[puppypower (OP)]

Water is the most studied substance in all of science. There are more published science papers written about water that any other material. Part of the appeal, even today, is that water turns out to be the most anomalous substance in all of nature. It displays over 70 different behaviors, and counting, that buck the trends found in other materials. For example, water expands when it freezes and hot water can freeze faster than cold water.

Water is a small molecule that is a very stable terminal product of combustion. Yet its hydrogen bonding network  is very dynamic and is responsible for water's anomalous nature. Water is very stable at the primary covalent bonding level, due to strong oxygen and hydrogen bond, but it is still very dynamic at the secondary bonding level; hydrogen bonding. Water provides a matrix where the hydrogen protons become dynamic.

If we were to burn life, like in a forest fire, all the fancy organics would break down into gases and charcoal. The water from life would vaporize and lose its secondary bonding dynamics but it would still remain water.  Water was there before life, and has not changed or been altered by life or  nature. It remains forever the same. These properties of water make it the cornerstone of life. Water can impart additional properties to the molecules of life, via its secondary bonding network, to create the state we call life.

If place DNA in water, the DNA becomes bioactive. If we removed the water and/or replaced the water with any other solvent, DNA would remain inert, no longer functioning. The same is true of protein and RNA. Their life dynamics depend on water's secondary bonding network. However,  the dynamics of water is not dependent on any of these organics.

Water was the nano environment for the evolution of life from scratch, with the hydrogen bonding network of water running the molecular selection process. This is inferred by the observation that none of the active biomaterial of life work without water. Water picked the team, that could work with it. Evolution is not about random events, but about milestones with respect to water.

Modern biology is still too dependent on random assumptions and statistical modeling. This gambling and whims of the god approach is needed because the logic of water is not fully understood, in biology, resulting in empirical theory that lacks full understand of that one stable eternal cornerstone variable that was always there, and which makes everything work.
 

[Bored chemist]

So what?
It's not as of any of that is news.

[puppypower (OP)]

So what?
It's not as of any of that is news.

I agree. However, why is there so much resistance to the basic changes needed to advance the life sciences into the next century? Think logically. If DNA does not work without water, and no other solvent can be used as a substitute, why do textbooks still insist that the DNA be shown in its dehydrated form, while also describing this as the template material? This is alternate theory and not fact.

It can be demonstrated that water is essential to the correct DNA conformation as well as to its  function. B-DNA requires a very specific degree of hydration. Yet we are still stuck in the 1940's, in terms of education. Why is the obsolete being clung to, when it has been demonstrated as false? Most of the life sciences should be moved to alternate theory, yet a double standard is allowed.   

The Covid 19 virus would not be a problem without water, since none of its dynamic properties, as a virus, would work if it was dehydrated or placed in any other solvent. Alcohol will mess it up due to altered surface free energy.  Yet we show the dehydrated form of the virus as being deadly. Who is in charge of this nonsense!

The question is, has casino science caused brain damage? In this philosophy of science cards and slot machines, anyone can be winner, on any give day, doing no more than pushing buttons and pumping in money. Is this what is being protected?

My opinion is, science does not have its own resources, but is beholden to others such as government and industry to provide. Science is like the child who gets an allowance and has do chores before the child can spend on their own desires. These others control science by controlling the purse.

Casino science allows more people to participate in applied biology. In the practical sense, anyone can be taught to "black box it " , since the same math can be used, anywhere. Rational theory that included water, is more specialized and targets and this could impact the labor market, thereby impacting the labor force in science government and business models. Scientists should not be carrying the water for the bureaucrats, but it should be the other way around. However, before you can go to the beach, you need to clean the garage.
 

[puppypower (OP)]

Rather than whine about casino science, it may be better to show how life is rationally organized by water. 

The Covid-19 virus will not be able to do anything without water. Water binds to and hydrates the virus so its correct conformations form, and these material shapes have the access to the free energy needed to do its duty as a virus.  Without water support the debate about whether this virus is alive,  will not be relevant. It is pile of inert chemicals.

Say we added another solvent, to the dehydrated covid virus, to replace the water, such as isopropyl alcohol. This makes things worse, since the alcohol will alter its viral configurations and change its surface free energy in an irreversible way, that even water cannot fix; hand sanitizer for sweaty hands  Solvent choice for life is very important to life, since as the majority component of life, the solvent is the big dog. It is straw that stirs the drink of life.

Water by itself cannot form life. Life also requires the organic materials. The organics are sturdy covalently bonded materials that can hold up to the dynamic secondary bonding environment of water. These organic materials, in turn, have an impact on the local and global water via their surface characteristics. This will alter the activity of the water, among other things, and therefore alter how the water can further interact with the organics. Activity is defined as 1.0 for pure water and as we add things, these lower the activity. Water is the major component of life, so there is still residual activity needed to get the job done. If we remove the water, life ends, even if all the organic are protected in place.

The various differences within different cells, such as different organelles, proteins and structural compositions, will attract water and impact the local water in different ways. This allows local activity to be different from average global activity. This difference helps to organize the cell into priories, such as for the flow of materials.  If we remove the water, this all stops.

There are other materials, such as ions in cells. Monopoles are not common to nature. Physics continues to look for monopoles. Ions tend to cluster as opposite charges; NaCl, instead of exist as isolated ions; only Na+ monopoles. But water sort of changes this, allowing solvation into monopoles, which then can impact the water, locally, altering the activity of the water near the ions that exist near specific proteins.

For example, ion pumps segregate sodium and potassium ions on each side of the membrane, with each ion causing a different impact in water. As new protein are added, they align with the water free energy gradient. Each ion changes the free energy of the water, allowing the outside of the cell to behave differently from the inside. If we remove the water this ends. The organics are very dependent on water, while water adapts to any organic or ionic state,  you can dish out. The hydrogen bonding matrix will find a sweet spot.

Again if we remove the water, all this is moot. The organics will lose their dynamics and then the cell will lose its life. If we add water back, each different thing will come back and the same priorities will appear again. Each alters the hydrogen bonding matrix of water and water will always find the same sweet spot when it returns to help.

Things like cell cycles, where cells divide into daughter cells, are driven by shifts in the various organics materials and their concentrations, which in turn, stem from the real time activity of the water. The changes impact the activity and gradients, due to the new materials and configurations.   If we remove the water at any point in the cell cycle, it is all dead in the water, so to speak. The cell cycle needs the water to quickly adapt and then micromanage the changes in compositions, configurations, and activity in a dynamic parallel. If we added alcohol to the water, this alters the water potential and all bets are off.

Evolution was driven by the needs of water, since all change would be dead in the water, without water. The idea of random change on the DNA makes no sense, since all change will impact the water and the water will become altered for all the rest of the organics, including the DNA.

A better model is based on the wild cards that enter a cell from the outside, which the cells has less control over There are transport protein frequencies and budding into cells for bulk material transport. These dynamics wild cards alter the activity of water and then the conformational grid all the way to the DNA. If this alters the water potential, on certain genes, they may need to lower or increase free energy to maintain equilibrium. Again if we take away the water,  this is all inert and lifeless.

[Kryptid]

Think logically. If DNA does not work without water, and no other solvent can be used as a substitute, why do textbooks still insist that the DNA be shown in its dehydrated form, while also describing this as the template material? This is alternate theory and not fact.

I assume this is the kind of diagram you are talking about? https://simple.wikipedia.org/wiki/DNA#/media/File:DNA_chemical_structure.svg

It's not an alternative theory. It's a simplification to make it easier to understand. Sticking a bunch of H₂O molecules on that diagram wouldn't really add anything. One could just as easily argue that the diagram is inaccurate because it's a two-dimensional drawing and thus doesn't show DNA's true shape, or that molecules aren't actually a bunch of letters connected by lines. It's not like that matters, because biochemists already know that DNA is suspended in water in cells. It's not exactly a secret.

[Bored chemist]

If DNA does not work without water, and no other solvent can be used as a substitute, why do textbooks still insist that the DNA be shown in its dehydrated form

They don't.
The dehydrated form is different.
They just don't bother showing the water because everyone knows that it is there, and it clutters the picture.

You may notice that chemists are even lazier; we often don't bother to draw hydrogens in molecules.
https://en.wikipedia.org/wiki/Paraffin_wax#/media/File:Hentriacontane.svg
They are taken as read by the experienced users.

The Covid 19 virus would not be a problem without water,

Well, yes.
Obviously.
Because people are mainly water, and covid is only a problem if it in people.

Did you somehow think that was some mystical hidden truth?

[Bored chemist]

Evolution was driven by the needs of water,

Water has no "needs".

[Zer0]

Hiya @puppypower
😊

Are You complaining that the Artists are drawing a Dolphin but not the Sea that it lives in?
🐬
Is this a classical case of defining a " Fish " but out of the Water?
🤔

I Do get Your point thou...Water is Life!
👍
Elixir!

P.S. - I really Like your Nickname.
😇

[puppypower (OP)]

Think logically. If DNA does not work without water, and no other solvent can be used as a substitute, why do textbooks still insist that the DNA be shown in its dehydrated form, while also describing this as the template material? This is alternate theory and not fact.

I assume this is the kind of diagram you are talking about? https://simple.wikipedia.org/wiki/DNA#/media/File:DNA_chemical_structure.svg

It's not an alternative theory. It's a simplification to make it easier to understand. Sticking a bunch of H₂O molecules on that diagram wouldn't really add anything. One could just as easily argue that the diagram is inaccurate because it's a two-dimensional drawing and thus doesn't show DNA's true shape, or that molecules aren't actually a bunch of letters connected by lines. It's not like that matters, because biochemists already know that DNA is suspended in water in cells. It's not exactly a secret.

The analogy would be like showing only the reactive site of an enzyme, and ignoring the rest of the enzyme, to simplify the drawing. This would create the impression the rest of the enzyme is there for decoration and can be ignored. In reality, the rest of the enzyme plays a critical integrated part in the enzymatic affect, which would not occur without it. The same is true of DNA and water.

A better way would be to show naked DNA, side-by-side with DNA with a semi-transparent halo of water, so the DNA is still easy to to see. Next you tell the student only the picture with the water works, and other is half baked and can do nothing. This would stimulate thinking.  I would ask myself ,what is water actually doing to change the game? This type of question is not being stimulated by the modem teaching methods. Not a single person sees any reason to explore the reason naked DNA needs water to do everything it does. We know water is there and DNA can do nothing without water, but water can be ignored. This is bad education for robot students.

 

If DNA does not work without water, and no other solvent can be used as a substitute, why do textbooks still insist that the DNA be shown in its dehydrated form

They don't.
The dehydrated form is different.
They just don't bother showing the water because everyone knows that it is there, and it clutters the picture.

You may notice that chemists are even lazier; we often don't bother to draw hydrogens in molecules.
https://en.wikipedia.org/wiki/Paraffin_wax#/media/File:Hentriacontane.svg
They are taken as read by the experienced users.

Chemists also know that different chemical reactions do better in different solvents, as well as with the additions of acids and bases. Simply changes like the solvent or to the solvent can make all the difference, including targeted differences. This can get very complicated but that is the topic I am trying to simplify for life.

The Covid 19 virus would not be a problem without water,

Well, yes.
Obviously.
Because people are mainly water, and covid is only a problem if it in people.

Did you somehow think that was some mystical hidden truth?


Water is needed to make all active material in cells work, including virus like Covid. Modifying the water around vulnerable cells, with chemical additions to the water, can alter the equilibrium for covid's configuration and reactions. One can reverse engineer medicine based on any of the critical points where water helps covid enter cells and propagate.

The value of this is, water is one simple thing that can reflect at any level; local or bulk, any and all  organic and ionic equilibria, no matter how complex. One can simulate life, using just water without all the organic clutter since any level of the organic clutter is reflected in the water. We only have to get past the poor educational systemic bias.

Last year when Covid first appeared on the scene, I started a parallel water analysis, to show that all the medical conditions of the most vulnerable people were consistent with a single equilibrium water analysis. This same analysis could have also put a muzzle on the bogey man affect that was encouraged by the casino approach. The young people were never consistent with the needed equilibria at the level of water. It is not coincidence that politics also uses the casino approach. It was painful watching the blind leading blind, waiting for their oracles to give advice.

[Bored chemist]

Are You complaining that the Artists are drawing a Dolphin but not the Sea that it lives in?

That seems to sum up the problem nicely.

[Bored chemist]

Chemists also know that different chemical reactions do better in different solvents

And, since we know, we don't need to be told about it.
In particular we know that the only solvent in which life (on Earth) works is water.
So there really is no need to keep mentioning it, is there?

[Bored chemist]

, I started a parallel water analysis,

What did you actually do?

[Kryptid]

The analogy would be like showing only the reactive site of an enzyme, and ignoring the rest of the enzyme, to simplify the drawing.

Depending on what is being taught at that moment, that could be a perfectly acceptable thing to do.

This would create the impression the rest of the enzyme is there for decoration and can be ignored. In reality, the rest of the enzyme plays a critical integrated part in the enzymatic affect, which would not occur without it. The same is true of DNA and water.

No, it wouldn't. If you are going to go down that track, then you might as well argue that showing DNA without showing the histones, enzymes and everything else in the cell gives the impression that DNA works all by itself without any of the other cellular machinery required. It's extraordinarily nit-picky and pointless. Anyone who actually becomes a biologist will know that DNA is in water.

[puppypower (OP)]

The analogy would be like showing only the reactive site of an enzyme, and ignoring the rest of the enzyme, to simplify the drawing.

Depending on what is being taught at that moment, that could be a perfectly acceptable thing to do.

This would create the impression the rest of the enzyme is there for decoration and can be ignored. In reality, the rest of the enzyme plays a critical integrated part in the enzymatic affect, which would not occur without it. The same is true of DNA and water.

No, it wouldn't. If you are going to go down that track, then you might as well argue that showing DNA without showing the histones, enzymes and everything else in the cell gives the impression that DNA works all by itself without any of the other cellular machinery required. It's extraordinarily nit-picky and pointless. Anyone who actually becomes a biologist will know that DNA is in water.

There is a difference between pure and applied science. Showing just the reactive site of an enzyme or the dehydrated state of the DNA, may be useful and even practical for applied science.  The rest you can black box with statistics.

Pure science is not allowed this practical short cut. The fact that water is critical to all aspects of life down to enzymes and below is pure. The odds are 1.0. Statistics is useful to applied science, because it can ignore what is pure in favor of what is probable. If this makes money, why not do it? 

If you take a pure approach, there is another way to do bio-physical chemistry, that is far more rational and it centers on water. There is no black box needed. I am taking a pure approach to the DNA, so I cannot ignore the one variable that makes the DNA and all its support enzymes and chemistry, alive. You all have been taught to ignore this, as everyone is demonstrating, since pure science is not critical to manufacturing drugs. However, once the pure science approach is made clear, there will be a new set of protocols that will be more efficient.


Let me start at the beginning. If we react oxygen and hydrogen gases, we get one of the hottest flames, with the result being the production of water molecules. Water molecules are very stable being the product of this fiery reaction.

If we place water molecules together, in the liquid state, these very stable molecules become a very dynamic matrix that can self ionize; pH affect. This paradox of self ionizing dynamics coming from extreme stability, is partially due to oxygen being very electronegative. Oxygen is able to hold more electrons than it has positive charges. Charge balance is not important to the oxygen atom, since it can form O-2 quite easily. This is very stable in mineral oxides.

The reason this occurs is the EM force, in general, is both electrostatic and magnetic. In oxygen, the magnetic attraction of its octet of elections, around the oxygen nucleus, is able to offset the electrostatic repulsion so two extra electrons are stable. The oxygen atom is magnetic heavy in terms of the EM force. The advantage of this is, in the liquid state, oxygen does not need the positive charge of the hydrogen proton to balance the local charge, since it can do this by itself with its orbital induced magnetic force. This allows the hydrogen more flexibility and mobility in the liquid matrix. 

Although water is a poor conductor of electricity, due to oxygen, the hydrogen proton becomes quite mobile, The hydrogen proton and is the fastest ion or entity dissolved in water, able to beat even sodium and potassium ions in any race, in water. When nerve impulses move sodium and potassium ions around, hydrogen gets there first, but never get credit. This is placed in the black box of applied science. However, It prepares the way, conducting information. It is easier to keep track of the sodium ions so this is the way used by applied science. This is not pure so I cannot just stop there.

[Kryptid]

You are still being nitpicky. Do you honestly think that lack of water molecules on a diagram of DNA is a genuine science problem? Please explain how that has caused observable problems in science.

[evan_au]

Do you honestly think that lack of water molecules on a diagram of DNA is a genuine science problem? Please explain how that has caused observable problems in science.

Getting the right level of hydration was critical in Franklin & Gosling getting the famous photo 51, which first revealed DNA's spiral structure.
- At different hydration levels, DNA forms different structures
- But ever since then, the presence of the right amount of water in a living cell was a given
See: https://en.wikipedia.org/wiki/Molecular_models_of_DNA#DNA_structure_determination_using_molecular_modeling_and_DNA_X-ray_patterns

PS: I would be fascinated to see the structure of tardigrade DNA when in it's dehydrated state. Apparently, tardigrades can survive in "suspended animation" for years with only 1% of the normal amount of water in their cells.
https://en.wikipedia.org/wiki/Tardigrade#Physiology

[puppypower (OP)]

You are still being nitpicky. Do you honestly think that lack of water molecules on a diagram of DNA is a genuine science problem? Please explain how that has caused observable problems in science.

I made a distinction between applied science and pure science. Applied science does not need to be pure to be practical and cost affective. Newtonian gravity is sufficient for a designing a pitching machine for baseball or cricket, even though relativity is a pure science way to describe the motion of the ball. No pitching machine business will waste their resources trying to be pure if semi-clean is good enough and cheaper.

The reason I would show DNA in both dehydrated and hydrated states, with a blue semi-transparent halo to represent the water that hydrates the DNA, side-by-side in textbooks, is to encourage the students to ask some questions. I can see these questions being a problem only if the teachers know current applied science simplifications, but are not knowledgable about of life in it's pure state with water. These questions are being discouraged because it was never taught. This has been taboo since the 1950's. It is time to change this.

I realize that having to express the DNA, with its hydrating water, although pure science, will be more cumbersome for applied science.  However, that can be simplified. If water is needed for all the dynamic shapes and reactions in the cell, then water is like a halo reflection of the organics and their induced dynamics. A more advanced applied science approach could model cells using only the water side, as we now do with only the organic side. In each case, the other can be ignore, but implied. Water is one thing with various hats. Organic is very complex. Water simplifies modeling by orders of magnitude.

In a business sense, this will create an applied bio-market monopoly, since complexity of organic modeling, will become too cumbersome and slow. The new push will be to translate the organics into their water halo, to create the water equivalent of the same thing. 

Quote from: Kryptid
Do you honestly think that lack of water molecules on a diagram of DNA is a genuine science problem? Please explain how that has caused observable problems in science.
Getting the right level of hydration was critical in Franklin & Gosling getting the famous photo 51, which first revealed DNA's spiral structure.
- At different hydration levels, DNA forms different structures
- But ever since then, the presence of the right amount of water in a living cell was a given
See: https://en.wikipedia.org/wiki/Molecular_models_of_DNA#DNA_structure_determination_using_molecular_modeling_and_DNA_X-ray_patterns

PS: I would be fascinated to see the structure of tardigrade DNA when in it's dehydrated state. Apparently, tardigrades can survive in "suspended animation" for years with only 1% of the normal amount of water in their cells.
https://en.wikipedia.org/wiki/Tardigrade#Physiology

Suspended animation is not alive. However, this state of these integrated organics is capable of becoming fully hydrated and alive, when the correct amount of water is added. This may be a good test subject to define the water halo for preliminary applied water models; two distinct final states and some transitional states for the reflected model halo.

Back to the theoretical foundation.

Hydrogen bonding is not unique to water. For example, hydrogen chloride and ammonia can boht form hydrogen bonds. However, the hydrogen bonding in water is unique in the sense water molecules can form up to four hydrogen bonds with other water. This allows an expansive 3-D network of water held together by transient hydrogen bonds. The other example cannot polymerize to the same degree, such as through out an entire cell.

In a loose sense, water is like a cousin of carbon, both able to form four bonds allowing extended structuring. Carbon does this at the primary covalent bonding level, using electrons for binding,  while water does this at the secondary bonding level using hydrogen protons to bind. While the pH affect of water shows water can also transition between primary and secondary bonding. There is a natural interface between water and carbon at the concentrations used by enzymes.

The hydrogen bonds show both polar and covalent bonding characteristics. Both are expressed in the pH affect. One water molecule will form a hydrogen bond with another water molecule. This often begins as a polar attraction between charges; hydrogen proton and oxygen electrons.

This brings the neighboring hydrogen proton close to the oxygen atom of the other water. As discussed before, oxygen is heavy on the magnetic side of the EM force, to maintain its extra electrons, beyond the positive charge of its nucleus. The hydrogen proton, being shared, can get wrapped up in the stabilizing magnetic field of the extra oxygen electrons. This transitions the polar hydrogen bond into the covalent aspect of a hydrogen bond.  If it goes even further, the hydrogen proton will become covalently attached to the new oxygen. Oxygen is important to the hydrogen bond's full nature.   

Water molecules in the liquid state have a very short life span; nanoseconds, before the protons switch partners; pH affect and others. This entire short lived water matrix, appears to be driven by the second law; the movement and switching of hydrogen protons. Life lower the entropy of pure water, using organics. This creates an entropic potential in the water, among other things. A potential is created, to increase entropy; complexity, elsewhere; evolution.  Water does not change, so carbon has the burden to meets the needs of the second law.

[Bored chemist]

Both are expressed in the pH affect.

Not really.

Rather than posting reams of obvious stuff (we know the water is there, and we know it behaves weirdly), perhaps you could actually answer this.

, I started a parallel water analysis,

What did you actually do?

[Kryptid]

This has been taboo since the 1950's.

You're going to need to back that up with evidence. I don't believe it.

Getting the right level of hydration was critical in Franklin & Gosling getting the famous photo 51, which first revealed DNA's spiral structure.

Depicting DNA with water molecules around it in books would not have helped with that.

[Petrochemicals]

Is this a "water is inherant to all life including aliens" post?

 Water is very good as a refrigerant to the temperature we are used to, its latent heat is rather high,  it is lighter in solid hexagonal form than its liquid meaning it floats at a pressure on a planet with gravity enough to hold an atmosphere meaning it floats rather than sinking, it has a humongous heat capacity to act as a buffer. Plus it seems to be fairly abundent.