The cell in one variable, i.e., hydrogen bonding

[pioneer]

It is possible to model the cell in terms of one variable, i.e., hydrogen bonding. To make this possible, hydrogen bonding needs to be revised. To build some background for this revision, consider the two bases Cl- and OH-. Both have one extra negative charge, but OH- is a stronger base. The reason this is so, is that charge alone is not sufficient to explain relative basicity. One also needs to include the affect of the magnetic fields around the atoms to get the entire electromagnetic affect.

 

A magnetic field is generated by a charge in motion. Writing these anions, in the simple way above, does not give one a good feel for the fact that this extra negative charge or electron is moving about 1/14 the speed of light. At that speed it is giving off a magnetic field as it circulates within these anions. With the electomagnetic force, a unified force composed of both electo-static (charge) and magnetic (charge in motion) aspects, the relative basicity implies that although both give off the same electro-static forces, i.e., both have an extra electron, the Cl- is more stabilized because of its extra magnetic stability lowering the affect of the negative charge. Or its has a lower electromagnetic potential and therefore lower basicity.

 

This electromagnetic (EM) affect is the basis for electronegativity. Atoms with the highest electronegativity have better magnetic addition, which in turn, lowers the impact of the electro-static repulsion between electrons. When Cl- gains its extra electron the octet is full allowing extra magnetic addtion that allows the Cl to compensate for the extra charge.

 

That being said, let us look at the most important molecule of life, i.e., water. Because the O atom is more electronegative than H (offers much better magnetic addition), the water molecule will develop a slight dipole, with the O becoming negative and the H becoming positive. Although the charges are equal and opposite, the EM force fields coming from each side are not the same. The H carries more EM potential than the O. It has to, since O is more electonegative and stabilzed the extra charge.

 

An easier way to see this is consider the molecule HCl or hydrochloric acid. This molecule is a strong acid with a very weak conjugate base. That means that the H side has far more potential than the Cl side even though the dipole charge is equal and opposite. It is not the charge dipole that is causing this disparity in potential, but the magnetic addition.

 

With respect to H2O, a similar affect occurs due to the much higher electronegativity of the oxygen. The O has excellent magnetic addition which diminishes the EM potential of the slight negative charge. The H is left holding the primary burden of the potential since it has both positive charge exposed and has lost magnetic additon to the O. When a H bond forms, the H has more to gain than the O, or else O would not have taken the extra charge in the first place within the single H2O molecule. As such, when looking at H-bonds one only needs to consider how much residual potential is left in the H since it is the one carrying the burden.

 

A hydrogen bond will minimize potential if the H-bond is linear at a critical bond length. Any deviation away from this optimum will mean the hydrogen is carrying some residual potential. The reason this is so is that hydrogen bonds have partial covalent character. The straight bond angle of 180 degrees is needed to optimize magnetic addition. It is due to the magnetic force following the right hand rule of perpendicular affect. If the angle is off one can't get the magnetic fields to add perfectly. The result is that the H will retain some of its residual EM potential.

 

If you look at the average run of the mill enzyme, a large proportion of the H-bonds are not at 180 degrees. This stores H potential, which amount to electrophilic potential within the structure of the enzyme. One way the enzyme tries to lower this is to pull the reactant into an excited state in an attempt to feed electron density to the hungry H. This mechanism is very generic with enzymes developing lock-key specificity so the generic need of the H can lead to very specific results.

 

If we look at ice. The hydrogen bonds are all, more or less, formed in the perfect way with the vast majority at minimum potential. Even though the prefect ice crystal, as a system, is at minimum energy, because the O still has the highest electronegativity, the H are still not at their minimum potential. The ice is at minimum potential with respect to the system of H and O, and with respect to the hydrogen bonds, but the hydrogen still has potential.

 

As an analogy, picture two lionesses sharing a piece of meat. The stronger lioness will get more of the meat. The two lioness system will end up at minimum potential, even thought the stronger lioness will get more. As such, even though the system is at minimum potential, this does not mean the weaker lioness is as full as the dominant lioness. In this case, minimum system potential will still leave the weaker lioness hungry.

 

If H was the only atom in the universe, H2 would be closer to minimum potential relative to the EM needs of H. It is not competing with the highly electronegative oxygen but with a similar lioness that will share equally. The relatively low electronegativity of C, which is close to H, offers H the best way to reach a state of minimal potential. Again, I am not talking about system potential in our environment with the hungry O, but I am talking about, if the goal was to lower H potential to a minimum using the ideal system for the H. The sun, by helping to make reduce C or C-H, i.e, photosynthesis, essentially helps the H get about as low in potential as possible, inspite of the needs of the O system. The O wants to increase the H potential so it becomes part of H2O with much higher potential.

 

If we look at the H in cells, they have a wide range of potential relative to the ideal EM needs of H in its own perfect system. The perfect hydrogen bond is in the middle at minimum system potential but will leave the ideal H with some potential relative to the ideal. A free H+ is at the highest potential and will lower its potential as the hydrogen bond get more and more perfect in distance and angle. While reduce H, such as C-H ,is a state where the hydrogen drops below system potential to where it its own potential is much close to the ideal minimum. Unfortunately for H this creates a potential to be oxidized so hydrogen can carry the burden.

 

When modelling the cell in terms of one variable H, is it easier in one thinks in terms of needs or potential in H instead of the usual O. It makes things much easier to conceptualize and model. I am not suggesting converting all of chemistry to H normalization, only the life sciences.

[foodchain]

Breaking and forming bonds in an organism for say energy to do work is constant, thus you have find vacuoles in a cell for such a purpose, or issues like a proton gradient or an electron transport chain. ATP for instance in many cases is not to be reduced to simply say the energy currency but can be also thought of as an activator to other things that actually do work. As for your description of H, or using it really as the anchor to talk of other aspects of a cell or the chemistry in cell is off for a couple of reasons. One is that elements react, its not just everything reacting to hydrogen. Plus the cell is not just hydrogen nor uses just hydrogen. Its one of the reasons thermal energy can be used to denature say an enzyme is by basically destroying its structure and thusly for one reasons is activation sites, but they enzyme for instance can be much much more then simply a single elemental ion. You can find glands in an organism that are nothing more then a cell, which can be rather small, but for regarding a cell from the viewpoint of it being organized just around hydrogen, well I don’t really think you can do that. For just how you explain the natural behavior of say hydrogen, other elements also posses such, which then basically brings you to nothing more then a system with a structure, and function and or course an origin. I think you would be interested to look into the roles of say Ca2+ in the life sciences.

[John Cuthber]

What does this mean?

"It is possible to model the cell in terms of one variable, i.e., hydrogen bonding."

I suspect the answer is no because cells are really very complicated.

I also think that most of the species he has talked about like H2O, OH- Cl- and so on are non-magnetic. And, I think the idea of electrons in nice circular orbits at 1/14 C are a rather simplistic way to think about orbitals in atoms and molecules.

[pioneer]

I am not saying that H is the only reason for cellular activity. The more well established traditons of bio-chemistry plays its own role. But H is the organizing factor that integrates the cell. Empiricism is currently required because this organizing factor is not included as part of the analysis.

 

Let me present a bulk observation to show both affects working together. The most ATP energy intensive process of the cell is the pumping of ions, especially the Na-K pumps. In neurons, this reaches 90% of the cell's energy. It has to be of primary importance to be given so much energy. The affect is to set up a charge gradient across the exterior membrane of the cell, with the outside positive and the inside negative. At the level of water, this means the H of water will have more potential outside the membrane, due to the competitions with the exterior positive charge, and less potential inside the membrane, due to the helpful affect of the inside negative charge.

 

Relative to the outside H of water, this high potential H affect will conduct away from the cell into the exterior water, until it reaches steady-state H potential with the exterior environment. This implies an electrophilic potential gradient that is highest at the exterior of the cell and decays at some distance into the exterior water. This is the universal way for a cell to begin attracting food, which is high in electron density, at a distance, well before the transport proteins do their thing. The transport protein will cherry pick from this generic abundance of electron density. The reduced material also implies a source lowered potential H, that can help lower the outside H potential, even when electron-density is not very obvious.

 

If you look at a transport protein, its equilibrium position in the membrane will require that it set itself up to minimize its potential across the membrane. That is why the business end of the transport protein always ends up in the correct orientation. It is not random. It too is held together with hydrogen bonding and things that have an impact on the potential within all this hydrogen bonding. It offers a way to conduct H potential from the higher potential outside of the cell toward the lower potential inside. This occurs during transport. Both affects are occurring, i.e., chemical and H potential, at the same time with the H affect helping the more traditional chemical observation.

 

When something is transported, the cationic potential stored with the membrane is used as the source of energy. This means the outside of the membrane, near the transport protein, will temporarily become less positive since this potential is being used as transport energy. This little zone will be induced to lower H potential than the bulk exterior cell membrane during a transport cycle. The exterior surface of the membrane has a time average bulk postive charge that is superimposed with smaller islands of dynamically lowered H (charge) potential. The result is a very complex interference H signal being transmitted into the exterior water that is both generic for bulk food, but also semi-specific due to the H-bonding interference patterns in the exterior water from very specific types of protein affects. This does not discount the importance of the traditonal wisdom, it adds a prescreening tool that makes the traditional wisdom more affective-directed and much less emprical.

 

One may say that even if H potentials are occurring, these are small. How can very large affects occurs that require far more energy? The easiest observation are thunderstorms and lightning. With lightning, one is dealing with positive charge connected to H, creating amplifed affects. The hydrogen are small as individuals, but because they work as an integrated team they can display far more strength than expected. That is why ATP energy can break bonds an order of magnitude stronger. It uses the help of the hydrogen bonded protein structures. The energy of ATP is a little stronger than the best hydrogen bonds. That is not coincidence! It is just enough to get the integrated H-bonding to discharge affects. The energy level of ATP should have made this obvious decades ago.

[John Cuthber]

What does this mean?

"It is possible to model the cell in terms of one variable, i.e., hydrogen bonding."

[pioneer]

Yes it does. This type of model would be the base layer so help us see how the cell integrates in space and time. To be useful, these results would be tranlated to the existing science to give specific chemicals. But what it brings different to the table is the ability to exploit the nervous system for medical treatment. The nervous system implies memory based tissue throughout the body. This is near all the cells of the body, more or less. There is not enough chemical transmission from much of this local nervous tissue to exploit it with conventional wisdom. But at the level of hydrogen bonding we have a way to transmit affect.

 

If we look at the body and cells, three types of important tissues are everywhere, circulatory, lymphatic and nervous. The current state of the art does a good job with the circulatory and lymphatic via medicine. But the need for empiricm is because the third tissue is not exploited. This can be addressed with an H style analysis.

 

This is sci-fi at this time, but say the kidney was sick, we trace its nerve connections to the larger branches that connect to the spine. Based on kidney-nervous profiles of H-potentials that stem from opimum kidney function, we transmit these artifically into the nervous control system of the kidney and induce the kidney back to health. Since the H affect has a biochemical parallel, this may still require medicines to work and may act more like a way to increase their affectiveness in difficult situations.

 

That is way in the future. For now we need to crawl with the basics.

[John Cuthber]

If I ask the same question a 3rd time will you get the message and answer it?

 

What does this mean?

"It is possible to model the cell in terms of one variable, i.e., hydrogen bonding."

[pioneer]

Yes it is possible to model the cell in one variable, i.e., hydrogen bonding. About ten years ago I took a freshman level biology text book and translated it into the hydrogen bonding model. What I didn't have at that time was a good way to explain the nature of the hydrogen potential. But intuitively, I knew it was possible and decided to work under this assumption to see how far I could go. There were no limits.

 

I original called my variable hydrogen potential. But it was theorized as a physics variable, instead of something simple in chemistry. I extrapolated with this nebulous variable and figured I could close the physics with the help of others, once I got things rolling. I also did a lot of work modeling the brain in terms of H. In the end, I just could never figure out how to open a door for myself to turn the idea into a living. There is no review process for a new branch of science, especially one that covers the entire scope of living state, i..e, in potentia. Working from the outside, nobody knew me, or my abilities, and nobody wanted to learn. After my final, of many disappointments, due to the lack of imagination in science, I gave up and stopped trying.

 

About two years ago I decided to give my various theories one more try. I was approaching 50 and rather than chase young females, I decided to give the theories of my youth one more try. I had put everything on the back burner for 5-7 years and I had fresh eyes and began from square one. I was able to make a contact at the National Academy of Science in US and was asked to submit at paper based on my outline. I redefined DNA in terms of hydrogen potentials. I tried to limit my scope to one thing, which was hard for me, since the model was being treated in 3-D. It was not published since the format was expecting experimental data.

 

I finally realized I needed to be able to define my variable in a way, where I could not be given the bum's rush due to experimental protocol. It took many trials and reactions within science and physics forums to finally iron it out. Now the variable should be easy enough to see. Since I developed this independantly, and since noone had the vision to help, that gives me a future zillion dollar monopoly within this new life science, state of the art. I need partners who would not be upset about hard work for insane pay. I can see the big picture, but many others will be needed for the details and proofs. It is going to start out like Microsoft in a garage and built to an empire.

[insane_alien]

It was not published since the format was expecting experimental data.

 

says it all really.

[Paralith]

"It was not published since the format was expecting experimental data."

 

says it all really.

 

Let me see if I understand your situation, pioneer. You don't like theories etc based off of experimental/observational data - aka, what you disparagingly call "empiricism" - because that data by it's very nature is almost never exact, especially in the life sciences. So you have come up with a theory based on an armchair model involving hydrogen, that is supposed to revolutionize the way life science is understood, but that has never been tested experimentally because you don't like experimental data. And the life sciences community in general has insofar rejected your theory until it has been backed up by experimental data. Thus you started a thread talking about how this experimental "empiricism" is an inferior way of going about science.

 

Let me offer you a bit of advice, if I may be so bold. It's not very easy to change people's opinions about something if you approach them in the manner of: "Your opinion is inferior and wrong. My opinion is better and right and the only reason that I stand alone is that no one with a vision as great as mine has yet to come forward." Especially if you're talking about revolutionizing a huge branch of science. Life science as it is today depends on testing theories against empirical, experimental/observational data. Because biological systems are so complex and variable, usually this data results in percentages and correlations, but at least it usually leads us in the right direction if we carry out our experiments with good science. It's not as though all the biological knowledge gathered in the last several hundred years is completely useless because much of it was based on empirical observations. So if your theory is as illuminating as you say it is, then it should be able to explain/predict a lot of observable biological phenomena. And when you show that it does, people WILL sit up and pay attention. And once you show the merit of your theory in a way that is understood by the science minds of today, then those people will begin to change if change is in fact what is best. After all, the National Academy of Science was clearly interested in your theory if they asked for a paper about it, but they know that experimental data is required if they want the papers they publish to be taken seriously by the scientists who read them.

[insane_alien]

okay, now that i have managed to get a few hours sleep, i'll make a meaningful response.

 

you have this idea. you claim it is revolutionary and will change the way science works etc. etc. etc. yada yada yada... but you have no actual evidence that it works in real life and are somehow surprised when people don't immediately go 'oh wow you theory is so brilliant! here have a nobel prize and that girl over there wants to sleep with you because your so smart!'

 

you haven't seen much of what most of us call reality have you?

 

i mean, if i came to you and said i have a revolutionary theory that explains everything its that everything is done by tiny invisible fairies but i don't trust experiments so i have no proof. what would you say to me?

 

if its not along the lines of '**** off you ****ing looney' then there is something wrong with the way you view science.

 

do you think that the theories that exist today would be classed as theories if they didn't have a small mountain of experimentation and observations to back up the initial hypothesis, and thats all you have: a hypothesis.

 

come back once you have done some experiments, posted to a peer review journal and got someone to confirm your results.

[pioneer]

I agree that experiment proof would make it easier for others to see. I have no problem with that. But I am in a catch-22 situation of no resources to create the data until I present data which needs resources to generate. The work around this guard dog of science is to use the highest form of science which is based on logic and rational arguments.

 

If you go back to my first post of this discussion, which discussed the basis for hydrogen potential, and how it carries the burden of potential, an experiment would be nice. It could help define relative potential in a range of situations. But it is not essential to be able to rationally extrapolate from there in a qualitative way. That is the strength of this analysis. One can do more science with less resources. Maybe the mistake some are making is assuming this is the same as the current empirical nature of the life sciences, which needs a a bunch of statistical experiments to be able to say anything with certainty.

 

The analogy that we have is, I have developed the equations needed to define projectile motion in a world where only experiments are assumed to be able to predict the place where the projectile is going to land. Before the experiment I know where it is going to go, in a world where that is considered impossible until the arrow lands. A cheap way to prove the analysis this would be to get me on a team that is already doing some type of experiment and I will predict results. I will use reason to tell them what will happen in their experiment before they do the experiement. Ijust need to get up to steam so I can understand what they need.

 

Enough soap box let's talk about an advanced application. If you look at the DNA it forms a double helix, which is held together with H-bonds. There are only two base pairs, one has three H-bonds and the other two. The basic section of the DNA is called a gene, with spacer zones between each of the genes so these genetic memories are separated.

 

With the hydrogen model we can now address features of the H-coding within the DNA. It is not a binary code like a computer that will always use an on-off switches between two states. Instead it is code that uses 2 or 3 hydrogen for a more complex signal. There is an on-off feature when the DNA double helix separates for transcription. But there is also a variable feature, that allows the gene to give off a signal that is more dependant on its environment. For example, packing proteins add more positive charge to the DNA, which is how they bind, changing the potential defined by the variable switches at the level of the H. It is the same gene but in variable H-states depending on its environment.

 

The DNA is even fancier than that. If you look closely, the hydrogen bonding within the base pairs of the double helix have extra H nearby that can also form a hydrogen bond. But there is only room for one h-bond in places where there are two possible H. The result is another aspect of the H signal, where either H can be on or off or both can be partially on. It allows for another variable signal feature at each H-bond.

 

There is one additional feature that requires going out on the limb. This would definately require experiments to prove if it occurs or not. Here is the theory, the DNA double helix is able to conduct H potential down its length sort of like electricity going through a wire. It is not H current but an energy signal at the level of H potential. There are aspects of the DNA that stay packed all the time. This is the highest potential pole of DNA's H-gradient that transmits current signals down the active gradient.

 

When genes are undergoing transcription these are gaps in the circuit. The genes have their own start-stop hydrogen bonding, with the start and stop defining the base current signal within the gene. There is also bulk current due to the gradient between levels of packing down to transcription gaps. The DNA constantly makes itself known with a complex H profile.The DNA is a elaborate hard-drive that can be pertubated by the rest of the cell and vice versa.

 

We would have to bring in the physicists and mathematicians in to model even the DNA with H-potential accuracy. It sounds very complex but there is way to simplify the hierarchy to make it easier to begin. I ready to rock-n roll, but I am a little awkward at the waltz. That was a long time ago. I have to think back.

[Skye]

It is possible to model the cell in terms of one variable, i.e., hydrogen bonding.

Explain carbon monoxide poisoning.

[John Cuthber]

Never mind CO poisoning.

Explain what you mean by "It is possible to model the cell in terms of one variable, i.e., hydrogen bonding. "

Trust me, the lack of experimental data isn't the real issue here as far as I can see; it's the fact that you don't seem able to explain what you are on about.

[foodchain]

Never mind CO poisoning.

Explain what you mean by "It is possible to model the cell in terms of one variable, i.e., hydrogen bonding. "

Trust me, the lack of experimental data isn't the real issue here as far as I can see; it's the fact that you don't seem able to explain what you are on about.

 

 

I think he is trying to talk about the behavior of say hydrogen in regards to cellular function, or using hydrogen as a basis of cellular function. Such as how you would use DNA as a basis of explaining life for example.

[Paralith]

I think he is trying to talk about the behavior of say hydrogen in regards to cellular function, or using hydrogen as a basis of cellular function. Such as how you would use DNA as a basis of explaining life for example.

 

He's trying to make a theoretical model to completely explain and predict everything that happens in a cell without having to actually go and observe that cell. Which is a mighty tall order.

[Bluenoise]

Why is it that every year or so someone comes onto these forums who is convinced that everything can be explained by hydrogen bonding?

I swear this is the third time I've seen something like this proposed.

 

My question is: What is it about hydrogen bonding that elicits these wild ideas?

[foodchain]

Why is it that every year or so someone comes onto these forums who is convinced that everything can be explained by hydrogen bonding?

I swear this is the third time I've seen something like this proposed.

 

My question is: What is it about hydrogen bonding that elicits these wild ideas?

 

 

I have not been around that long so this is my first time seeing such:D

 

I have not idea why people get onto hydrogen in the way you purpose, maybe because we have so much of it as a constitute of our structure, but even then its not just floating about freely. My overall best guess comes down to a perceptual issue. You have people educated as chemists, then biologists educated as biologists working the chemistry of life issue, the same with physics. I read the wiki link on biophysics, and it seems that crossing over to various fields, all of which in the natural sciences study basically nature, but there seems to be some kind of a wall people cant breech, they can only view the objects from there scholarly training. Lastly the chemistry of life has to work, but even in microbes the use of protons to generate movement of a flagella is not typically either physics or chemistry, but some grey area that’s basically nature in action.

[pioneer]

The idea of modelling the cell in terms of H-bonds is not something I came up with out of the blue. When I was taken O-Chem as part of my ChemE curriculum, the text book we used was Morrison and Boyd. My specialty was polymers. In a brief few chapters on bio-polymers, the author stressed that work was needed on the affect of H-bonds on bio-polymers. That was in spring of 1976.

 

In polymers, the unique poperties of plastics are often due to small secondary forces. For example, teflon is just weak F interactions. This gives it it non-stick properties. So, I could see how H-bonds should have an impact on the bulk properties of bio-polymers like DNA. But, at that time, I had never taken any biology. I was more practical minded and didn't like memorizing all the $10 latin words, so I avoid it. I was not allowed to skip biology and go right into bio-chemistry, so I stopped. It wasn't until another 6-7 years, that the idea was resurrected again.

 

I was now a development engineer. One of my projects was to see if it is possible to do an anaerobic denitrification in open waste acid ponds, as a cheap way to clean up acids ponds common the nuke trades. I was still stupid when it came to biology and bacteria. But I had creative ingenuity. The experts in the field said, it was impossible. The consultants were nice and all but they knew how hard it was to control bacteria even with tight standards. Little blips could make the bio-reactors shut down. I was asked to do it where there was very little control over variables, in open ponds subject to weather, leaching, they had almost the entire periodic table of the elements due to decades of R&D, nitrates that were 10-100 times what were considered optimized in the bio-reactors, etc., Because I was stupid in biology, I was also ignorant of what couldn't be done. My job was to make it work. As it turned out, I not only had a green thumb but a slimey thumb for bacteria and the impossible became the new way.

 

This gave me a sense of confidence that traditional wisdom has room for improvement. It also required that I learn something about biology for presentations. After the success of the project, it started to make me think about the H-bond model again. About a years or so later I began one my first passes through single and multicellular situations. At that time, my biology knowledge was disjointed, so I made use of idiot biology, i.e., the thing-a-ma-jig has an extra OH group compared to the widget. It was more geared toward figuring out how to connect things at the chemical level via H-potentials. I could see in terms of chemical structure, but the bio-lingo just wouldn't stick.

 

It was almost ten years later that I decided I needed to bite the bullet and learn bio-lingo and see if my basic theory could work within established biology, at least at a freshman level textbook. It worked fine with me able to translated the book and explain unexplained things, at the time, like how the parts of the Na-K pumps find each other. The problem was my physics treatment of the base variable needed an elaborate research study to help me define the basic variable. I figured a few hundren applications would make the base research a viable thing. But it was hard to find an audience due to my overlapping branches of science. The applications meant nothing to the physicists and the physics meants nothing to the biologist. The biologist is more by the book so even the applications seemed to go over poorly, without experimental proof.

 

This last pass, about 6-7 years later, was connected to trying to establish the variable without needing any physical resources other than using the well established principles of physical-chem. I was good at P-chem. But now I have forgotten much of the biology lingo. I see the structures and can can see the connections to the H-bonding and can extrapolate. I need help making sure my next and final translation is by the biology book.

 

Explain carbon monoxide poisoning.

 

Carbonoxide is not a poison per se. What it does is absorb oxygen to form carbon dioxide, which in the cell becomes bi-carbonate. You have two affects going on, the first reduces the metabolic oxidation potential by capturing O2 that should be the terminal electron acceptor. The cell has to go into an anaerobic mode so it can continue to make energy. But it can't do that for too long compared to having more O2 to drive the metabolism.

 

Secondly, bi-carbonate is HCO3-. Normally the waste products of metabolism should be CO2 and H2O which equals H2CO3 if there is plenty of O2. The H2CO3 becomes HCO3- which theoretically gives off an H. But with CO and O2, the result is also HCO3-, but now it needs to gain an H. This loss of the H from the local water, will mess things up at the level of hydrogen potential. This is more connected to the so-called poison affect of CO.

 

I am not a biologist and I am sure there are enzymatic things also going on. But with the H-analysis, I would assume gradients. The loss of H can change an entire H gradient potential within a range of proteins causing affects that could even be a little more distant than one might expect. The future hope of the H-model is to see how far the affect goes so we can predict which proteins lose efficiency. What that does is give the research team valuable insight to help narrow a search. We will still need both teams, the H-team to narrow the search and the other team to get into the trenches, like they do now, but the latter will have more certainty up front.

 

I think he is trying to talk about the behavior of say hydrogen in regards to cellular function, or using hydrogen as a basis of cellular function. Such as how you would use DNA as a basis of explaining life for example.

 

This is essentially what I am saying. Picture this, instead of worrying about H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., we model all of these only in terms of the final H potential states all these induce. Now we only have one variable to worry about, that has a range of possible potentials. This gives us sort of the ghost (for the lack of a better term) of life. We model the ghost. Since we modeled H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., in terms of H, when we pertubate the ghost system with H, we should eventually be able to back translate to H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., and the use that to predict the particular molecule that implies the H pertubation needed to create an affect. The bio-team gets into the trenches and tries the prediction helping to tweak both systems.

[insane_alien]

I have not been around that long so this is my first time seeing such:D

 

heh, this isn't the worst of it(this might have been on a different forum but i'm pretty sure it was this one) there was this one guy that came on trying to tell everybody that everything was made of hydrogen atoms. not as a product of the fusion of hydrogen atoms but chemical bonding of hydrogen atoms. passed of helium as H2 as well as molecular hydrogen.

 

he also didn't believe in the neutron, or quarks. oh yeah, and there is no such thing as electromagnetism as it is all accounted for by hydrogen pushing other molecules ofhydrogen in the right direction.

 

he also had some issues with einstein being 'the great hydrogen suppressor' apparently einstein is alive and well and raiding his house on a weekly basis to prevent his 'god like theory' from reaching the public. that would be something to see. old albert barging through his house and burning everything.

 

there seems to be a fixation on hydrogen. it can probably be explained but i doubt its hydrogen bonding.

[foodchain]

heh, this isn't the worst of it(this might have been on a different forum but i'm pretty sure it was this one) there was this one guy that came on trying to tell everybody that everything was made of hydrogen atoms. not as a product of the fusion of hydrogen atoms but chemical bonding of hydrogen atoms. passed of helium as H2 as well as molecular hydrogen.

 

he also didn't believe in the neutron, or quarks. oh yeah, and there is no such thing as electromagnetism as it is all accounted for by hydrogen pushing other molecules ofhydrogen in the right direction.

 

he also had some issues with einstein being 'the great hydrogen suppressor' apparently einstein is alive and well and raiding his house on a weekly basis to prevent his 'god like theory' from reaching the public. that would be something to see. old albert barging through his house and burning everything.

 

there seems to be a fixation on hydrogen. it can probably be explained but i doubt its hydrogen bonding.

 

If that thread is still around or if you have a link to such I would die to see it.

 

The idea of modelling the cell in terms of H-bonds is not something I came up with out of the blue. When I was taken O-Chem as part of my ChemE curriculum, the text book we used was Morrison and Boyd. My specialty was polymers. In a brief few chapters on bio-polymers, the author stressed that work was needed on the affect of H-bonds on bio-polymers. That was in spring of 1976.

 

In polymers, the unique poperties of plastics are often due to small secondary forces. For example, teflon is just weak F interactions. This gives it it non-stick properties. So, I could see how H-bonds should have an impact on the bulk properties of bio-polymers like DNA. But, at that time, I had never taken any biology. I was more practical minded and didn't like memorizing all the $10 latin words, so I avoid it. I was not allowed to skip biology and go right into bio-chemistry, so I stopped. It wasn't until another 6-7 years, that the idea was resurrected again.

 

I was now a development engineer. One of my projects was to see if it is possible to do an anaerobic denitrification in open waste acid ponds, as a cheap way to clean up acids ponds common the nuke trades. I was still stupid when it came to biology and bacteria. But I had creative ingenuity. The experts in the field said, it was impossible. The consultants were nice and all but they knew how hard it was to control bacteria even with tight standards. Little blips could make the bio-reactors shut down. I was asked to do it where there was very little control over variables, in open ponds subject to weather, leaching, they had almost the entire periodic table of the elements due to decades of R&D, nitrates that were 10-100 times what were considered optimized in the bio-reactors, etc., Because I was stupid in biology, I was also ignorant of what couldn't be done. My job was to make it work. As it turned out, I not only had a green thumb but a slimey thumb for bacteria and the impossible became the new way.

 

This gave me a sense of confidence that traditional wisdom has room for improvement. It also required that I learn something about biology for presentations. After the success of the project, it started to make me think about the H-bond model again. About a years or so later I began one my first passes through single and multicellular situations. At that time, my biology knowledge was disjointed, so I made use of idiot biology, i.e., the thing-a-ma-jig has an extra OH group compared to the widget. It was more geared toward figuring out how to connect things at the chemical level via H-potentials. I could see in terms of chemical structure, but the bio-lingo just wouldn't stick.

 

It was almost ten years later that I decided I needed to bite the bullet and learn bio-lingo and see if my basic theory could work within established biology, at least at a freshman level textbook. It worked fine with me able to translated the book and explain unexplained things, at the time, like how the parts of the Na-K pumps find each other. The problem was my physics treatment of the base variable needed an elaborate research study to help me define the basic variable. I figured a few hundren applications would make the base research a viable thing. But it was hard to find an audience due to my overlapping branches of science. The applications meant nothing to the physicists and the physics meants nothing to the biologist. The biologist is more by the book so even the applications seemed to go over poorly, without experimental proof.

 

This last pass, about 6-7 years later, was connected to trying to establish the variable without needing any physical resources other than using the well established principles of physical-chem. I was good at P-chem. But now I have forgotten much of the biology lingo. I see the structures and can can see the connections to the H-bonding and can extrapolate. I need help making sure my next and final translation is by the biology book.

 

 

 

Carbonoxide is not a poison per se. What it does is absorb oxygen to form carbon dioxide, which in the cell becomes bi-carbonate. You have two affects going on, the first reduces the metabolic oxidation potential by capturing O2 that should be the terminal electron acceptor. The cell has to go into an anaerobic mode so it can continue to make energy. But it can't do that for too long compared to having more O2 to drive the metabolism.

 

Secondly, bi-carbonate is HCO3-. Normally the waste products of metabolism should be CO2 and H2O which equals H2CO3 if there is plenty of O2. The H2CO3 becomes HCO3- which theoretically gives off an H. But with CO and O2, the result is also HCO3-, but now it needs to gain an H. This loss of the H from the local water, will mess things up at the level of hydrogen potential. This is more connected to the so-called poison affect of CO.

 

I am not a biologist and I am sure there are enzymatic things also going on. But with the H-analysis, I would assume gradients. The loss of H can change an entire H gradient potential within a range of proteins causing affects that could even be a little more distant than one might expect. The future hope of the H-model is to see how far the affect goes so we can predict which proteins lose efficiency. What that does is give the research team valuable insight to help narrow a search. We will still need both teams, the H-team to narrow the search and the other team to get into the trenches, like they do now, but the latter will have more certainty up front.

 

 

 

This is essentially what I am saying. Picture this, instead of worrying about H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., we model all of these only in terms of the final H potential states all these induce. Now we only have one variable to worry about, that has a range of possible potentials. This gives us sort of the ghost (for the lack of a better term) of life. We model the ghost. Since we modeled H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., in terms of H, when we pertubate the ghost system with H, we should eventually be able to back translate to H, C,O, N, Na, K, Ca, Mg, P, S, Fe, Cu, etc., and the use that to predict the particular molecule that implies the H pertubation needed to create an affect. The bio-team gets into the trenches and tries the prediction helping to tweak both systems.

 

 

I get where you are going with some aspects, like the overall lack of interdisciplinary fields within the natural sciences basically, such as an environmental biochemist for example. On the biology lingo though, yes biology practically has its own language, but on the more basic premise of it the B.S level of biology really is to introduce to the field as a whole, and then from this massive field of fields you typically will specialize. Also, if you study the lingo for a little bit, say just read about stuff related to such for about an hour a day, you will start to find patterns and stuff will start to look easier really. Such as having four limbs, in biology you might get the term tetrapod tossed at you instead, but there is usually a reason for such which goes back into a working theory and so on.

[pioneer]

heh, this isn't the worst of it(this might have been on a different forum but i'm pretty sure it was this one) there was this one guy that came on trying to tell everybody that everything was made of hydrogen atoms. not as a product of the fusion of hydrogen atoms but chemical bonding of hydrogen atoms. passed of helium as H2 as well as molecular hydrogen.

 

he also didn't believe in the neutron, or quarks. oh yeah, and there is no such thing as electromagnetism as it is all accounted for by hydrogen pushing other molecules ofhydrogen in the right direction.

 

he also had some issues with einstein being 'the great hydrogen suppressor' apparently einstein is alive and well and raiding his house on a weekly basis to prevent his 'god like theory' from reaching the public. that would be something to see. old albert barging through his house and burning everything.

 

there seems to be a fixation on hydrogen. it can probably be explained but i doubt its hydrogen bonding.

 

There is a difference between nuke states and chemical states. But if you think about, it how does an nuclear proton different from a H-proton? The only difference might be a little mass due to the mass burn. In that case, the nuclear proton is only a lower potential state of an H-proton. So he are not talking about apples and oranges but red apples and yellow ones.

 

 

 

 

The life sciences are observational and empirical. The observational took and takes a lot of hard effort to iron down something. Each little thing is treated as it own little special thing, each being given a power word. One can see something and identify it even if one doesn't know what it does at first. This becomes the seed of future investigations. From all these things one begins to see patterns and how they relate.

 

What I have tried to do is reduce dozens if not hundreds of patterns down to just one basic pattern, which is common to all the patterns. Maybe my brain fart is connected to not wishing to fill my memory with too much data to where I lose track of the forest because of all the trees. There are thousands of people already doing that. I prefer to look at the forest as a whole and work downward toward the largest bulk patterns. There are not many trying to do that. This is where extra helpers are needed

 

If you were in the woods, you can see the bark on the trees and the small differences between two trees of the same speciies. But from that perpective the only patterns you can see are those right in front of you. But looking at the forest from a satelite view, one can see bulk patterns that may not be very obvious to someone who is bush wacking. I may see a wedge of similar trees of about the same color. The specialist can help me by telling me, what you see is actually three types of trees. Thanks, I now know what I need to do to be consistent with you. The specialist may say, really, these trees go all the way to the river. Thanks, that changes the center of where we thought these three tree types originated.

[Bluenoise]

Now pioneer your view is definitely much better founded than those threads that follow. Though I still don't exactly agree/believe your view...

 

But maybe after this you'll understand why we're so skeptical.

http://www.scienceforums.net/forum/showthread.php?t=20734&highlight=hydrogen+bonds

http://www.scienceforums.net/forum/showthread.php?t=19209&highlight=hydrogen+bonds

http://www.scienceforums.net/forum/showthread.php?t=19472&highlight=hydrogen+bonds

 

I guess sunspot was the one I was thinking of.

[Skye]

Carbonoxide is not a poison per se. What it does is absorb oxygen to form carbon dioxide, which in the cell becomes bi-carbonate. You have two affects going on, the first reduces the metabolic oxidation potential by capturing O2 that should be the terminal electron acceptor. The cell has to go into an anaerobic mode so it can continue to make energy. But it can't do that for too long compared to having more O2 to drive the metabolism.

 

Secondly, bi-carbonate is HCO3-. Normally the waste products of metabolism should be CO2 and H2O which equals H2CO3 if there is plenty of O2. The H2CO3 becomes HCO3- which theoretically gives off an H. But with CO and O2, the result is also HCO3-, but now it needs to gain an H. This loss of the H from the local water, will mess things up at the level of hydrogen potential. This is more connected to the so-called poison affect of CO.

 

I am not a biologist and I am sure there are enzymatic things also going on. But with the H-analysis, I would assume gradients. The loss of H can change an entire H gradient potential within a range of proteins causing affects that could even be a little more distant than one might expect. The future hope of the H-model is to see how far the affect goes so we can predict which proteins lose efficiency. What that does is give the research team valuable insight to help narrow a search. We will still need both teams, the H-team to narrow the search and the other team to get into the trenches, like they do now, but the latter will have more certainty up front.

Carbon monoxide is a poison, poison is a fairly broadly defined term and CO definitely fits in it. CO binds very strongly to transition metals to form complexes. By doing so it makes certain enzymes where the transition metal is the active site inactive, since they are now bound to the Co rather doing what they normally do. This includes things like heme, which transports oxygen around the body. The effect is independent of H-bonding. It would also occur at reasonably low concentrations, not like the effect on H like you present (due to the amount of buffering of bicarb in cells).

[lucaspa]

It is possible to model the cell in terms of one variable, i.e., hydrogen bonding. To make this possible, hydrogen bonding needs to be revised.

 

LOL! So, no, it is NOT possible to model the cell in terms of hydrogen bonding, because you have to change hydrogen bonding to something else.

 

I suggest you write your idea up and send it to Bioessays or Journal of Biological Chemistry and see if it can get past peer review.

 

If you would like a taste of what the reviewers are likely to say, I am a biochemist and can give you some general comments -- all I can since your "modeling" doesn't really do anything in this post.

 

To build some background for this revision, consider the two bases Cl- and OH-. Both have one extra negative charge, but OH- is a stronger base.

 

Please tell us how you measured the "strength" of Cl- and OH- as a "base".

 

I would think that Cl- is a stronger "base", since it will give off an H+ ion a lot better than HOH does.

 

That being said, let us look at the most important molecule of life, i.e., water. Because the O atom is more electronegative than H (offers much better magnetic addition), the water molecule will develop a slight dipole, with the O becoming negative and the H becoming positive. Although the charges are equal and opposite, the EM force fields coming from each side are not the same. The H carries more EM potential than the O. It has to, since O is more electonegative and stabilzed the extra charge.

 

The same happens in HCl, only more so. In HCl the H has a much larger partial positive charge than HOH.

 

An easier way to see this is consider the molecule HCl or hydrochloric acid. This molecule is a strong acid with a very weak conjugate base.

 

I would say that this makes Cl- a stronger base, not a weak one.

 

Basically, you are reinventing the wheel here in biochemistry, since polarity of water has long been known. See the first chapter in Lehninger's Biochemistry; it is devoted to the importance of polar water for life. All you have done is add some mumbo-jumbo about EM fields that are totally unnecessary to explain the polarity. It is well explained simply be noting that the electrons in the covalent bond spend more time around O or Cl than around H.

 

When a H bond forms, the H has more to gain than the O, or else O would not have taken the extra charge in the first place within the single H2O molecule. As such, when looking at H-bonds one only needs to consider how much residual potential is left in the H since it is the one carrying the burden.

 

Hydrogen bonding is well known. It is about 7 kcal/mole. Very weak. But useful. THe complementarity of bases in DNA is maintained by hydrogen bonding.

 

If you look at the average run of the mill enzyme, a large proportion of the H-bonds are not at 180 degrees.

 

Document this, please. Cite papers where this has been demonstrated. How many amino acids can develop hydrogen bonding? Do you know?

 

One way the enzyme tries to lower this is to pull the reactant into an excited state in an attempt to feed electron density to the hungry H.

 

No, it doesn't. You need to read some basic biochemistry since the chemical mechanisms for enzymes acting as catalysts are well known.

 

You seem to be ignoring proteins that are not enzymes.

 

This mechanism is very generic with enzymes developing lock-key specificity so the generic need of the H can lead to very specific results.

 

The relatively low electronegativity of C, which is close to H, offers H the best way to reach a state of minimal potential.

 

Again, the electronegativity of C is not that close to H. C is very close to O in the periodic table. You need to look at electron orbitals, not "electronegativity".

 

The sun, by helping to make reduce C or C-H, i.e, photosynthesis, essentially helps the H get about as low in potential as possible, inspite of the needs of the O system.

 

That isn't really what photosynthesis does. You forget the C-C and C-O bonds that have nothing to do with C-H bonds.

 

The O wants to increase the H potential so it becomes part of H2O with much higher potential.

 

There's way too much teleology here and way too little chemistry.