Water As The Co-Partner Of Life

[Moontanman]

If i had a dollar for everytime you have spun off on one of these water worshiping rants..  

[CraigD]

I am interested in water and life, and Martin Chaplin's web site is an excellent source of information about water.

Martin Chaplin’s “Water Structure and Science” does appear to be a nice web site, especially its “Memory of Water” page, which presents this controversial subject in a level-headed way. Chaplin has been criticized because of publishing papers in journals of Homeopathy, and lending support to Homeopathic medicine, which many people, including me, consider to be a scam, but I think this webpage of his presents the subject in a scientific, unbiased way.

 

However, Chaplin’s writing is published under a Creative Commons Attribution-Noncommercial-No Derivs license, which requires you to give credit to Chaplin when copying it. The easiest way to do this is to provide a link to the pages from which you copy. This is a matter of copyright law, which Hypography requires its members to follow. Please do!

 

In terms of evolution, increasing hydration was the direction the DNA needed to evolve before it could work properly.

You seem to be suggesting that DNA was once found more in its A form, then evolved via selection pressures to be found mostly in its B form, as is the case today. However, I’ve heard of not theory or evidence suggesting this to be the cases, of that, except for small sections in strand that is mostly B form, DNA can be biologically active in any of its other forms. Do you have links or references to any credible scientific publication suggesting otherwise?

 

This was not random but by design; copartner water.

You seem to be suggesting that DNA did not evolve naturally, but was artificially designed. Do you believe this?

 

This binary nature of hydrogen bonding allows water to transmit information.

I think it’s important to note that the kind transmitting information to which you’re referring, HBond, as described in Chaplin’s “hyrogen bonding”, involves carrying “information about solutes and surfaces over significant distances in liquid water” over very short time intervals. This is very different than the kind of transmitting information that involved in DNA or computers, which can store and repeatedly transmit the information many times over very long time intervals.

 

While the transmission of information in biological systems requires liquid water, this doesn’t mean that the most important information, such as the genetic information that determines the kind and arrangement of cells in a plant or animal, is stored or transmitted by water. In the case of genetic information, it’s stored in DNA, and transmitted by the various microbiological mechanisms involved in its expression.

[HydrogenBond]

It is easier to develop ideas if I know where the audience is getting stuck.

 

The idea of other solvents, also being the basis for alternate life, is an example of accepted pseudo-science based on a dual standard.  

 

The reason I can claim this is pseudo science, that use a dual standard, is nobody has ever claimed to have formed life in water, from scratch, even though we know water works and we know much more of what to expect. Since water is  easier and more definitive, yet this has not been accomplished, there is no way an alternate solvent path, with so many wild cards, could have been done first, to show this is even possible.  How about showing us any proof beyond the prestige offered by the dual standard? 

 

As far as Professor Chaplin's web site, has anyone gone to the site to see what it looks like? The topic of homeopathic represents about 1% of the site, and is connected to a summary of research done in science about this subject. The bulk of the web site is about the chemistry of water down to the tinies detail covering the entire range of science that has been done with water, including discussions of hydration in life. Below is paragraph of the summary that he offers about the subject of homeopathic effects, which is more objective than that given by alternate solvents and life. The real problem is water poses a threat to the status quo. 

 

 

A thorough investigation into the structural differences previously reported between homeopathically potentized (that is, succussed and extremely diluted) and unpotentized nitric acid solutions showed that the effect was lost or changed if different glassware was used [495]. Changes in the thermoluminescence of ice produced from ultra-diluted water have been noted [500a] but can be explained by remaining trace amounts of material (due to poor mixing, impurities, absorption, nanobubbles (that is, nanocavities) [500d] or other causes) being concentrated between ice crystals [500b]; an explanation supported by later work [500c]. A series of papers from Academician Konovalov has proposed that physical and biological effects of highly diluted aqueous solutions differ from those expected from simple dilution and may be due to the formation of nano-sized (up to 400 nm) molecular assemblies [2207]. Also, maxima in the biological activity at very diluted concentrations (~ 10^-15 - 10^-18 M), below measurable concentrations, have been widely reported [2232]. Changes in the NMR relaxation times [1620a, 1620c], thermochemistry [1644] and UV absorption [1620b] of water in some homeopathic preparations remain unexplained and require confirmation. A systematic assessment of the in vitro research on high potency effects has shown positive, if only partially reproducible, effects [2238]. This may indicate a stochastic influence similar to that ocurring in the (now accepted) Mpemba effect.

Edited April 26, 2015 by HydrogenBond

[HydrogenBond]

I will be quoting Chaplin's web site using quote boxes. I also use his images which have the image address in the HTML.  I like this site because he shares and has the best summary of information I could find on the web. Beyond this data set, I am also creating my own ideas based on my ingenuity. The idea of cells being phase diagrams is from my background in chemical engineering. The oil and water foundation is also my idea. But I also make sure extrapolation is consistent with the latest thinking on water and its interaction with organics.

 

Water has been so wildly investigated Chaplin's web site has over 2200 papers used a reference, to back up all the data and claims he presents in this summary of water.  I have been removing the reference links but I will leave them in for those who like to read journals for details. The links to the papers above, appear to work with copy and paste. 

Edited April 26, 2015 by HydrogenBond

[Moontanman]

It is easier to develop ideas if I know where the audience is getting stuck.

 

The idea of other solvents, also being the basis for alternate life, is an example of accepted pseudo-science based on a dual standard.  

 

The reason I can claim this is pseudo science, that use a dual standard, is nobody has ever claimed to have formed life in water, from scratch, even though we know water works and we know much more of what to expect. Since water is  easier and more definitive, yet this has not been accomplished, there is no way an alternate solvent path, with so many wild cards, could have been done first, to show this is even possible.  How about showing us any proof beyond the prestige offered by the dual standard? 

 

As far as Professor Chaplin's web site, has anyone gone to the site to see what it looks like? The topic of homeopathic represents about 1% of the site, and is connected to a summary of research done in science about this subject. The bulk of the web site is about the chemistry of water down to the tinies detail covering the entire range of science that has been done with water, including discussions of hydration in life. Below is paragraph of the summary that he offers about the subject of homeopathic effects, which is more objective than that given by alternate solvents and life. The real problem is water poses a threat to the status quo. 

 

 

So since you never seen a black swan all swans must be white?

 

We have one data point for life, no trend can be drawn from one data point! Life on Earth has evolved in water and takes advantage of all the properties of water, if life on earth had evolved in sulfuric acid i would expect it to have taken advantage of all the properties of sulfuric acid, many of which we have no way of knowing unless we actually encounter life in sulfuric acid. 

 

Speculation is not pseudo science, making unsupported claims and trying to pass them off as being supported is pseudo science! That is what the works of Chaplin are, pseudo science..  

[HydrogenBond]

Have you gone to Professor Chaplin's water web site? It is called, Water Structure and Science. It is about a summary of all the state of the art water research, with water the most investigated substance in all of science. There is not even a close second. His site is not about homeopathic medicine, although it summarizes all the valid research studies in one small sub-section. This site may not be for the layman. Because of the amount of detail, it assumes proficiency in all areas of chemistry, often at a graduate level. It often summarizes research of professors and Nobel prize winners. 

 

I think your sour grapes is because I treated the idea of other solvents for life in a dismissing way. Logic is often cool. Maybe a better way to address alternate solvents is, both others solvents for life and homeopathic medicine are being investigated in accredited science labs. Both are considered blue sky research.

 

Blue sky research is where a frontier hypothesis is investigated, since if is true, it could have significant implications. It is worth the money and resources to settle the idea in a proper science environment to avoid political science and/or free market exploitation; power and money science. In the case of homeopathic effects, Professors Chaplin summarizes the results of all the blue sky teams, in an objective way. Go to the site and read the entire small section. He is not selling anything, he is only summarizing all this water based research since this done in a valid setting. 

 

Maybe you can show us a summary of the alternate solvents for life research to see where that blue sky research stands. In all honesty, the only research I am aware of is life from earth, such as bacteria, were dehydrated and even dissected and placed in other solvents. What they found was nothing works properly, done to most enzymes, with all signs of integrated life gone. Beyond that, I am not aware of later research and what results they may have achieved. I did a quick search, but research summaries are not easy to find. 

 

 

Water and life is based on what we know to work. If you scan the web site of Professor Chaplin the amount of things we know about water, allows one to get a feel for all the possibilities that water brings to the table, that other solvents do not possess. If they do possess extra properties these are so in the distance future of investigation it will not happen anytime soon. 

 

If you look at the universe, after the big bang, there was only hydrogen and helium. After the first generation of stars, until the present, the third most abundant atom in the universe was/is oxygen. The fourth is carbon. The chemistry from hydrogen and oxygen, to water was defined, early, with frozen water how second generation stars formed; abundance of ice. 

 

The energy value of carbon chemistry is between that of the reaction between oxygen O2 and hydrogen H2, with water the floor of both systems of chemicals due to oxygen atoms being number 3 in universal abundance. In the beginning, it was not about life, but it was settling the energy bandwidth of chemistry. More recently in the lab, some forms of earth life has been able to generate hydrogen gas, completing the chemical energy loop of life and the universe.

 

Life in water is not an isolate anomaly. It ties life into the chemical energy economy of the universe. I am trying to attach water to carbon and organics, in an intimate way, that give logic to what now appears to be random universe of life's organics. 

Edited April 28, 2015 by HydrogenBond

[Moontanman]

 

 

Life in water is not an isolate anomaly. It ties life into the chemical energy economy of the universe. I am trying to attach water to carbon and organics, in an intimate way, that give logic to what now appears to be random universe of life's organics. 

 

You have absolutely no evidence whatsoever to make that assertion. You have one example of life and that life is evolved to fit the environment it is in. You cannot draw a curve from one data point..   

[HydrogenBond]

Let me pose an observation and question to those more proficient in biology and the assumption of statistical science? I will be quoting a paper by John Grant Watterson 18 Tomanbil Terrace Ashmore, Qld 2412 AUSTRALIA, who got me thinking. 

 

It has been known since the early work of Kauzmann (1959) and Tanford (1968) on the thermodynamics and kinetics of protein denaturation, that proteins are not very stable. In thermodynamic terms, the stabilities lie in the range 20 – 60 kJ/mol. However, H-bond energies are quoted also in the range 12 – 38 kJ/mol (Fersht, 1999). Comparing these figures, one is struck by their apparent incongruity – they mean that protein stability relies on a few H-bonds. It is even conceivable that some H-bonds are more stable than small proteins. For example, Finney (1982) gives the stability of lysozyme and ribonuclease as equivalent to 4 H-bonds each. One naturally asks, how can a molecule containing thousands of atoms be held together by a few H-bonds? I am not saying that these figures are wrong, but rather that another energetic mechanism for protein stability has to be found – one that has not been detected by classical methods. 

 

Proteins are held together, weakly, with the binding energy quite small, being the same energy as about  1-4  hydrogen bonds. This has been known for some time. Because of this weak binding holding proteins together, it was assumed that protein folds were based on an average folding. The thermal energy in the water alone, should have been sufficient to tweak protein folds. But as equipment got better, it was observed that proteins maintain a unique fold? 

 

One is reminded here of the problem of protein folding. As I have pointed out elsewhere (Watterson, 1997), that problem also arises from applying classical theories, since they predict an average, not a unique fold. That these questions remain unsolved still today after 50 years of intense research effort, highlights a two-fold failing of statistical methods: firstly, they did not predict the existence of a stable folded state, and secondly, once given as an experimental fact, they cannot explain it. 

 

The statistical methods and assumptions, predicted an average fold, due to how weakly protein are bound together. This was considered done deal,  until scientific equipment was developed that proved otherwise; protein maintain a unique fold. This meant the statistical assumption was not correct, at least in this case. Something else was at work. Even today, after 50 years of foot dragging, nobody has a good statistical explanation for this. It is not based on statistics. 

 

Since protein shapes/folds are critical to their enzymatic activity, something not statistical in origin, underlies the very shapes, that define the chemistry of life. 

 

The water and oil analogy is used to show how water can force organics to assume shapes that they will not assume on their own. The binding and order within water, forces order upon organics, with the water keeping the weakly held protein as a unique fold. 

 

Even if we stop there, the impact of water is critical, since shape holding eliminates an entire layer of  randomness through the entire cell. 

Edited April 28, 2015 by HydrogenBond

[HydrogenBond]

You have absolutely no evidence whatsoever to make that assertion. You have one example of life and that life is evolved to fit the environment it is in. You cannot draw a curve from one data point..   

 

You brought up other solvents first, so you have the burden of proof. If you show me proof for your claim I will integrate it. 

Edited April 28, 2015 by HydrogenBond

[Moontanman]

You brought up other solvents first, so you have the burden of proof. If you show me proof for your claim I will integrate it. 

 

 

I never claimed there was another solvent, I simply claim that if there were life would exploit what ever properties it has as thoroughly was it has water.. 

[Moontanman]

You brought up other solvents first, so you have the burden of proof. If you show me proof for your claim I will integrate it. 

 

 

HB you seem to be assuming life has to be exactly the way we see it on Earth, there is no reason to assume this is true. We don't know what chemicals life has to have to exist, Carbon seems like a pretty good bet but DNA is not a sure bet, there are other self replicating molecules and DNA could be a fluke, we just don't know, to assert otherwise at this point is dishonest.. 

[HydrogenBond]

HB you seem to be assuming life has to be exactly the way we see it on Earth, there is no reason to assume this is true. We don't know what chemicals life has to have to exist, Carbon seems like a pretty good bet but DNA is not a sure bet, there are other self replicating molecules and DNA could be a fluke, we just don't know, to assert otherwise at this point is dishonest.. 

 

Fair enough! Since we don't know anything about other forms of life, beyond water based, nor do we know anything of the materials these life forms may contain, I prefer stick to the proven, which is life on earth. Life on earth, makes use of water, which was the original topic. I was hoping to show some of the unique connections between water and organics needed for earth life. 

 

If we go back to may last post, which was about protein folding, protein fold and are held together by weak binding forces, equivalent to 1-4 hydrogen bonds in total energy. Because this binding is so weak, spread over thousands of atoms in 3-D, science originally assumed average folding of protein in cells. This assumption, was before there were instruments sensitive enough to prove otherwise. This hypothesis was consistent with the random universe theory, which was popular, as well as the random assumptions used in solvent chemistry; thermal agitation.  

 

As instruments progressed, about 50 years ago, a team of scientist observed proteins had exact folds. This was not expected, based on the assumption of the random universe model. Even after 50 years, there is no statistical explanation for why proteins fold with probability of 1.0. Probability of 1.0 is more connected to the assumptions of cause and effect, not random. 

 

I don't understand why the status quo never changed their approach, after this flaw was found in the random theory of life? I can see a reluctance at first, to make 100% sure, but why is this still the case after 50 years of no explanation and consistent data?

 

If we extrapolate proteins fold with exact folds and these folds impact reactions on enzymes and catalytic activity, then even more aspects of life is based on cause and effect; exact leading to exact. Why do we use random, when the deck is stacked in so many ways? 

Edited April 28, 2015 by HydrogenBond

[Moontanman]

Who has ever said random? 

[sman]

Observers in a given universe may observe that the universe they find themselves in is appropriate for the evolution of observers, however rare that might seem. This is not surprising. It’s called the anthropic principle, as I’ve been saying.

 

And life is not random. It’s targeted by evolution: an idea you’ve denied yourself many opportunities to learn about. I’ve no faith you’re receptive to it now.

[HydrogenBond]

Observers in a given universe may observe that the universe they find themselves in is appropriate for the evolution of observers, however rare that might seem. This is not surprising. It’s called the anthropic principle, as I’ve been saying.

 

And life is not random. It’s targeted by evolution: an idea you’ve denied yourself many opportunities to learn about. I’ve no faith you’re receptive to it now.

 

Who has ever said random? 

 

Evolution is where the assumption of random still persist. Since the theory of evolution is the foundation theory for life, random also becomes the foundation theory for life. Evolution is not considered a path of cause and effect or even order, yet experiments showed that protein have evolved to fold, in unique ways where chaos does not apply.

 

Protein folds, in turn, are critical to all the reactions and enzymatic affects behind life. This also means statistics was replaced by cause and effect. There was sense of direction relative to proteins folds, which define the nuts and bolts of cellular activity, yet evolution is still assumed to random and without a sense of direction. Humans are not built on potentials but a random event. I have always been presented ordered arguments for evolution even before I knew about this repressed science. I was right. The next step is how do you explain the cause and effect of life that allows exact folds and all the implication of this? The answer is water. 

Edited April 29, 2015 by HydrogenBond

[HydrogenBond]

One possible reason biology never evolved or progressed from random to ordered evolution, even after the key experimental fact of protein folds, may have been due to atheism. Most scientists appear to subscribe to atheism. Atheism defines itself by taking a stand against anything religion claims; sees itself in a mirror with a reverse image. 

 

Religion has always maintained an ordered approach to evolution. I am not saying Creationism is consistent with science. What I am saying is Creationism is built upon an ordered foundation theory; God was about order; omniscience, not dice. Atheism to be contrary, for its own mirror identity, had to assume randomness, via a principle that is not called a god; chaos.

 

Even after experiments showed that there was unique order, on a wide scale, in their cellular world of chaos via evolution, the tradition of atheism could not deny its not God of chaos, in favor of other god in the mirror, who was always about order.They denied a science fact, for 50 years, proving atheism was a religion. Public sector funding needs to stop funding atheist science, due to separation of church and state.

 

Conceptually the only difference between creationism theory and the random evolution theory is creation has the right foundation premise; order, consistent with state of the art observation, but it uses  wrong science and observation. Evolution has the right science and observational data, but makes use of a wrong foundation premise; god of chaos. Both fall short, because religion in a mirror, is also a religion, even if this is denied; opposite of a god of truth is a god of lying; relative truth. Any scientist who claims a connection to either religion, as being their POV for science, should be defunded. Unless the dual standard of atheism is in effect because truth and lying are relative. 

Edited April 29, 2015 by HydrogenBond

[HydrogenBond]

The question becomes, how and why do protein folds become exact and unique, even though there is only weak binding, equal to the energy value of 1-4 hydrogen bonds, spread over thousands of atoms in 3-D? The thermal energy in the water should be enough to tweak this, but it does not. This original assumption was reasonable until this was disproven. This cool design of nature, allows the protein to be stable and perfect, yet easy to manipulate when needed. 

 

To answer this, I will use the simple system of water and oil. Water and oil do not mix, unless we add a lot of energy. If we add energy we can form an emulsion, which still segregates the water and oil, but as tiny bubbles, that look somewhat mixed.

 

When protein, like enzymes fold, the hydrophobic organics will fold into the core. This is less due to these groups avoiding water, but rather these fold into the core, because they are being excluded by the water, as water binds with itself and the hydrophilic groups on the surface. 

 

Relative to the core materials, these moieties are primarily non polar organics groups loosely analogous to oil. Along with these groups, are the peptide linkages of the protein, which binds via hydrogen bonds to each other. This polar hydrogen bonding backbone allows some water to bind in the core as the protein is folding. The non polar core is not afraid of the water, since water can form weak hydrogen bonds with even reduced organics, so the water is accepted. But this is a one sided love fair. 

 

The water, on the other hand, feels somewhat trapped in the non polar or "oil" core and feels the need to separate. It was lured by the hydrogen bonding but is now trapped. This needs of this water to avoid and separate helps to keep the insides loose, because water and oil don't want to remain mixed, due to the water.   

 

The outside of the protein, due to the hydrophilic surface groups, binds with the water via hydrogen bonding. This water binds even further with other water (water can form four hydrogen bonds) into a network. This network can then form cooperative hydrogen bonding.

 

Cooperative hydrogen bonding is where the water network shifts more into the covalent state, where the hydrogen bond of the network will expand. This slight expansion helps release the pressure of the water repulsion of the innards, while also binding the surface, tightly. The result is a stable yet delicate balance. The binding energy of the protein may be only equal to 1-4 hydrogen bonds; innards pushing out, but the water network, attached to and beyond the protein, adds hundreds of hydrogen bonds. It like putting a jello egg inside of a plastic case, making it more durable than expected of jello. This is not subject to random collisions due to the case. 

 

ATP is important because it has two uses. The second use is much less well know. The movement from ATP to ADP and P requires the absorption of water. The water molecule that is absorbed is part of the cooperative network. The unique thing about a cooperative hydrogen bonding network, is the first bond broken, is the strongest bond. The network works as a team to fortify any point of breech. If the castle is stormed left or right, this is the focus of the network.

 

The absorption of water by ATP is a point of breech, and once this is broken, it is like a cut in a net under tension; surface tension. The breech propagates and the network breaks. Another analogy is a run in a nylon stocking. If you cut even one string, a run forms quickly over distances as hundreds of bonds become broken due to the force of the surface tension. Now the jello is out until water regroups. 

Edited April 29, 2015 by HydrogenBond