Dna And Water

[Turtle]

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 That is obsolete science, that your have memorized as dogma science.

My memory is of your posting here and indeed you repeat the same bias and behavior. Invoking chemistry does not make it about chemistry.

 

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.

There you go hiding behind misdirection again. Craig brought up homeopathy and I discounted it as your tune. It's not my argument and never was.

 

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.

More misrepresentation. Soooo dishonest! The science of genetics is in its infancy and declaring it invalid as a whole is as ludicrous as declaring a toddler not a human just because you can't predict what the child will grow up to be and do.

 

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.

And again you misrepresent science. Science is no more creationism than you are brave.

 

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.

More deceit, but at least you make a veiled admission that all this is about god for you, and not about chemistry. You start with the assumption of a god and then do your damndest to clothe it in flashy garb that disguise.

 

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[sic], 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.

And here we find more deceit and cowardice raises her ugly head again. Science is never complete and you never lay out your 'model'.

 

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!

Good grief! No one is claiming that water does not accompany life. Just another of your lies of misdirection. You use chemistry as a disguise for your theistic beliefs because you are a chemist; if you were a geologist you would use geology, if a linguist, language, if a yada yada yada, pseudoscience up the wazzoo.

[HydrogenBond]

Rather than get into the chemistry, which you are trying to distract from, I will stay more along the lines where you seem to feel more comfortable. Make a prediction using conventional evolutionary theory; genetic mutations followed by natural selection. For example, what will be the next stage of human evolution? Or what new species will appear next? 

 

Next, make a prediction as to how far a ball will go, that is shot from a tube out of the ground, at 100 mph at a 45 degree angle? This prediction can be made use projectile motion equations. Or predict the amount of rocket fuel needed to send a man to the moon? The weakest theory, of these three, in terms of making a prediction, is evolutionary theory.

 

The current theory of evolution is a good theory for cataloging and organizing data, from the past and/or after the fact. It is not useful for making predictions of the future. In terms of making predictions, it is at the stage of science, where shooting the ball from the tube in ground, would be treated like a mystery or random event, which you can record and catalog, after the fact. But it would be considered luck or taboo to make a prediction, and get it right. 

 

If you do enough cataloging of the ball shooting from the tube, you would able to infer that if we shoot the ball from the tube, it will land somewhere and not keep going forever. But we still can't tell, in advance, based on this cataloging, exactly where it will land, even after 60 years of the same theory and procedure. Science is not about appearance, due to lab coats, but the goal is practical utility. 

 

Other than collecting and organizing evolutionary data, using the methods of science, the utility of contemporary evolutionary theory, in terms of making predictions, is not much different from Creationism. They also catalog changes in the universe and to life, based on their theory. Like evolutionary theory, even with cataloging, Creationism cannot be used to make predictions. Repeatable prediction is the litmus test of sound theory. It is not just about cataloging bigger and better than another theory. 

 

The theory of natural selection is acceptable, because it can be used to make predictions. Once a change occurs, one can make a prediction, as to whether this change will allow advantages or disadvantages, based on the environment. The front end of evolution, connected predicting the change, is not as advanced, as the tail end; natural selection, in terms of making predictions. The overall theory is lopsided. 

 

You don't seem to understand the difference between science and religion. Religion is based on formal traditions, which are not allowed to change, since these define the very nature of the religion. Once changed, a religion becomes something new. Science is different, since science is not about defending the traditions of a religion, but accepting change if better. Change is acceptable if it lead to greater utility. 

 

The truth is experimental results, especially over the past 20 years, have been able to investigate and show the importance of water in terms of the structures and dynamics of the DNA, as well as all cellular materials. You appear to resist any change to the cell in a vacuum dogma, and appear to treat evolution as a religion, that would lose its identity if anything was to change. You do no wish the goddess of chaos and chance to be displaced, with a new testament based on water and logic. The water science is sound and peer reviewed. Your argument is about defending the essence of a dogma. You have not once even tried to refute any of the science I have presented. You don't want the dogma touched in any form, even if the  science presented is sound. 

 

I have been consistent with this since the beginning. I have tried to develop different approaches to make it better. It was of late that I found the key to the future; prediction. 

Edited January 18, 2017 by HydrogenBond

[CraigD]

HBond, many members of hypography believe you are dishonest, attempting to discredit science in favor a religions creationism through persistent pseudoscientific arguments such as the one in this thread.

 

Before making more posts, please answer the following questions, each with a “yes” or a “no”.

• Do you believe that liquid water can hold multiple bits of information that can be retrieved after long (60 sec +) periods?
• Do you believe that genetic information in biological cells is contained in part or completely in water, rather than entirely in the cell’s DNA?
• Do you believe that information in a cell’s DNA is transferred to other parts of the cell via some interaction with the water, rather than via messenger RNA transcribed from its DNA?

Consider this a request from a moderator, which you are not allowed to ignore.

[exchemist]

Rather than get into the chemistry, which you are trying to distract from, I will stay more along the lines where you seem to feel more comfortable. Make a prediction using conventional evolutionary theory; genetic mutations followed by natural selection. For example, what will be the next stage of human evolution? Or what new species will appear next? 

 

Next, make a prediction as to how far a ball will go, that is shot from a tube out of the ground, at 100 mph at a 45 degree angle? This prediction can be made use projectile motion equations. Or predict the amount of rocket fuel needed to send a man to the moon? The weakest theory, of these three, in terms of making a prediction, is evolutionary theory.

 

The current theory of evolution is a good theory for cataloging and organizing data, from the past and/or after the fact. It is not useful for making predictions of the future. In terms of making predictions, it is at the stage of science, where shooting the ball from the tube in ground, would be treated like a mystery or random event, which you can record and catalog, after the fact. But it would be considered luck or taboo to make a prediction, and get it right. 

 

If you do enough cataloging of the ball shooting from the tube, you would able to infer that if we shoot the ball from the tube, it will land somewhere and not keep going forever. But we still can't tell, in advance, based on this cataloging, exactly where it will land, even after 60 years of the same theory and procedure. Science is not about appearance, due to lab coats, but the goal is practical utility. 

 

Other than collecting and organizing evolutionary data, using the methods of science, the utility of contemporary evolutionary theory, in terms of making predictions, is not much different from Creationism. They also catalog changes in the universe and to life, based on their theory. Like evolutionary theory, even with cataloging, Creationism cannot be used to make predictions. Repeatable prediction is the litmus test of sound theory. It is not just about cataloging bigger and better than another theory. 

 

The theory of natural selection is acceptable, because it can be used to make predictions. Once a change occurs, one can make a prediction, as to whether this change will allow advantages or disadvantages, based on the environment. The front end of evolution, connected predicting the change, is not as advanced, as the tail end; natural selection, in terms of making predictions. The overall theory is lopsided. 

 

You don't seem to understand the difference between science and religion. Religion is based on formal traditions, which are not allowed to change, since these define the very nature of the religion. Once changed, a religion becomes something new. Science is different, since science is not about defending the traditions of a religion, but accepting change if better. Change is acceptable if it lead to greater utility. 

 

The truth is experimental results, especially over the past 20 years, have been able to investigate and show the importance of water in terms of the structures and dynamics of the DNA, as well as all cellular materials. You appear to resist any change to the cell in a vacuum dogma, and appear to treat evolution as a religion, that would lose its identity if anything was to change. You do no wish the goddess of chaos and chance to be displaced, with a new testament based on water and logic. The water science is sound and peer reviewed. Your argument is about defending the essence of a dogma. You have not once even tried to refute any of the science I have presented. You don't want the dogma touched in any form, even if the  science presented is sound. 

 

I have been consistent with this since the beginning. I have tried to develop different approaches to make it better. It was of late that I found the key to the future; prediction. 

This is balls.

 

Evolution makes predictions all the time. It predicts high similarity between the DNA of creatures it considers to be close relatives. It predicts where to find fossils of particular types (no rabbits in the Cambrian, for example). It predicts the existence of transitional fossils between types, many of which have been found (e.g. Pakicetus). These are all different sorts of prediction made by the theory, with great success. So it is utter rubbish to claim it does not make predictions, and thus to imply it is not really a proper theory of science.  

 

As for it being "dogma", that is rubbish too. The theory is constantly changing in light of new discoveries, for example the whole area of epigenetics, which was unknown 20 or so years ago. 

[HydrogenBond]

This is balls.

 

Evolution makes predictions all the time. It predicts high similarity between the DNA of creatures it considers to be close relatives. It predicts where to find fossils of particular types (no rabbits in the Cambrian, for example). It predicts the existence of transitional fossils between types, many of which have been found (e.g. Pakicetus). These are all different sorts of prediction made by the theory, with great success. So it is utter rubbish to claim it does not make predictions, and thus to imply it is not really a proper theory of science.  

 

As for it being "dogma", that is rubbish too. The theory is constantly changing in light of new discoveries, for example the whole area of epigenetics, which was unknown 20 or so years ago. 

 

 I narrowed my discussion to predicting the future, not the past or finding new places between other places in a catalog. We could do that with rocks without knowing anything about the chemistry of rocks. If you gather enough samples, from different terrains and environments you can anticipate the rocks in similar environments. This is not the same as predicting a future rock, that is not in the catalog, yet. That requires knowledge of the chemistry of rocks. It has to be complete chemistry, or else the prediction will be  a crap shoot. 

 

If you needed to put a man on the moon, and this had never been done before, inferring from cataloging is useless. You will need to break the goal  down into steps, and define the logic for each step and the logic that connects the steps. Random will not do, since there is no room for compounding errors. 

 

Settle this by making a future prediction using evolutionary theory, as is?  I am not trying to be contrary. I am trying to be evolutionary in terms of the utility of evolution. You need to include the properties of water to make the happen. 

Edited January 18, 2017 by HydrogenBond

[exchemist]

 I narrowed my discussion to predicting the future, not the past or finding new places between other places in a catalog. We could do that with rocks without knowing anything about the chemistry of rocks. If you gather enough samples, from different terrains and environments you can anticipate the rocks in similar environments. This is not the same as predicting a future rock, that is not in the catalog, yet. That requires knowledge of the chemistry of rocks. It has to be complete chemistry, or else the prediction will be  a crap shoot. 

 

If you needed to put a man on the moon, and this had never been done before, inferring from cataloging is useless. You will need to break the goal  down into steps, and define the logic for each step and the logic that connects the steps. Random will not do, since there is no room for compounding errors. 

 

Settle this by making a future prediction using evolutionary theory, as is?  I am not trying to be contrary. I am trying to be evolutionary in terms of the utility of evolution. You need to include the properties of water to make the happen. 

Well then you narrowed it tendentiously, with a view to making the false claim that evolution cannot predict. The prediction requirement for a scientific theory is that it can predict what future observations can be expected, not that it can see generally into the future. Obviously. 

Edited January 18, 2017 by exchemist

[Turtle]

Still waiting...

HBond, many members of hypography believe you are dishonest, attempting to discredit science in favor a religions creationism through persistent pseudoscientific arguments such as the one in this thread.

 

Before making more posts, please answer the following questions, each with a “yes” or a “no”.

• Do you believe that liquid water can hold multiple bits of information that can be retrieved after long (60 sec +) periods?
• Do you believe that genetic information in biological cells is contained in part or completely in water, rather than entirely in the cell’s DNA?
• Do you believe that information in a cell’s DNA is transferred to other parts of the cell via some interaction with the water, rather than via messenger RNA transcribed from its DNA?

Consider this a request from a moderator, which you are not allowed to ignore.

 

[CraigD]

Still waiting...

H-Bond will be on a 1-week suspension ‘til Wed 25 Jan, so the wait will be at least a couple more days.

 

H-Bond, if when your suspension is lifted, you still chose to post at hypography, begin by immediately answering these questions, and any other direct questions from any member asking for clarification of the intentions and meaning of your posts. We find it frustrating and unpleasant to have our questions ignored, and it makes us suspicious that you are sneakily promoting an anti-science agenda akin to the “wedge strategy” pursued by the Discovery Institute in the 1990s. Honesty and understanding in discussions of science is vitally important, and directly answering direct question is an important tool for being honest and understood.

[HydrogenBond]

HBond, many members of hypography believe you are dishonest, attempting to discredit science in favor a religions creationism through persistent pseudoscientific arguments such as the one in this thread.

 

Before making more posts, please answer the following questions, each with a “yes” or a “no”.

• Do you believe that liquid water can hold multiple bits of information that can be retrieved after long (60 sec +) periods?
• Do you believe that genetic information in biological cells is contained in part or completely in water, rather than entirely in the cell’s DNA?
• Do you believe that information in a cell’s DNA is transferred to other parts of the cell via some interaction with the water, rather than via messenger RNA transcribed from its DNA?

Consider this a request from a moderator, which you are not allowed to ignore.

 

 

The water that is hydrogen bonded to the bases of the DNA and is therefore part of its structure, reflects the information contained on the bases and therefore on the genes. This water plays a role in gene recognition and therefore contains reflected information that persists since it is bonded to the DNA in very specific ways. The analogy is clay does not contain information. However if you press the clay onto your face, it now looks like you, This is not my opinion, but is based on peer reviewed papers in the journal of biophysical chemistry. 

 

I have made such claims in the past, based on my own inferences. Over the past year or two I found proof, I found Dr Chaplin's web site about water and found that my claims had a basis in peer reviewed science. 

 

The processing of the genetic information within DNA is facilitated by highly discriminatory and strong protein binding. It has been shown that the interfacial water molecules can serve as 'hydration fingerprints' of a given DNA sequence [889].

 

The normal 'hydration fingerprint' of the DNA will clearly be disrupted by DNA damage and this will facilitate repair protein attachment. The hydration spine (see above) is capable of carrying messages, as facilitated proton movement down the water wire, between binding sites in a similar, if complementary, manner to the electron transfer through the DNA residues [2258] and so coordinate the repair process.

 

http://www1.lsbu.ac.uk/water/nucleic_acid_hydration.html

 

Ref 889: S. Magazù, F. Migliardo, C.Mondelli and M. Vadalà, Correlation between bioprotective effectiveness and dynamic properties of trehalose-water, maltose-water and sucrose-water mixtures, Carbohydr. Res. 340 (2005) 2796-2801; ( :cool: S. Magazù, F. Migliardo and A. J. Ramirez-Cuesta, Changes in vibrational modes of water and bioprotectants in solution, Biophys. Chem. 125 (2007)138-142; © F. Affouard, P. Bordat, M. Descamps, A. Lerbret, S. Magazù, F. Migliardo, A. J. Ramirez-Cuesta and M. F. T. Telling, A combined neutron scattering and simulation study on bioprotectant systems, Chem. Phys. 317 (2005) 258 -266.

 

The system of pure DNA, without water, is not bioactive. Information is contained on the genes, but you cannot access this information using pure DNA alone. The DNA needs water to help induce the active state. Water also plays a role in gene recognition as well as providing free energy for protein binding. 

 

The major driving force for the specificity of protein binding is the entropy increase due to the release of bound water molecules (estimated at 3.6 kJ mol^-1 for minor groove water and 2.3 kJ mol^-1 for major groove water, both at 300 K [1096]), ^c with the DNA sequence determining the hydration pattern in the major and minor grooves (see above). Less perfect (that is, weaker) binding involves mainly secondary hydration water loss and so would allow sliding of the protein along the DNA [1176], facilitated by the remaining primary hydration water molecules [889]. For example, about 110 water molecules are released on binding of the restriction endonuclease EcoRI to its site GAATTC leaving an essentially dry interface and firmly bound complex (with binding constant ~10,000 times that for nonspecific binding), whereas changing just one base out of the recognition sequence leaves those water molecules mostly unaffected and only little different from EcoRI non-specifically binding to DNA [1176b]. Thus, the key to the formation of specific links between proteins and DNA is that the interfacial water molecules allow the protein facile movement along the binding cleft whilst retaining contact information [1443]. Final binding makes use of both direct and water-mediated hydrogen bonds; for example, the restriction endonuclease MspI makes specific contacts with all eight bases in the four base pair recognition sequence (5'-CCGG-3' and complementary 3'-GGCC-5'), by six direct and five water-mediated hydrogen bonds and thirteen water-mediated links to the phosphates [1444].

 

 

http://www1.lsbu.ac.uk/water/ref15.html#r1443

 

Protein configurations are also dependent on water. 

 

Protein hydration is very important for their three-dimensional structure, dynamic ensemble of conformations [2249] and activity [472, 1093, 1345, 2005]. Fluctuations of the protein surface groups drive and are driven and controlled by the surrounding network of water molecules [2648]. Indeed, proteins lack biological activity in the absence of sufficient hydrating water (usually at least a monolayer covering; > 1.5 mols H₂O mol^-1 amino acid residue). High resolution X-ray diffraction detects about one H₂O mol^-1 amino acid that are relatively static [2677]. The aqueous structuring around proteins is affected out to at least 1 - 1.5 nm from its surface or 2 - 3 nm between neighboring proteins, as shown by terahertz spectroscopy [1368, 2102], ^e with even small proteins (e.g. bovine serum albumin, 66,463 Da) affecting the whole of its unstirred (Nernst) layer of about 20,000 neighboring water molecules [2102]. Certainly, the range of these interactions is governed by directed hydrogen bonding interactions that extend further than the electrostatics dependent Debye screening length (< 1 nm). Additionally, the presence of glycans attached to (glyco)proteins impose a long-range order on the water structure out to several nanometers, dependent on the orientation of the glycan [2104]. Some water molecules interact with the surface, reorienting both themselves and the surface groups whereas other water molecules link these to the bulk in an ordered manner whilst remaining in dynamically active [1695]. In solution proteins possess a conformational flexibility, which encompasses a wide range of hydration states, not seen in the crystal ^a or in non-aqueous environments. Equilibrium between these states will depend on the activity of the water within its microenvironment; that is, the freedom that the water has to hydrate the protein [434].

 

To answer the last question, what always puzzled me is how does everything know where go in the cell. Why is this not random with nucleus protein ending near the membrane and membrane protein near the DNA? You have the DNA, making mRNA, which then goes to the ribosomes to make protein. The protein can be all types and these go every which way, yet they all find their proper places in the cell. The question is how is this possible?

 

Water offers a medium that can make this possible. Proteins need to become hydrated to become active; see above. The protein, in turn, will impose order in the water, which depending on the surface groups, can extend considerable distances, at the nanoscale. If this ordered water is next to another protein, the water order can become more continuous between the two. As with the DNA, water plays a role in recognition and energetics. 

 

http://www1.lsbu.ac.uk/water/protein_hydration.html

 

 

Water molecules form an integral part of most protein-protein [1339], protein-DNA [1340] and protein-ligand [1341] interactions, aiding the mutual recognition and both the binding thermodynamics and binding kinetics [1338]. Generally, hydrophilic residues make up the protein−protein and protein−DNA binding surfaces and these interact via water molecules. The relative diameters of the binding cavity and the ligand determine the kinetics and thermodynamics of (hydrophobic) binding cavity-ligand systems, involving a sharp (cooperative) dewetting transition in formation and a continuous dewetting transition on ligand loss [2575].

The water at the interface of the tightly bound barnase-barnstar enzyme- inhibitor complex (see right) shows highly slowed dynamics (> 100-fold, [2797], from 20 bridging and 74 interfacial water molecules compared with 459 non-interfacial water molecules, reminiscent of glassy water even at ambient temperatures. Similar effects were noted at protein−DNA interfaces. The strength of these effects is thought due to the presence of a strong electrostatic field, driven by the binding surface’s electrostatic complementariyy [2797].

 

The last line about strong electric fields reminds of the study I posted about million volt electric fields on the surface water of DNA. These extend about a nanometer out from the DNA. 

 

The problem we appear to have, is connected to biology and biochemistry education rarely mentioning the latest life water research. Water considerations for life, although peer reviewed science, therefore appears like it is all made up. Many assume that their education would include this if it was true. Then again, the state of the art takes time to reach education.