Hydrogen proton and life

[sunspot]

This is something I have presented to the biologists, but they seem to be waiting for the chemists to OK it. So I went to the chemists, but they seem to be dragging their feet. Maybe they are waiting for the physicists. The premise is the hydrogen proton is the basis for life. It is even more findamental than DNA. From the perspective of the universe, the hydrogen proton or hydrogen is the main component of the universe. It is the most likely candidate for life.

 

If we look at the water molecule, hydrogen is bonded to oxygen, with strong covalent bonds, among the strongest for a single bond. But in liquid water, the hydrogen proton is able to jump around from oxygen to oxygen as reflected by pH. In pH, H2O actually exist as OH- and H3O+, at a moderate level of 10-7 moles/liter at neutral conditions. The hydrogen moves in and out of strong covalent bond fairly easily. The hydrogen proton is the fastest thing in water by almost two orders of magnitude.

 

One way to look at this affect, is that the hydrogen of liquid water is sort of floating, in a figurative way, above the electron clouds. It uses the electron orbitals of oxygen almost like a negative nucleus. The orbital electrons within water, don't migrate much in water since water is a poor conductor of electricity, but the hydrogen proton sitting on the top of the fixed electron clouds, defines a special layer of chemisty.

 

Most thing like rocks, minerials, oil, are based on electrons. But life is different in that it has the hydrogen layer floating on the top of water. The hydrogen proton, via hydrogen bonding, is the basis for the properties of DNA (base pairing, helicial structure, reacticity, etc.), RNA, protein and water. This extra layer of potential, defined by the hydrogen proton, the most abundant material in the universe, is what makes the living state tick. If we take away hydrogen bonding, all the activity of life would end.

 

The chemist ignors the nucleus, once they know the atom, and they ignor all the electrons in atoms except only those on the top that participate in chemical bonds. Chemistry only require working on the top. The same can be done with a hydrogen proton model of life. In other words, as a first good approximation, one can define molecules, like DNA, RNA, proteins, etc., in terms of their hydrogen protons

[SkepticLance]

You are neither right nor wrong, since it is all a matter of how you look at it.

 

From one viewpoint, you can quite correctly say that the hydrogen proton is the basis for life, since its special properties permit water, with its special properties. Water, of course, is a very unusual molecule, and that special nature is due to the weak hydrogen bonding between molecules.

 

I would prefer, myself, to say that water is the basis for life, taking the statement one step higher to molecular level. However, as I said, it depends how you look at it.

[ecoli]

or you could break it down even further and say that quarks and gluons are the basis for all life... it's pretty meaningless.

[kenshin]

I beg to disagree with SkepticLance and ecoli.IMHO,way of looking at the things makes a big difference( things like field concept,forces as space-time geometry..................).I liked your view point sunspot.It makes sence to me and may be,it may help us define life itself(have you tried it?It may provide a boost to your concept).

 

Most thing like rocks, minerials, oil, are based on electrons. But life is different in that it has the hydrogen layer floating on the top of water

 

This may really be the differentiating statement.I liked your view point very much.At least it has given me a new way to look at things.I totally agree with you.

[swansont]

One way to look at this affect' date=' is that the hydrogen of liquid water is sort of floating, in a figurative way, above the electron clouds. It uses the electron orbitals of oxygen almost like a negative nucleus. The orbital electrons within water, don't migrate much in water since water is a poor conductor of electricity, but the hydrogen proton sitting on the top of the fixed electron clouds, defines a special layer of chemisty.

[/quote']

 

 

PLEASE, FOR THE LOVE OF MIKE, POST THIS SPECULATIVE CRAP IN "SPECULATIONS," NOT IN THE SCIENCE FORUMS.

[Ragib]

Yea exactly, how is this in anyway relating to ANY form of science, let alone Modern/Theoretical Physics...its meaningless..Even more fundamental than quarks and gluons then, stings, pure energy. It doesn't matter.

[sunspot]

The value of any orientation is based on its practical value. One could model life in terms of subparticles but it would be impractical in the field. Currently life is based on life molecules, like DNA, RNA, proteins, etc., which does have practical value since it is easier to investigate this level of interactions. What the hydrogen proton brings to the table is a variable that is common to all the life molecules. This would be a practical way to simulate cells since it is a global variable that it easy to investigate.

 

Let me give an example. The main component of life is liquid water. It properties are based on hydrogen bonding. When a protein is dissolved in water and begins to form its structure, hydrogen bonds cause it to form a helix, while hydrophobic and hydrophillic affects typically place the hydrophobic organic groups in the center and the hydrophillic polar groups on the surface. Changes in the hydrogen bonding potential within water due to anything floating around within the water (most things exists with hydration spheres), will have an impact on the surface hydrogen bonding potential of the protein.

 

Water is everywhere in the cell (90%). Everthing within the water will impact the local and the global hydrogen bonding potential of the water. With all the big wigs of the cell, i.e., DNA, RNA, proteins, dependant on hydrogen bonding to define their shapes and dynamics, while also induced by water to expose polarized areas, I can see the cell being coordinated through the water via the hydrogen proton. This is not speculation, it is common sense. The thing that needs to be ironed out is how to define the basis for a hydrogen interaction that can make it a global variable.

 

The idea of floating on top is not exactly rigorous but has practical value. In water it is evident by the pH affect. In the DNA double helix, during transcription the floating is only a half affect. The hydrogen stays attached at one side but will float away from the base pairing into the arms of the transcription complex. The full floating of the hydrogen of water implies an higher potential that helps the partial hydrogen float.

[sunspot]

The hydrogen bonding model of the cell is practical because it simplifies complex chemicals, like DNA, into their hydrogen bonding ghosts. In other words, if we were to take a picture of DNA and color all the hydrogen green and everything else red and then put on a pair of red sun glasses, all we would see would be the hydrogen. If we do this for the whole cell, we would only see hydrogen protons interacting and corrdinating, from the cell membrane to the DNA. This is the ghost of life. The hydrogen ghost simulation is possible with current computers.

[ecoli]

The hydrogen bonding model of the cell is practical because it simplifies complex chemicals, like DNA, into their hydrogen bonding ghosts. In other words, if we were to take a picture of DNA and color all the hydrogen green and everything else red and then put on a pair of red sun glasses, all we would see would be the hydrogen. If we do this for the whole cell, we would only see hydrogen protons interacting and corrdinating, from the cell membrane to the DNA. This is the ghost of life. The hydrogen ghost simulation is possible with current computers.

 

By reducing DNA down to hydrogen bonding, you are ignoring the parts of DNA that don't involve H-bonds.

 

The same goes for proteins and everything else. You need to work with a suffeintly big model, or risk loosing the big picture.

[YT2095]

sunspot, keep it up dude,

and you`ll find ALL your posts/threads in here

[sunspot]

The hydrogen ghost was not meant ot be taken literally but was only used to create a visual image of the hydrogen.

 

This is true. However, as a first approximation, I would like to assume that these molecules are set up to cater to the needs of the hydrogen protons. In other words, to ignor the nucleus of the atoms within DNA does not have an negavitve affect on modelling the DNA. To be more rigorous these need to be taken into account since different atoms set up the conditions that will define their bonding properties. But as a first approximation, bio-chem ignors the nucleus and lower electrons by averaging the affects. The hydrogen model does the same thing by averaging the affects of covalent chemistry into the states of hydrogen protons that are created. The secondary bonding, hydrogen bonding, is why DNA does what it does while remaining a stable molecule.

 

If one goes back to the archives of hydrogen bonding from the late 1950's hydrogen bonding was not limited to N-H and O-H, but C-H bonds were also thought to participate. As time went on, H-bonding was made more restricted to O and N. But more recently, science has rerecorded the old 1950's data. Essentially, all the hydrogen within the cell are involved at some level with some hydrogen protons at very low interaction potential.

 

This is new/old perception is important because it suggests a physical basis for the potential. It has to do with electronegativity.

 

Electronegativity is a term to describe the affinity of an atom for electrons. Something more than simple charge balance occurs within different atoms. Some atoms, like oxygen, is able to hold more electrons that it has protons (anions). While most metals prefer to have more protons that electrons (cations). In other words, if we mix oxygen atoms and most metals atoms, they do not remain with zero charge. Oxygen takes more than it needs while the metal gives up more than it needs to stay neutral. This can not be explain with electrostatic force alone.

 

I asked myself, self, what could be tipping the scales? The first thing that came to mind was the magnetic force. In other words, electron orbitals are the result of the EM force. If the electrostatic force is out of proportion, when cations and anions form, then maybe magnetic force subtraction or magnetic force addition was tipping the scales toward cations and anions, respectively. This premise is not without precident. If one adds same spin electrons to an orbital an excited state will result. Opposite spin electrons are more stable due to magnetic addition. The charge balance is the same in both cases, yet simple magnetic considerations result in two different atomic scenarios.

 

The next question was how is this possible while also having the electrons with additive spin in all the orbitals? What came to mind, recently, was the shape of atomic orbitals. The S-orbital is spherical, while the P-orbitals are 3-dimensional (x,y,z) dumbell shape. What the P-orbitals allow is magnetic addition in 3-dimensions for greater magnetic addition. The x-lobe has two opposite spin electrons. Because these two are perpendicular to the y and z-lobes, there is further magnetic addition between these additive spin electron and those in the y and z-lobes. The S-orbital only has the electron pair magnetic adding.

 

The extra magnetic addtion in the 2P orbitals explains why F, O, N, are three of the top four in electronegativity. The last of the top four is Cl which has 3P orbitals. All these attempt to gain extra electrons so they can benfit by the 3-Dimensional magnetic addition. The magnetic addition is more significant for lowering energy than the electrosptatic potential created due to having too many electrons with respect to protons.

 

The D-orbitals and F-orbitals are not so 3-Dimensionally perfect, with respect to magnetically adding all the electrons in the atom. They will actually cause magnetic subtraction which will result in most metals becoming cations. It pushes electrons away against the electrostatic force attraction of equal charge.

 

As we layer atoms within orbitals to make higher atoms, one gets a atomic composite orbital strucuture composed of layers of magnetic addition and magnetic substraction, with the outer orbital layer influenced by the summation affect beneath it. This explains why Cl is less electronegative that F. It has a 2S-orbtial between the 2P and 3P orbitals, which takes a little bit away from the 3P-orbital. Distance may play a role but with all atoms nearly the same size this affect is small.

 

Getting back to hydrogen. It has an 1S orbital with one electron. When it reacts with oxygen to form water, the 2P stability of O attempts to take the electron away for more magnetic addition. This magnetic stability within oxygen is part of the reason hydrogen can float among the oxygen. Some become more cationic instead of covalent.

 

The hydrogen that stick to the oxygen faces another problem. The orbitals of oxygen are hybridized into SP3 orbtials. What this means is that the bonding orbitals behave as though the 2S and 2P orbitals of oxygen have merged into a new type of pseudo-orbtal that has some character of both. This partially screws up oxygens full P stability because it is 25% S. This helps hydrogen to share by making O less magnetic stable.

 

But on the other hand, the 1S orbital of hydrogen is sharing electrons with the SP3 hybrid orbitals. This imparts 2P character onto the electrons shared by hydrogen. This is the kicker. This causes the electrons that hydrogen is sharing to exist further away from hydrogen (on the average) than is indicative of a 1S orbital.

 

What is significant about this, although an O-H bond has a charge dipole, the negative oxygen end is magnetically stablized to some extent. While the positive charge of H is not only due to less electron density, but also due to the electron density it has, partially existing outside the 1S orbital. If we add it together, every hydrogen proton in water carries a net burden of additional potential.

 

This is how the hydrogen ghost is modelled. All the hydrogen are energized relative to O, N since these are more electronegative and will benefit by being slightly anionic. The hydrogen can lower potential by forming a hydrogen bond with O and N. But since this will destabolize the magnetic stability of O and N the O and N will resist or pass on the burden to its own covalent hydrogen, causing some form of hydrogen to retain at least some residual potential.

[sunspot]

It is a sad day when good science is called speculation. I often attempt to build a conceptual understanding to create a meeting of the minds. I am hoping to stimulate fresh discussions without criticizing of the limitation of existing ideas. If the machine is not broken don't fix until it is broken.

[insane_alien]

It is a sad day when good science is called speculation.

 

Are we reading the same thread?

[sunspot]

I am trying to offer a way to model the cell in terms of hydrogen bonding. I did not make up the fact that hydrogen bonding is the basis for the DNA double helix, template relationships, the secondary structure of protein, the translation of proteins, the usual properties of water, to name a few. Observation has also shown this is a dynamic variable as the DNA helix separates, new complexes are added, etc.. Why is focusing on this fundamental variable of life considered speculation?

 

Personally, selling my hydrogen bonding model of the cell to the highest bidder, would be better for me. But what happens to all the empirical dinosaurs when they are made obsolete? I am trying to give everyone a heads up first. Unfortuneately, the blind man's prophesy called statistics is clouding common sense.

[ecoli]

and what about all the process that H-bonding has NOTHING to do with? Are you just going to pretend that it doesn't exist?

[swansont]

Why is focusing on this fundamental variable of life considered speculation?

 

Because it so far lacks any testable aspects. You haven't made any specific predictions with it, of phenomena that are not already explained by standard science.