[Bored chemist]

Right here on this forum I predicted Omikron as a coronavirus with a lot less intense symptoms and and making a lot more people ill

You do realise that  a more readily transmitted, but less lethal version of the virus is exactly what Darwinian evolution predicts, don't you?

We got lucky with omicron.
There was no guarantee that we wouldn't get a more lethal version- and there still isn't any such guarantee.

[Origin]

The problem with "there is no proof for IT" - look again. The title of this forum is "new ideas", so go find yourself those proofs..

If you can't be bothered to support your position why in the world do you think I would?
Based on your answer I will assume your claim is untrue and just some thing you made up.

the rest - I'm not answering this, 'cause I'm right, you're not!

Acting like a 10 year old is not conducive to a scientific discussion.

[alancalverd]

If only a few specimens of an extinct species are left,

...then it isn't extinct.

[puppypower]

The result is the over dependence on casino math to supply fudge factors for the DNA brain.

Nonsense.

it gives too much credit to the DNA, for being like a brain, and not enough credit to the interactive protein grid that interfaces the DNA

All that protein was produced because it was encoded for in the DNA.
That's why the DNA is typically given priority.

The hard drive of a computer has all the data including the code for the operating system. However, once the operating system is functional, it now runs the show, with the hard drive more passive, with extra data that might be needed.

This priority makes a difference. Protein, such as enzymes, can do work and catalyze reactions such as getting data from the DNA. This why the mother cell undergoes a lot of synthesis first to gather enough protein for two protein based operating systems. She then finishes by  duplicating and packing the DNA, since the daughter cells will first need logic and muscle and then access to more data to build from there.

In multicellular differentiation, all cells have the same DNA, yet the expression is unique for each cell type. This is easier to control at the level of the operating system; protein grid, since the operating system come in contact with the environment, and can it use the DNA hard drive to add to the protein muscle, to deal with any scenario, while also maintaining the needs of cellular differentiation control; base layer of logic.

The random changes on the DNA is different if we compare the DNA is the brain scenario, to the protein grid is the brain. In the latter, the operating system would also be making changes to the DNA that reflect the long term activity that has built up a capacitance over time; read and write instead of just read only.

[Bored chemist]

The hard drive of a computer has all the data including the code for the operating system. However, once the operating system is functional, it now runs the show, with the hard drive more passive

No
https://en.wikipedia.org/wiki/Virtual_memory

[puppypower]

The hard drive of a computer has all the data including the code for the operating system. However, once the operating system is functional, it now runs the show, with the hard drive more passive

No
https://en.wikipedia.org/wiki/Virtual_memory

The DNA cannot do anything without enzymes; protein. The DNA is packed into chromosomes via packing protein and is unpacked via unpacking  protein; enzymes. This basic mechanics is how the DNA hard drive is organized by the protein grid for read, write and long term data storage.

When cells interact with the environment, the protein grid is the interactive switching mechanism that mediate needs, to the DNA. Signals, from the environment do not go directly to the DNA. The protein grid can even make protein that are not coded on the DNA. It is one step above.

If you look at the DNA, its code is based on base pairing via hydrogen bonding. There are four bases, the various combinations of which can be used as templates for RNA, which are then used as templates for protein.

The functionality of the DNA is limited to acting as a template. This hard drive is organized with configurational capacitance; junk genes, that helps the organize the data for more efficient read and write. There is far more variety to the protein in terms of form and function. This is needed for the operating system.

The one thing all proteins have in common, is once they are synthesized on  mRNA templates, that were coded from the DNA hard drive, they need to pack and organize in space, based on the potential in the water; energy landscape.

Water is also important to the functionality on the DNA hard drive. It assists the protein for recognition; fingerprinting, as well as for free energy. In your link about virtual memory,  water would be the equivalent to the virtual memory, since it is the reflected and interacting part of the DNA, the protein grid, and the external environment.

Evolution has the problem of doing this backwards since the two top layers of virtual memory; water, and operating system ; protein grid, is what controls the DNA, even for forward seeking change.

When the DNA hard drive is duplicated, proof reader enzymes go up and down the DNA making sure there are no typo's. If you ever download an update the operating system of your device, the download is checked to make sure it is a clean copy. The question is how can mutations on the DNA get by that, for a forward looking affect called evolution?

The answer is DNA is not alone in terms of potential. The full template potential also includes the protein grid and the water. As an analogy the words "way" and "weigh", sound the same, but will give different meanings. Neither is a spelling error, but both create a different instructions, that are the sum of a three pronged approach; forward integration.

[Bored chemist]

The hard drive of a computer has all the data including the code for the operating system. However, once the operating system is functional, it now runs the show, with the hard drive more passive

No
https://en.wikipedia.org/wiki/Virtual_memory

The DNA cannot do anything without enzymes; protein. The DNA is packed into chromosomes via packing protein and is unpacked via unpacking  protein; enzymes. This basic mechanics is how the DNA hard drive is organized by the protein grid for read, write and long term data storage.

When cells interact with the environment, the protein grid is the interactive switching mechanism that mediate needs, to the DNA. Signals, from the environment do not go directly to the DNA. The protein grid can even make protein that are not coded on the DNA. It is one step above.

If you look at the DNA, its code is based on base pairing via hydrogen bonding. There are four bases, the various combinations of which can be used as templates for RNA, which are then used as templates for protein.

The functionality of the DNA is limited to acting as a template. This hard drive is organized with configurational capacitance; junk genes, that helps the organize the data for more efficient read and write. There is far more variety to the protein in terms of form and function. This is needed for the operating system.

The one thing all proteins have in common, is once they are synthesized on  mRNA templates, that were coded from the DNA hard drive, they need to pack and organize in space, based on the potential in the water; energy landscape.

Water is also important to the functionality on the DNA hard drive. It assists the protein for recognition; fingerprinting, as well as for free energy. In your link about virtual memory,  water would be the equivalent to the virtual memory, since it is the reflected and interacting part of the DNA, the protein grid, and the external environment.

Evolution has the problem of doing this backwards since the two top layers of virtual memory; water, and operating system ; protein grid, is what controls the DNA, even for forward seeking change.

When the DNA hard drive is duplicated, proof reader enzymes go up and down the DNA making sure there are no typo's. If you ever download an update the operating system of your device, the download is checked to make sure it is a clean copy. The question is how can mutations on the DNA get by that, for a forward looking affect called evolution?

The answer is DNA is not alone in terms of potential. The full template potential also includes the protein grid and the water. As an analogy the words "way" and "weigh", sound the same, but will give different meanings. Neither is a spelling error, but both create a different instructions, that are the sum of a three pronged approach; forward integration.

Talk the simple smile
Such platonic eye
How they drown in incomplete capacity
Strangest of them all
When the feeling calls
How we drown in stylistic audacity
Charge the common ground
Round and round and round
We living in gravity
Shake
We shake so hard
How we laugh so loud
When we reach
We believe in eternity

[puppypower]

The topic is about evolution, which in contemporary science is connected to changes on the DNA and Darwin's theory of natural selection. The current approach places the DNA at the top of the food chain. This is where I depart from science since DNA at the top, does not make sense if you think it through.

The DNA at the top of the hierarchy does not make conceptual sense, since the DNA, alone, can do nothing. All that occurs at the DNA requires support by a range of protein and enzymes. The DNA is more like a hard drive with all the data, but it has no means of it own, to do much else. It is passive and needs to be acted upon by enzymes; protein, before its data can be accessed and used. The DNA is not the CPU. A CPU gets hot due to expended energy.

Errors on the DNA, often deemed as the basis for evolution and natural selection, cannot get there without enzymes, or some other outside activity; carcinogenic chemicals. The cell body or the protein grid; how the protein of cells organize, has control over the data on the DNA, on the Ribosomes,  and then to its final placement. This energy intensive approach makes the protein grid the CPU, with even mutations mediated by proteins.

Another key observation is that  enzymes, will not work, if they are not packed properly. Experiments were done and it  has been found that no solvent, other than water, is able to pack protein properly, so they can function as designed. There is something about the molecule properties of water that make it unique to the needs of life.

Water will form up to four hydrogen bonds, with other water, to form extended but transient 3-D water structuring. When you add materials to this liquid water matrix, such as newly manufactured protein, hot off the ribosome press, all the side groups along the protein, will create different potentials in the 3D hydrogen bonding matrix of water; energy landscape diagram.

The most reduced moieties, will create the most potential and surface tension in the water. These will bead up like little balls of oil in water and start to pack as the core of the enzyme. This continues in energy priority, from highest  to lowest potential. The final shape of the protein has been prioritized by water, to minimize its potential in water.

Once the enzyme is properly packed by the water; high to low energy is very repeatable and defined by the water, the protein is moved to its proper place in the protein grid. Water will hydrogen bonds onto the surface, forming cooperative hydrogen bonding.

Cooperative hydrogen bonding is where the water on the surface becomes like a large connected 3-D shell; resonance structure of sorts  These 3-D shapes go way beyond what water can do by itself in pure water. This is due to the packed proteins forced to linger in time by the water. These water surfaces contain free energy, that can help enzymatic reactions. The cooperative of water lowers local water entropy; lingering order in time, and sets a free energy potential with the second law. Covalent hydrogen bonding used by cooperative define lower entropy then polar hydrogen bonding.

This water cooperative effect occurs cell wide, including on the DNA. In terms of the entire cell, these water cooperative reflect an integrated water based expression, that includes all things within the cell. This is the top of the food chain, but it only exists because the DNA and protein grid set the stage with materials, that can allow the water to linger in unique states.

If you look at the DNA, the number of coding genes is limited. Most of the DNA is based on noncoding genes. The question that came to my mind was, why use such a large hard drive of DNA material, when all you need is a tiny hard drive, to contain the coding genes?

The reason is the majority of the DNA.; noncoding, is there to help organize the coding genes in space, though configurational potential. Like packing a protein in water, where proteins are packed, based on highest potential first, the noncoding genes are hare and there, so the coding genes can be spread out in 3-D space, based on water potential priories; chromosomes.  These water potential priorities extend into the protein grid and beyond, since the water is continuous to the outside. Information flow in water is the fastest method in any cell.

Conceptually, you could model cells by just the cooperative water shells, since the surface shapes of water reflects specific material surfaces. This way you only need work in one variable.  The organic-centric approach is too cumbersome; enormous catalog of organic details. These can all be replaced by water surfaces, to do fast paced simulations with water as the one variable CPU.

[evan_au]

it  has been found that no solvent, other than water, is able to pack protein properly

That is what you would expect for water-based life.

If we imagine some other form of life, based on (say) ammonia, I expect that no solvent, other than ammonia, would be able to pack their proteins properly.

The current approach places the DNA at the top of the food chain

In a sense, the cell is DNA's way of reproducing itself. This is the concept behind "The Selfish Gene".

There are various views about which came first: Data storage (DNA or RNA), structure (proteins), process (enzymes) or energy/metabolism.
- To some extent, they are all required for life as we know it
- But the origins are now lost to the sands of time.
- Perhaps we might discover more on Europa....

[alancalverd]

Errors on the DNA, often deemed as the basis for evolution and natural selection, cannot get there without enzymes, or some other outside activity; carcinogenic chemicals.

Most of them are actually triggered by free water radicals. The hydrogen bond is a wonderful thing, and the DNA molecule is interestingly both fragile (prone to alteration) and robust (able to function with significant changes). The fact that life evolved on a radioacitve planet may also partially account for the status quo.

[Bored chemist]

Puppypower,
if we just tell you that we already knew that water is weird, will you stop banging on about it?

However, you don't get life without some means to make 2 copies of the same blueprint.
And that's the unique selling point of the nucleic acids.

And that is why people looking at evolution focus on the DNA (and RNA).

Reverse transcription does happen but it's from RNA to DNA.
It doesn't start with protein.
So proteins can't copy themselves.
So they can't evolve.

[puppypower]

Puppypower,
if we just tell you that we already knew that water is weird, will you stop banging on about it?

However, you don't get life without some means to make 2 copies of the same blueprint.
And that's the unique selling point of the nucleic acids.

And that is why people looking at evolution focus on the DNA (and RNA).

Reverse transcription does happen but it's from RNA to DNA.
It doesn't start with protein.
So proteins can't copy themselves.
So they can't evolve.

If you look at any scientific definition of life, life is not defined by replication alone. All the rest of the attributes of life like metabolism, signally, growth, etc, come from the protein. This is why I like the hard drive analogy for the DNA. The DNA contains all the data needed to define, say a human. But this data is only information. It needs to be translated, transcribed, packed and then positioned, before it can do all the work required to be called the living state.

A computer hard drive may have all the code needed for our music collection. We can make copies of this music to give to our friends. But to become music, you can hear and appreciate, you need hardware to access the data and then scale the code, all the way into the action of speakers used for the HD-sound. Evolution is about changes in the hardware, that express the changes in code on the hard drive. The unicorn is different from the horse by a protein horn. Fossil remains are about calcium from the protein grid.

The protein grid, as the CPU, accounts for differences, from the beginning, even with the same DNA. Adding water to the DNA hard drive and protein grid, to make this a trinity, is more subtle, but water is what drives evolution.

Protein, DNA and RNA only work properly in water.  They will not work in any other solvents. This has been tried without success. This is expected, since these categories of molecules all evolved in water. Water set the potential for molecular selection at the nanoscale. All life on earth works in water, because water selected all these chemicals. If an alcohol was in charge, it would have selected differently. DNA would not be chosen as the template by alcohols, since it does not work with alcohols.

When we mix water and oil, they separate since the potential is minimized for both materials.

This molecular selection in water; abiogenesis, follows the same schema as macro-scale evolution. If we look at a desert, the types of life one would expect to see, will all need to accommodate the lacks, needs, and surpluses of the desert. They are tuned to what the desert can offer. DNA, RNA and protein are turned to water and were selected.

In the case of water, the direction of evolution, at the nanoscale, heads in ways that reinforce the potentials offered by a water environment.  When protein are packed in the water environment, the final selected protein needs a hydroponic core and hydrophilic surface. This shape s tuned to the nature of water. Water can even form lingering  cooperative hydrogen bonding in space. If we try a new protein and its falls short of the water test it not selected but recycled.

Environmental stresses on life, from many sources, alter the balance between water and all its many selected and organized chemicals. Rain, in the desert, for example, adds a wild card that throws things off balance. New things may enter for the water. Dormant plants may now grow from their roots, and the former bugs may become overwhelmed with new birds. The selective process begins again.

The nanoscale target of the water's selective nature appears to be the DNA hard drive, since it is pliable and water can alter potential with simple changes. Improper base pairing adds energy point to reflect the stresses.

[Bored chemist]

If you look at any scientific definition of life, life is not defined by replication alone.

Nobody said it was.
However the thread is about evolution an, for that, you need replication.

This is why I like the hard drive analogy for the DNA. The DNA contains all the data needed to define, say a human. But this data is only information. It needs to be translated, transcribed, packed and then positioned, before it can do all the work required to be called the living state.

A computer hard drive may have all the code needed for our music collection. We can make copies of this music to give to our friends. But to become music, you can hear and appreciate, you need hardware to access the data and then scale the code, all the way into the action of speakers used for the HD-sound

Why do you keep repeating that bit?

We know how biology (and computers) work.
You are just wasting time and bandwidth.

but water is what drives evolution.

No, it isn't.
Evolution requires change.
Water does not change.
It It may facilitate it (for life on Earth as we know it).
I'm even prepared to accept that life elsewhere in the universe probably uses water.

But it's still just a cheap solvent with some useful properties.

When we mix water and oil, they separate since the potential is minimized for both materials.

Your repeating this statement just makes me wonder if you forgot that you already said it.
It doesn't actually help the discussion, because everyone already knows it.

DNA, RNA and protein are turned to water and were selected.

That makes no sense.

In the case of water, the direction of evolution, at the nanoscale, heads in ways that reinforce the potentials offered by a water environment. 

No, it does not.
Apart from anything else, if that was true, we would still be in the oceans where water is more abundant.

Do you see how your posts seem to me to consist of repeating the obvious, and then interspersing stuff that a bright schoolkid would spot the errors in?

[alancalverd]

Fossil remains are about calcium from the protein grid.

Calcium in protein? Collect your Nobel Prize at the door. Or maybe read some biochemistry.

[puppypower]

No, it isn't.
Evolution requires change.
Water does not change.
It It may facilitate it (for life on Earth as we know it).
I'm even prepared to accept that life elsewhere in the universe probably uses water.

But it's still just a cheap solvent with some useful properties.

Quote from: puppypower on 10/07/2022 20:52:16
When we mix water and oil, they separate since the potential is minimized for both materials.
Your repeating this statement just makes me wonder if you forgot that you already said it.
It doesn't actually help the discussion, because everyone already knows it.

Water does not change in terms of being H2O. Water is a sturdy bookend that is important to life, since carbon based molecules; like DNA, RNA and protein can and do change, and have nearly infinite variety. The stable water bookend offers a constant steering mechanism, for all life, as new carbon compounds appear for packing and placement.

Life in other solvents, like alcohols, would not start with a stable bookend since alcohols would ultimately be metabolized down to CO2 and H2O. Now we have a stable water bookend and a gas that departs. Ammonia would be metabolized down to NOx and H2O. Now we have a water based bookend that will not change further.

I often repeat the water and oil experiment, since it is simple key to a deeper understanding that is still not getting through. This example shows what happens to a simple class of organics; oil, when placed in water and agitated. The surface tension between the water and oil, add energy and force the water and oil to separate into two phases to lower the surface tension. Surface tension allows water to manhandle organics.

Pure water has both polar and covalent hydrogen bonding character. Oil creates surface tension, which implies a shift more to the covalent side of water. The phase separation is due to pure water preferring to stay more on the polar side at steady state. It will do what it takes, to get back toward the ideal balance such as separate out to lower surface contact.

In the case of a protein, which is a more complex organic molecule; reduced groups, polar groups and hydrogen bonds, the phase separation is also based on the surface tension in water, and the need of water to get back to being more polar and less covalent.

As the complexity of the protein increases, the amount of steps increases before the reaching the final packed protein bubble. It is the same water. It does not change and still it wishes to reach that sweet spot; more polar to covalent bonding ratio. Like army ants, many little things all with the same agenda can move large objects into coordinated compliance.

Different organics; from oil to protein to DNA, will each force the water to behave with different amounts of potential and selectivity, based on the unique circumstance set by the specific organics in question. This is why a water bookend is so useful. Selection by water at the nanoscale, is based on organic molecules and packed surfaces that allow water to minimize its potential. These can peacefully coexist with water. This is true of packing   DNA with packing protein, to form low surface area chromosome bubbles. Unpacking reverses this and adds potential for enzymatic affects.

My guess, based on how water packs protein, packed chromosomes are packed based on water priority; best way to reach the magic ratio. This consistency of packing is useful for organizing the DNA data the same from  mother to daughters.
 
If we look at an entire cell, full of its organic variety, that creates various  pockets and zones of surface tension in water.  We still have one water bookend, with all the water molecules; ants, with the same sweet spot in mind, in terms of their magic polar/covalent hydrogen bonding ratio. However, each has to perform a different range of tasks, based on where it is in the cell. The water helps itself, by organizing the protein grid into gradients, just as it does with a single protein or with chromosome being packed. Shifts in water potential; input food, can send information through the water that can alter the packing by the water down stream. Mutations on the DNA are just another job for the bookend of ants that never stops trying to find its sweet spot.

Life is simpler  to model from the water bookend side, since how the water is behaving, near any the organics, reflects the complexity of the organics, but in one stable variable. Evolution, driven by water would be based on selection that allows the sweet spot of the bookend to be reached even under the most complex senarios.

[Bored chemist]

Life in other solvents, like alcohols, would not start with a stable bookend since alcohols would ultimately be metabolized down to CO2 and H2O

How?
Where would the required oxygen come from?
Oxygen is only present in meaningful quantities on Earth because it is formed by splitting water.

Did you not realise that your idea is wrong?

I often repeat the water and oil experiment, since it is simple key to a deeper understanding that is still not getting through.

It got through to us the first time.
What you are not "explaining" is the other nonsense you talk (see above for an example).
Because it's rubbish, you won't "get it through" to us- because we spot that it's trash.

My guess, based on how water packs protein, packed chromosomes are packed based on water priority; best way to reach the magic ratio.

Your guess is word salad.

[alancalverd]

Water does not change in terms of being H2O.

Oh but it does! In the liquid state it forms umpteen different temporary polymers, the individual molecules are electrically polarised, and there are always a few ions and free radicals floating about. It's a highly reactive substance with some absolutely unique physical properties. It just happens that there is a lot of it about, in all three states, on this planet. It  is responsible for pretty much everything that happens in the biosphere (indeed water is the biosphere) and most of what goes in in the atmosphere.

[puppypower]

Life in other solvents, like alcohols, would not start with a stable bookend since alcohols would ultimately be metabolized down to CO2 and H2O

How?
Where would the required oxygen come from?
Oxygen is only present in meaningful quantities on Earth because it is formed by splitting water.

Did you not realise that your idea is wrong?

I often repeat the water and oil experiment, since it is simple key to a deeper understanding that is still not getting through.

It got through to us the first time.
What you are not "explaining" is the other nonsense you talk (see above for an example).
Because it's rubbish, you won't "get it through" to us- because we spot that it's trash.

My guess, based on how water packs protein, packed chromosomes are packed based on water priority; best way to reach the magic ratio.

Your guess is word salad.

Most of the proposed solvents, that are assumed to support life on other planets, have a chemical potential higher than water. This topic is about evolution and the assumptions of biology, that do not add up. Water has a selective advantage by being at the bottom of the solvent energy hill. Grinding down other solvents, all the way to water, will be exothermic and increase entropy.  We add alcohol to gasoline to extract energy and get CO2 and water. Organic based solvents for life will eventually be used for metabolic energy. Water is the last solvent standing.

The black box and probability approach of biology gets them into trouble, with the solvent assumption more about gambling than about common sense. If we used an organic or polar organic solvent, proteins will not pack the same way. The energy landscape diagrams will be different for each solvent. Ammonia is a good degreaser, which means you will not get the correct hydrophobic core nor the correct surfaces on forming proteins.

Protein were not selected by ammonia, but by water. Only water can fold them into useful things. The has been proven in the lab. What replacement for protein polymers would ammonia select, so life in ammonia can get repeatable enzymatic surfaces, even with its higher energy solvent floor? The DNA has similar problems with ammonia and other organic solvents. What would be the new template material that can function in an alcohol; selected by the alcohol to work properly? There is no answer just a lottery ticket, dreams and magical assumptions.

Water can be broken down to O2, such as during photosynthesis. However, this is endothermic and oxygen is a gas. O2 gas can never take over as the solvent, since it can only concentrate in small amounts in liquid water. It is not easy way to alter water all the way to a replacement, since unlike all the organic solvents, there is no good exothermic energy hill for water. We need to add energy to push water up the hill to make even O2. If we burn or retrieve all the energy within the O2 , we end up with water.

[puppypower]

Water does not change in terms of being H2O.

Oh but it does! In the liquid state it forms umpteen different temporary polymers, the individual molecules are electrically polarised, and there are always a few ions and free radicals floating about. It's a highly reactive substance with some absolutely unique physical properties. It just happens that there is a lot of it about, in all three states, on this planet. It  is responsible for pretty much everything that happens in the biosphere (indeed water is the biosphere) and most of what goes in in the atmosphere.

The hydrogen bonding matrix of liquid water, alters water in many different ways such as the pH affect and 3-D water polymers. In fact, H2O molecules to not exist more than a tiny fraction of a second before the atoms are swapped out. H20 molecules are more enduring in the gas and solid state. But in the liquid state, things are different, allowing hydrogen bonding to constantly break the covalent bonds of water; pH. Liquid water takes the second law to new levels; very complex matrix.

The question then become how can a molecule, like water, that is very stable in fire, be able to do things like break strong water bonds, that should require a lot of energy? It has to do with oxygen of water able to hold two more electrons than it has protons; complete the octet.

Electrostatic and polar potential arguments alone cannot explain the stable charge unbalance of oxygen, that oxygen strives for. The analysis also requires magnetic considerations; electrons in orbital motion, and partial covalent character. The oxygen of water can hold the electrons of water tighter, making hydrogen more free to find other electrons. This can reverse the magnetic impact of oxygen, on another water molecule, so the bonds  becomes more polar. The binary switch within the hydrogen bonds of water, via oxygen, allows water molecules to have a potential range at each hydrogen bond.

Organics are often called hydrophobic. However, this is misnomer, since organic are not afraid of water. Water can share via the weaker van Der Waals forces that also bind organic materials. The problem is the water will gain potential, in the presence of organics, through surface tension. The hydrogen of water can shares the electron density of the organics. This causes the oxygen of water, to amplify its magnetic orbital affect; covalent nature. The organics like this, arrangement, but water would prefer lower potential and be more polar, since polar better expresses the 2nd law. Polar  is only a function of distance, but not position. Covalent is based on the proper positioning and distances in space for orbital overlap; lower entropy.

Say we have a protein that is hot off the press, all stretched out. It is surrounded by water molecules; army ants. The various amino acids will each has a different impact on the water, based on the side groups along the protein. Gradients will form in the local water, based on polar and covalent hydrogen bonding settings, with the more covalent having higher surface tension, near the reduced moieties on the protein.

The covalent side of the hydrogen bonding switch lowers water entropy, while the polar side is at higher entropy. Entropy can increase if the water can become more polar within the gradient. This can occur if the oxygen of water shares electrons with its own hydrogen. This disconnects the protein, which then starts to pack The entropy of the water can increase, prioritized by the potential lowering along the gradient toward  higher entropy polar. This packing lowers the entropy of the protein.

The difference between water and the protein is, water molecules are small army ants, and have more degrees of atomic freedom in liquid water; constantly swapping partners and shapes. The proteins are large with less atomic freedom due to being a covalent polymer than cannot self ionize to any great degree. Water become more polar to resolve the total entropic potential of the system even though protein packing lowers some entropy.  The smaller residual entropic potential, within the folded protein; very specific shape instead of random folding, makes the protein subject to entropic change; entropic based aspect of enzymatic potential.

Alcohols and organic solvents add more randomness or entropy to protein folding, resulting on less entropic potential in the final enzymes. But with water lowering surface tension, so water can become more polar with higher entropy, the many polymers of life are forced into order to maximize the entropic potential of the protein. We get a situation expressed by the continuous activities of life; reversible surface expressions reactions, due to water running a high entropy ship; maximizes the second law. 

Evolution is about maximizing the entropy of water by minimizing the entropy of protein and organic surfaces. This order gives the organic dynamics of life a renewable entropic potential. Increasingly complex life is driven by the unusually high entropy background potential set by the water. as the pieces of puzzle fill in better and better, water is better off.

[alancalverd]

The hydrogen bonding matrix of liquid water, alters water in many different ways such as the pH affect

Rubbish. The pH of pure water is always 7. Sadly, drivel in the first sentence makes one wonder whether it is worth reading any more.