Naked Science Forum

Non Life Sciences => Chemistry => Topic started by: puppypower on 29/03/2017 13:02:33

Title: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 29/03/2017 13:02:33
If you do a Google search for the DNA double helix, what is shown is a dehydrated double helix, which is not bioactive or how it exists in nature. The same is true of textbooks.

The reason I ask is, ever since Watson and Crick discovered the structure of DNA, it has been known that water plays a major role in the structure and function of the DNA. In fact, there are places on all the bases of DNA and RNA that are earmarked for hydrogen bonding to water. Water is an important part of the structure. Why do textbook not show this reality, but rather misrepresent DNA? It makes a big difference on how the mind will process and extrapolate the DNA and its activity.

Below is chemical representation of the water that has been proven to be hydrogen bonded to the bases of the DNA. These water also hydrogen bond to each other, to form a double helix of water, one helix in each the major and minor grooves of the DNA double helix. The reality is, active DNA is a quadruple helix. Why is reality still repressed by educational science? Why stay dumbed down and not upgrade the textbooks to the latest proven science?

This is not a new theory, but is well documented science. Maybe the question should be, who benefits by the dumb down and the constant aborting of all attempts to upgrade to the latest data. 

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fnuclei.gif&hash=5a231e78c151e6b5f59a7808a36702ee)
Title: Re: Why don't textbook show DNA with it's hydrating water?
Post by: PhysBang on 29/03/2017 15:18:42
People benefit from learning a little at a time. They also benefit from not hearing your bonkers theory of magic water.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: chris on 29/03/2017 19:05:20
You are right that DNA is active in the aqueous state, but I think it would make it very hard - and highly confusing - for people trying to see the structure with all the flanking water molecules in the way.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: alancalverd on 29/03/2017 19:36:54
If you add lots of water molecules, you have to explain why they don't confound the stereochemistry of mitosis, and you end up with a whole chapter of hypothesis to explain one sentence of observation. 
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: evan_au on 29/03/2017 21:42:07
Quote from: puppypower
Why don't textbooks show DNA with its hydrating water?
1. Because the chapter title is "DNA", not "Water" or "Hydrogen Bonding"
2. Because the title on the cover is "Biology", not "Chemistry".
3. Because water is transparent  ;)
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 30/03/2017 12:00:58
If you add lots of water molecules, you have to explain why they don't confound the stereochemistry of mitosis, and you end up with a whole chapter of hypothesis to explain one sentence of observation. 

So you are saying that truth is not important to science, but rather oversimplified convenience is more important? This would make practical sense if the purpose of biology was make money, such that factory speed and efficiency is the goal. I was taught that science seeks the truth of nature. Water is still part of the naked DNA, but it is placed in the black box for statistics.

Let me explain one chemical purpose for the hydrogen bonded water, using an electron density analysis. If you look Guanine, for example, as shown in the opening diagram labelled as G, notice the double bonded oxygen atom at the top. Because this oxygen is the most electronegative atom in guanine, electron density is pulled toward this oxygen. 

If we now hydrogen bond water to this oxygen, as shown, the positive charge of the hydrogen will increase the electron withdrawing ability of this oxygen. It sort of add a couple of extra hands. If we place water in the black box, the oxygen of guanine appears to act as though it has a higher electronegativity than is normally expected. This impacts the entire molecule.

The hydrogen bonded water also hydrogen bonds to other water molecules, attached to the other bases, to form a double helix of water that follows the major and minor grooves of the DNA. Water has a property called cooperative hydrogen bonding. As more and more water, hydrogen bond polymerize, all the hydrogen bonds get stronger and stronger. In fact, cooperative hydrogen bonding can double the hydrogen bond strength compared to a single hydrogen bond.

The net effect is the double helix of water, as a cooperative, increases the electron withdrawing nature of that oxygen even more. Conceptually, one can tweak the effective electronegativity of this oxygen by tweaking the extent of the cooperative. A similar analysis is true for each atom of the bases, the water hydrogen bonds. In some places there is more electron release. This has an impact on template strength, which is not always uniform, due to tweaks in extended cooperatives.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: PhysBang on 30/03/2017 12:17:54
If you add lots of water molecules, you have to explain why they don't confound the stereochemistry of mitosis, and you end up with a whole chapter of hypothesis to explain one sentence of observation. 

So you are saying that truth is not important to science, but rather oversimplified convenience is more important? This would make practical sense if the purpose of biology was make money, such that factory speed and efficiency is the goal. I was taught that science seeks the truth of nature. Water is still part of the naked DNA, but it is placed in the black box for statistics.
Nobody is saying that except you. You have a limited knowledge of the science and you only look at the most basic of textbooks, so you find simplifications that you do not understand.

And none of the chemistry of DNA, which practicing scientists who work with it understand in great detail, justifies your claims that water is intelligent and chooses the mutations that happen.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: tkadm30 on 30/03/2017 13:23:55
My guess is that the configuration of DNA by water molecules is essentially a current research topic, and that science must adapt itself with the latest data.  This takes time, and requires new experiments to confirm this hypothesis.

See: https://www.sciencedaily.com/releases/2011/04/110426091122.htm
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 31/03/2017 13:24:10
My guess is that the configuration of DNA by water molecules is essentially a current research topic, and that science must adapt itself with the latest data.  This takes time, and requires new experiments to confirm this hypothesis.

See: https://www.sciencedaily.com/releases/2011/04/110426091122.htm

Science is not self sufficient when it comes to resources. Science is beholden to government, industry and private donations for its resources. That being said, science has to do research based on the objective of the donors. In terms of medical research, industry donates a lot of money and resources to science. These industries are there to make money, with many of their products subject to regulatory compliance. Statistical modeling simplifies both tasks. It offer compliance wiggle room, and as a science procedure, it can be used for mass production.

Although adding the impact of water, will bring these models much closer to reality, it adds complications to the business needs, in the short term. The net result is, it is never the proper time for the change, even if it can lead to a new ways to address old problems. Competition is tough, so any disruption of research, can break a business. However, any company that has this ace in the hole, will have a future market advantage. Money makers are not working for ther future CEO, but the needs of todays profits.


The DNA double helix is held together with hydrogen bonding between base pairs. This is not new. These hydrogen bonding hydrogen on the DNA, can also form cooperative hydrogen bonding. While the proximity of the hydrogen bonded water, to these same bases, allows a cooperative to be shared between the water and the DNA.

Below is a representation of the DNA double helix. The large green and red balls represent some of the oxygen of the hydrogen bonded water, attached to the bases, that run along the spine of the double helix. The yellow and red tetrahedrons are also water. There is more water than is shown.

(https://www.thenakedscientists.com/forum/proxy.php?request=http%3A%2F%2Fwww1.lsbu.ac.uk%2Fwater%2Fimages%2Fdna_minor_groove.gif&hash=7707157b6a57e9351592fe0e7f47db55)

Another important use for the cooperative hydrogen bonding of water (and DNA), is to supply free energy and finger prints for substrate binding and template reactions. A cooperative is highly ordered, similar to chemical resonance; benzene. When you disrupt the cooperative, the result is in an increase in entropy; order to disorder.

For entropy to increase in any system, the system needs to absorb energy. In a loose sense, a cooperative disruption, among other things, pulls an energy vacuum; pulls things up a free energy hill. Enthalpy/energy output can push things up an energy hill. In life, entropy acts like a partner, that can pull as the other pushes. The hydrogen bonding cooperative are reversible and not random, turning entropy into a reusable tool.

[B. Jana, S. Pal, P. K. Maiti, S. T. Lin, J. T. Hynes and B. Bagchi, Entropy of water in the hydration layer of major and minor grooves of DNA. J. Phys. Chem. B Condens. Matter Mater. Surf. Interfaces Biophys. 110 (2006) 19611-19618.

 
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 01/04/2017 13:29:20
This topic title is, why isn't water included in textbook pictures of DNA? I am showing water is not just an inert solvent but plays a major role in the dynamics on the DNA. It is not overly complicated, to where one can justify the suppression of evidence due to headaches for thinking.

Why would science want to suppress truth, if the goal of science is to seek the truth? Science is mostly mercenary. Most people who work science jobs do so to earn a good living and build a pension. They will not make waves, if the truth is not a goal of management. Little Johnny needs braces.

Let me add another layer to the water analysis. I don't wish anyone to get in trouble with the taboos of science religion  so turn the lights down and pretend you are web surfing.

This layer is connected to the difference between the impact of potassium ions and sodium ions on water. The hydrogen bonding of water is in a unique chemical potential spot, relative to the impact of these two cations on water. Potassium cations will bind to water slightly weaker than water-water hydrogen bonding, while Sodium cations bind to water stronger than water-water hydrogen bonds. This is part of a natural design, critical to life. Each cation, although both having one positive charge, impact the structuring of water in opposite ways.

Potassium ions; K+, which accumulate in cells, are chaotropic. They add chaos or entropy to the large scale structuring of water. While Sodium ions; Na+, which accumulate outside the cell, are kosmotropic and will add order to the structuring of the water. The net result of cation pumping is the cel will create two distinct water environments, inside and outside the cell, each with a specialty task.

If nature had decreased the hydrogen bonding strength in water by only 11%, K+ would become kosmotropic. If nature had increased the strength of hydrogen bonding in water by 11%, Na+ would become chaotropic. Neither scenario would support modern life. Like in the fable of Goldilocks and the three bears, the choice for water was in the middle and just right for life.

Relative to the DNA, the impact of the internal  cellular K+, is to add chaos or entropy to the water. This helps to limit the extent of the cooperative hydrogen bonding of the water, around the DNA, so the water does not become overly structured and inhibiting. The water cooperatives around the DNA have a more limited scope, based on potassium concentrations.

During cell cycles, the cell membrane becomes more unsaturated and fluid and the Na+-K+ pumps are more reversible. The result is the sodium ion concentration increases in the mother cell, to help cancel out some of the potassium ion chaotropic impact. Water becomes somewhat more ordered, and cooperative around the DNA. This leads to the DNA complex behaving differently. Condensed Chromosomes is not a magic trick of life, but is an artifact of water structuring changes.

As the daughter cells restore the higher potassium ion environment, the potential of the water changes, again, and new equilibria are defined on the DNA. These involve unpacking and template translation into RNA.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: PhysBang on 01/04/2017 13:37:57
Statistical modeling simplifies both tasks. It offer compliance wiggle room, and as a science procedure, it can be used for mass production.
No, it doesn't. Statistics allows people to accurately reflect the error and uncertainty in any scientific endeavor. Like any tool, it is sometimes used incorrectly. However, almost any scientific paper that fails to take error and uncertainty into account is poor science. The only exception to this are those papers that are relying wholly on the ramifications of existing theory and, as such, they are supported only as much as the existing theory, which must rely on some sort of statistical understanding.

Quote
Although adding the impact of water, will bring these models much closer to reality,
This is your claim. You have not offered any evidence of this. You haven't provided any source for your claim that textbooks leave out water; you merely produce one picture from one textbook. You haven't provided any source that is an analysis of these textbooks. You haven't given any sources for the effect of water on DNA that supports your wild claim that water chooses mutations. Since pretty much every study on the chemistry of DNA is done in water, your claim that biochemists ignore water seems so far-fetched as to leave the realm of the reasonable.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 03/04/2017 11:58:52
Statistical modeling simplifies both tasks. It offer compliance wiggle room, and as a science procedure, it can be used for mass production.
No, it doesn't. Statistics allows people to accurately reflect the error and uncertainty in any scientific endeavor. Like any tool, it is sometimes used incorrectly. However, almost any scientific paper that fails to take error and uncertainty into account is poor science. The only exception to this are those papers that are relying wholly on the ramifications of existing theory and, as such, they are supported only as much as the existing theory, which must rely on some sort of statistical understanding.

Quote
Although adding the impact of water, will bring these models much closer to reality,
This is your claim. You have not offered any evidence of this. You haven't provided any source for your claim that textbooks leave out water; you merely produce one picture from one textbook. You haven't provided any source that is an analysis of these textbooks. You haven't given any sources for the effect of water on DNA that supports your wild claim that water chooses mutations. Since pretty much every study on the chemistry of DNA is done in water, your claim that biochemists ignore water seems so far-fetched as to leave the realm of the reasonable.


I have proven that water is critical to life. The problem is you can't grasp the evidence. This is why statistics appeals to you. A lessor theory can't make accurate prediction and therefore will need wiggle room that can be supplied by statistics. That is why I have to admit that statistics is good for science mass production. A good free market tool. Statistics allows coffee to be good for you today, and the bad for you tomorrow, based on which industry you work for. You don't have to explain why, like I am doing. My approach will look magical but it is old fashion logic.

I was going to talk about ATP and enzymes to show an example where we need both an organic and a water explanation to paint a complete picture. Before doing that I would like to look at enzymes in general. Enzymes can be easily denatured, due to their weak binding energy, that is equivalent to the strength of a couple of hydrogen bonds. In spite of this weak binding energy, enzymes will fold with exact foldings, not defined by statistics. The probability is 1.0. Water takes away the uncertainty. That is the primary purpose of the water when it comes to life.

Traditionally, enzymes folding was thought to be governed by statistics, with enzymes assumed to have average folding.   Everyone knows the binding forces are weak and there was enough thermal energy and vibration,in water to expect average folding defined by statistics. Yet analytical studies have proven that enzymes fold with exact folds. Although proven as a fact, there is still no statistical explanation for this. The reason is, this is not governed by statistics, yet it is still treated that way, due to traditions.

The reason enzymes fold with exact folds is connected to water. Below are the free energy landscape diagrams for an unfolded and folded protein. The peaks on the first diagram are the various hydrophobic groups which create an oil-water affect in water, which makes these groups want to phase separate, first, to help lower free energy. These become the core of the protein. The water is displaced as these groups fold, with the waters cascading down the falling peaks toward lower peaks. The sequence of folding is about lower the free energy of the enzyme until the energy landscape diagram collapse into a funnel of very low free energy.

(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: Why don't textbooks show DNA with its hydrating water?
Post by: PhysBang on 03/04/2017 16:24:10
I have proven that water is critical to life.
Well, no, because you haven't shown us anything about life that might be on other planets or about possible artificial life forms on this planet.

You have established the trivial claim that active cells on our planet contain water. Nobody denies this. You want to make it a magical basis for your wild claims, but you have absolutely no support. All you have is rants against textbooks without any evidence.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 04/04/2017 12:09:52
I have proven that water is critical to life.
Well, no, because you haven't shown us anything about life that might be on other planets or about possible artificial life forms on this planet.

You have established the trivial claim that active cells on our planet contain water. Nobody denies this. You want to make it a magical basis for your wild claims, but you have absolutely no support. All you have is rants against textbooks without any evidence.

Life on other planets is interesting, because everyone with credibility is looking for water based planets, since life in water has plenty of evidence. This is direct evidence that goes beyond the probability claims, that life can form in other solvents besides water.

The reason I can make this assertion, against life in others solvents, is nobody has ever made life from scratch using water, which is already fully characterized. We already know what to expect in water and can reverse engineer. But even with this much head start, nobody has formed life from scratch in water. The claim that one can prove life in another solvent, requires we start from scratch, with no characterization, and nevertheless exceed that which we have not been able to do in water. Life in other solvent is all based on speculation, using lottery odds assumptions. If you assume someone will win, than anything appears possible. This is misleading. 

Let me get back to enzyme folding in water. If we were to use another solvent, the two free energy landscape diagrams above would be different, since the free energy potential between the solvent and enzyme would change. For one thing you would not have the same peak distribution to help define the folding order priority leading to a functional enzyme. If you did a folding experiment, in any other solvent, statistics would more than likely apply. I will grant yo that. Only water beat the odds every time. Water is still not allowed in the science casinos, since it cheats and does not play by the rules of the house. One could conclude that protein, that evolved in water, have a limited number of amino acids, to allow exact folding of any protein in water; card counting.

If we look at a folded enzyme, the core is composed of hydrophobic groups, while the surface is composed of hydrophilic groups. These hydrophilic surface will hydrogen bond to surface water and then that water will hydrogen bond to other water up to several nanometers from the protein surface. This surface cage of hydrogen bonded water helps the exact folding to persist so the enzyme is consistent.

To remove that scaffolding of hydrogen bonded water, so the enzyme can change conformation during a reaction, dozens upon dozens of aqueous hydrogen bonds need to be broken. However, ATP, which is the most common energy molecule for enzymes, has the energy equivalence of about 2 hydrogen bonds. The energy of ATP does not add up to strength of the hydrogen bonded water, that helps hold the enzyme in its exact fold. So where is the extra energy coming from? The answer is the water.

Based on hydrogen bonding, I have a theory that ATP has a dual function. ATP reacts with an -OH group attached to the enzyme, to leave behind an electron withdrawing phosphate group. To form ADP from ATP, the ATP needs to absorb a molecule of water. This is standard theory. Unlike the random assumption models used for the water source, the local water near the enzyme, has hydrogen bonded order. Therefore, the ATP has to pull a water molecule out of a fixed cooperative matrix of water.

The affect is similar to a nylon stocking on the shapely leg of a female dancer. The ATP not only reacts with the enzyme but to get the water molecules, it acts like a bolt cutter, cutting out a fixed water molecule out of an ordered matrix of water. The result is like a run in the nylon stocking, which disrupts the cooperative, and generates free energy via the entropy increase. Now the enzyme has the free needed to change conformation, until the water reforms the matrix and refolds the enzyme, back, for another cycle. Now we need another bolt cutter, ATP.

During cell cycles, the amount of ATP being used rises to a peak. This reflects the level of aqueous cooperation that is used to supply free energy.
 
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: evan_au on 04/04/2017 12:30:50
Quote from: puppypower
Life in other solvent is all based on speculation
Lack of evidence for life in other solvents is not evidence that there is no life in other solvents.

Especially since we have examined precisely 0 planets on which there may be another solvent.
Which is even less than the number we have examined for water-based life around 1.01: this consists of Earth plus a very cursory look at Mars, which may occasionally have liquid water today (but not near any of the places we have looked).

A look at the hydrocarbon lakes of Titan would be instructive, but our space probes would probably evaporate the hydrocarbons as soon as they got close enough to take a sample.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 12/04/2017 12:41:12
Quote from: puppypower
Life in other solvent is all based on speculation
Lack of evidence for life in other solvents is not evidence that there is no life in other solvents.

Especially since we have examined precisely 0 planets on which there may be another solvent.
Which is even less than the number we have examined for water-based life around 1.01: this consists of Earth plus a very cursory look at Mars, which may occasionally have liquid water today (but not near any of the places we have looked).

A look at the hydrocarbon lakes of Titan would be instructive, but our space probes would probably evaporate the hydrocarbons as soon as they got close enough to take a sample.

Life in other solvents has no direct evidence or chemical logic, other than being based on the bookie odds offered by statistics. In any given day, even the horse with the lowest odds can win the race. That is the basis fro this claim. That is the assumption of a tool not of reality. Life is not a horse race, where Sea Biscuit can win the second race if the track is muddy.

Life in water is not about playing the odds or winning a lottery. Water loads the dice to remove the randomness in favor of a sure thing. For example, protein fold with exact folds in water. This is not about randomness. Protein folding would be random in other solvents. Your statement is based on the traditional assumption that the impact of water is based on odds, therefore other solvents have their own odds. That is the assumption of a tool, not based on observing life at the nanoscale. 

One of the main reasons for the unique life given properties of water is hydrogen bonding. It is also connected to the ability of water molecules to form up to four hydrogen bonds to create extended water structures  A single ammonia molecule can form up to four hydrogen bonds, but since it has three hydrogen and one electron releasing group (water has two and two) ammonia can't form the same degree of extended hydrogen bonding.

In terms of water, just as the four covalent bonds of carbon allow for extended organics structures; polymers, the four hydrogen bonds of water allow for extended hydrogen bonding structuring. This hydrogen bonding polymerization of water is why water and oil will phase separate. The self bonding of water, to water, is so energetically favorable, organic substances need to cooperate. Other solvents don't show this same level of self organization using the bond strength of hydrogen bonds. This would allow more randomness to occur, such as in protein folding. The result is life in other solvents, even if it started, will build an unreliable foundation of random footings. Water allows for the high quality control needed for life to keep evolving.

You can build a one story house with a poorly mixed concrete foundation. But if you start to add a few more levels to the house, cracks will appear in the poor foundation. Water builds with first grade concrete and therefore is designed to become a sky scraper. It all comes back to order in water imposing order in organics.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: tkadm30 on 12/04/2017 13:05:23
I'm pretty sure the existence of liquid water in distant exoplanets is a sure evidence of water-based organic life forms. The water spectrum and resonance in biological systems is surely a proof of quantum-like interactions (tunnelling) in water molecules acting as intracellular messengers for quantum information processing of DNA/water entanglement.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 13/04/2017 12:59:56
Water has ways to transmit information even without quantum entanglements. This is not to say quantum entanglements do not play a role. The former is much easier to investigate using existing technology. The latter is harder to investigate in situ.

The hydrogen bond is a unique form of chemical bond. It is somewhere between a covalent bond and a polar bond in terms of strength. It also shows both polar and covalent character. Hydrogen bonds can go both ways, or be one or the other, depending on the circumstances.

The advantage of this dual nature of the hydrogen bond, is a hydrogen bond can act like a binary switch, like used in computer memory. A hydrogen bond can form, and without breaking the bond, shift between its polar or covalent character, with each of the two switch setting defining different physical parameters.

The polar state is denser, has higher entropy and enthalpy (internal energy). The covalent state is less dense, has lower entropy and enthalpy. Below is a representation of high and low density water cluster where the binary switches act together within Icosahedral water clusters; 280 water molecules. This change in cluster density can be seen with existing technology.

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

The hydrogen bonding switch of water is a much more advanced switch compare to what is used in computer memory. The reason is, it is more than an on-off switch. Each state of the switch, on or off, defines different physical parameters; pressure, volume, entropy and enthalpy. If you flip the hydrogen bond switch, it will have a physical impact on its local environment based on volume and free energy. 

Alternately, changes in the local environment, due to chemical reactions or the movement of material, since these have  have physical properties, they can flip switches. This new information is transmitted. This is harder to investigate with existing technology, but follows from the nature of this unique binary switch. A cell can remain in integrated communication, even with the environment shifting switch patterns. Other solvents that lack hydrogen bonding don't have this communication advantage. Water allows the most extensive hydrogen bonding networks of all the hydrogen bonding solvents.
.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 14/04/2017 12:07:50
There is another important feature of water, useful to life, that becomes possible due to the partnership between the organics and water. This feature, which is generated via osmosis, which is common at membranes, is what I like to refer to as the fifth force of nature; entropic force.  The entropic force is a directed force generated by entropy.

Osmosis is a colligative property meaning the osmotic pressure is dependent on the concentration; number of units of solute, but not on the character of the solute.  The same concentration of Na+, Cl-, Ca++, glucose will all generate the same osmotic pressure, where pressure equals force/area. The force or entropic force is not electromagnetic force dependent; defines solute character. The water defuses, through the membrane to increase the entropy on the solute side no matter what the solute. This entropy driven diffusion can generate a pressure head, which is connected to the entropic force.

(https://imcurious.wikispaces.com/file/view/osmosis.jpg/98343667/360x252/osmosis.jpg)

Reverse osmosis occurs when we add pressure to the solute side, to reverse the direction of the water. In this case, the pressure causes the entropy of the water to lower. Relative to water, this direction implies a negative entropic force.

All liquids can generate osmotic pressure if we use a suitable membrane and solute. Water has a wild card. In the last discussion of the binary switch nature of hydrogen bonding; covalent and polar, the covalent state is more expanded and defines lower entropy, while the polar state is more contracted and defines higher entropy. The net affect is the binary switching of water, which reflects changes in information, can also locally generate higher and lower pressure to locally tweak the global entropic forces due to osmosis.

The term entropic force is not standard nomenclature nor is the entropic force considered the firth force of nature by science. But it should be, since this force is easy to measure and can be used to regulate entropy. This has also been called the life force, since life makes so much use of it to regulate entropy; load the dice.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: Tomassci on 16/06/2017 08:52:45
With water, the DNA will be mistaken as... Chaotic.
Title: Re: Why don't textbooks show DNA with its hydrating water?
Post by: puppypower on 16/06/2017 20:16:31
With water, the DNA will be mistaken as... Chaotic.

This is not exactly true. Water contributes to the structure and the activity of the DNA. For example;

Quote
The DNA double helix can take up a number of 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.

If you were to dehydrate DNA, it would no longer work. If you were to replace the water with any other solvent, you would get chaos. You argument is true of all others solvents and DNA, but not water.

One reason the water is not include is, the life sciences are too dependent on the random assumption, whereas water eliminates randomness. The DNA does not randomly shift between A and B conformations. This is regulated by the water. You can control this by controlling the hydration.

Another reason is, science is not self sufficient when it comes to resources. Rather it is beholden to others, like business, for its resources. Big Money does not want anything to change, since change, even for the good, creates instability for the big players in the market place. The horse and buggy companies never wanted the automobile to succeed, even if better, because they could not evolve with the times. Instead new players would be expected to appear who were not bogged down by loyalty to a dinosaur tradition.

Including water with the DNA in textbooks would be good for the young people, who will start to see the DNA in new ways, from which there will be the innovation for the future.