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Dna And Water


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#1 HydrogenBond

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Posted 08 January 2017 - 07:50 AM

I started a topic, in chemistry, about the impact of water on evolution at the nanoscale. This was a too large a topic since it parallels all of biology and evolution. That broader topic required I build background, which bogged down and detoured the discussion. I decided to narrow this topic down to just one thing, which is the impact of water and DNA. 

 

To begin, the importance of water on the structure of DNA has been known since the Watson and Crick. Their original model of DNA was a triple helix bridged by Mg+2 ions, between the phosphate backbone on the three helixes.

 

Crick and Watson's first model was a triple helix with its bases on the outside of the molecule. The sugar-phosphate backbones ran down the centre, with the phosphate groups of each chain bound to one another by magnesium ions. Crick and Watson hoped that the low water content of the molecule would mean that magnesium ions were in abundance.

 

The  model predicted repeat structure distances and showed promise. However, it did not equate properly to chemical analysis studies which showed that DNA contained far more water than assumed by Watson.

 

They had some difficulty making the model fit together, but found that it repeated its structure every 2.8 nanometres along its length. This was very encouraging, as both this 2.8 nanometre repeat and the helical structure would fit with Franklin's X-ray photograph. Crick and Watson needed to check their model accurately against the photograph, so they invited Wilkins and his colleagues from King's College to the Cavendish Laboratory.

 

When they arrived Franklin was still very dismissive of Crick's support for a helical structure. She pointed out that the proposed three-chained molecule couldn't exist, as any available magnesium ions would be tightly bound to water molecules. DNA actually contained ten times as many water molecules as Watson had thought. Franklin had stated the correct amount at her talk in London, but Watson had forgotten on the way back to Cambridge.

 

With the correct water content in mind, a more logical model eventually appears; double helix of base pairs. 

 

J. D. Watson and F. H. C. Crick, Molecular structure of nucleic acids, A structure for deoxyribose nucleic acid, Nature 171 (1953) 737-738.



#2 CraigD

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Posted 08 January 2017 - 12:13 PM

Your link is to itself, this webpage. You seem to have made a mistake creating it.

The text you quote appears to be from this webpage from the Cavendish Lab’s Cambridge Physics outreach website. The 1953 Nature article you cite is available here.

Please feel free to correct you post with these links, or let me know if you would like me to. Once it is corrected, I’ll delete this post.

#3 HydrogenBond

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Posted 10 January 2017 - 03:05 PM

Your link is to itself, this webpage. You seem to have made a mistake creating it.

The text you quote appears to be from this webpage from the Cavendish Lab’s Cambridge Physics outreach website. The 1953 Nature article you cite is available here.

Please feel free to correct you post with these links, or let me know if you would like me to. Once it is corrected, I’ll delete this post.

 

I think the link got rerouted, because it was never a hyperlink, but just a reference from Martin Chaplin's, Water Structure and Science web site. I must have inserted it as a link. The quotes were originally from the site you mentioned, but when I was thinking how to begin I used another site that said basically the same thing. I could not remember where I read it but knew it was true. 

 

My whole point for this opening, was that the importance of water, in terms of the structure of DNA, goes back to the very beginning investigations of DNA; Watson, Crick and Franklin. Water considerations help them change track, and find the correct solution. Water and DNA is not new, but is treated like this is alien; strange? I was trying to avoid speculations by showing I am following the leaders. 



#4 exchemist

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Posted 11 January 2017 - 01:59 AM

This seems to be tedious, bears-****-in-the-woods stuff.

 

Everyone knows that biochemistry takes place in an aqueous environment and that the configurations taken up by large biochemical molecules depends on how they are solvated. There is nothing remarkable here, surely?



#5 HydrogenBond

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Posted 11 January 2017 - 05:54 AM

This seems to be tedious, bears-****-in-the-woods stuff.

 

Everyone knows that biochemistry takes place in an aqueous environment and that the configurations taken up by large biochemical molecules depends on how they are solvated. There is nothing remarkable here, surely?

I agree with you. However, as unremarkable as you say, this does not explain why DNA is always misrepresented in textbooks. Do an image search on Google, for DNA, and count how many images include the structural water that is part of the DNA. Textbooks and all Google images show the DNA in a vacuum, as though that is the end of the story. The students are led astray. Water is a critical part of the structure, chemically bonded to the DNA. You cannot centrifuge this water away. When DNA is shown as a just double helix in a vacuum, this should be called alternate theory and speculation, since this is not reality. It has been proven not be true for decades. 

 

Below are two sets of images for the base pairing, one which is more like the textbook traditions, and the second is connected to reality. The base pairing of DNA and RNA have evolved to include sites which hydrogen bond to water. These water are part of the base pairing and play a critical role in the structure and dynamics. The water molecules bind with the bases and to other water to form a double helix of water, with one helix in each in the major and minor grooves. This water, by forming cooperative hydrogen bonding, expands the DNA double helix, by about 1%, weakening the base pairing by about 50%.  The original paper for this last claim is below. 

 

J. Poater, M. Swart, l. F. Guerra and F. M. Bickelhaupt, Solvent effects on hydrogen bonds in Watson-Crick, mismatched, and modified DNA base pairs, Comput. Theor. Chem. 998 (2012) 57-63

 

 

 

 

basepair.gif

 

 

 nuclei.gif

 

 

Below is the real DNA with its base paired water included. The oxygen of water are in yellow, and the hydrogen of water are small red. This is only the first layer of water, with more water attached to the phosphate and sugars. 

 

dna_minor_groove.gif


Edited by HydrogenBond, 12 January 2017 - 06:04 AM.


#6 HydrogenBond

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Posted 12 January 2017 - 06:50 AM

I have been working on hydrogen bonding and water and life for years, and have had to absorb a lot of flack, abuse and censor, based on a consensus acceptance of the pseudo science of a DNA double helix in a vacuum. If you start with a poor foundation, the house will eventually form cracks and then sag.

 

The (DNA) structure is an open one, and its water content is rather high'     

 

The above quote is from Watson and Crick 1953. I am not sure when science fell off the reservation, since the importance of water was known from the beginning, when the configuration of the DNA was inferred.  I would guess the technology for investigating the water was not there is 1953, due to the difficulty of investigating tiny water molecules, in situ. They went with what was known. 

 

But breakthroughs in technology have made it possible to investigate the real system of DNA and water. However, the life sciences are staying retro and pseudo; stuck in the past. This may be do to the random assumptions, used for evolution and assemble line science. If you add water, random starts to fall apart, and the assembly line could be made obsolete. 

 

 

 

 



#7 HydrogenBond

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Posted 13 January 2017 - 07:21 AM

Nucleic acid hydration is crucially important for their conformation and utility [1093], as noted by Watson and Crick [828]. The strength of these aqueous interactions is far greater than those for proteins due to their highly ionic character [542b]. The DNA double helix can take up a number of conformations (for example, right handed A-DNA pitch 28.2 Å 11 bp, B-DNA pitch 34 Å 10 bp, C-DNA pitch 31Å 9.33 bp, D-DNA pitch 24.2 Å 8 bp and the left handed Z-DNA pitch 43Å 12 bp) with differing hydration. The predominant natural DNA, B-DNA, has a wide and deep major groove and a narrow and deep minor groove and requires the greatest hydration.

 

The above quote is from the Martin Chaplin web site about Water structure and chemistry. The links should work if you need references for the various claims in the quote. 

 

The quote shows how the conformation of the DNA is dependent on the amount of hydrating water. This water is chemically bonded to the DNA and is part of the structure. The predominant natural DNA, or beta DNA, used by most cells, has the most chemically bonded water.

 

Water can form up to four hydrogen bonds; two receivers and two acceptors. When water hydrogen bonds to the DNA, it has up to three hydrogen bonds left over to bond with other water. The water, has to bond to other water, in predefined way, due to the way the bonding orbitals are optimized; tetrahedral. The result is the water bonded to the DNA and the to the next layer of bulk water, becomes sort of a  scaffolding for the DNA, inducing and holding the DNA into a given conformation, based on how much water is present.

 

The water also has a dynamic aspect, like the parent who holds the child while they drive the bike. If the parent was to let go; DNA in a vacuum, the child falls to the ground. Below is scaffolding around the capital so work can be done, efficiently. The workers are like the enzymes that use the scaffolding to locate and use the templates. 

 

 

hqdefault.jpg

 

 

 



#8 Turtle

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Posted 13 January 2017 - 12:24 PM

The above quote is from the Martin Chaplin web site about Water structure and chemistry. The links should work if you need references for the various claims in the quote. 
 
The quote shows how the conformation of the DNA is dependent on the amount of hydrating water. This water is chemically bonded to the DNA and is part of the structure. The predominant natural DNA, or beta DNA, used by most cells, has the most chemically bonded water.
 
Water can form up to four hydrogen bonds; two receivers and two acceptors. When water hydrogen bonds to the DNA, it has up to three hydrogen bonds left over to bond with other water. The water, has to bond to other water, in predefined way, due to the way the bonding orbitals are optimized; tetrahedral. The result is the water bonded to the DNA and the to the next layer of bulk water, becomes sort of a  scaffolding for the DNA, inducing and holding the DNA into a given conformation, based on how much water is present.
 
The water also has a dynamic aspect, like the parent who holds the child while they drive the bike. If the parent was to let go; DNA in a vacuum, the child falls to the ground. Below is scaffolding around the capital so work can be done, efficiently. The workers are like the enzymes that use the scaffolding to locate and use the templates.


Booooorrrrrring! Please move on to your claims for how all this water information supports creationism and debunks evolution.

#9 HydrogenBond

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Posted 14 January 2017 - 06:02 AM

Booooorrrrrring! Please move on to your claims for how all this water information supports creationism and debunks evolution.

 

Contemporary evolution is based on a random assumption of change on the DNA, followed by the logic of natural selection. I have no problem with the logic of natural selection, since it makes sense and can be observed and even predicted. However,  I do have a problem with the random assumption that is based on DNA in a vacuum, where water is nothing but a solvent that can be ignored or replaced. That erroneous assumption is followed by the gods of gambling casinos; random assumptions, using the oracle of statistics.  The question is how is this different from a random form of creationism? 

 

Where I differ, is I don't use either version of creationism; god or order or god of chaos. It does no matter to me if you define random as not a form of creationism, if it quacks it is a duck. Science is not covered under PC word games. 

 

Let me create a mythology. There where two goddess, who could both do anything and/or make anything happen. One goddess was ordered and could do most of the calculations in her head. After she pondered, it would produce integrated results. The other goddess could do the same things, but had not control over the creative process other than output results like a burp, without any forethought. Both goddess could create a universe. The first goddess would think, plan, and brood, and it would appear. The second goddess would belch to get a bunch of different results, until eventually, she could also make a universe. 

 

Followers of Discordianism, who venerate Eris the Greco-Roman goddess of chaos, have a strong belief in randomness and unpredictability.

 

In discordian mythology, Aneris is described as the sister of Eris aka Discordia. Whereas Eris/Discordia is the Goddess of Disorder and Being, Aneris/Harmonia is the Goddess of Order and Non-Being. 


Edited by HydrogenBond, 14 January 2017 - 06:05 AM.


#10 Turtle

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Posted 14 January 2017 - 10:35 AM

Contemporary evolution is based on a random assumption of change on the DNA, ...

'On' the DNA? No doubt your non-standard syntax 'on the DNA' is yet another of your veiled meanings. So too 'random assumption'? I consider this habit of yours simple cowardice. Moreover, your failure to provide a contemporary citation for your assertion about evolution is another example of your habit of intellectual dishonesty.
 

...followed by the logic of natural selection. I have no problem with the logic of natural selection, since it makes sense and can be observed and even predicted. However,  I do have a problem with the random assumption that is based on DNA in a vacuum, where water is nothing but a solvent that can be ignored or replaced. That erroneous assumption is followed by the gods of gambling casinos; random assumptions, using the oracle of statistics.  The question is how is this different from a random form of creationism?

Pot calls kettle black, which is to say you demonize statistics for science, but vaunt it for your god. While statistical calculations regarding evolution can be formed, presented, and checked, no such evidence can be presented for creationism or god.
 

Where I differ, is I don't use either version of creationism; god or[sic] order or god of chaos. It does no matter to me if you define random as not a form of creationism, if it quacks it is a duck. Science is not covered under PC word games.

But your entire kit-and-caboodle is word games! If you don't use either version of creationism -god of order or god of chaos- then stop your dissembling and tell us what version of creationism you use and name your god.
 

Let me create a mythology. There where two goddess, who could both do anything and/or make anything happen. One goddess was ordered and could do most of the calculations in her head. After she pondered, it would produce integrated results. The other goddess could do the same things, but had not control over the creative process other than output results like a burp, without any forethought. Both goddess could create a universe. The first goddess would think, plan, and brood, and it would appear. The second goddess would belch to get a bunch of different results, until eventually, she could also make a universe. 
 
Followers of Discordianism, who venerate Eris the Greco-Roman goddess of, have a strong belief in randomness and unpredictability.
 
In discordian mythology, is described as the sister of Eris aka Discordia. Whereas Eris/Discordia is the Goddess of Disorder and Being, Aneris/Harmonia is the Goddess of Order and Non-Being.

Now you cobble up a false dichotomy for the grand finish, and yet still falter when faced with having to present your god. It is a fallacy to assert that using mathematics implies fellowship in Discordianism. Intellectual dishonesty is your sword and cowardice your shield.

#11 HydrogenBond

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Posted 15 January 2017 - 06:16 AM

Your going way off topic. I only answered your accusation, to be polite, and engage the audience. Your detour question was curious to me, because I figured a turtle would like to discuss water. You're not really a turtle, right?

 

Statistics is a tool, and not a fact of reality. The tools offer a way to model reality, based on a random philosophy. This is the pitfall you and many others have fallen into. You assume the tool define reality. 

 

Statistics can be a very useful tool, when you don't understand something, but still need to explain it. If you are screening new medicines, the body is very complicated with many unknowns in terms of 3-D affects. You place the unknown details in a black box, and only look at input and outputs. This tool can be very useful for complicated situations. 

 

However, the utility of the tool, does not mean what is inside the black box is always random, just because the tool uses that assumption in all cases. Random is an assumption used by the tool. It would be much better to open the black box and look inside to find the reasons for why we get the output from the input. Just because a hammer is necessary to build a house, does not mean the house was designed around the assumptions of how a hammer works. I suppose their may be architects that build this way. The goddess Eris/Discordia is a way to describe those who assume the assumption of a tool defines reality. A tool is used for fabrication. 

 

This is way off topic, but relevant. We live in a quantum universe. What a quantum universe implies is the number of possible option is finite, or there are only a small set of possible outcomes, relative to all conjectured outcomes. Not all things are possible in a quantum universe. For example, there are only 5 energy levels for the hydrogen atom, each with specific energy, and not an endless number of states. The dice of the universe are heavily loaded; quantum universe. Life cannot form unless the chemicals that integrate are parts of the loaded dice; allowable quantum states. All these allowable pieces need to fit with other quanta, which further limits what is possible.

 

Do a google image search for DNA. What you will see is the isolated DNA double helix, without the chemically bonded water. What is shown is not bioactive.  That is not a valid quanta in terms of life. It is like assuming there is a 1.5 energy level for hydrogen. Water is part of the structure of the DNA and is needed to maintain the active conformation; right quanta.  The amount of attached water will also determine whether the DNA is alpha or beta DNA; which quanta of DNA. 

 

 

Discordianism is a religion and subsequent philosophy based on the veneration or worship of Eris, a.k.a. Discordia, the Goddess of chaos, or archetypes or ideals associated with her. It was founded after the 1963 publication of its holy book, the Principia Discordia,[1] written by Greg Hill with Kerry Wendell Thornley, the two working under the pseudonyms Malaclypse the Younger and Omar Khayyam Ravenhurst.

There is some division as to whether it should be regarded as a parody religion, and if so, to what degree.[2] It is difficult to estimate the number of Discordians because they are not required to hold Discordianism as their only belief system,[3] and because there is an encouragement to form schisms and cabals.[4][5]

 

Again I recognize the usefulness and utility of the statistical tool. The black box approach allows us to still do science when things are shrouded in mystery. We can keep moving forward until the tools evolve. Random is an assumption of the tool. This is useful because it maintains all the options and does not try to skimp. However, we live in a quantum universe where all options are not possible. There are only certain options, possible. If we knew nothing of the hydrogen atom, we could place hydrogen in the black box. We would then assume random, even though there are only five energy levels with each level having a very specific quantized energy. Those who directly and indirectly worship ERIS, will argue that all states are possible; have odds, and this would appear if we did enough experiments. If we did enough experiment, some states would be given very small but not zero odds. However, in a quantum universe  zero odds is part of reality. Water is part of the genetic quanta. 


Edited by HydrogenBond, 15 January 2017 - 06:25 AM.


#12 HydrogenBond

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Posted 15 January 2017 - 07:04 AM

I brought up the article, below, in my discuss of water and life at the nanoscale. I will bring it up again, because it shows things that will help to make the importance of water, for the activity of DNA, more clear cut. 

 

The structure and dynamics of the DNA double helix are influenced in a decisive way by the surrounding water shell. New experiments in the ultrafast time domain show that the first two water layers at the DNA surface generate electric fields of up to 100 megavolts/cm which fluctuate on the femtosecond time scale and are limited to a spatial range on the order of 1 nm.

Read more at: https://phys.org/new...fields.html#jCp

 

The water that is hydrogen bonded to the DNA; first two layers, generates substantial electric fields in order of 100 million volts that last about a femto-second. The DNA and water is a very energetic team. The DNA and water is not a passive situation. Water is more than a scaffolding that holds the DNA in the correct way to be bioactive. 

 

The reason is, the atomic composition and the shape of the DNA, and therefore the way the water hydrogen bonds to DNA, allows the water to form cooperative hydrogen bonding. What cooperative hydrogen bonding means is the elections of the surface water of DNA, are able to delocalize to form extended resonance, based on hydrogen bonding. 

 

The value of the cooperative hydrogen bonding, relative to the evolution of the DNA, is not all theoretical bases, base pairs and base precursors will allow the surface water to generate these high voltages. Most will inhibit, to various degrees, the extensive cooperative hydrogen bonding in the surface water. The cooperative hydrogen bonding on the DNA is a state of stability. I would guess the electric fields are due to the potential with the bulk water. The bulk water can also form cooperative structures, but as well as the water bonded to the DNA. There is constant discharge between, followed by the reestablishment of the cooperative on the DNA, since the water is fixed to the DNA. 

 

If the DNA was anything less than its modern based pairs, the discharge potential would disrupt the water cooperative on the surface of the DNA, for longer periods of time, if not all together. The result would be the DNA becomes more energized, so there is room for evolutionary change. But eventually, the DNA and water became the modern team; cooperative water on stable DNA. 


Edited by HydrogenBond, 15 January 2017 - 07:21 AM.


#13 Turtle

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Posted 15 January 2017 - 12:06 PM

Your going way off topic. I only answered your accusation, to be polite, and engage the audience. Your detour question was curious to me, because I figured a turtle would like to discuss water. You're not really a turtle, right?...


No. I am not off topic. You have been obsessed with water for years and you have some theistic beliefs about water that you think contradict evolution. However, because you are afraid of the scientific debunking of your beliefs you never state your beliefs, and that is cowardice.

Because you are afraid, you attack science and scientists using metaphoric misrepresentations, i.e. you lie. That is intellectual dishonesty.

Cut to the chase and stop wasting peoples' time.

#14 CraigD

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Posted 16 January 2017 - 04:33 PM

This seems to be tedious, bears-shit-in-the-woods stuff.

Booooorrrrrring! Please move on to your claims for how all this water information supports creationism and debunks evolution.

H-Bond and Martin Chaplin’s fringe neo-homeopathy aside :thumbs_do, the Cavendish lab’s “Structure of DNA” webpages gives a brief account of the history of the discovery of the structure of DNA, from which H-Bond took his first quoted text, and is an interesting read. :thumbs_up

The gist of this history is that in their earliest attempts at a model of the structure of DNA, Wilkins, Watson, and Crick of 1962 medicine Nobel prize fame assumed the 4 nucleotides were attached to the outside of an inner sugar-phosphate-magnesium backbone (“BOTI”). Due to x-ray crystallography (from Rosalind Franklin and and her graduate student assistant Raymond Gosling), they knew that these molecules were present, but not how they were arranged. Their first intuitions were to place the important, information-carry nucleotide molecules facing outward, leading to a model that required 3 spirals.

How different this is than the model they finally arrived at, with 2 sugar-phosphate backbones on the outside (“BOTO”), and the nucleotides on the inside, is hard to overstate. The backbone-on-the-inside model provided no explanation for how DNA can replicate. The on-the-outside model, on the other hand, immediately suggest that DNA can be “unzipped”, and 2 new, identical ones created by attaching complementary (A-T, G-C) nucleotides to the exposed nucleotides.

To put it more starkly, W,W & C didn’t initially understand base pairs, only bases! In 1951, these top biochemical scientist understood DNA less well than a precocious present-day preschooler. By 1953, they had its basic structure right.

The correct, BOTO model contains much more - about 10 times – water than the incorrect, BOTI one. This wasn’t accidental – Watson and Crick worried that too much water would result in not enough magnesium for the proposed inner spine.

Franklin pointed out to Watson and Crick that her x-ray photos showed too much water for their BOTI model. This had the effect of getting them embarrassed in front of their boss at the Cavendish lab, William Bragg of 1915 physics Nobel prize (for the x-ray crystallography) and stopping their work on finding the structure of DNA for a while.

While problems with to the amount of water in DNA model stopped Watson and Crick from continuing down the wrong path with their BOTI model, I think what really got them on the track of the right model was a combination of academic competition – Linus Pauling at Caltech proposed his own BOTI model, which Bragg, Watson and Crick knew would quickly be corrected, so if they didn’t resume looking for the structure of DNA, Pauling would likely find it first – and input from the chemist Erwin Chargaff, who pointed out that there were about equal amounts of A and T, and equal amounts of G and C, in DNA that could be explained other than by there being a A-T and G-C relationship. Once this relationship was in their minds, the BOTO model with its A-T G-C base pairs, make compelling sense.

A further example of Watson and Crick in early 1953 knowing less about DNA than a present-day precocious preschooler is that that they originally assumed “like for like” (A-A, T-T, G-G, C-C) pair bonding.

I tend to think of the structure of DNA as something Wilkins, Watson, and Crick just figured out withough complications from 1951 to 1953. The real history is full or mistakes, rivalries, and less famous people making important contributions.

No homeopaths, though, as best I can tell. While the role of water in causing DNA to have its active, B form was important and understood in the 1950s, they didn’t believe that water stores information, or carried it from DNA to other parts of the cell. These ideas are fringe science, unsupported by any credible research or theory of which I’m aware.

#15 Turtle

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Posted 16 January 2017 - 05:25 PM

H-Bond and Martin Chaplin’s fringe neo-homeopathy aside :thumbs_do, the Cavendish lab’s “Structure of DNA” webpages gives a brief account of the history of the discovery of the structure of DNA, from which H-Bond took his first quoted text, and is an interesting read. :thumbs_up
...
No homeopaths, though, as best I can tell. While the role of water in causing DNA to have its active, B form was important and understood in the 1950s, they didn’t believe that water stores information, or carried it from DNA to other parts of the cell. These ideas are fringe science, unsupported by any credible research or theory of which I’m aware.

While the interesting read is...well, interesting, that is not the issue of my concern. HBoned has denied he is on about homeopathy while continuing to evade declaring what his pseudoscientific claims actually are, which -as I have pointed out repeatedly- are in essence creationism. As I have also pointed out, this board is littered with this crapola covering a span of at least a decade and enough ought to be enough.
Your thoughtful corrections Craig, as well as those of others, have done nothing to forestall this ongoing broach of both the rules and intent of this science forum. Same too, your direct admonitions as a moderator and administrator which HBoned patently ignores.

All-in-all, allowing this to go on is more disservice to science and the board than aid. Second chances are one thing, 876th chances another thing altogether and I urge you Craig and staffers to reconsider such allowances.

As clearly I am not the only one of this opinion, I invite other members to weigh in in no uncertain terms. See something, say something.

#16 HydrogenBond

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Posted 17 January 2017 - 06:39 AM

Turtle, if you had more competence in chemistry, you would see where I am going. Your critique is based on bias memory and repeat, with very little demonstrated understanding of chemistry. The DNA double helix, as shown in text books, and in any google image search, is not bioactive. That is obsolete science, that your have memorized as dogma science.

 

Water is a necessary part of the active structure of the DNA. There are places reserved on all the bases of DNA and RNA, earmarked for water. The water hydrogen bonds to these reserved places, and then to each other, to form a double helix of water, that occupies the major and minor grooves of the DNA double helix. This is called reality, based on proven science. This has nothing to do with homeopathy. I am not even sure where that comparison comes from other than a buzz word to sour opinion and confuse the facts. 

 

Say you designed a theory of evolutionary change, based on a DNA double helix, that is not bioactive. Your theory will be incorrect, by default. It is not because DNA is not a template material, nor that DNA is not subject to change. This is also not due to the fact that the DNA in all cells is bioactive. Rather double helix DNA, without the necessary water, is not bioactive. This is overlay simplified and flawed. 

 

You cannot substitute other solvents for water, because places are reserved for water to be included on the DNA. Other solvents will not hold the double helix of DNA in the correct conformation for the DNA to be bioactive. But if you persist in the double helix, only, fairy tale, the result is the need for a random assumption to compensate for a poor foundation premise. 

 

Let me do this a different way. Predict a future evolutionary change for any living system? According to the scientific method, a theory should be able to make predictions, that are repeatable by others. The current model; front end for evolution, does not live up to the standards of a theory that can make a prediction! The theory is not that advanced. 

 

Once a change does occur, we can point it out. But that is not prediction. That is 20/20 hindsight. A backwoods native, with no modern science education, can point out weather, after it happens. He can't make predictions. He can keep track of the weather in cave writings.  And he can also say this is proof that his god of the winds and rain is responsible for all weather. If you ask how his god doe this, he can say his god is fickle, so humans can't know her mind. The front end of the current evolutionary model is a form of creationism. 

 

There are two creationism models, neither of which can make predictions in terms of evolution, before the fact. One is based on the god of order and the other based on the god of random. I chose order instead of random, because natural selection uses order. Natural selection is based on the logic of known environmental potentials not throwing dice. 

 

The part of the evolutionary model that does work is the second aspect; natural selection. If we have a change, due to the god of wind/rain or gambling casinos,  you can use logic to determine if this change will help to hurt, relative to what already exists. There is a logical order from which one can infer. The upfront random change approach does not satisfy the needs of prediction.  This has been my focus. This is where I have contented, from the beginning, the model is flawed. Not the entire model, but the front end. I am an applied engineer and I can tell if a theory is useful or useless. If useless, the goal is to make it workable. To make it workable you need to make it real. To make it real you need the latest water science. 

 

If you read the last article I presented about megavolts electric fields on the surface water of DNA, the surface water on the DNA is very energized, Youneed to read the background I developed, that was moved to the speculations. In that background, I discuss how hydrogen bonds are binary, with both polar and covalent character. Like with computer memory, binary switches can be use to store and transmit information. The DNA is a solid chemically bonded structure that is very stable. When water attaches to this, the  water is aligned to by solid structure, allowing persistence for the binary switches. 

 

Show me a reference that demonstrates a DNA double helix is bioactive without bonded water!


Edited by HydrogenBond, 17 January 2017 - 07:28 AM.


#17 HydrogenBond

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Posted 17 January 2017 - 07:07 AM

The changes in the free energy of the surrounding water aids the conversion of single-stranded DNA (ssDNA) into double stranded DNA (dsDNA) as the water molecules are more stable around dsDNA than around ssDNA even out to about 0.65 nm (3 hydration layers) [2693].

 

After that long detour, I would like to add a brief discussion of the above quote. The free energy change in the water aids in the conversion of single stranded DNA, into the more common DNA double helix. Water can hydrogen bond to both single or double stranded DNA, with water part of both structures. The double helix is preferred because this lowers the energy of the water the most, all the way to three hydration layers; cooperative hydrogen bonding. 

 

It is not the DNA double helix, due to base pairing, being stable on its own; in a  vacuum, in spite of the water or any solvent. Water is not just a solvent used to loosen the DNA. The DNA double helix is more stable, because this conformation benefits both the free energy of the water. The DNA double helix plus water system is at minimum energy, with the water is making the base pairs 50% weaker. The DNA is energized by the water, with the water at very low free energy. 

 

What this also means is if we were to energize the nucleus water, so the nucleus water has to maintain a higher level free energy floor, then single stranded DNA becomes more favorable at equilibrium. If we then lower the energy floor of the nucleus water, then the DNA double helix wants to form to meet the needs of the lower free energy floor. 

 

This is useful for replication on the DNA, since tweaking the local and bulk water can help or inhibit enzyme complexes by loosening or tightening the DNA double helix. One could also argue, that you can inhibit genes by making the local water too stable, since the double helix will not want to separate, easily, and if it does, it will prefer to reform the double helix very quickly. 


Edited by HydrogenBond, 17 January 2017 - 07:44 AM.