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On the Lighter Side => New Theories => Topic started by: puppypower on 14/11/2019 20:11:15

Title: Are Water and the Organics copartners in life?
Post by: puppypower on 14/11/2019 20:11:15
If you started with a packet of baker's yeast, the yeast cells are initially dehydrated and show no signs of life. All the organics and ions needed for life are present, but there is no life. All we have an in inanimate powder. If we add water, suddenly the yeast come alive. Water is the like the straw that stirs the drink.

If we start with twenty packets of yeast, and to each we add a different solvent besides water, such as a variety of alcohols, aliphatic and aromatic hydrocarbons, aldehydes, ketones, liquid CO2, etc., life will not appear in any of these experiments.  In fact, nothing works properly down to enzymes. Even the DNA remains paralyzed.

The questions become what is so special about water? How can water animate all the organics and ions and then coordinate these so life can return? Since water is so special and a appears to be copartner for life, why doesn't medicine approach sickness and disease, from the water side?
Title: Re: Are Water and the Organics copartners in life?
Post by: Halc on 14/11/2019 20:48:04
If you started with a packet of baker's yeast, the yeast cells are initially dehydrated and show no signs of life. All the organics and ions needed for life are present, but there is no life.
It is very much alive (and not heavily dehydrated), but dormant, not particularly consuming resources, but that's why it helps to keep it in a cool place.  Frogs do this as well.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 14/11/2019 21:21:46
The questions become what is so special about water?
Two things, one is that it's an uncommonly good hydrogen bond former.
The other is that it's the solvent that life evolved to work with.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 14/11/2019 21:54:43
The questions become what is so special about water?
Two things, one is that it's an uncommonly good hydrogen bond former.
The other is that it's the solvent that life evolved to work with.

Water is the nanoscale environment, which set the potentials, in which organic life molecules formed and  evolved into life. If we started with a different solvent, with different potentials, the selection process is different. 

If we place life in the desert, that environment sets unique potentials. That which will be selected needs to harmonize with that environment. If we start with a nanoscale water environment, the potentials set by the water, runs the nanoscale selection process. Everything is hand picked by water which is why everything works, individually and globally, when water is added.  Other solvents would not select the same molecules as water and therefore will not be able to animate water base life organics, properly.

The question becomes what does a nanoscale water environment bring to the table? The DNA was selected. It is the most hydrated molecules in the cell. This is not coincidental but reflects a  goal of the water selection process.

One way to understand this last statement is to consider the system of water and oil. Water and oil to not want to blend but rather will try to separate to lower the surface tension that forms. The highly hydrated nature of the DNA reflects a molecule with low water surface tension. The DNA  hardly causes water any pain, in terms of induced potential. The DNA was a molecular sweet spot that also works well as a template.

Water and the organics of life are a type of tension of opposites; like water and oil. The water prefers organic molecules that don't create too much tension and potential. If they appear they will be modified to lower the potential. Al roads are leading to the same place. 
Title: Re: Are Water and the Organics copartners in life?
Post by: Kryptid on 14/11/2019 22:16:22
We don't know that alien life doesn't exist out there somewhere that utilizes something other than water.
Title: Re: Are Water and the Organics copartners in life?
Post by: evan_au on 15/11/2019 01:17:49
Quote from: puppypower
organics of life
Echoing Kryptid, we don't know that there isn't life out there that is non-organic (ie primarily based on some chemical other than carbon).
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 15/11/2019 11:50:54
We don't know that alien life doesn't exist out there somewhere that utilizes something other than water.

What you are saying has never been proven, even though it is science consensus convention. What we do know for certain is no other solvent, besides water, can make use of DNA as a template material. Therefore, one would need, at the very least, to engineer an alternate genetic material, suitable for another solvent, before an alternate solvent theory can be considered  more than consensus speculation. Nature already engineered DNA which makes my job easier. I only need to reverse engineer to figure out why DNA should be the default.

What water brings to the table is the water-oil affect. This mutually opposing affect between water and organics, allows water to pack protein with repeatable folds. Water is selfish and will fully or partially exclude organics, in various ways, to maintain its own stability. Most of the others solvents are too energy friendly with organics, resulting in too much randomness during packing and operations. Water is at the only one who is able to force the proteins to pack is a repeatable way, due to the needs of water; nano-environment, coming first. The packing of protein has been shown to involve no randomization. Even after over 50 years of the first demonstration of this, there is still no statistical explanation for a packing probability of 1.0; water-oil affect.

Below are two energy landscape diagrams which show  unpacked and packed protein in water, respectively. The peaks in the top diagram represent the energy potential between water and the various organic side groups of the protein, with hydrophobic groups the tallest peaks. These will pack first and then the lower peaks will pack next, etc., reduce this potential in the most efficient way.

The second diagram is a packed protein in harmony with the energy needs of water. There is a deep trench.  This is very stable and helps to maintain the protein during its busy day. Water packs the protein with a sequential and repeatable energy based priority. Organic solvents, speculated for alternate life, will generate a different first and second diagram, with the peaks reversed and/or smaller. This results in different packing priorities and more randomness. After making an alternate solvent version of DNA, you might even need to make a new protein replacement to mimic water's energy landscape diagrams, so you can eliminate randomness, as does water.

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fdry_surface.gif&hash=ca26beafa189a7bb5bc8e0c30e78b26a)

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fwet_surface.gif&hash=8cffe8ebc13a8ff63ef455b29240c52f)
Title: Re: Are Water and the Organics copartners in life?
Post by: Kryptid on 15/11/2019 17:22:38
What you are saying has never been proven

I never said that it had been.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 16/11/2019 12:04:09
The discussion of possible alien life with other materials, although interesting, is not critical to the discussion at hand. The topic is whether water and organics are copartners in life. If we wished to speculate about possible life on other planets, the question would become, If we used other solvents to evolve life on another planet, would the structural phase be copartners with the solvent phase?

This question is inferred from the observation that all the structures will need to evolve within that solvent. There will be a natural selection process at the nanoscale. For life or form the selection process will be such that the structural phase and the solvent phase need to be able to take advantage of the properties of each other, so the team can become more than the sum of its parts; something extra called life. 

In the case of water-solvent phase and organics-structural phase, neither can create life without the other, but combined something special happens, that is more than the sum of its parts. In terms of life on earth, what water brings to the game is connected to hydrogen bonding. More specifically, it is connected to hydrogen bonding connected to the oxygen atom. Not all solvent phase based hydrogen bonding is created equal.

If we look  methane, ammonia and water, although  they all have the same molecular weight, their  boiling points are -161.5C, -33.34C and +100C, respectively. These difference reflect the strength of the intermolecular liquid bonding forces. Liquid Methane is held together by van der Waals forces which are weak binding forces, Ammonia is held together by hydrogen bonding, which is an improvement over methane in terms of strength, but ammonia is well below the binding forces within water. Hydrogen bonding is not the entire story.

Although Oxygen; water and Nitrogen; ammonia can both can form hydrogen bonds, the electronegativity of Oxygen is stronger than Nitrogen. Electronegativity is a relative measure  of how strong an atom attracts and binds electrons. Oxygen's has a slightly higher affinity for the electrons of its hydrogen in water, than Nitrogen has for the electrons of its hydrogen in ammonia. The result si the hydrogen of water end up with a slightly stronger positive charge, and oxygen ends up with slightly more negative charge for the hydrogen bonds.

But beyond that, since water is H2O and ammonia is H3N, water has a symmetry in terms of hydrogen and available electrons for hydrogen bonding; 2 and 2, whereas  ammonia is asymmetrical with respect to hydrogen and available electrons; 3 to 1. The result is water can form extended structuring in the liquid phase; fours hydrogen bonds loosely similar to carbon's four covalent bonds. Ammonia's hydrogen bonding is more restricted to nearest neighbors due to steric  problems causes by the asymmetry. This is main reason  ammonia has such a low boiling point even with hydrogen bonds. 

The higher boiling point of water, with is considered an anomaly in nature, reflects the liquid matrix of water having tremendous self adhesion, stabilized by an extended hydrogen bonding matrix; water polymers based on hydrogen bonding. This unique  liquid phase stability is a strict selection environment for organic materials since few organics can coexists with the water and not cause the water potential to increase. Water is always pushing and pulling, tugging and tucking, and even reacting, to minimize internal potential.

Other solvents would do the same but with less strength than water. Water is the most strict, in terms of selection process, based on Free Energy Potential considerations. DNA was going to be the choice even when this all started since it is very cooperative; extreme hydration. 

 

Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 17/11/2019 12:44:49
To understand water, and hydrogen bonding in water, you need to look at oxygen. Oxygen, which is  highly electronegative (second behind only Fluorine), can form oxide which is O-2. This is a state of an oxygen atom where it has two more electrons than it has nucleus protons.

If you think in terms of the electrostatic force, this should be very unstable. The two extra electrons should charge repel due to the excess of negative charge beyond the number of nucleus  protons. Yet, oxygen can greedily scavenger extra electron density, beyond neutral charge, from almost all other atoms. This is called oxidation. Oxygen can take electrons from neutral atoms to form charge imbalances everywhere in nature. This includes carbon and nitrogen.

The reason this can occur is the electromagnetic force or EM force, has both electrostatic as well as magnetic components. These are separate forces, but in the EM force they work together as a team. In the case of oxygen, even though the electrostatic force aspects is repulsive and unstable; oxide, the magnetic component, due to the extra electrons in orbital motion, is much stronger than the electrostatic repulsion, making this stable in terms the unified EM force. Oxygen is heavy on the magnetic side of the EM force, when it completes the octet of electrons.  A charge in motion will create a magnetic field, that can add with other magnetic fields; right hand rule.  The three p-orbitals (x,y,z) create a 3-D magnetic addition which is very strong in oxygen.

A hydrogen bond has both electrostatic; polar, as well as covalent bonding character. The strong magnetic component of the EM force of the oxygen atom, puts shared electrons  into play as part of its internal magnetic addition. The self ionization of water to form the phenomena we call pH, is based on the oxygen able to magnetically hold the extra electron and turn the covalent bond with  the hydrogen into a polar bond. H2O ----> H+. and OH-. In water, the line between covalent and polar bonding become blurred because of oxygen.  This is mediated by hydrogen bonding.

The blurring of the line between covalent and polar bonding within water imparts some unique properties to water that are centered on hydrogen bonding. A hydrogen bond can form between two waters molecules. This hydrogen bond can stay polar; charge attraction, or the oxygen can change the EM equilibrium from polar to a covalent attachment, while giving up the covalent bond of one of this other hydrogen, which now becomes a covalent part of another water molecule; swap partners.

In terms of life, this switching in bonding states can be used as a binary switch to transmit information, without disrupting basic structural states. The hydrogen bond junction maintains stability as it switches between these two bonding states. These different states have slightly different properties in terms of bond length, entropy and enthalpy.

These switches do not just have the potential to transmit binary information, but the switch also has local energy and muscle. Below is water clusters, where many of the hydrogen bonds in the cluster are flipping switches, causing the cluster to expand or pucker. It becomes a little binary information pump, with mechanical-free energy. Liquid water is a crowded place, with an expanded cluster able to expand and muscle its neighbors, will also decreasing the local entropy and enthalpy. This can useful to enzymatic actions while also reflecting global information flow.

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fcluster_equilibrium_2.gif&hash=f239deea87c5e020e05a82a42e27554e)



Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 19/11/2019 11:55:26
Picture a pure aqueous continuum of liquid water where the water molecules are hydrogen bonded in extended water structuring. This extended structuring imparts extra free energy stability to the continuum, leading to a very high boiling point for such a small molecule. One needs to add energy to break through the various layers of ordering.

Also the oxygen atom, due to being heavy on the magnetic side of the EM force, is able to blur the line between polar and covalent bonding between oxygen and hydrogen. This can result in resonance type structures with hydrogen bonding, referred to as cooperative hydrogen bonding, where electrons become share with a cooperative of water molecules. This is very stable. More about cooperative hydrogen bonding another time.

If we were to add any carbon compound, polar or non polar, these will all have a detrimental affect on the aqueous continuum, at some level of the extended structuring. This will cause free energy to rise to various degree within the water. The water will respond, through information transfer and attempt to minimize the impact, often locally, with water clustering around the invader, trying to shield the continuum.

In terms of a living cell, the organic material are numerous, and many are composed of large structures of various compositions, arranged with a type of order; organelles. This structuring is placed throughout the aqueous continuum. The aqueous continuum extends from inside to outside the cell. Water is continuous and can freely flow through the membrane in both directions.

What this situation does is impact a range of potentials within the aqueous continuum.The scaffolding protein help to  set this up as a fixed gradient from the membrane to the DNA. The water in the cell is induced to more or less a permanent free energy potential gradient by the organics.

This aqueous potential gradient imparts free energy potential to the organic surfaces through surface tension and other affects. While information transfer through the hydrogen bonding of water will attempt to equilibrate and minimize the potential gradient. This strategy cannot easily be accomplished due to the fixed organic structuring. It has to be accomplished via the movement of smaller materials. However, the catalytic action of enzymes, by changing these smaller materials,  reestablishes the potential gradient. It is loosely like water and oil trying to separate but each time we add a shot term surfactant to disrupt the growing bubbles. .

When we dehydrate a yeast cell, life is made dormant; hibernation. There is not enough water to establish all the potentials throughout all the organic gradients at sufficient levels. As we rehydrate the cells the potentials build as the organic grid reforms fully hydrated configurations. Then life returns as water tries to equilibrate and lower the potentials within a catalytic grid.

 
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 20/11/2019 15:09:05
Cells pump and exchange cations at the outer membrane. This action results in the inside of the cell accumulating Potassium Ions and the outside of the cell accumulating Sodium ions. Although both ions have a single positive charge, each ion impacts water in different ways. This is based on the strength of hydrogen bonding being in the middle between the two. The Potassium ion than Sodium, is larger which changes the charge affect, slightly.

Sodium ions are considered kosmotropic or they will create more order in water than water creates in its pure from hydrogen bonding. Potassium ions are chaotropic and will create more disorder in water than is found in pure water using hydrogen bonding. When cells expend energy pumping, exchanging and concentrating these ions, they also will create different aqueous environments inside and outside the cell, separated by the cell membrane.

Cells help attract food toward their outside surfaces, by establishing a kosmotropic external aqueous environment; Sodium ions, outside the cell. The kosmotropic affects adds more order and stability to the water, than pure water. This means water can give up some of this stability, and still be just as good as pure water. Therefore the outer water can handle a modest amount of organic material in solution, since it can absorb the added potential. The transport proteins will continually lower the concentration, thereby resetting the long range fetch potential.

The inside of the cell, by accumulating Potassium ions, which is chaotropic, has the opposite affect. The water now has too much potential compared to pure water. The water has to work harder on everything inside the cell to compensate for the Potassium ions. One important affect occurs on active surfaces. Cooperative aqueous hydrogen bonding will occur. This can be exploited to provide free energy in the form of entropy.

In cooperative hydrogen bonding, as more hydrogen bonds form this water polymer, each dded bond makes the cooperative stronger and stronger. This reflects a type of resonance with extended electron sharing via the Oxygen and hydrogen bonding. The line between polar and covalent bonding breaks down and electrons start to cooperate over distance in the cooperative. This adds more partial covalent character to the cooperative making it very stable; low energy.

Essentially, because of the chaotropic affect of the Potassium, active surfaces become covered with a cooperative net of water; surface tension. This helps to balance it out. ATP is important in terms of these water cooperatives. When ATP reacts with the enzyme, a water molecule is added to the ADP residue. This water molecule is extracted from the cooperative. The affect is similar to a bolt cutter, cutting a high tension cable; recoil. This recoil increase the local water entropy;  free energy boost for the enzyme action.

An interesting observation is that if you were to take off the outer membrane of a cell, Potassium ions still accumulate in the cell. This implies there is a water equilibrium between the Potassium and the protein surfaces in terms of the potentials needs of water. In other words, the protein surfaces appear to be kosmotropic and adds stability to the water so it can handle the extra Potassium to balance things out.

This creates plausible scenario for the early protein selection process. If you had ion pumping forming early, and potassium was forced to accumulate inside the cell, proteins with kosmotropic surfaces would be selected since they would have an water energy advantage. 
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 24/11/2019 14:30:12
Water also brings to the table, a fifth force of nature, that is common to life. This force has been referred to as the life force. The fifth force, in physics terms, is the entropic force or a force that is generated by entropy. This fifth force can be demonstrated in the lab and can be explained with osmosis.

Osmosis is a colligative property. What that means is osmosis and osmotic pressure is not dependent on the character of the solute that is dissolved in water. It is only dependent on the concentration. This means if we used positive or negative ions or neutral molecules, as the solute, as long as the concentration is the same, the same osmotic pressure will be generated.

What a colligative property means is the force, that creates the osmotic pressure =entropic force/area, is not dependent on the EM force, or else charge and magnetic affects would make a difference. It is independent of the EM force. It is a separate force created by entropy.

Osmosis requires a semi-permeable membrane, separating water with different concentrations of solute on either side of the membrane. The water can move freely through the membrane, but the solutes cannot. The movement of the water will be in response to the concentration gradient, with the goal of balancing the concentration of solute on both sides of the membrane. This diffusion of the water reflects the second law in action. During the nanoscale selection process, water picked membrane molecules that were tailored to its own needs; it is the mobile phase.

Reverse osmosis allows us to use mechanical pressure, to reverse this situation. We can add pressure to push water back in reverse and selectively decrease the water entropy, by a very exact amount based on the pressure we apply. This induced entropic potential, can use for various things. Entropy is often associated with randomness and complexity, but water, via osmosis, has a way to stockpile entropy and reverse complexity, which is a good tool for selection processes.

This entropic potential can be exploited as entropic force; mechanical muscle. Or it can be expressed as entropy, not connected to entropic force. Water for example, demonstrates quantum tunneling affects with the hydrogen proton. This often occurs with proton pairs, which is somewhat unique. Theoretically, free energy within the entropic potential could be used for quantum affects, rapid bleed off. The entropic force is not your average force since it is not based on attraction, per se. It has more in common with repulsion. Mutations would be a possible application.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 24/11/2019 16:59:12
Water also brings to the table, a fifth force of nature, that is common to life. This force has been referred to as the life force. The fifth force, in physics terms, is the entropic force or a force that is generated by entropy. This fifth force can be demonstrated in the lab and can be explained with osmosis.

Osmosis is a colligative property. What that means is osmosis and osmotic pressure is not dependent on the character of the solute that is dissolved in water. It is only dependent on the concentration. This means if we used positive or negative ions or neutral molecules, as the solute, as long as the concentration is the same, the same osmotic pressure will be generated.

What a colligative property means is the force, that creates the osmotic pressure =entropic force/area, is not dependent on the EM force, or else charge and magnetic affects would make a difference. It is independent of the EM force. It is a separate force created by entropy.

Osmosis requires a semi-permeable membrane, separating water with different concentrations of solute on either side of the membrane. The water can move freely through the membrane, but the solutes cannot. The movement of the water will be in response to the concentration gradient, with the goal of balancing the concentration of solute on both sides of the membrane. This diffusion of the water reflects the second law in action. During the nanoscale selection process, water picked membrane molecules that were tailored to its own needs; it is the mobile phase.

Reverse osmosis allows us to use mechanical pressure, to reverse this situation. We can add pressure to push water back in reverse and selectively decrease the water entropy, by a very exact amount based on the pressure we apply. This induced entropic potential, can use for various things. Entropy is often associated with randomness and complexity, but water, via osmosis, has a way to stockpile entropy and reverse complexity, which is a good tool for selection processes.

This entropic potential can be exploited as entropic force; mechanical muscle. Or it can be expressed as entropy, not connected to entropic force. Water for example, demonstrates quantum tunneling affects with the hydrogen proton. This often occurs with proton pairs, which is somewhat unique. Theoretically, free energy within the entropic potential could be used for quantum affects, rapid bleed off. The entropic force is not your average force since it is not based on attraction, per se. It has more in common with repulsion. Mutations would be a possible application.
Reverse osmosis can be made to work with essentially any solvent.
There's nothing special about water and RO.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 25/11/2019 12:41:14
Water also brings to the table, a fifth force of nature, that is common to life. This force has been referred to as the life force. The fifth force, in physics terms, is the entropic force or a force that is generated by entropy. This fifth force can be demonstrated in the lab and can be explained with osmosis.

Osmosis is a colligative property. What that means is osmosis and osmotic pressure is not dependent on the character of the solute that is dissolved in water. It is only dependent on the concentration. This means if we used positive or negative ions or neutral molecules, as the solute, as long as the concentration is the same, the same osmotic pressure will be generated.

What a colligative property means is the force, that creates the osmotic pressure =entropic force/area, is not dependent on the EM force, or else charge and magnetic affects would make a difference. It is independent of the EM force. It is a separate force created by entropy.

Osmosis requires a semi-permeable membrane, separating water with different concentrations of solute on either side of the membrane. The water can move freely through the membrane, but the solutes cannot. The movement of the water will be in response to the concentration gradient, with the goal of balancing the concentration of solute on both sides of the membrane. This diffusion of the water reflects the second law in action. During the nanoscale selection process, water picked membrane molecules that were tailored to its own needs; it is the mobile phase.

Reverse osmosis allows us to use mechanical pressure, to reverse this situation. We can add pressure to push water back in reverse and selectively decrease the water entropy, by a very exact amount based on the pressure we apply. This induced entropic potential, can use for various things. Entropy is often associated with randomness and complexity, but water, via osmosis, has a way to stockpile entropy and reverse complexity, which is a good tool for selection processes.

This entropic potential can be exploited as entropic force; mechanical muscle. Or it can be expressed as entropy, not connected to entropic force. Water for example, demonstrates quantum tunneling affects with the hydrogen proton. This often occurs with proton pairs, which is somewhat unique. Theoretically, free energy within the entropic potential could be used for quantum affects, rapid bleed off. The entropic force is not your average force since it is not based on attraction, per se. It has more in common with repulsion. Mutations would be a possible application.
Reverse osmosis can be made to work with essentially any solvent.
There's nothing special about water and RO.

This is true and can be demonstrated in the lab. However,  life as we know it evolved in water and water was able to select suitable membrane material that makes the entropic force possible, without the need for synthetic materials.

Life forming in other solvents not only requires new and unique genetic material, it also requires ways to form protein equivalents. It also requires ways to induce and take advantage of the entropic force so it can control entropy. Unique protein packing controls entropy so this can be repeatable and not subject to randomness.

The term, hydrophobic, is a misnomer when it comes to water and organics. Water does not have a phobia for organic materials. Water can form weak hydrogen bonds with any organic materials including graphite nanotubes. These bonds are not as optimized as in pure water. Water is not afraid to do this, but can do better if it sticks with other water.

If water has to form hydrogen bonds with organic materials these bonds are shifted more to the polar side of hydrogen bonding; van der Waals. The water can compensate, internally, by forming more covalent character in the remaining hydrogen bonds it has with other water.

This covalent reassignment is based on the magnetic aspect of oxygen This stretches the water to water hydrogen bonding into tension, so the partial covalent bonding orbitals can overlap properly; surface tension. The net affect is water can deal with organic membranes in a way that allows semi-permeable membranes while helping the affect. Water has a backup plan for everything it selects.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 25/11/2019 13:19:17
However,  life as we know it evolved in water
What about life as we don't know it?

It's entirely possible (though unlikely) that tomorrow, someone will make the discovery of a life form that doesn't depend on water .

At that point it will become as clear to you that you are posting nonsense as it is already clear to the rest of us.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 28/11/2019 00:28:19
However,  life as we know it evolved in water
What about life as we don't know it?

It's entirely possible (though unlikely) that tomorrow, someone will make the discovery of a life form that doesn't depend on water .

At that point it will become as clear to you that you are posting nonsense as it is already clear to the rest of us.


Science is supposed to be grounded on fact and evidence, and not a consensus of believers. I respect religions of all kinds, and I am trying to be respectful of other people's faith. However, everyone can offer proof that life can form in water, but nobody from the consensus of faith, can offer hard proof that life can form in other solvents. Everyone is assuming a random event can make this happen, but the god of random is under control within life due regulating the entropic force.

At the very least the consensus should be able to show a type of genetic material that can copartner with a proposed alternate solvent, since DNA does not work without water. That would make it more than just faith. I am trying to offer chemical logic for my belief.

Let me build a bridge and create an educational scenario, where I will parter with the consensus of faith. In this scenario, we are on planet of that has a wide range of  conditions, such that life somehow appears in a wide range of solvents. If this was to happen, water would have selective advantage and be the last life standing.The main reason is, if you burn any organic solvent, in the presence of oxygen, one of the terminal products is water.

Most organic solvents and ammonia have too much internal energy; reduced. If life could somehow form in alcohols, ammonia, and hydrocarbons, etc., there would come a day where that life would starts to extract energy from its solvent; eat is own solvent. It wont be long until that life would burst into flames. Water based life, cannot extract energy from water, since this is a terminal chemical product, already. Oxygen cant go much further.

But before this happened, the energy bandwidth between other organic solvent and cellular synthesis would be smaller, compared to water. Water life woul be more vigorous.  Water based life can burn any organic as food, with the terminal products of combustion added to the solvent pool.

Hydrogen, helium,  oxygen then carbon are the four most abundant atoms in the universe, respectively. While hydrogen; H2 and H2O are the two most abundant molecules in the universe. Between H2 and H2O is the entire energy bandwidth of water based life. Although it is very rare to find life that can eat hydrogen gas since this is very hot. However, water does have excellent heat capacity.





Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 28/11/2019 00:47:41
Science is supposed to be grounded on fact and evidence,
That's right.
Now, please show me the evidence that life without water is impossible.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 28/11/2019 00:50:08
Oxygen cant go much further.
Nor can nitrogen, in a hypothetical world based on ammonia, rather than water.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 28/11/2019 16:40:23
Science is supposed to be grounded on fact and evidence,
That's right.
Now, please show me the evidence that life without water is impossible.

It is hard to prove a negative, which is why science is more geared to proving a positive; tangible and repeatable. For example, we cannot disprove God, since it would take infinite experiments to make sure we cover all the bases. Anything less still leaves reasonable and unreasonable doubt. 

I have been building chemical background in terms of water and hydrogen bonding. Now I would like to discuss some practical equilibrium applications beginning with DNA. DNA is the most hydrated molecule in the cell. This is due to the phosphate, sugar and nucleic acid aspects, all able to form hydrogen bonds with water, leading to secondary and tertiary water structuring around the DNA. Water even forms a double helix along the minor and major grooves.

Although DNA is considered the most hydrated molecule in the cell, pound for pound, RNA is even more hydrated than DNA.  DNA has the status of being the most hydrated due to its huge double helix nature and size. RNA, although smaller, contains a slightly different base distribution and an extra -OH group in its sugar  group compared to the DNA. This adds even more hydrogen bonded water for any given length.

When RNA is formed on the DNA, extra hydration is added to the nucleus water, compared to pure DNA and water. The use of the DNA as a template to form RNA brings the nucleus water even closer to the stability of pure water. The formation of RNA on DNA was inevitable, since it assists in the furthering of water stability.

Organics in water create potential in water; surface tension. This creates a self induced potential for change. This change does not apply to water, since water is already a  stabile terminal product of high energy reactions. The organics will need to change, with the formation of RNA reflecting a lowering of the slight residual potential between DNA and water. 

DNA does not maintain a linear configuration within the water of cells. It is usually packed with packing proteins, which are rich in the amino acids arginine, lysine and histidine. These are basic proteins. As shown below, the polar end can hydrogen bond to water which increases water stability. However, these amino acid also contain organic separators that create surface tension closer to the peptide linkage. To optimize water potential, in the nucleus, the packing proteins become shielded by the DNA; wrap around and pack. 

The water is inducing this elaborate co-polymer packing arrangement to minimize the water potential; high and low potential molecules are combine to make medium potential co-polymers. When unpacking enzymes reverse this and unpack the DNA, for RNA transcription, this reflects a movement down the slight energy hill of packed DNA;  lowering the water potential.

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww.cryst.bbk.ac.uk%2FPPS2%2Fcourse%2Fsection2%2FSideChains%2Fbasic.gif&hash=847efe31c7006595f1b1f38392524c13)
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 28/11/2019 17:07:37
DNA is the most hydrated molecule in the cell.
Says who?
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 29/11/2019 11:57:10
DNA is the most hydrated molecule in the cell.
Says who?

http://www1.lsbu.ac.uk/water/nucleic_acid_hydration.html (http://www1.lsbu.ac.uk/water/nucleic_acid_hydration.html)

Quote
Nucleic acid hydration is crucially important for their conformation and utility [1093], as noted by Watson and Crick [828]. The organized hydration extends to several nanometers from the surface. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character [542b]. The DNA double helix can take up several conformations (for example, right-handed A-DNA pitch 28.2 11 bp, B-DNA pitch 34 10 bp, C-DNA pitch 31 9.33 bp, D-DNA pitch 24.2 8 bp and the left-handed Z-DNA pitch 43 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration. Lowering the hydration (for example by adding ethanol) may cause transitions from B-DNA to A-DNA [2784] to Z-DNA.

This can be inferred from the huge size of the DNA, in conjunction with organized hydrogen bonding extending several nanometers beyond the DNA, with these aqueous intersections far greater than in proteins due to their ionic content on DNA.

What is also cool is DNA exists in many conformation with the dominate conformation of life; B-DNA, the most hydrated, Water has been moving the scale over time such that the present reflects maximum hydration in terms of the 3-D DNA conformation.

The bases of DNA have also been designed with water in mind.  Below are the base pairs and the hydration sites connected to thebasl pairs. Years ago I wondered why there were more hydrogen bonding sites than needed by the base pairs, since DNA in textbooks was always shown as being water free. It turns out these extra sites had been earmarked for water.

In the context of the entire DNA, these hydration sites within the base pairs, are all connected with other water and form a double helix of water that runs along the axis of the DNA, in the major and minor grooves. DNA is actually a copolymer of DNA-water with each having a double helix. This should be how DNA is presented in text books, so the students will start to ask new questions.

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fnuclei.gif&hash=5a231e78c151e6b5f59a7808a36702ee)

Quote
The processing of the genetic information within DNA is facilitated by highly discriminatory and strong protein binding. It has been shown that the interfacial water molecules can serve as 'hydration fingerprints' of a given DNA sequence [889]. The usual 'hydration fingerprint' of the DNA is disrupted by DNA damage, and this facilitates repair protein attachment. The hydration spine (see above) is capable of carrying messages, as facilitated proton movement down the water wire, between binding sites in a similar, if complementary, manner to the electron transfer through the DNA residues [2258] and so coordinate the repair process.
 
The primary driving force for the specificity of protein binding is the entropy increase due to the release of bound water molecules (estimated at 3.6 kJ ˣ mol-1 for minor groove water and 2.3 kJ ˣ mol-1 for major groove water, both at 300 K [1096]), c with the DNA sequence determining the hydration pattern in the major and minor grooves (see above).

This bring us back to entropy and the control of entropy. The aqueous hydrogen bonding on the DNA allows water to form cooperative hydrogen bonds, which are similar to partial resonance structures. Oxygen is mediating the blur between polar and covalent bonding. This organization of the water, lowers the water's entropy. The cooperative is low enthalpy and low entropy, but free energy favorable. Protein attachment disrupts the cooperative; bolt cutter and recoil, causing an entropy increase in the water. This change in free energy helps the enzyme.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 29/11/2019 12:31:48
Quote from: Bored chemist on Yesterday at 17:07:37
    Quote from: puppypower on Yesterday at 16:40:23
        DNA is the most hydrated molecule in the cell.
    Says who?

http://www1.lsbu.ac.uk/water/nucleic_acid_hydration.html


So, nobody actually said it (that page doesn't).

DNA is actually held together by hydrophobic interactions
https://phys.org/news/2019-09-dna-held-hydrophobic.html


Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 30/11/2019 11:50:10
Quote from: Bored chemist on Yesterday at 17:07:37
    Quote from: puppypower on Yesterday at 16:40:23
        DNA is the most hydrated molecule in the cell.
    Says who?

http://www1.lsbu.ac.uk/water/nucleic_acid_hydration.html


So, nobody actually said it (that page doesn't).

DNA is actually held together by hydrophobic interactions
https://phys.org/news/2019-09-dna-held-hydrophobic.html

I did read somewhere in Dr Chaplin's online book that DNA is the most hydrated molecule in the cell, however i cannot find it quickly. It can also be inferred from what I posted since the DNA of a human cell is about 2-3 meters long, which in longer than proteins.

As far as DNA held together with hydrophobic interactions this is true. However, it does not tell the whole story of why DNA has been designed as it is. In a way, similar to protein folding, the hydrophobic groups on the sugar and bases on a single helix of DNA, are peaks on the energy landscape diagram for DNA. These energy peaks are with respect to water. Water can lower its internal potential; surface tension, by having the hydrophobic groups pack so they can be shielded from the aqueous continuum. This forms the double helix.

The bases and sugars of the DNA not only have hydrophobic groups, but also contain polar groups which can form hydrogen bonds with water as well as base pairs. The net affect is the hydrophobic interactions are moderated, by the hydrogen bonded water, making the DNA more reversible. Unlike the proteins which are designed to maintain a more permanent configuration, the DNA is designed to be reversible because of the internal aqueous hydrogen bonding that is working in opposition to the hydrophobic interactions.

This energy landscape situation places the phosphate groups on the outside, with the many oxygen of phosphate able to participate in hydrogen bonding with the bulk water. The  (PO4)-1 group is considered chaotropic, or binds to water weaker than water binds to itself via hydrogen bonding The net affect is the surface phosphate groups participates in hydrogen bonding with the aqueous continuum, but in a slightly weakened way, which also helps reversibility.  The chaotropic nature of the  (PO4)-1 group also makes it easier to shift to and from packing proteins.

The observed methylation and carboxylation of the DNA have opposite affects in terms of reversibility. Methylation by adding additional organic; methyl groups, increases the hydrophobic impact of the core and makes it harder to reverse. While carboxylation, by adding a hydrogen bonding group shifts the interior of the helix toward water side and makes it easier to reverse.

If we look at RNA versus DNA, RNA has an extra -OH group on its sugar; ribose. This adds to the hydrogen bonding of the water side and increases reversibility. RNA also contains one different base; uracil compared to the DNA; thymine, which differs by the loss of a methyl group of thymine.  These combined affects allows the RNA to overcome the weaker hydrophobic bindings making it a single helix in water.

(https://www.thoughtco.com/thmb/1cwY848JIA9rCh2wtz45ZPfG6y0=/768x0/filters:no_upscale():max_bytes(150000):strip_icc()/dna-versus-rna-608191_sketch_Final-54acdd8f8af04c73817e8811c32905fa.png)
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 30/11/2019 11:59:29
DNA is the most hydrated molecule in the cell.
Define "most hydrated".
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 02/12/2019 20:39:34
DNA is the most hydrated molecule in the cell.
Define "most hydrated".


One way to define to hydration is connected to the water that remains, attached to a molecule, after the molecule has been centrifuged. The water that does not come off with a centrifuge, is  chemically bound, whereas physically bound water will be removed by a centrifuge.

Wet cotton clothes in the wash machine can hold a lot of physically bound water. This water is released during the spin cycle. Chemically bound water is water that will remain chemically bonded, via hydrogen bonds, even if the spin cycle used a centrifuge. In the case of the DNA, because it such a long molecule with a lot of hydrogen bonding sites, the chemically bound water is very large in terms of total number of water molecules.

Another way to define hydration is with a physical chemical term called activity. The activity of water is defined as the amount of available hydrogen bonding capacity, within a water solution. The activity of pure water s defined as 1.0, and as we add things to the water, and water interact via aqueous hydrogen bonding, the activity falls below 1.0.

Say we started with a hundred beakers each with a small amount of water; 1ml.  The water begins as pure water with an activity of 1.0. To each beadier we add "one" molecule of various substances, The beaker with the DNA will lower the activity the most. DNA is so huge and has many places to directly bind water. This orders the water and also impacts secondary water, so the activity of that beaker lowers the most.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 02/12/2019 22:20:46
So, the water in a test tube, since it will stay in the tube if it is centrifuged is water of hydration by your definition.
You seem not to have noticed that your statements are contradictory.
A spin dryer is a centrifuge.

Say we started with a hundred beakers each with a small amount of water; 1ml.  The water begins as pure water with an activity of 1.0. To each beadier we add "one" molecule of various substances, The beaker with the DNA will lower the activity the most. DNA is so huge and has many places to directly bind water.

Imagine, instead that you add 1 milligram  of various substances.
Sugar and salt will be more hydrated than DNA.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 04/12/2019 12:04:34
So, the water in a test tube, since it will stay in the tube if it is centrifuged is water of hydration by your definition.
You seem not to have noticed that your statements are contradictory.
A spin dryer is a centrifuge.

Say we started with a hundred beakers each with a small amount of water; 1ml.  The water begins as pure water with an activity of 1.0. To each beadier we add "one" molecule of various substances, The beaker with the DNA will lower the activity the most. DNA is so huge and has many places to directly bind water.

Imagine, instead that you add 1 milligram  of various substances.
Sugar and salt will be more hydrated than DNA.

I think we can add jello to the list.

I think we are loosing track of the forest because of the trees. My original claim was "most hydrated molecule in the cell". I was comparing DNA, RNA, protein and other large molecules in the cell. This status as most hydrated is important because it implies the DNA represents one pole of the cellular aqueous gradient. It has a place on top of the aqueous hierarchy. In other words, organics in water create potential as surface tension in water. The internal structures within cells, by being different, impact different the local potentials in water, differently. DNA is at the low end of this potential grid. This grid is important for coordination and it sets the potentials for directional material flow as a way to lower the potential. The catalytic grid resets the potentials.

The topic is the copartnership of the organics of life and the water of life. I am trying to rough in the bigger picture since life exists from cells to multicellular. SInce, you are interested in the hydration of DNA, below is a more detailed analysis.

Quote
Thus, in B-DNA, guanine will hydrogen-bond to a water molecule from both the minor groove 2-amino- and major groove 6-keto-groups with further single hydration on the free ring nitrogen atoms (minor groove N3 and major groove N7). Cytosine will hydrogen-bond to a water molecule from both the major groove 4-amino- and minor groove 2-keto-groups. Adenine will hydrogen-bond to a water molecule from the major groove 6-amino-group with further single hydration on the free ring nitrogen atoms (minor groove N3 and major groove N7). Thymine (and uracil, if base-paired in RNA) will hydrogen-bond to a water molecule from both the minor groove 2-keto- and major groove 4-keto-groups. Phosphate hydration in the major groove is thermodynamically stronger but exchanges faster. There are six (from crystal structures, [143]) or seven (from molecular dynamics, [144]) hydration sites per phosphate a, not including hydration of the linking oxygen atoms to the deoxyribose or ribose residues. The deoxyribose oxygen atoms (O3' phosphodiester, ring O4' and O5' phosphodiester) all hydrogen-bond to one water molecule whereas the free 2'-OH in ribose is much more capable of hydration and may hold on to about 2.5 water molecules. b The total for all these hydrations, in a G3 H-bondsC duplex, would be about 26-27 but about 14 of these water molecules are shared. There are many ways in which these water molecules can be arranged with B-DNA possessing 22 possible primary hydration sites per base pair in a G3 H-bondsC duplex but only occupying 19 of them [144]. The DNA structure depends on how these sites are occupied; water providing the zip, holding the two strands together. It should be noted that cations may transiently replace about 2% of the hydrating water molecule sites.

Quote
In DNA, the bases are involved in hydrogen-bonded pairings, close to the 0.28 nm bond length found between hydrogen-bonded water molecules in liquid water. The aqueous environment causes a slight lengthening (≈ 1%) of the DNA hydrogen bonds and weakens them significantly (≈ 50%) [1867].d All these groups, except for the hydrogen-bonded ring nitrogen atoms (pyrimidine N3 and purine N1) are capable of one further hydrogen-bonding link to water within the major or minor grooves in B-DNA.

The starter sequences for genes on the DNA are rich in Adenine. Water hydration plays a role in both energetics and protein recognition.

Quote
The hydration of the B-DNA minor groove is dependent on the DNA sequence with water-bridge lifetimes varying from 1 to 300 ps [1767], depending on the sequence. The hydration usually involves single water molecules connecting the strands. However, connection via pairs of water molecules, with varying interchange between these forms, may allow greater structural flexibility in the DNA and interactions with specific proteins [1605]. There is a spine of hydration running down the bottom of the B-DNA minor groove, particularly where there is the A=T duplex [145] (see right, where the water oxygen atoms are shown large green and red, where the red atoms are the primary hydration water and the green atoms are the secondary hydration water, [1136]), which is important in stabilizing it [146]. Thus, A=T duplex sequences favor water binding in the minor groove and also protein binding there driven by the large entropy release on this low entropy water's release [1136].



 
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 04/12/2019 19:50:02
The catalytic grid resets the potentials.
Word salad

I was comparing DNA, RNA, protein and other large molecules in the cell.
And I guess you missed out glycogen (in animals) and starch (in plants) because it didn't fit with your idea.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 05/12/2019 20:59:55
The catalytic grid resets the potentials.
Word salad

I was comparing DNA, RNA, protein and other large molecules in the cell.
And I guess you missed out glycogen (in animals) and starch (in plants) because it didn't fit with your idea.

Glycogen is a good transitional molecule to discuss, so we can move forward with the topic, which is, are water and organics copartners in life. Glycogen is a polymer of glucose. It is used for energy storage. Energy rich organic molecules within the cell; reduced, imply a free energy potential will be induced within the cellular water. The polymerization into glycogen lowers the potential, somewhat, but it does not fully remove it. Glycogen is on the oil side of the water-oil analogy. It increases the potential within the cellular water, relative to pure water.

Energy storage in cells, when taken to the limit, potentiates the water, causing equilibrium changes within the organics, that are dissolved and are in contact with the water. One important global equilibrium result are cell cycles. The water by being the continuos phase, allows the change in water potential to impact equilibria throughout the cell. The energy storage helps the cell change gears via the global water potential. All forms of cancer use water equilibria.

One way the cellular water potential can shift the organic equilibrium, more in its favor, is to burn the extra energy and increase production of ATP. The burning of the energy is self explanatory, while ATP is a water friendly molecule, that can also be used to increase water entropy; lowers aqueous free energy. Favorable equilibria can also increase the production of RNA, since RNA is favorably hydrated on the water side of the potential. This allows the cell to make all the extra proteins needed for two daughter cells.

DNA is normally packed with histone packing protein into various levels of packing. This packing can go all the way to condensed chromosomes. The packing proteins are basic proteins with organic tails separating their charges. DNA packs with the packing protein to shelter the water from the surface tension causes by the packing protein. The various levels of DNA and packing protein are like larger and larger bubbles, combining in water-oil, to lower surface tension.

During the cell cycles the DNA becomes unpacked and the DNA double helix is separated for DNA duplication.

Quote
The change in the free energy of the surrounding water aids the conversion of single-stranded DNA (ssDNA) into double-stranded DNA (dsDNA) as the water molecules are more stable around dsDNA than around ssDNA even out to about 0.65 nm (3 hydration layers) [2693].

Double strand DNA; dsDNA is more stable than single strand DNA; ssDNA, because water is more stable around dsDNA. The double helix minimizes the water potential. In cell cycles, because the  the water potential is higher and the equilibrium is different, this allowing the ssDNA to stay open for duplication with less resistance. Once the DNA is doubled, this creates excess potential via four higher potential ssDNA, requiring two dsDNA to lower the excess potential.

The condensing of the DNA into chromosomes, near the end of cycle cycles, suggests the water has induced new equilibrium changes. Now the water potential is favorable to the water, causing inducing DNA to pack (shield packing protein) all the way to condensed chromosomes. There is now a new equilibria sheriff in town; divide the DNA and the two daughter cells.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 21/12/2019 17:38:06
Quote
Quote from: ron123456 on 17/12/2019 21:54:19
Does the Na+K+ pump not provide 3Na+ out and 2K+ in across the cellular membrane leading to a specific potential difference?......and is this potential difference not less in a cancer cell?......and is this not due to the mitochondria not functioning up to par in a cancer cell  according to Otto Warburg? Is this lower membrane potential differences due to damaged local nerve endings or a biofilm coating? Is this what is being suggested here? I don't know and if you could elaborate perhaps it's a start which should be considered.....



The Na+K+ pumps segregate and concentrate these ions on the opposite sides of the cellular membrane. This results in a lowering of entropy at the membrane, since left to their own devices both of these ions would prefer form a uniform concentration; highest entropy. The net affect is the Na+K+ pumps create an entropy potential at the membrane. There is an induced potential for entropy to increase at the membrane, which can be expressed by dynamics on both sides of the membrane. These dynamics are all mediated by water. 

Sodium ions are kosmotropic which means they can bind to water stronger than water molecules blind to each other via hydrogen bonding. While Potassium ions are chaotropic which means they can bind to water weaker than water binds to itself. The net effect is the Potassiums ions in water; hydrated ions, are time average smaller than hydrated Sodiums ions in water. Both carry hydration spheres, but the weaker binding of Potassium ions in water makes its hydration sphere more transient and less specific. This allows Potassium ions to flow through the membrane easier, by  changing water partners, in response to the concentration gradient and the induced entropy potential.

In terms of water and hydrogen bonding, hydrogen bonds have both covalent and polar character. They are similar to binary switch since they can flip back and forth without breaking the hydrogen bond.  The polar aspect of hydrogen bonding is smaller in bond length and higher in both entropy and enthalpy, compared to the covalent aspect. The entropy potential induced by the ion pumping flips in the switch toward the polar side. This helps to skinny down the Potassium ions. It also helps with other transport affects.

The impact of the nerve tissue near cells is to increase the Sodium ion concentration outside the cell as well lower the Potassium ion concentration, similar to the Na+K+ pumps. The nerves do this because of its status of among the highest membrane potential cells, and its own Na+K+ pumps, This provides a backup plan, even if there are problems with cellular Mitochondria, which could a;er the cellular membrane potential. Damaged nerve endings remove the back up plan, making it easier for the propagation of cancer, all else being equal.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 21/12/2019 18:31:13
, imply a free energy potential will be induced within the cellular water.
Word salad
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 22/12/2019 13:32:01
, imply a free energy potential will be induced within the cellular water.
Word salad


In terms of Na+K+ pumping and a free energy potential forming in the water, a good example is osmosis. This has been explained in an earlier post. In the case of the membrane, ions do not move without coming in intimate contact with water, thereby transmitting potential and information in water, as water regroups in space; flip the binary hydrogen bonding switches. 

The Na+K+ pumping and the preliminary discussion of cancer, is a good step off point to a very important application of the water-oil model for life. In particular, the brain and nervous system epitomize the water side of the potential. Even consciousness is on the water side potential, since this is essentially ions and the binary switches of hydrogen bonding in water transmitting information.

Since water and organics are copartners in life, the brain and nervous system; water side, can influence the oil side; organics. At the same time, the oil side; organics can influence the brain and nervous system. Medicine is currently a predominately an oil side approach to life. There is also a water side approach to medicine, connected to the brain and nervous system. This approach is both ancient and futuristic; witch doctor and water chemistry. Faith healing uses consciousness for a water based induction. A good attitude is fat free and useful to healing.

Neurons are unique cells in that they stop reproducing at about the time of birth. They are self renewing and can live for decades and even longer. The cellular change, at birth, into eternal cells is useful for cellular differentiation control, since neurons, once they stop reproducing, are never taken off-line by cell cycles. This allows for a more consistent control system.

Before birth; fetus and embryo, neurons can and do replicate. The impact of this ability to replicate,  earlier, in terms of the cellular differentiation control system, is the control system moves between being on-line and off-line. This provides a cycling water potential for cellular differentiation and proliferation of stem cells.

From embryo to birth, dividing and multiplying neurons form sort of a sine wave of fluctuating potential, that is climbing an energy ramp. The climb reflects the combined signals of more and more neurons. This control profile tweaks the potential around stem cells in a systematic fashion. Below is a crude approximation for the affect. At birth, the sine wave collapses, into more or less a line with real time noise; neuron firing and recovery based on consciousness and unconscious feedback with the internal and external environments.

Interaction with the control cells occurs via nerve endings and the water and ions which are shared with the control cell. This impacts the free energy in the shared water. The organic side of medicine does not deal wth this very much, since its affect lacks organics and may seem like magic. However, there are organics involved, that reflect equilibrium affects.

(https://www.researchgate.net/profile/Louise_Crocker/publication/281283566/figure/download/fig2/AS:614213995204651@1523451436955/Increasing-amplitude-waveform-applied-using-the-IPTM.png)

 
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 22/12/2019 14:18:44
Do you plan to make a point at some stage?

I ask because this thread starts off with something that's not true
If you started with a packet of baker's yeast, the yeast cells are initially dehydrated and show no signs of life.
and doesn't seem to get better
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 22/12/2019 14:20:11
This has been explained in an earlier post. In the case of the membrane, ions do not move without coming in intimate contact with water
Osmosis works with other solvents.
Water is weird, but not magic.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 22/12/2019 14:46:43
In terms of cellular differentiation control and the nervous system of the human body, all cells in the human body have the same DNA. Different cells are differentiated based on using different proportions of the genes available to all cells. What this suggests is each dynamic DNA differentiation, for each differentiated cell, is nothing but an equilibrium configuration with a given water potential. If you can control the water potential, than any differentiated dynamic DNA packing shape will hold firm.

The analogy is packing and folding protein. When unpacked and unfolded, proteins create an energy landscape diagram with the water. The packing priority is based on lowering the potential of the water and protein in the most efficient way. This sweet path is always the same, leading to reproducible protein configurations with probability of 1.0. Statistics does not apply when water is in charge. This is more needed for the oil side approach.

With the DNA and cellular differentiation control, this is done in reverse. We start with condensed chromosomes, which is DNA that is efficiently packed with various levels of packing protein. The condensed chromosomes are equivalent, in the water and oil analogy, to oil that has phased separated from the water into one layer. This minimizes the potential of the water by lowering the surface area with the packing proteins.

Based on the water and oil analogy of the condensed chromosomes being analogous to two layers; chromosomes and water, what we now need to do is add agitation and break up the one layer of oil; condensed chromosomes, back into bubbles. Depending on how hard and fast we agitate, we can get more or less bubbles, as well as control the size distribution. This is assisted by equilibrium enzymes, based on the global water potential, which can be assisted by the nervous control interface.

When the chromosomes are condensed, the DNA is offline and unable to do anything. The DNA is not part of the control system. The DNA is passive and receptive with all its genes off-line. We need an outside potential for change to occur, os we can put the DNA back online, in a differentiated way; unique equilibrium dynamic packing configuration.

One of the keys to induced DNA differentiation, from a commonly packed DNA, is the DNA is not uniform along its length, but rather it is set up with internal gradients. One stable anchor or pole for the gradient is the centromere region, where the spindle attaches. The nucleolus region is another. In terms of unpacking a gradient DNA, the affect is similar to heating a composite material with a stable pole, where the state pole is only responsive to extreme heating. At weaker levels of heating, the outer most layers of the packing, fluff out. The rest stays packed. If we control the heating, we can stop the reversible packing, at any given unpacking differentiation. For this to be possible, you need to be able to dial in the water potential, in a precise way, so any dynamic equilibrium packing shape; in water, stays where you put it.

During the late stages of cell cycles, after the DNA is duplicated, condensed into chromosomes,  and taken off-line, the nuclear membrane disappears. This is useful since the aqueous impact of the outer cell membrane, is less obstructed, by the nuclear membrane. The spindle firms up the centromere pole. This stable pole makes it easier to create an unpacking equilibrium image, onto the condensed chromosomes.

Since the DNA has to unpack, for the DNA to come back on line, and unpacked DNA exposes packing protein, increasing the water potential, the equilibrium in the water needs to be impacted by the oil side to create the potential. The materials needed for the daughter cells has an impact on the global water potential, which "heats" the water to achieve a parallel equilibrium DNA configuration to its proteins.

If we start with a mother cell, with her nerve ending nearby, if we assume the nerve is helping to inhibit cell cycles, as part of its role in cellular differentiation control, that means it generates potential on the water side of the water-oil analogy. Our two daughter cells are generating  potential on the oil side. The impact of the nerve is to discourage DNA unpacking beyond a certain point induced by the cells protein and organic materials; secondary control.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 22/12/2019 14:59:10
This has been explained in an earlier post. In the case of the membrane, ions do not move without coming in intimate contact with water
Osmosis works with other solvents.
Water is weird, but not magic.

What makes water magical is water molecules can form up to four hydrogen bonds. This creates a situation similar to carbon, but based on secondary bonding. Carbon can form extended structures in space; polymers, while water can also form extended structures, that allow information and potential to distribute over larger areas via changes in hydrogen bonding. Water can open up a path for the Potassium ions, to get then through membrane, to help lower the shared free energy potential, due to the cationic pumping.

Carbon can form extended structures, but covalent bonding, besides resonance, is more or less restricted to local information and potential. 

Part of the problem is this is a new theory, which means it does not yet have resources needed to do it the easy way. Anyone can do empirical. This only requiresa lets see wha happens attitude. I have chose to develop it from basic logic, observation and theory, so the audience can follow, but without the ease money can buy. I am not trying to mimic others, but rather wish to be unique, since this area of science needs a push in a unprecedented way.

What I probably need is a way to supplement the water based analysis, with more organic and oil side detail. I can apply the model to anything in life, but my knowledge of the oil side details is limited. The oil side is a composite of tens of thousands of scientists over a hundred years. I can't be expected to do the same all by myself. Nor do I wish to get bogged down in the weeds and lose track of the big picture. However, the model has to run parallel through all the data to prove the premise of the topic. I have to choose my battles, everywhere, even in places where the oil side cannot yet go, without the water side.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 22/12/2019 15:02:25
What this suggests is each dynamic DNA differentiation, for each differentiated cell, is nothing but an equilibrium configuration with a given water potential.
No.
It does not suggest that.
If it was water availability that decided which DNA was expressed and thus what cells became then every time you needed a pee, your bladder would turn into a different organ.

The idea really is that stupid.


Why are you persisting with it?
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 22/12/2019 15:23:47
What this suggests is each dynamic DNA differentiation, for each differentiated cell, is nothing but an equilibrium configuration with a given water potential.
No.
It does not suggest that.
If it was water availability that decided which DNA was expressed and thus what cells became then every time you needed a pee, your bladder would turn into a different organ.

The idea really is that stupid.


Why are you persisting with it?

If you go back to the beginning, I did an analysis of dehydrating cells and replacing water with other solvents. Nothing works. You would not be able to induce any differentiation, with any other solvent, even if all the organics were present. Water works, because everything has had to evolved within an aqueous nano-environment. All the structures in the cell are in equilibrium with water; water-oil affect, with the goal is minimizing the water potential since water is the majority component. Most of life science is from the oil side and water side is less developed. My goal is to introduce th water side with a wide range of applications.
Title: Re: Are Water and the Organics copartners in life?
Post by: Bored chemist on 22/12/2019 15:51:20
I did an analysis of dehydrating cells and replacing water with other solvents. Nothing works.

That makes about as much sense as trying to fit a spark plug into a diesel engine, finding that there isn't a place for it and concluding that diesel engines can't work.

Just because life here is based on water doesn't mean that all life must be.

On some hypothetical planet "Water Ammonia works, because everything has had to evolved within an aqueous amoniacal nano-environment. ".
You can't rule that out so you can't say that water is a requirement for life.

If you did find a planet with ammonia based life it's possible that water would screw things up.


Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 24/12/2019 11:37:20
I did an analysis of dehydrating cells and replacing water with other solvents. Nothing works.

That makes about as much sense as trying to fit a spark plug into a diesel engine, finding that there isn't a place for it and concluding that diesel engines can't work.

Just because life here is based on water doesn't mean that all life must be.

On some hypothetical planet "Water Ammonia works, because everything has had to evolved within an aqueous amoniacal nano-environment. ".
You can't rule that out so you can't say that water is a requirement for life.

If you did find a planet with ammonia based life it's possible that water would screw things up.

I would suggest that you start a topic "Can ammonia or other solvents, besides water, be the basis for life?" Then you can develop your logic and arguments to see if it adds up. I would not mind helping out. I am doing this analysis with water, becuase this job is much easier, since the organic side of this equation is well known. All I need to do is infer the role of water in the equation starting with known things. Your job will be much more difficult.

The most obvious role of water is connected to the water and oil analogy, that I have been using. Water and oil do not spontaneously mix, and remain an emulsion, because mixing creates surface tension and adds free energy potential to the system. When the free energy is allowed to minimize we get a phase separation of the organics (of aqueous based life) into organelles and other types of cellular structures and water.  The free energy potential is high enough for this to be repeatable, such as is observed in repeatable protein folding and daughters cells that look like mom.

This analogy is one of the main problem for others solvents, such as ammonia. An ammonia-oil analogy does not phase separate quite the same way. Ammonia is both a good polar solvent as well as an excellent degreaser. It would maintain an emulsion with most of the organics used for water based life. Instead of repeatable ordering, that is needed for consistent life, we would get far more transient randomness.

I am not an expert with ammonia, but I sense you would need to come up with a way to force a clean phase separation by controlling the organic solvent power of ammonia. Alternately, you may have to  come up with a replacement set of materials for the normal organic materials of water based life. These new materials will not be as obvious, as amino acid and nucleic acid base polymers, that are found naturally in the universe, such as in asteroids.
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 24/12/2019 12:04:16
My time is limited, today, but I would like to look at neurons in light of the water- oil analogy. Neurons, besides never replicating, have among the highest membrane potentials of all cells. They use up to 90% of their ATP energy maintaining membrane potential. They burn so many calories maintaining the membrane potential they are never able to store sufficient energy to increase the internal potential and initiate cell cycles. Instead, the water side dominates inside the neurons for the rest of its life.

The membrane is a different animal in terms of a neuron, This is the zone where 90% of its energy is being constantly inputted. Therefore, the neuron membrane is slanted toward the oil side of the equation. One observed affect are "bubbles" will form, in the oil analogy; membrane, that we call axons and dendrite branches.

The energy pumped into the membrane is like an agitator which adds membrane surface area in contact with the outside water; surface tension value equivalent. The internal neuron water side dominance creates a unique environment for the neuron DNA, relative to other cells, allowing the DNA to play an information storage role; water side information; memory. In other words, a strong internal water side potential, forces the protein and other structures into near perfect phase separation; no bubbles, that reflects the impact of the external neural information environment; memory storage into structures.

If we look at synapses, we have two areas of neuron membrane "bubbles", in near contact, but separated by a gap; synaptic gap. This gap also reflects the oil side of the potential. Instead of the bubbles induced to combine to reflect a water side potential, the surface tension is maintained by an oil side potential. There is sustained potential in the water that is bathing the synaptic matrix.

If we return to a single neuron, the Na+K+ pumping adds energy to the membrane that is reflected in the membrane potential, as well as ion concentration gradients. If the membrane was a perfect barrier the membrane potential could keep on increasing. In the real world, the free energy in the membrane potential, animates the water, allowing neurons to spontaneously discharge potential, if and when the potential reaches a threshold. This threshold is regulated via neurotransmitters that can help destabilize or stabilize the water.

Once a neuron fires, the potential within the membrane is discharged. The discharge potential goes in two directions; into the inside and outside water. The outside energy aspect of the discharge, energizes the synaptic grid, while the discharge inside adds potential to the material grid that stores memory; forms inner bubbles. These short term bubbles are useful for updating the material memory grid. The neuron quickly restores the membrane potential, completing the writing process as the water reforms the more stable material configurations.

The concentration gradient, that is induced at the membrane, reflects an entropy potential. In other words, left to the their own devices, these segregated membrane cations would spontaneously form uniform solutions driven by the second law; entropy. The Na+K+ pumps use energy to reversed the direction of cationic entropy creating an entropy potential; too low. When the membrane discharges, entropy potential is released, within the membrane as well as inside and outside membrane. There is a push=wave to increase complexity in the water on both the inside and outside of the membrane. Since hydrogen bonds are like little switches, this increase in water entropy reflects a flip of switches to the polar side, which has a different impact on the synaptic grid and internal material configurations.
 




 
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 28/12/2019 13:53:16
 If you look at male and female, the female human, on the average, have more natural body fat, while the male have more muscle mass. This distinction implies women are naturally designed to be on the oil side of the potential. Men are more designed to be on the water side in terms of the water-oil analogy.

The enhanced oil side of the female body potential has an impact on amplifying cell cycles, which is designed for having babies. The embryo/fetus is not wired into the mother's nervous system allowing the mother body and blood potential to have an enhanced external influence over the cell proliferation of her unborn. The unborn also uses its own nervous system, for cellular differentiation induction and control.

In nature, the female or mother animal has more things to do connected to her offspring. Her higher oil side potential; body, sets a higher potential with her brain, causing more brain discharge to her body, for instinct and action. The male has less body induced brain discharge to the body, which allows the male brain to lower brain potential, internally within the brain; thought, imagination and willpower.

In terms of neural potential flow within the brain, all potential flow goes to the thalamus region in the center of the brain. This is the most wired part of the brain and acts like a central switching station for distributing the potential to the body and for recycle to other parts of the brain. The male and female brains, due to the difference in natural body potential, have sightly different natural switching priorities. These can be altered with willpower.

The female menstrual cycle and the associated emotions is related to her higher body induction causing thalamus potential to the limbic system. Males are better at repressing emotions, due to the natural flow thalamus switched more to the brain stem; colder blooded intellect and muscle potential.

With will power the thalamus priorities can be tweaked. A feminized male can shift priority more to the limbic system; warmer, at the expense of common sense; feeling first. The brain stem is more bare bones cold blooded survival, where facts are important for triggering instinct. The cute lion; limbic emotions, may not be the appropriate feedback for survival. Lion is bad; period, is better.

 
Title: Re: Are Water and the Organics copartners in life?
Post by: Origin on 28/12/2019 16:08:01
That post is so damn stupid I think I lost 10 IQ points just reading it. 
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 29/12/2019 23:32:55
That post is so damn stupid I think I lost 10 IQ points just reading it. 


You need to go back to the very first posts, where I develop the basic chemical background needed to understand the relationship of water to the organics of life. Life evolved in water, therefore water was nano-environment in which the organics of life evolve, from day one. This environment help the natural selection process, for the organic chemicals of life.

An an analogy, physical environments, such as the hot desert or the frozen tundra, sets constraints for life. Not all life will be selected by each environment. What will be selected needs to able to adapt to the unique potentials of that environment. The same is true with water and life at the nanoscale. The organics of life were naturally selected based on an aqueous environment.

This can be demonstrated in the lab by taking a single cell and dehydrating it and then adding others solvent to see if it will come back to life. Since the molecules of the cell evolved in water, all the biomaterials are unresponsive in any other solvent. The organics are all there but there is no life. No enzyme or the DNA works properly. These materials were hand picked by water over the eons. If we add water, everything works and life appears. My goal is to show how the organic hand fits in the water glove.

My last post was just a broad based application, contrasting the stereotypical male and female, in terms of the potential in the water, induced by the organics difference of each; fat venus muscle,  and how that potential environment impacts the water of the brain. This will makes more sense, if you start from the beginning, since none of this is convention taught in school. Water is the most researched substance known to science. I have tried to rearranged this data in a new way so it can better interface life, via the selected organics of life.


 
Title: Re: Are Water and the Organics copartners in life?
Post by: puppypower on 02/01/2020 19:03:13
The thalamus region of the brain, in the center of the brain, is the most wired region of the brain. It is the central switching station where nearly all brain signals goes. This status, as most wired means it has the most "bubbles" and therefore the most surface tension, making it the zone where the water has the highest potential. This zone of highest potential is the center of consciousness; inner self. The potential of the thalamus water attempts to lower, with potential flow down a wide range of reverse pathways some into the body.

The neurons of the brain add potential to their outer membranes; ion pumping. When neurons fire this potential is released and finds it way to the thalamus, keeping this zone at highest potential; amplification. The amplification of potential at the thalamus is more than just raw potential energy, since it also contains information. 

If we go back to the hydrogen bond, it is binary switch, that can shift between polar and covalent character, with both settings forming stable hydrogen bonds. Each setting contains different amounts of enthalpy and entropy, and each expresses different volumes, with the polar switch smaller. The former aspects defines free energy, while the latter defines mechanical muscle through volume changes.

In the case of water, binary information stored in switch settings not only contains the character of information, but this character of information, is also paralleled by the potentials in the switch settings. The information is manipulated by the process of adjusting potentials in the hydrogen bonds, as a way to lower the potential. The water and oil bubble analogy still applies, with the information switches undergoing a lowering or increase in surface tension; bubbles combine or break up; integrating or differentiating data. 

This is much different from computer memory. With computer memory the on-off switches are a one trick pony. Hydrogen bonding switches have free energy based differences at each switch setting. In the case of hydrogen bonding, by manipulating the free energy aspects of the switches the contained binary information aligns with the laws of physics; natural instinct and inner self.  Computer information aligns with human convention; ego consciousness.