Water As The Co-Partner Of Life

[HydrogenBond]

Intracellular water is the water inside cells that bathes all the necessary biological molecules including the proteins and nucleic acids. Cells contain differing amounts of water dependent more on their purpose (and hence expressed proteins) rather than their source organism (for example, the % water contents of red blood cells are about 64% whether from man or dog whereas frog heart contains 80% but a frog egg only 49% water).

 

This water is not solely a medium but a metabolic reactant, product, catalyst, chaperone, messenger and controller . The water is essential for biomolecular recognition and orchestrates the cell machinery . The complexity and organization within the cytoplasm is expressed in an adaptability of intracellular water in engaging in a wide range of cellular biochemistry. 

 

Water is more than just the solvent of life. Water is more like a copartner to the organics of life. If we remove the water and replace it with any other solvent nothing works properly, and what we call life,  disappears. If we rehydrate life appears again. This is due to the many roles water places, including some properties connected to liquid state physics. 

 

The DNA, for example, has a double helix of water that hydrogen bonds along the major and minor grooves of the double helix. The four bases of the DNA have extra hydrogen bonding sites that have evolved to accommodate this water. The water also hydrogen bonds to water, to form a double helix of water that parallels the DNA double helix. 

 

 

Nucleic acid hydration is crucially important for their conformation and utility , as noted by Watson and Crick. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character. The DNA double helix can take up a number of conformations (for example, right handed A-DNA pitch 28.2 Å 11 bp, B-DNA pitch 34 Å 10 bp, C-DNA pitch 31Å 9.33 bp, D-DNA pitch 24.2 Å 8 bp and the left handed Z-DNA pitch 43Å 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.

 

 

The conformation or the 3-D structure of the DNA is dependent on the degree of hydration and not just the DNA double helix. The DNA containing the most water is B-DNA. The B-DNA needs that much water to make it active as a template.

 

In terms of evolution, increasing hydration was the direction the DNA needed to evolve before it could work properly. This was not random but by design; copartner water. 

Edited April 20, 2015 by HydrogenBond

[sman]

Not the first time you've referenced Martin Chaplin's webpage, I've noticed.

[HydrogenBond]

I am interested in water and life, and Martin Chaplin's web site is an excellent source of information about water. Those who are not aware that I often quote his site, assume I am making things up. The idea of a double helix of water, intertwined with the DNA double helix, with the amount of water of hydration, controlling the conformation of the DNA and its activity, is not the stuff of most text books. 

 

This has to do with the life sciences only teaching half the story of life; organic side. Because they leave out water, in proportion to is contribution, and teach disproportionate organics, life appear to be governed by randomness. If you add water, as the copartner of life; finger in every pie, the random POV goes away and life becomes more logical.  

 

The foundation theory for the co-partnership of water and organics, leading to life, is based on the simple system of water and oil. 

 

If we add oil to water and agitate, we can form an emulsion. The emulsion is a state of high entropy or disorder, due to the energy added via the agitator. If we let the emulsion settle, it will separate into two layers. This separation causes order to appear from the chaos of the emulsion; entropy decreases. The interaction of the organics of life, with the majority component of water, create all types of phase separations, such as enzyme and organelles. Water allows order to appear from chaos.

 

A cell is like a phase diagram of water and organics; various oil and water analogies. The DNA is the most hydrated of all the molecules in the cell. It stands at one extreme in the phase diagram; as a function of water. The lipid bilayer membrane is the least hydrated, being more like an oil. This is the other extreme on the phase diagram. These two bookends define a potential gradient, for the equilibrium phases in the middle of the phase diagram called the cell. 

Edited April 21, 2015 by HydrogenBond

[Buffy]

Goodness gracious, I just had fun Googling "water memory" and Dr. Champlin. Very humorous. Goes off into Homeopathy too.

 

 

Some of them wanted to sell me snake oil and I'm not necessarily going to dismiss all of these, as I have never found a rusty snake, :phones:

Buffy

[HydrogenBond]

Water is the most investigated substance in all of science. Water appears so simple yet it is the most complicated of all substances having 72 known anomalies, like expanding when it freezes. Dr Chaplin's web site is a good overview of all the water based research, which to be comprehensive, includes a summary of investigations into water and homeopathy. The intent of his site is not PC sanitation, to appear politically legitimate to the propaganda of the uninformed. Rather it is intended for scientists who prefer a summary of all the latest water research, to can get a complete picture. 

 

Let me get back to water and oil, which is my own unique foundation for the copartners of life. This is based on applying and extrapolating water chemistry. Oil is called hydrophobic, which means water fearing. This term is actually a misnomer, because oil and other hydrophobic organic materials, do not fear water, as much as water tends to exclude oil. Water can form low energy bonds with oil. However, it can form much stronger hydrogen bonds with other water. Based on energy considerations, the oil becomes excluded in favor of water-water binding. The oil does to fear the water, as much as liquid water will not let it play. This exclusion is good for life, because water can exclude organics into phases while still being in touch, allowing the entire cell to become integrated zones. 

 

In chemical engineering, there is a trick called steam distillation, which is a way to boil high boiling point oils at much lower temperature, using steam. Oil is quite soluble in steam, and oil that boils at 200C will boil off with the steam at 100C. The reason is, at the boiling point of water, the hydrogen bonding matrix of water is disrupted. Water is no longer excluding the oil, but will now form weak bonds with more of the oil, making the oil soluble in the steam.

 

Steam distillation is one way to tweak the hydrogen bonding strength of the water matrix, so organics become more soluble. This can also be done chemically, by means of a class of chemicals that are called chaotropic. These create chaos in the hydrogen bonding matrix of water, allowing organics to be less excluded from the water. For example, the potassium cation, which all cells accumulate, disrupts the order of water so the organics are less excluded and water can penetrate. Cells can tweak the concentration of chaotropes for specialty phase shifts; cell cycles. 

Edited April 22, 2015 by HydrogenBond

[HydrogenBond]

The key to water lies within the unique nature of hydrogen bonding. Hydrogen bonds have both ionic and covalent character. The ionic character allows dipole interactions between opposite charges. While the covalent character allows water to bind via covalent bonding orbitals.

 

The ionic state of hydrogen bonding benefits by hydrogen bonding getting close as possible, since charge potential lowers with less distance. The covalent state of hydrogen bonding benefits by the hydrogen bonds moving away, since covalent bonding orbitals require the overlay of specific wave functions. There is a sweet distance for optimum wave interaction.

 

As water switches between ionic and covalent hydrogen bonding states, water will contract and expand, making extra room in the water continuum, or placing things under pressure. The expansion of ice, when water freezes, is due to the hydrogen bonding network favoring the covalent state. This causes a 10% volume expansion. When we melt ice, to liquid water, the water contracts by 10% as more ionic hydrogen bonding begins to form again.

 

This 10% shift can also occur in the liquid state, locally, as local hydrogen bonds shift between the two bonding states. This local change in volume is how the water makes room for enzymes to shape shift, or put them under the squeeze for reset. The hydrogen bonding shift of the water volume can also occur in waves to coordinate an enzyme train. 

 

The energy value of the ionic and covalent states of the hydrogen bonds are fairly close in energy. They exist in either aside of a potential energy barrier and can shift between the two states with very little energy. In the diagram below, state a represent the ionic state, and state b the covalent state. This binary nature of hydrogen bonding allows water to transmit information. 

 

 

Edited April 22, 2015 by HydrogenBond

[sman]

I don’t understand much of the chemistry, but I don’t have to in order to call Non sequitur:

 

In terms of evolution, increasing hydration was the direction the DNA needed to evolve before it could work properly. This was not random but by design; copartner water.

This is rather as if you imagine a puddle waking up one morning and thinking, 'This is an interesting world I find myself in — an interesting hole I find myself in — fits me rather neatly, doesn't it? In fact it fits me staggeringly well, must have been made to have me in it!, :phones:

[Moontanman]

I am interested in water and life, and Martin Chaplin's web site is an excellent source of information about water. Those who are not aware that I often quote his site, assume I am making things up. The idea of a double helix of water, intertwined with the DNA double helix, with the amount of water of hydration, controlling the conformation of the DNA and its activity, is not the stuff of most text books. 

 

This has to do with the life sciences only teaching half the story of life; organic side. Because they leave out water, in proportion to is contribution, and teach disproportionate organics, life appear to be governed by randomness. If you add water, as the copartner of life; finger in every pie, the random POV goes away and life becomes more logical.  

 

The foundation theory for the co-partnership of water and organics, leading to life, is based on the simple system of water and oil. 

 

If we add oil to water and agitate, we can form an emulsion. The emulsion is a state of high entropy or disorder, due to the energy added via the agitator. If we let the emulsion settle, it will separate into two layers. This separation causes order to appear from the chaos of the emulsion; entropy decreases. The interaction of the organics of life, with the majority component of water, create all types of phase separations, such as enzyme and organelles. Water allows order to appear from chaos.

 

A cell is like a phase diagram of water and organics; various oil and water analogies. The DNA is the most hydrated of all the molecules in the cell. It stands at one extreme in the phase diagram; as a function of water. The lipid bilayer membrane is the least hydrated, being more like an oil. This is the other extreme on the phase diagram. These two bookends define a potential gradient, for the equilibrium phases in the middle of the phase diagram called the cell. 

 

 

Exact of course when that life is not based in water!

 

http://en.wikipedia.org/wiki/Life_on_Titan

 

A hypothetical cell membrane capable of functioning in liquid methane was modeled in February 2015. It is composed of small molecules containing carbon, hydrogen, and nitrogen and would have the same stability and flexibility as cell membranes on Earth, which are composed of phospholipids—compounds of carbon, hydrogen, oxygen and phosphorus. This cell membrane was termed an "azotosome" ('nitrogen body'), formed from "azote", French for nitrogen, and "soma", Greek for body.^[2]

Comparative habitability[edit]

In order to assess the likelihood of finding any sort of life on various planets and moons, Dirk Schulze-Makuch and other scientists have developed a Planetary Habitability Index which takes into account factors including characteristics of the surface and atmosphere, availability of energy, solvents and organic compounds.^[27] Using this index, based on data available in late 2011, the model suggests that Titan has the highest current habitability rating of any known world, other than Earth.^[27]

 

 

 

Titan as a test case[edit]

While the Cassini–Huygens mission was not equipped to provide evidence for biosignatures or complex organics, it showed an environment on Titan that is similar, in some ways, to ones theorized for the primordial Earth.^[28] Scientists think that the atmosphere of early Earth was similar in composition to the current atmosphere on Titan, with the important exception of a lack of water vapor on Titan.^[29] Many hypotheses have developed that attempt to bridge the step from chemical to biological evolution.

Titan is presented as a test case for the relation between chemical reactivity and life, in a 2007 report on life's limiting conditions prepared by a committee of scientists under the United States National Research Council. The committee, chaired by John Baross, considered that "if life is an intrinsic property of chemical reactivity, life should exist on Titan. Indeed, for life not to exist on Titan, we would have to argue that life is not an intrinsic property of the reactivity of carbon-containing molecules under conditions where they are stable..."^[30]

David Grinspoon, one of the scientists who in 2005 proposed that hypothetical organisms on Titan might use hydrogen and acetylene as an energy source,^[31] has mentioned the Gaia hypothesis in the context of discussion about Titan life. He suggests that, just as Earth's environment and its organisms have evolved together, the same thing is likely to have happened on other worlds with life on them. In Grinspoon's view, worlds that are "geologically and meteorologically alive are much more likely to be biologically alive as well".^[32]

 

[HydrogenBond]

Life in other solvents, besides water, is all speculation. They have not even made life in water from scratch never mind in other solvents to show this is possible. The idea that any solvent can work is there to diminish the impact of modern water research, so organics remain alone, as the king of the hill. Water is how cancer will be cured; change the phase diagram into something not as dynamic. 

 

The main problem with other solvents, is life on earth uses water as its solvent , with the solvent water a terminal product of metabolism. Say you start with methane as the solvent, what does the metabolism look like, if methane is as far as the metabolism can go; before it digests the solvent?

 

There is almost nothing one can burn or digest that has more energy value than methane; pound for pound, except things like  acetylene. All organic solvents have this metabolic energy bottleneck that sets the energy floor too high due to the energy value of organic solvents. What will eventually happen are enzymes will evolve that will eat its solvent; combustion.

 

Water is different because it is the end product of the most fiery of combustion, using any organic solvent. Water is sturdy, stable and durable and allows life the use the full range of organics for energy. All life, even of it could start in other solvents, will evolve  into a water economy, as it eats all solvents downward to this final stability. 

Edited April 23, 2015 by HydrogenBond

[HydrogenBond]

The system of water and oil was chosen as the foundation of thought, because this simple system allows life to evolve from scratch. Because water and oil don't mix, this sets a ceiling on system or state entropy. Since entropy still needs to increase, due to the second law, there will be the need and push for chemical changes in the oil, that allow the water and oil to mix, better. It is hard to change water, since this is already barebones. Water remains as the floor on which the building of life will be constructed. However, water will also be incorporated into organics such as in amino acids.  

 

One quick and simple way to mix water and oil is to add/extract other solvents/materials, that can mix in the water, that can pull oil into the water, or solvents that can mix in the oil and pull water into the oil. We can also add hydrogen bonds to materials; protein, RNA, DNA, with the DNA so hydrated, the needs of entropy have been maximized; at the leading edge.  

Edited April 23, 2015 by HydrogenBond

[sman]

Not all compounds are of equal utility for organization. They’re all different. That water is particularly suited for life and life makes particular use of water surprises me no more than any of many contrivable anthropic coincidences.

[HydrogenBond]

Hydrogen bonding in water is finely tuned to the needs of life; Below is a table of the impact of changing the hydrogen bonding strength of water even a few percent, up or down. The copy and paste of the table did not formant properly. The first data point is water will boil at 37C with a 29% decrease in hydrogen bonding strength. This is about a 6 KJ /mole decrease, which is small. 

 

 

The major effects of changes to water’s hydrogen bond strength are summarized below, where they are considered individually. It is apparent that small changes of a few percent would not be threatening to life in general but changes in excess of 10% (equivalent to just 2 kJ mol^-1) may cause a significant threat. The overall conclusion to be drawn is that water’s hydrogen bond strength is poised centrally within a narrow window of its suitability for life.

 

Effect of H-bond strength on water's physical properties 

% Change in H-bond strength

Effect at 37 °C

Decrease 29%

Water boils

Decrease 18%

Most proteins heat denature

Decrease 11%

K⁺ becomes kosmotropic

Decrease 7%

pK_w up 3

Decrease 5%

CO₂ 70% less soluble 

Decrease 5%

O₂ 27% less soluble

Decrease 2%

No density maximum

No change

No effect

Increase 2%

Significant metabolic effects

Increase 3%

Viscosity increase 23%

Increase 3%

Diffusivity reduced by 19%

Increase 5%

O₂ 270% more soluble

Increase 5%

CO₂ 440% more soluble 

Increase 7%

pK_w down 1.7

Increase 11%

Na⁺ becomes chaotropic

Increase 18%

Water freezes

Increase 51%

Most proteins cold denature

 

 

 

[HydrogenBond]

Let me try to explain the basis for hydrogen bonding in water, and why the hydrogen bonding of water makes water so unique. This background is useful for conceptualizing.  Hydrogen bonding occurs when hydrogen is covalently bonded to a highly electronegative atom, with fluorine=4.0 and oxygen=3.5 the top two in terms of electronegativity.

 

Electronegativity is a measure of an atom's affinity for electrons. If you react an atom with high electronegativity with one that has lower, the higher tends to get the electrons, while the lower loses the electrons. The numbers are relative and are shown on the chart below. This is a good chart to predict reactivity between any atoms; quick guess.

 

Fluorine and Oxygen are the king and queen, and can strip electrons from almost everything. Whereas, Fluorine can strip one electron, Oxygen can strip up to two electrons, thereby giving oxygen a central role in chemistry. The oxygen is also one of the most stable atomic nuclei being the third most abundant atom of the universe. Metabolism will use oxygen as a terminal electron acceptor, because O=3.5 plus it can hold two electrons and is number three in the universe. This is as good as it gets. 

 

 

The reason oxygen is so electronegative is oxygen tries to complete its octet of electrons, by filling in the two remaining places in the 2P orbitals. This allows oxygen to exist as O-2 or oxide. The reason oxygen can firmly hold two more electrons, than it has protons, and not lose these electrons to other atoms, are the extra electrons, that fill the 2P orbital will create magnetic attraction with all the other electrons, in 3-D. This allow the total magnetic attraction, to be stronger than the electrostatic repulsion of having two extra  electrons. This has to do with the unique shape of the p-orbitals in 3-D, and right hand rule that defines magnetic attraction and the movement of the electrons. This all adds up in 3-D. 

 

 

When oxygen=3.5 reacts with hydrogen=2.1, the oxygen dominates the electrons. In water, the oxygen and hydrogen form a covalent bond, with oxygen taking the lions share of the electron density, into its magnetic addition. This leaves hydrogen with a positive charge. 

 

The hydrogen to lowers its potential, will now need to share the unbounded electrons of other oxygen atoms. These electrons of other oxygen are attracted via charge attraction, where the other oxygen has less control over the electrons, compared to its own covalent hydrogen.

 

This attachment of the hydrogen, to the oxygen, pulls electron density away from the oxygen, causing the oxygen to try and make up this loss by taking it out on own hydrogen bonded hydrogen. It own hydrogen get even more positive charge. These hydrogen will now need even more electron density from other oxygen, to eventually the oxygen forms a covalent bond so it can have more control. The hydrogen bond can shift between covalent and ionic, based on the needs of Oxygen and Hydrogen as they compete for electrons. 

 

The hydrogen bonding in water can form cooperative hydrogen bonds, where the binding between water molecules can escalate until order water structures begin to form that are all covalently bonded sharing the electrons among the entire group. 

 

Edited April 25, 2015 by HydrogenBond

[sman]

This is not your personal blog. It’s a discussion forum. What are you discussing? And with whom?

 

If you mean merely to wax on about water you can retract your opening statement concluding design. You’ve already linked us to Chaplin’s webpage on the subject (well… I did it for you, you’re welcome… otherwise you were just plagiarizing it). Continuing to copy/paste its contents is pointless and redundant.

[Moontanman]

HB, what is the point of all this proselytizing? We have known for years that you seem to have this super natural love for water but as I pointed out if there is no water and another liquid is present then water is irrelevant. You seem to think life can only exist in water and you might be correct but nothing you have typed has any bearing on anything but water and how life has evolved to fit water not the other way around. 

 

Water may indeed be perfect for life and no other fluid will do but your post does not indicate that no matter how much you want it to. Your source for this water love affair (Chaplin) is nothing but pseudoscience. 

[Moontanman]

Life in other solvents, besides water, is all speculation. They have not even made life in water from scratch never mind in other solvents to show this is possible. The idea that any solvent can work is there to diminish the impact of modern water research, so organics remain alone, as the king of the hill. Water is how cancer will be cured; change the phase diagram into something not as dynamic. 

 

The main problem with other solvents, is life on earth uses water as its solvent , with the solvent water a terminal product of metabolism. Say you start with methane as the solvent, what does the metabolism look like, if methane is as far as the metabolism can go; before it digests the solvent?

 

There is almost nothing one can burn or digest that has more energy value than methane; pound for pound, except things like  acetylene. All organic solvents have this metabolic energy bottleneck that sets the energy floor too high due to the energy value of organic solvents. What will eventually happen are enzymes will evolve that will eat its solvent; combustion.

 

Water is different because it is the end product of the most fiery of combustion, using any organic solvent. Water is sturdy, stable and durable and allows life the use the full range of organics for energy. All life, even of it could start in other solvents, will evolve  into a water economy, as it eats all solvents downward to this final stability. 

 

Can you give any support for this than your own assertions? 

[Moontanman]

Hydrogen bonding in water is finely tuned to the needs of life; Below is a table of the impact of changing the hydrogen bonding strength of water even a few percent, up or down. The copy and paste of the table did not formant properly. The first data point is water will boil at 37C with a 29% decrease in hydrogen bonding strength. This is about a 6 KJ /mole decrease, which is small. 

 

 

The major effects of changes to water’s hydrogen bond strength are summarized below, where they are considered individually. It is apparent that small changes of a few percent would not be threatening to life in general but changes in excess of 10% (equivalent to just 2 kJ mol^-1) may cause a significant threat. The overall conclusion to be drawn is that water’s hydrogen bond strength is poised centrally within a narrow window of its suitability for life.

 

Effect of H-bond strength on water's physical properties 

% Change in H-bond strength

Effect at 37 °C

Decrease 29%

Water boils

Decrease 18%

Most proteins heat denature

Decrease 11%

K⁺ becomes kosmotropic

Decrease 7%

pK_w up 3

Decrease 5%

CO₂ 70% less soluble 

Decrease 5%

O₂ 27% less soluble

Decrease 2%

No density maximum

No change

No effect

Increase 2%

Significant metabolic effects

Increase 3%

Viscosity increase 23%

Increase 3%

Diffusivity reduced by 19%

Increase 5%

O₂ 270% more soluble

Increase 5%

CO₂ 440% more soluble 

Increase 7%

pK_w down 1.7

Increase 11%

Na⁺ becomes chaotropic

Increase 18%

Water freezes

Increase 51%

Most proteins cold denature

 

 

No life is finely tuned to the properties of water, another solvent would appear to be just as well matched to it's life forms...