Enzymes lower the activation energy hill of reactions, but this only true in water. If we take out the water, enzymes don't work in a dehydrated state or in other solvents. We need chain cutting and a rapid aqueous entropy rise.

 

[Dinosaur]

A few blank lines makes text much easier to read.

 

[mjs]

yazata: i think that generally, you understand me very well. What i am saying is pretty simple and one doesn't have to be a professional to understand! The only problem is that maybe it is far too simple.
However, with respect to entropy, i am not saying that the entropy of a subsystem cannot decrease, but a subsystem in which entropy is always decreasing is not very probable to occur spontaneously in nature. It is more likely that actually the subsystems entropy is actually increasing, but the subsystem cannot realize this.

And yes! I think that subjectivity can play a role in the interpretation of entropy. I will give you an example: Imagine there is a large number of birds that are flying one next to other to the same direction.If we make them to fly one far from the other,so the group will start separating, the entropy of the system will start increasing.Imagine also that there are three birds inside the system that are very close to each other.If they separate with less speed than the others and we consider these 3 birds as a subsystem,the subsystems entropy will actually decrease relatively to the whole system of the birds.
In the same way, if a small subsystem of chemical reactions inside a bigger system is the reference frame for things like entropy of parts or the whole in this particular system, one can talk about entropy only in relativistic terms.

 

[wellwisher]

However, with respect to entropy, i am not saying that the entropy of a subsystem cannot decrease, but a subsystem in which entropy is always decreasing is not very probable to occur spontaneously in nature. It is more likely that actually the subsystems entropy is actually increasing, but the subsystem cannot realize this.

Entropy creates a bottleneck for the theory of RNA replicators as the starting point for evolution. Replicators will cause the local entropy to lower because the freedom of small monomers molecules is going into the restrictions of polymers. What allows this to work in modern cells, is there is free energy contained within the tri-phosphate moiety attached to the monomers. Being high energy this needs to be generated as you need it since it would be subject to reversal (move back to lower energy and higher entropy).

This suggests that some form of metabolism (the main source of modern cell entropy) needed to occur first, so the local system entropy increase is high enough to balance, and an energy output exists to generate tri-phosphate faster than the reverse reaction.

The main source of entropy increase, in modern cells is via the metabolism. Even if you could come up with a scenario for base replicators, the cell can't continue to build protein and cell order from templates, until the metabolism generates the needed entropy increase, to act as a counterweight. I would bet on protein first, which can generate a high entropy zone. Now we have the counterweight for lowering entropy into all types of order.

The mitochondria does it all, in the sense it generates high entropy via metabolism, allowing its internal DNA freedom to lower entropy into order, with replication of mitochondria increasing when metabolism is high.

 

[exchemist]

yazata: i think that generally, you understand me very well. What i am saying is pretty simple and one doesn't have to be a professional to understand! The only problem is that maybe it is far too simple.
However, with respect to entropy, i am not saying that the entropy of a subsystem cannot decrease, but a subsystem in which entropy is always decreasing is not very probable to occur spontaneously in nature. It is more likely that actually the subsystems entropy is actually increasing, but the subsystem cannot realize this.

And yes! I think that subjectivity can play a role in the interpretation of entropy. I will give you an example: Imagine there is a large number of birds that are flying one next to other to the same direction.If we make them to fly one far from the other,so the group will start separating, the entropy of the system will start increasing.Imagine also that there are three birds inside the system that are very close to each other.If they separate with less speed than the others and we consider these 3 birds as a subsystem,the subsystems entropy will actually decrease relatively to the whole system of the birds.
In the same way, if a small subsystem of chemical reactions inside a bigger system is the reference frame for things like entropy of parts or the whole in this particular system, one can talk about entropy only in relativistic terms.

I think Yazata is right (as usual) and that your contention that entropy is subjective is thermodynamically unsound.

You need to recall what entropy increase really is. It all goes back to the the basic c.19th definition dS = dQ/T. It seems to me there is nothing whatsoever that is relative about that.

It is true that Statistical Thermodynamic relates this to the kinetic theory of matter, as expressed in partition functions and S = k ln W and so forth, but as I recall you always need to be very careful in how you define what you are doing when you work out what "W" is, in a particular situation, or you can get silly results.

If your answer seems to depend on the viewpoint of the observer, then warning bells should sound that there is likely to be something wrong with your analysis.

 

[wellwisher]

Entropy is a quantitative variable that is measured experimentally. Sometimes when describing what entropy is, the explanation creates confusion and makes entropy appear like an old fashion variable that is not quite real. But it is used and is needed to close energy balances.

For example, when ice melts into water, entropy increases because the liquid has more disorder. When water freezes into ice the entropy decreases. Entropy needs energy to increase. When we chill water, we draw out the energy away from entropy, causing the entropy to fall. When we melt ice, thermal energy is made available and will increase the entropy leading to the liquid state. This is one example of reversible entropy.

Water in the liquid state also transitions between high and low density domaines (bonded clusters of water) with the high density cluster having higher entropy and the low density cluster having lower entropy. These constantly shift back and forth causing local entropy cycling. Like the liquid water to ice, the cycling between high and low density cluster absorbs or releases energy, which can increase or decrease the local entropy, which can then help or inhibit the local chemical reactions; reversible equilibrium.

 

[Aqueous Id]

Life cannot be spontaneously generated in a world that favors low energy states and increasing entropy.

Yes it can, and yes it does. This simply ignores the only case for which the law of increasing entropy applies: closed systems.

Organisms are open systems therefore this argument does not apply. That is, organisms can not exist unto themselves without external energy sources to nourish them. Organisms do NOT spontaneously build complexity out of nothing but through exploitation of external raw materials and energy. There is a net increase in entropy in the closed system which includes all energy sources and sinks that an organism depends on to survive, plus the organism itself, enclosed all together inside a valid system boundary.

It is therefore false and incorrect to claim that organisms by themselves constitute closed systems. This argument becomes a deliberate lie when used to prop up absurdities of superstition and myth which pretend to claim that abiogenesis violates the laws of thermodynamics, by application of the fallacies of pseudoscience.

 

[mjs]

exchemist:
You forget that we are judging life. A system in which we are included.
For instance, in the case of bowling water, are entropy changes equally evident if the reference frame are 1) you (as an outside observer), and 2) a moving molecule inside the bowling water?
Besides, how good can you observe entropy changes caused by the motion of our solar system, our galaxy, our group of galaxies etc, and generally of systems inside we ourselves participate?

Aqueous Id:
Solar energy is a random form of energy coming to earth. Life of course is not a closed system, and of course entropy of life can decrease. However, I am amazed how easily most you say: ok! It happens always. Entropy is decreasing when an external source provides the system with energy. Its like bombing a city and assume that the entropy of the city will always decrease.

 

[mjs]

Despite the fact that living organisms are far too complicating in terms of reactions, and the interreactions with the environment makes it difficult to test whether they are actually random automaton reactions i will propose some ideas to overcome the difficulties.
So here are some proposed experimental testing of the approach i have previoulsy explained.

(Experiments must be performed in the simpliest life forms that is possible).
A If a living organism is a sum of random automaton chemical reactions as we previously explained, then the components of food intake are the first substrates and the excreted products are the last elements. By changing the food and also the pace of feeding, one can observe the way the organism performs some functions, for instance if the organism is an automaton, in certain feeding conditions one can observe extreme reproducible outlier values. The latter won’t be observed if the organism is self-regulating (self sustained).
B) Testing if feeding identical organisms (clones) with the same food in an identical manner and under identical conditions would produce exactly the same amount of waste products plus the error factor ε, (also known as noise), produced by various unpredictable factors. Only if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results.
The factor ε must follow a normal distribution as known by statistics.
C) If we have clones of the same simple organism and we study them into the same conditions and we give the exact food, then if these organisms are just random chemical reactions, their lifespan could be predicted as a result of multiple linear regression. The dependent variable y (or else the lifespan) would be: y=a+a1x1+a2x2+…….aνxν+aωxω+ε where ε is the error variable and x1,x2…xν the various explanatory variables and a,a1,a2…av the effects or regressor coefficients and aωxω measures the feeding speed effect.
If these clones share everything in common(e.g environmental factors, temperature etc) except the pace with which they are fed and if we secure that actually these organisms absorb exactly the same nutrients, but differ only in the pace they absorb them, then all the parameters of the linear regression will be the same for all clones except the speed factor, or else lifespan=y=aωxω+B+ε (where B=a+a1x1+a2x2+….avxv and it is the same for all organisms), or else we have a simple linear regression. Thus, if we avoid extremes in feeding pace and we assume no collinearities caused by it, then at a certain pace range we would expect lifespan to be linearly correlated with the feeding pace. (ATTENTION: The regressors x do not represent the reactions, but rather represent the effects of some “x” factors. Once again, if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results. I agree that it is difficult to completely isolate the system from all possible disturbing factors, but if their influence is chaotic and random for all experimental individuals, i think that their influence as a total can be satisfactorily represented by ε , or else the error term or noise in the formula of the final linear regression.
D) One can also test the way the living forms and their functions are decaying when they move to more hostile conditions on earth, such as extreme temperatures, deep ocean etc. Do they decay as if they where random chemical reactions or in an other way, e.g. self-sustaining organisms?
Any comments?

 

[exchemist]

exchemist:
You forget that we are judging life. A system in which we are included.
For instance, in the case of bowling water, are entropy changes equally evident if the reference frame are 1) you (as an outside observer), and 2) a moving molecule inside the bowling water?
Besides, how good can you observe entropy changes caused by the motion of our solar system, our galaxy, our group of galaxies etc, and generally of systems inside we ourselves participate?

Aqueous Id:
Solar energy is a random form of energy coming to earth. Life of course is not a closed system, and of course entropy of life can decrease. However, I am amazed how easily most you say: ok! It happens always. Entropy is decreasing when an external source provides the system with energy. Its like bombing a city and assume that the entropy of the city will always decrease.

mjs these are imaginary difficulties.

With regard to "bowling" (=boiling?) water, yes of course the entropy change is the same whether you are external or sitting on one of the molecules. All that is required is that you properly identify the system involved. There is no reason to think this cannot be done from within. For example, we humans are perfectly capable of calculating the thermodynamics of the Earth or larger astronomical systems. It's just rubbish to argue we cannot do so because we happen to be within the system in question.

Secondly, WHY are you amazed as how easily we say entropy of life or other subsystems can decrease? It is NOT like bombing a city and seeing a reduction in entropy. Not AT ALL. Firstly bombing is very destructive whereas solar energy is gentle. But the key point to remember is that any entropy decrease in life occurs in absolutely tiny decrements from one generation of the organism in question to the next generation. All the time a given generation is in existence there are entropy increases going on that are massively huge by comparison, associated with the metabolism death and decay of that generation at the end of its life. There is no continuous entity whose entropy is constantly decreasing. That is a creationist's myth.

 

[exchemist]

Despite the fact that living organisms are far too complicating in terms of reactions, and the interreactions with the environment makes it difficult to test whether they are actually random automaton reactions i will propose some ideas to overcome the difficulties.
So here are some proposed experimental testing of the approach i have previoulsy explained.

(Experiments must be performed in the simpliest life forms that is possible).
A If a living organism is a sum of random automaton chemical reactions as we previously explained, then the components of food intake are the first substrates and the excreted products are the last elements. By changing the food and also the pace of feeding, one can observe the way the organism performs some functions, for instance if the organism is an automaton, in certain feeding conditions one can observe extreme reproducible outlier values. The latter won’t be observed if the organism is self-regulating (self sustained).
B) Testing if feeding identical organisms (clones) with the same food in an identical manner and under identical conditions would produce exactly the same amount of waste products plus the error factor ε, (also known as noise), produced by various unpredictable factors. Only if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results.
The factor ε must follow a normal distribution as known by statistics.
C) If we have clones of the same simple organism and we study them into the same conditions and we give the exact food, then if these organisms are just random chemical reactions, their lifespan could be predicted as a result of multiple linear regression. The dependent variable y (or else the lifespan) would be: y=a+a1x1+a2x2+…….aνxν+aωxω+ε where ε is the error variable and x1,x2…xν the various explanatory variables and a,a1,a2…av the effects or regressor coefficients and aωxω measures the feeding speed effect.
If these clones share everything in common(e.g environmental factors, temperature etc) except the pace with which they are fed and if we secure that actually these organisms absorb exactly the same nutrients, but differ only in the pace they absorb them, then all the parameters of the linear regression will be the same for all clones except the speed factor, or else lifespan=y=aωxω+B+ε (where B=a+a1x1+a2x2+….avxv and it is the same for all organisms), or else we have a simple linear regression. Thus, if we avoid extremes in feeding pace and we assume no collinearities caused by it, then at a certain pace range we would expect lifespan to be linearly correlated with the feeding pace. (ATTENTION: The regressors x do not represent the reactions, but rather represent the effects of some “x” factors. Once again, if the organism is a system of random chemical reactions, it will behave mechanistically and will produce reproducible results. I agree that it is difficult to completely isolate the system from all possible disturbing factors, but if their influence is chaotic and random for all experimental individuals, i think that their influence as a total can be satisfactorily represented by ε , or else the error term or noise in the formula of the final linear regression.
D) One can also test the way the living forms and their functions are decaying when they move to more hostile conditions on earth, such as extreme temperatures, deep ocean etc. Do they decay as if they where random chemical reactions or in an other way, e.g. self-sustaining organisms?
Any comments?

Yes. This whole exercise seems pointless unless you can clarify the distinction you make between " random automaton reactions" and "self-sustaining" and why it is important.

 

[wellwisher]

Entropy is reversible in many chemical and physical instances. For example, we can start with liquid water. If we freeze the liquid into ice, the entropy of the water will lower. We can then melt the ice and cause the entropy to rise back to the original level. We can do this again and again. The connecting valuable is based on energy, via the heat of fusion. For entropy to increase, it needs to absorb energy, which in the case of ice to water, is the heat of fusion. When we freeze water, we extract the same amount of the heat of fusion from the entropy. This cycling back and forth is not based on randomness but on reproducible results. Life can regulate entropy by reversible processes and energy. Life will build protein and recycle the same protein, to maintain an entropy balance.

Water is key to life, because even within liquid water, the hydrogen bonding of water has two distinct states. One state defines higher entropy in the water and one state defines lower entropy in the water, with these reversible into each other, requiring only the addition, or slight loss of energy. Osmosis and reverse osmosis, due to membranes, brings another feature to water, in that pressure or pressure drop, can be used to increase or decrease entropy. This too is totally reversible and is very predictable and not random.

In chemical engineering, we can use an entropy increase to extract work, with the expected entropy increase, decreasing by the amount of the work we extract. System work plus final system entropy will equal the total input entropy. Let me give you a practical example. Let us use steam to run a turbine, to generate work. We add energy to liquid water to create high entropy steam. If we released it into the air, it would vaporize to form a cloud. With the turbine extracting work, the exit entropy of the steam goes down by the amount of work. The steam will cool and condense into water to reflect the loss of entropy because the energy in the entropy when into work.

When life generates work cycles it converts entropy to work causing less entropy than expected, if one does not take into consideration work cycles. Water is useful because it can be used as part of work cycles to generate more order than expected.

If we mix water and gasoline, and blend them with an agitator, we can increase the system entropy; system will absorb the agitation energy into an entropy increase. If we let this sit, it will spontaneously lower entropy into two layers. This is because the energy of the system will be too high, with the loss of energy pushing harder than the loss of entropy.

Say we add dry gas or methanol to this blend. This allows water and gasoline to blend and increase system entropy. If we extract the methanol, the system will lower entropy again into two phases, There are many way to tweak the entropy in reversible ways, with life using many of these.

 

[Fraggle Rocker]

Entropy is reversible in many chemical and physical instances. For example, we can start with liquid water. If we freeze the liquid into ice, the entropy of the water will lower. We can then melt the ice and cause the entropy to rise back to the original level. We can do this again and again.

As I have noted several times, the Second Law of Thermodynamics only says that entropy tends to increase over time. Spatially and temporally local reversals of entropy are possible, and indeed common.

As you point out, life is a perfect example. Plants grow, greatly increasing the organization (reducing entropy) within them. But the only way they can do this is to metabolize the energy in solar radiation, which lowers its frequency and reduces its organization (increasing entropy). The total entropy of the whole system (the solar system, or even the universe) has increased.

 

[mjs]

Lets now see some further implications of our presented model
1) Means that living organisms normally not die because the chemical reactions that are composing them are continuing happening. If we analyze all these reactions we will have a very good view to their homeostasis. We think that homeostasis is a very magical and perfect mechanism, because we are the result of homeostasis, but the theory that we analyzed says that homeostasis simply is the catalogue of the chemical reactions that are still happening, and just because they keep happening, the organism is alive. Its only a matter of our specific "inside the system" point of view.
2) Due to the fact that human is a very complicated system of reactions that all depend from each other, its logical to assume that it is almost impossible to treat compeletely a chronic disease with a single drug. The human body is not a car that we fix the part that is wrong and everything is ok. Instead, its reactions are so complicated, that (unless the illness is caused by a foreign agent e.g. a microbe, or by that lack of a substance that can be replaced), if there is a problem with a reaction this will lead to a chain reaction of problems to other reactions of the body as well. This mechanism is responsible for chronic diseases. The only way to treat completely this disease is to put back the initial reaction with the problem the way it was. Every other method will only reduce symptoms, but not cure. Additionally, it may treat a problem and cause the creation of another. A good example for this is the treatment of high blood pressure or cholesterol. We are not talking about healing, but for statistically significant improvement. Some studies also shows that there is no decrease in mortality even with the treatment of the risk factors. Another good example are rheumatic diseases. No complete cure exists. Drugs have many side effects in such a way that while one hole is closed, another is opened. Even in major diseases there is a big dissociation between the pathogenetic mechanisms that are discovered and effective treatments. This diference will continue growing if we dont realize that the mechanism that organism works is more complicated.
3) Another implication of the theory is that because the sum of the chemical reactions is a chain, it means that the cause of a disease maybe come from the organ that has the symptoms, but maybe not. An initial problem causes its irregularity, but depends of the vulnerability of each organ to see in which organ the symptom will be seen, because all the reactions communicate with each other, and when a problem exists its like a volcano and we dont know where will it explode.