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Everything posted by sunspot

  1. I keep writing with the hopes that others can benefit by what will become the newest frontier in the life sciences. It should really speed up progress in medicine, since we should be able to target using equilibrium designs. The virus already does this. Its protein shell says one equilibrium state to help sneak into and out of the cell. When it sheds its skins, it is able to define another equilibrium zone close to the DNA. The cell gradient, as a whole, has its maximum potential between the inside of the cell membrane (negative) and the packed aspects of the DNA. The nuclear membrane acts as a buffer that breaks this primary internal gradient into two compartments. We already discuss the basics within the nucleus. From the nuclear membrane to the cell membrane, there are actually two overlapping gradients of parallel potential within the primary gradient. One aspect begins at the DNA and extends to the cell membrane. The second aspect starts at the cell membrane and extends to the nuclear membrane. The observed cell hierarchy of RNA/protein biosynthesis activity, starting at the DNA lines up with a decreasing hydrogen potential. From the DNA, to the rough ER, to the smooth ER, to the Golgi apparatus and then to the cell membrane reflects an ever lowering of structural hydrogen potential. There are also lateral branchings as proteins assume their equilibrium positions within the gradient. One interesting tidbit is the base uracil on RNA. It has a lower surface tension induction than the thymine of DNA. This lower aqueous hydrogen potential induction allows larger proteins to form on the ribosomes than if the RNA contained thymine. The thymine would increase the local water potential near the mRNA and ribosomes, and would decrease how much hydrogen potential the proteins could define before the entire translation complex reaches nonequilbrium. Smaller proteins would be one result. The other aspect of the gradient begins at the cell membrane with the protein flux from the DNA down gradient helping to populate it. The gradient from the cell membrane is actually two-fold. One aspect goes from inside to outside the cell membrane The second go from inside the cell membrane to the nuclear membrane. There is a high hydrogen potential difference between the inside and outside of the cell membrane, with the outside being at the higher hydrogen potential due to its positive charge. The parallel between high surface tension and high aqueous hydrogen potential allows external organics to form an equilibirun on the outer membrane surface. The aqueous signal from the external membrane surface is sort of a tracker beam for the organics to follow so they can reach this better equilibrium zone. The bulk exterior water, is also trying to lower its global potential, pushing organics toward the cell.
  2. Like any toy, it helps to build the imagination. These may also help one project their inner selves into the toy, bringing things to consciousness. Knolwledge of psychology could be useful. But even this can make one a closed loop, that makes it harder to deal with reality. The scientist working quietly in the lab plays with his toys and attempts to create new ideas and technology. The scientist needs to colaborate with others to add a dose of reality data to the loop. On the other hand, just living in sensory reality deprives one of the inner world of the imagination. Such people may actually benefit by a toy that stimulates the imagination so they can add inner data to the external data.
  3. At one time I had a good grasp of psychology. But the modern science equivilent of religion appeared to be suffering from a multiple personality disorder or scientific polytheism. Why are there so many opinions on even simple things like motivation. That is when I decided to go it alone. My standard data base of ideas has atrophied but my understanding is better than it was. What I called sensory expectation is more than the way we act on our instincts. It is also connected to how one percieves reality. One will use their sensors to reinforce this perception of reality. If one is a bigot, they will be able to see examples all around them. But their expectation will cause them to ignor, either consciously or unconsciously data that they do not expect to see (does not satisfy their expectation). Someone with a counter perception will ignor the bigot's data and only see what they perceieve to be reality. Reality is in the middle somewhere. If one takes a middle position to include all the data, very often neither side is able to see it, because their expectation needs one-sided data. Science is not immune. If we look at physics. The universe started as a big bang of the primordial atom, mass transfer from another dimension, matter giesers from black holes/white holes, from a primal energy field, out of the vacuum of space, etc.. These are all mutually exclusive, yet each camp can see data to support their position. Even if one is correct, I gave four other examples of science illusions that are considered reality due to using limted data that reinforces their belief. One would think that psycholgy woulld be advanced enough to step in and say, "hold your horses", your turning science into disney world. But psychology can't because they are doing the same thing. The relativity of behavior bias is the problem. We have all these architechs building sand castles. If one tries to point that out, only that person is out of touch with reality. If I was to guess it is due to psychology trying to replace religion. It took and is taken a polarized position. Religion teaches absolutes so psychology has to take the relative position. Religion taught divine design so psycholgy has to teach random occurance. The truth is probably in the middle. This current state of affairs was predicted by art in the 1950's. This work of art is called relativity. Each point of view appears valid but itself but all together they create many mutually exclusive references.
  4. If we look in nature usually the male is the more colorful or decorated of a species. But for humans, the female is more colorful and decorative. Both are connected to sexual attraction phenomena. Does anyone have an ideas of why the colorful lure switches for humans? It appears to show a cross sexual part of the brain being used for human animal sexuality.
  5. Here is a good link about AIDS progression in the US. http://www.thebody.com/asp/june01/lazarus.html
  6. Very little theoretical physics has any solid evidence. If we took only one or two data points to explain any phenomena on earth, it would be considered bull. But if one does that in space or subspace, it is considered proof. One finds a tiny particle anomaly and that is proof of other dimensions. One can't find strings but that means they are everywhere. Quarks are only found in the lab and hardly exist, so that means they are also everywhere. The CMB is microwaves. Atoms and molecules coming off stars will give off heat and microwaves in all direction too. Maybe CMB has nothing to do with the beginning of the universe. Excuse me, I forgot, physics only needs a couple of data point to prove anything.
  7. I might be projecting human traits into animals, but I chose dogs because some are quite ingenious. Scent tracking dogs can be given a scent to smell and will sniff around to find that scent, ignorring other interesting smells along the way that should trigger food tracking. They may go miles before smelling what they are looking for, ignorring instinctive triggers. The sensory systems are usually considered feedforward, like your example of the fox tracking anything that smells good enough to eat. What I call sensory expectation is an instinctive use of the sensors to make reality coordinate with sensory expectation. The architech has an image in his or her mind of a new building. Reality is shaped until the visual reality takes the form of the visual expectation. In this case the sensory systems are used for both feedback and feedforward. I do not mean to be long winded but to continue this analogy. Some architechs may design a building that is much more form than function and it may not be possbile to build this building using the existing principles of engineering and materials. Other building designs may stay within these parameters, but at the perimeter, and may still be limited by possible geology and weather considerations. While other designs can meet all these parameters. The way I look at it, we are architechs of our own sensory expectations. In everyday life we design our instinctive drives using various behaviors. One also designs the sensory expecation of the sensory systems to reinforce our beliefs and desires. If one believed that the world is flat one could find visual data that appears to reinforce this sensory expectation. The green zone of instincts are behavior designs that can meet all the natural parameters associated with our biochemistry. One can also live in the yellow zone at the margin whats physically possible, with unforseen events causing the structures to fall. Others can live in the red zone of behavioral design that exceed the limits of our body's engineering and material properties. The buffer zone map was an attempt to help people understand how various types of behavioral design relate to the body's practical parameters. There is a buffer but there is also a bulls eye. The sensory expectation within some branches of psychology appears to be relative behavior. This is what many people desire to see and some branches of psychology are helping to create this fanatasy world beyond the practical reality of our instincts.
  8. The extra hydrogen bonding hydrogen, within the base pairing of DNA, and the extra hydrogen bonding hydrogen of the DNA packing proteins, induce DNA packing structures to define the highest hydrogen potential, with more DNA packing meaning more hydrogen potential. The observed methylation of packed DNA is a simple reflection of packing equilibrium since the extra methyl groups add more surface tension to the DNA to reflected the higher hydrogen potential implicit of packing. What the relationship between packing and hydrogen potential implies is that the doubled condensed chromosomes are the highest hydrogen potential structures of the cell. After the doubled chromosomes condense, the nuclear membrane will disappear. This is a well documented observation. This observation is due, in part, to a surface tension affect that is created by the condensed chromosomes. The nuclear membrane is induced into nonequilibrium and needs to define a new equilibrium shape and position because of the aqueous hydrogen potential induction cause by this highly packed DNA. I not going to get into a detailed discussion of how all the observations of mitosis reflects a systematic lowering of the packing potential within the double packed DNA. Essentially, the ATP that runs the spindle focuses a lot of countering negative charge and low aqueous potential near the DNA. The result is a lower hydrogen potential DNA configuration implicit of two sets of separated condensed chromosomes. As each set of chromosomes continue to lower their hydrogen potential by unpacking further, the nuclear membrane will eventually reform around the DNA, due to a much more favorable aqueous equilibrium. The aspects of the DNA that remain packed, such as the centromere, will define the highest hydrogen potential structures within the nucleus of a nondividing cell and will create a hydrogen potential gradient with the lower hydrogen potential nuclear membrane. The rest of the structures within the nucleus will assume equilibrium positions within this dynamic nucleus gradient. It is not cooincidental that the active (unpacked genes) are often found near the nuclear membrane. These define a relatively low potential, due to lack of packing proteins. This state of the DNA is induced, in part, by the aqueous channels within the nuclear membrane. The lower hydrogen potential cytoplasm (due to the negatively charged inside of the cell membrane) sends global and specific aqueous hydrogen potential signals into the nuclear membrane. This lowers the potential of the DNA causing aspects to unpack and migrate toward the nuclear membrane. The unpacking of the DNA is resisted by the higher potential of the packed aspects of the DNA. These two countering hydrogen potentials help the nucleus maintain a specfic DNA packing/unpacking differentiation. If we look at DNA unpacking, this can not happen by itself due to steric hindrance within the DNA packing structures. What is typically required are unpacking enzymes. The low potential signal coming into the nucleus, from the cytoplasm, will create nonequilibrium for certain packed genes. It is nonequilibrium because these genes should be unpacked at that aqueous hydrogen potential but can not unpack spontaneously due to the steric hindrance. The unpacking enzymes find the most potentiated points on the packed DNA and combine to form the needed equilibrium. In the process, they unpack the DNA, altering the local equilbrium. This will cause the next batch of enzymes and biochemicals to flow to these newly created potential zones, etc., leading to the transription of RNA. One of the prominent features within the nucleus is the nucleolus. This is where the ribosomes are assembled. If we consider the long length of the ribosomal RNA, this area of the DNA define the longest continuous lengths of unpacked DNA. The mRNA of active genes are smaller by comparision, although many adjacent genes may add up to very similar lengths. The net affect of the long lengths of DNA unpacking is that the nucleolus is the lowest potential pole of the DNA. As the lower potential rRNA accumulates within this zone (RNA defines a lower hydrogen potential than DNA) the hydrogen potential of the DNA will drop further until the lower potential ribosomes begin to form to reflect equilibrium. These are lower potential, as inferred by the observation that they leave the nucleus to assume positions within the top of the cytoplasm gradient. The nucleolus's ribosomal production rate sort of coordinates with all the RNA production within the nucleus. All the formed RNA and unpacked DNA lowers the nucleus aqueous hydrogen potential, while being resisted by the packed DNA. The equilbrium seen by the nucleolus will coordinate the ribosomal production rate to maintain the needed proportions to the entire RNA production. One important consideration within respect to other subgradients within the nucleus is how hydrogen potential is conducted withing the nucleus. The most obvious means is via the water within the nucleus. This would explain why altering the transcription parameters of one gene can sometimes cause a distant gene to react. The gene grouping is part of a local aqueous cluster with its own little subgradients set up locally. It is not quite as simple as centromere to nucleolus to nuclear membrane to cytoplasm, although the subgradients are within these gradients. It also seems theoretically possible for hydrogen potential to conduct axially along the DNA double helix, via the hydrogen bonding of the base pairing. The extra hydrogen bonding hydrogen, within each base pair, might lower potential via an axial connection between adjacent base pairs on the DNA double helix. The DNA double helix might actually be a type of hydrogen potential wire.
  9. To understand how the cell creates an aqueous hydrogen potential gradient from the inside of the cell membrane to the DNA, one needs to understand why the DNA defines a high hydrogen potential. There are at least three causes within the DNA double helix. The first is connected to the hydrogen bonding within the base pairing. In the base pair thymine and adenine there is an extra hydrogen bonding hydrogen that can not fully participate within the base pair hydrogen bonding. In the base pair cytosine and guanine, there are two such hydrogen. Actually, these hydrogen sort of share electrons with a lot of steric hindrance. As such, every base pair has considerable hydrogen potential built into them. The second two reasons are easier to see by contrasting DNA and RNA. The DNA will form a double helix while the RNA typically has more variety often forming a single helix. The double helix of DNA is implicit of its higher hydrogen bonding potential. Both have the same extra hydrogen on all their bases. This makes them both sort of high with respect to their structural hydrogen potential. The extra hydrogen potential of the DNA is connected, in part, to the slight difference in the pentose sugars of DNA and RNA. The pentose sugars ribose and deoxyribose differ only by the ribose of RNA having an C-OH group and the deoxyribose of DNA having an C-H group at the same spot on the sugar. The polar C-OH creates a lower surface tension affect within the local water, while the nonpolar C-H creates a higher surface tension affect. Although both pentose sugars create some surface tension within the local water, due to their slight imbalanced polar/nonpolar natures, the higher surface tension defined by deoxyribose will increase the local aqueous hydrogen potential impact of DNA more than ribose does for RNA. The next difference has to do with DNA containing the base thymine and RNA containing the base uracil. The only difference between these two bases is a methyl -CH3 group for DNA's thymine, and a -H for RNA's uracil in the same position on the base. Everything else is the same. It comes down to the -CH3 of DNA's thymine creating more surface tension within the water, i.e., more aqueous hydrogen potential. The real kicker that makes the DNA the high hydrogen potential pole of the cell (inside of the cell membrane is the low hydrogen potential pole due to its dynamic negative charge), are the histone packing proteins. The lysine and arginine residues contain positive charges to neutralize the negative charges of phosphate groups along the DNA backbone. This amplifies others aspects of DNA. These packing proteins residues also both contain many extra hydrogen bonding hydrogen. These retain hydrogen potential within the packing structures. The result is that the packed DNA are the highest hydrogen potential structures within the cell. The more packed the DNA, the higher the hydrogen potential. The next time I will rough out the cellular gradient
  10. I guess my problem is that I don't use the standard definitions, which makes it difficult for others to know where I am coming from. I understand the phenomena but lose something in translation. If we look at what I called sensory expectation, that would be what pops into one's mind when a particular instinct sounds. It is a lead aspect of an instinctive human behavior. For humans it is partially hardwired and partially learned. If we get hungry we gather food. This is hardwired. But before we gather we see in our imagination what we desire to eat. Let me give another example of sensory expectation. If a wild dog begins to get hungry, he may have a hankering for the local rabbit. Even though he can eat nuts and berries, these will not catch his attention unless he is really hungry. The sensory expectation of eating rabbit has a certain expected smell, so he will sniff the ground looking for an overlapping scent stimulus. When he smells rabbit, he will begin tracking in the direction of increasing smell concentration. The final smell that correlates to his sensory expectation is the rabbit in his mouth being chewed. If while he is tracking, he smells a natural enemy, he will respond directly to the sensory stimulus in an instinctive way, trying to minimize the smell concentration by going the other way. In this case the survival instinct might overide the hunger behavior clearing the sensory expectation slate. When he feels safe, he may smell around looking for a food stimulus, with or without the same sensory expectation, and begin food tracking again. The sense of smell is not an instinct, but the sensory expectation, can lead or bias the instinctive behavior. In other words, the neural wiring that is created to due to instinctive experiences combined with the operation of the sensory systems, can add another layer at the top of the instinctive behavior of a species. This can bias the collective instinctive behavior to the experiences of individuial.
  11. I am a theoretical speculator and come up with new things. Along the line of this discussion I would like present something for discussion. It has to do with sensory expectation. It is something more associated with the psychology behind instinct than the biochemistry. One often assumes the sensory systems always behave in a cause and affect relationship. Or the sensory system inputs data and we react. With instinctive brain potentials, the sensory affect often comes before the sensory cause. For example, if it is evening and one gets a little hungry for a snack, they may picture a bowl of ice cream in their mind's eye. One might then go to the freezer to find the ice cream so it can satisfy the sensory expectations of taste, smell, cold, sweet, etc.. If there is no ice cream, for the craving, one may not be as satisfied with just some cookies and milk, even though they essentially contain the same chemical value. This is because they do not totally forfill the sensory expectations. They will satisfy the hunger but not that something else. A pregnant woman might get her husband to go to the store to get the ice cream because the sensory expectation is more important than simply the sum of the food components needed to satify the biochemical hunger.
  12. My name is Mark. When I was young I was called pencil mark by the adults because I was thin and fairly bright. As a teen I was dubbed Marcos and Marcos Supreme, by my closest friends, because I was good at academics, sports, partying, diplomacy. I preferred, just Mark so I could stay below the radar of attention. This allowed me to blend into all the various niche groups and have many types of friends without adversaries. Screen names often have to do with one's state of mind. Sunspot was chosen as a reflection of the discernment of truth and shadow becoming more important than my former youthful adaptation. Sometimes pointing out the truth and shadow can make one unacceptable to all the groups.
  13. The sense of smell is often combined with breathing yet both are distinct. If you could smell the same smell without harmful air, you could have the best of both worlds. I like to smoke some cigs, about 1/2 pk a day. I try not to smoke during the day only early morning and the evenings. I fugure it is in the buffer zone for me. There are two sides to our instincts. There is the purely biochemical as you pointed out. But there is also a psychological side; starts in the head. This is where the biochemical feedback loops comes to life. The psychology that is used to satisfy the biochemical potential is what I am trying to address. For example, the body has specific biochemical needs with respect to food. How we satisfy the needs comes down to our behavior. The body is quite flexible allowing variety. Science is learning what the optimum foods are, but many people's feeding behavior lead them to cake and chips inspite this biochemical optimium. The psychological aspect of the instinct is more flexible than the optimum biochemical. The body still survives indicating that there is probably a biochemical buffer zone that extends beyond the optimum. This makes room for nonoptimized choices. Humans are not delicate flowers that will wilt if they are put in a nonoptimized biochemical environment. I was hoping, as a discussion we can address the theoretical optimum and the less than optimum that still seems to work
  14. I chose sunspot as my forum name because I wanted to show that there are other ways of looking at things. The sun (cultural knowledge) is not just light or truth combined with constant solar flares of new insight, but there are also many unproven things, and many subjective opinions of the same phenomena, which are the sunspots.
  15. I would like to discuss two potential paradoxes, associated with cellular hydrogen bonding. If we look at water, the hydrogen has a partial positive charge and slightly ionized shared electrons due to sharing 2sp3 orbitals with the highly electronegative oxygen. The oxygen has less potential in its slight negative dipole charge, since it induced this dipole charge for better octet stability. In fact, oxygen is able to accommodate even more negative charge as reflected by the formation of the OH- anion at neutral pH. Even that does not fully satisfy oxygen’s need for electrons under all conditions. Oxygen can reach O-2 or oxide in many cases. If one considers oxides, it is very difficult to take electrons back from oxide. Typically the best that occurs is ionic sharing with cations. The crystals that form spread out the negative charge of oxide to many cations, due to the stability of the oxide octet and oxygen’s resistance to giving up the electrons. If we go back to water, the oxygen has little reason to share its puny excess electron density or negative dipole charge. In fact, it would like to have even more electron density all the way to the stable oxide. This is one of the potential paradoxes; a slightly negatively charged entity, oxygen of water, wanting more negative charge, i.e., wants even more electron density. The hydrogen is a horse of a different color. It is induced positive and has baggy electron clothes, i.e., slightly sp3 ionized. This double potential makes hydrogen look for electron density within the water. With oxygen being the only source of electrons, the hydrogen takes what it can, with the oxygen trying to twist away to retain it’s stabilized negative charge. The hydrogen bonding that does form within water lowers hydrogen’s potential, somewhat, but some potential still remains due to the constant evasiveness of the oxygen of water. This left over hydrogen potential is why metals will oxidize faster in water than in air. Hydrogen’s residual electrophilic potential acts as the catalyst. The continued potential within the hydrogen of liquid water is loosely analogous to an oxidation potential in that it contains an electrophilic potential just like molecular oxygen. They both are looking for electron density. This is evident in the increased corrosion of metals in water. The hydrogen tries to share the easy metal electrons, pulling these electrons into a slight excited state, with molecular oxygen scooping them up because of its higher electrophilic potential. If take a hydrocarbon and burn it with oxygen, this is highly exothermic because the reduced electrons within the hydrocarbon. Based on this reduced electron density within hydrocarbons, one might expect that this rich source of electrons should help lower the aqueous hydrogen bonding potential. The paradox is, the opposite will occur. The hydrocarbons will increase the potential of the aqueous hydrogen. The reason this occurs is that the hydrocarbon surface is not a good place for aqueous hydrogen to find electron density. It can actually do much better with the stubborn oxygen of water. The result is surface tension due to the hydrogen losing aqueous electron density by being in contact with the organic surface. This increases the local and global aqueous hydrogen potential. The hydrocarbons will lower their water contact surface area to help lower the increased aqueous hydrogen potential, while be pushed by the hydrogen to lower its local/global potential. If we look in a cell, all the membrane lipid material, both inside and at the perimeter of the cell acts to increase the aqueous hydrogen bonding potential. While the increased aqueous hydrogen bonding potential acts as an electrophilic catalyst for the metabolic oxidation potential, sort of a second cousin of corrosion. The potentiated hydrogen of the cellular water energizes the top end of the mitochondria’s proton pumps, as well as the hydrogen/electrons of the Krebs cycle, which combine with molecular oxygen to form water. This aqueous hydrogen bonding induction is directly reflected, during cell cycles. During cell cycles, the membrane potential will lower; implying the inside of the cell becomes less negative. This increases the impact of the high surface tension membrane materials. This results in the aqueous hydrogen potential increasing, thereby increasing the potential of all the hydrogen associated with the metabolic oxidation potential. The increased aqueous hydrogen bonding potential also changes the hydrogen bonding equilibrium of the metabolic enzymes (become more electrophilic), to increase reaction rates.
  16. The green zone of the hunger instinct appears to be centered on a varied and balanced diet, as outlined by the food pyramid. Humans are omnivores, which gave primative humans the ability to adapt and survive, even during the last Ice Age. A vegitarian diet is also in the green zone. Many people can live a very healthy life with nothing but veggies. If one adds milk, cheese, eggs, fish, etc., to the veggie diet one is also adding other nuitrients getting closer to the bull's eye, which allows maximum adaptation. The center of the bull's eye may also include the wide variety of cultural specialties, such as unique veggies. The soybean comes to mind and there are many others. Besides what enters the mouth, the green zone of the hunger instinct is also a function of quantity, the frequency of eating, even how one chews of prepares the food. The last point is interesting in that cutting fine or chewing small allows the body to digest better. Bigger prepared chucks or swallowing food in big gulps sends things in the digestive track that can take longer to digest. Cooking meat is definitely in the green zone. Food quantity is often a measure of body size and metabolism with so many calories per day being optimum for most. But size is sort of subjective, since some people can appear a little over or under weight and still live a long life, Quantity is even mmore flexible if one looks at longer terms cycles. Most people will eat much more during the holidays. Many will then diet as a New Years Resolve ,and then drop off the diet and eat moderately over the rest of the year. In a years time, this is probally green zone, but in a smaller time frame, the hunger instinct may fluctuate from the green to yellow to red and back to the green. The hunger instinct green zone is also dependant on the frequency of eating. The three meals a day is probally within the green zone but there may be other combinations that are also in the green zone, such as five smaller meals. The yellow zone is both a short and long term zone. If one only eats certain foods that do not contain a good balance, one can still survive and live long but this may create add edstresses to the body. Short term yellow zone eating probally does little harm in the long term, but it may be worse for one if it become a longer term average. The red zone may include malnutrition, spoiled food, raw meat, the ingestion of wild mushrooms, household cleaning products, lead paint, etc., It can also be extreme behavior that long term exceeds or does not meet the volume and quality requirements of yellow zone eating. The hunger instinct is fairly flexible, over the long term. It allows periods of yellow and even red zone eating. If one's long term eating allows one to average green, short term variety should have no long term affect. The closer to the bulls eyes for longer periods of time one places themselves, the more yellow maybe red zone periods that can be averaged, over the long term, and still allow one to end up in a average lifetime green zone. Maybe knowing the bulls eye allows one a better handle on how much of the good life or bad life is still good for you.
  17. The breathing is hardwired for sure, which is good. Communication is a good angle concerning breathing that I didn't really consider. I know some people who can talk a whole breath. They almost appear to be able to talk on the inhale. Breathing is different than eating in that our desire to breath is usually for healthy air. I don't not know anybody who desires to breath junk air or even harmfully poluted air. Most people like to breath sweet smelling air, but this is probably more connected to the instinctive sense of smell than it is to breathing. Smell and breathing may be a good example where two instincts sort of battle each other for dominance. Some people like to burn incense, while others like the smell but don't like to breath the smoke.
  18. Pardon the elementary approach to the chemistry of life atoms. I thought it might get the point across easiler without requiring overbroard science. What I would like to look at is the left handed nature of bioactive proteins. The two terms, lefthanded and bioactive, implies that lefthanded proteins have a natural built-in potential, that right handed proteins lack. This built in potential, within lefthanded bio-active proteins, stems from the potential within the hydrogen bonding hydrogen of the cell, with the cell water, local and global, playing a very important role. Even the manufacture of the animo acids feels this local and global hydrogen bonding tension causing them to form the slightly potentiated left handedness. This tension is compounded further as proteins form. In human culture, left handed people are stereo-typically considered more creative. If so, it may be due, in part, to the neural wiring into the right hemisphere. But it is also a function of simple needed adaptation. If one is left handed in a world which is primarily right handed, one, by necessity, needs to adapt themselves to the simple things of everyday cultural life that are easier for a righthanded person. In the past, a left handed child would soon realize that there are no left handed baseball gloves at the ball field. The choices were to learn to catch and throw the ball with only the left hand, or learn to throw the ball with the right hand. Nature is sort of similar in that lefthandedness required adaptation to the simple things of the inanimate world, which creates more of a balance between the left and righthanded amino acids and proteins. If we take a long protein and stretch it out in water and then let the protein recompress into a 3-d strucuture, there are several potentials at work. The protein has its own secondary bonding forces built in that will attempt to minimize potential. One of the most important is the internal hydrogen bonding that will twist the protein into a helix. The protein is also dissolved in water. The hydrogen bonding potential within the water, due to the potential within the water's hydrogen, will also have an impact. For example, surface tension will force all the hydrophobic side groups of the linear protein to immediately avoid the water. At the same time, the protein is trying to minimize its own molecular potential. The result might be a compromise between the external and the internal potentials. It we take the same protein and manufacture it fresh on a ribosome, it starts out as a little end piece, which is surrounded by water. Under these conditions, with the overall protein still in the works, the little protein fragment becomes the whole internal potential. This is being molded by the external water potential. If the needs of the water potential stores additional packing potential into the fragment, as new protein comes out hot off the press, its new internal potential is the sum of the internal potential of the new fragment, the hot internal molded potential of the old fragment, and the external potential. The final assembled 3-D protein can become something that is different than the 3-D isolated protein in water. It has built in potential that is quite useful for catalytic purposes. What these packing stresses and strains essentially do is place internal hydrogen bonding hydrogen in nonoptimized orientations. If an internal hydrogen bond length is too long, or the bond angle is nonlinear, or if the hydrogen is place in a position where it is surround by a bunch of high surface tension hydrophobic moities, etc., each little hydrogen maintains residual potential for electron density. The overall sum makes the protein configuration electrophilic or needing electron density to lower the stress and strain. Unfortuneately, the structure is often very stable so the innternal potential remains. In enzymes, this electrophilc strain helps the surface active site pull a substrate into an excited state. In other words, the excited state of the substrate is an attempt to share its electrons with the protein. The surface active side still needs the proper lock and key relationship to work right, but the calaysis potential is amplified by the structural stress and strain. If we took a nano-scissors and cut out the surface active site, the reaction rate would drop because the active would lose the extra electrophic affect stemming from the protein's structural electrophilic potential.
  19. I have nothing against gays, live and let live. Culture in an attempt to protect groups from bigoted intolerance makes certain areas of discussion taboo, less it feeds into the narrow minded thinking. But I also believe the data and truth gives everyone the only real perspective. One thing that everyone loses track of is that STD's in any population group appears to be a natural way to discourage unnatural behavior. Even if one knew nothing about science, symptoms of STD, gets one's attention and helps one pull in the reins. It may even take them out of the breeding population. Or it makes potential partners look elsewhere. It's nature's way of funnelling people down a better path. With science and medicine, we can create counter measures to undermine this cause and affect relationship of nature. This helps perpetuate the myth that all behavior is relative because there are no real permanent consequences that science can not cure. AIDS is different in that counter measures have yet to be developed. Maybe the cure to help satisfy the cultural illusion of the relativity of sexual behavior will lead to even worse diseases due to the orginal cause and affect of nature once again trying to restore a natural order to human sexual behavior. Whether gay or straight, monogamy or limited diversity contatc seems lto be the natural fail safe approach that does not create disasterous natural counter measures. As a parallel example, if one wanted to eat broken glass and had a built in zipper in their abdomen so doctors could clean one out daily to prevent any ill affects, glass eating could eventually become a part of our daily life and would eventually be considered a part of the food pyramid, especially since it would create jobs and wealth.
  20. I am going to change gears and look at the five atoms of life; C,N,O,H,P. There are others but this set is the vast bulk of biochemistry. I do not have time to patent or copyright any of my ideas. My mind stays in flux making it difficult to focus on one thing for too long. Everyone is free to make use of my seed ideas. Here is the breakthrough stuff. If we look at H covalently bonded to O, N and C, this occurs via sp3 hybrid orbitals. What this means is the 2S and 2P orbitals of each of these three atoms, combine to make four similar orbitals with blended S and P character, instead of one S and three P's. When hydrogen covalently bonds into an sp3 orbtial, it shares electrons but at P orbital distance. The hydrogen atom is actually optimized for 1S orbitals and can only be truly optimized as H2. Sharing within sp3 hybrid orbitals sort of gives hydrogen slightly ionized electrons to balance its positve charge, due to the P character of the shared electrons. Within the living state, hydrogen essentially lives in the land of sp3 orbital giants (O,N,C) and is induced by these giants to wear baggy electron clothes. The result is that hydrogen is not only induced slightly positive, due to their higher electronegativity, but also carries the burden of the sp3 ionization. As such, going into a hydrogen bond it carries more burden of potential than any of the big three. Technically, only O and N will form hydrogen bonds in the traditional sense. However, newer and older studies indicate that C-H actually forms lower potential versions of hydrogen bonds due to the lower electronegativity of C compared to N or O. The charge within C-H is tiny but the baggy clothes is still there. Although one little H is no match in the land of giants, H has numbers of its side and as a team is a formidable force. The team effort adds another layer to the biochemistry of the three giants. If we look at a cell, the biochemistry is manhandled by the vast numbers of little H, each with a potential chip on its shoulder. This is not standard chemisty lingo but is intended to draw a picture of the force that organizes everything in the cell. The biochemistry of the giants has the capactance of life, but the H is light weight choreographer that integrates everything. Before gettiing into particulars I would like to look at P. Phosphorus is very important to the cell. It is part of DNA and RNA and is the basis for the ATP molecule. If we look P, it is a bigger giant among the smaller giants. It has electrons in the 3S and 3P orbitals. When its reacts to make phosphate PO4, it essentially loses all its 3 orbital electrons and is forced to share the level 2 orbital electrons of oxygen. Within phosphate, P is a giant wearing the tight electron clothes of the slightly smaller O giant. This is not exactly true. P will stretch out its electron clothes a little bit and O's electron clothes will get a little baggy. P sort of does to oxygen what oxygen does to H. When ATP forms from ADP, the extra P adds a slight potential to the O (baggy clothes), which is the stored energy value within ATP. Oxygen wants better fitting electron clothes and will team up with other oxygen atoms to get them. The phospate in DNA and RNA is a little under stress. The O is slightly ionized with baggy P clothes. As such, although it has a negative charge for membrane repulsion, it is does not put out a full charge signal with respect to the hydrogen bonding hydrogen. In other words, the electrons of the oxygen of phosphate are even baggier for the H and is not their first choice. Someone like K+ is a different story, since these baggy clothes fit better for this series 3 atom.
  21. I was only talking about the how AIDS progressed in the USA. I stand corrected about how it was spawned. Do you have an idea when and where the first deaths from AIDS occurred? This was when AIDS really matured and became much more of a problem. But doesn't Gay servicemen bringing it to American suggest overseas gays being the first carriers?
  22. I was going to go into the cell and discuss the gradient between the membrane and the DNA, but before doing that I would like to stay outside the cell to discuss the nervous and lymphatic connection. The primary gradient for cellular differentation control lies between nervous tissue and the blood supply. This is inferred by the high positive surface of nervous tissue and the negative or slightly alkaline pH of the blood. Aqueous hydrogen bonding connects the potential. The lymphatic tissue is within this range but much closer to the nervous potential. This is inferred from the observation that baby brain cells crawl with amaeboid motion. This implies the bottom end of nervous tissue is sort of close to the top end of blood cells. This leads to the theory of making new brain cells from the blood cells within brain. How that can be done, I haven't figure out yet, but it appears theoretically possible. Sorry for the detour. Getting back on path, the potential between the lymphatic tissue and the nervous tissue is a way to charge up the blood cells for the immune response. When they reach a certain potential they become attracted to the lower blood potential. Once in the blood or around cells, they begin to lower potential. This changes their aqueous hydrogen bonding output, allowing a spectrum of attraction and surface potential. Once they discharge their potential, they now become attracted to the higher nervous potential and begin to flow back up the gradient into the lymphatic tissue. Here they get powered up again. They increasing surface charge allows them to alter the internal protein gradients to digest a very wide range of complex food patterns. This is very over simplified and is intended to show what is happening at the hydrogen bonding potential level. The biochemistry makes use of the changing external and internal hydrogen bonding gradients for an integrated response. If we look at cancer cells, many replicate out of control. When a cell is in the cell cycle, the membrane potential lowers. One theory for some types of cancer is due to defects in local nervous tissue control system. Certain cells can lose the high end of cellular differentiation control and are only seeing the lower blood potential. This one sided control system (bottom end) not only pulls them down into the cell cycle, but continues to feed food into in the constant cell division. I have no proof of this, just logic. But if it is true, the corrective measure is simple. Grow nervous tissue into cancers. This should not only slow the cell cycle turn-over, but it will keep the local immune system powered up for a better local response.
  23. I was not sure where to put this topic. But since instincts are as much psychological as physical I thought this might be a good place. The idea came to me yesterday when I realized that there is no one size fits all when it comes to our instincts. There appears to be a buffer that allows for variety around an optimum. Let me just start with an example. If we look at the breathing instinct. This is the most important instinct since after about 7min without air, tragic results can occur in most people. Luckily, this instinct is done for us, unconsciously, to assure not too much tampering. Exercise, although beneficial to good breathing is not essential. Many people can live sedate lifestyles and still live to a ripe old age. Such people live in the green zone of the breathing instinct. Exercise is a little better than normal breathing because it can expand the lungs for better air flow and even adding extra lung cells compared to a sedate lifestyle. Exercise is the bright green center of the green zone with respect to the breathing instinct. Normal breathing is the rest of the green zone. Breathing is more than the mechanics of the in-out of air. Air quality can also have an impact on the breathing instinct. The ideal air may be in a remote forest after a rain. The air is not only clean of pollen and dust because of the rain, but also from polution because of remoteness. Also the trees are producing fresh oxygen for us to breath. Fresh new oxygen may not be important but it can't hurt. Very few people have the luxury to live in a remote forest. Most live in cities and suburbs and can still live to a ripe all age. Much of this may also be in the green zone or at the perimeter of the green zone. In very poluted cites we begin to enter the yellow zone. Some people can still exist within this buffer with few ill affects. While others begin to show signs of respiratory problems. With some precautions the yellow zone is still within the buffer zone of the breathing instinct. Beyond the yellow zone is the red zone. This may be jobs like coal mining. Or circumstances that bring us in contact with a lot of smoke from fires. The red zone is an area where the natural instinct begins to get damaged with various degrees of exposure. There may well be an orange zone between the yellow/red, where short term exposure is reversible but beyond a certain amount of time is permenantly damaging. One thing that comes to mind is breathing radioactivity. One is allowed so much per year. Cigarette smoking lies somewhere in the range from the yellow to the red zone. It is definitely not in the green zone. If someone didn't start smoking until they were 21 and only smoked 5-cigs/per day and quit at 40, they would probally never leave the yellow zone, especially if they also exercised. On the other hand, a child who starts smoking at 10 and is up to 2pk/day by 16 may actually stay in the yellow zone until the twenties, because of their young lungs, and then enter the red zone in their thirties as their lungs begin to reach a steady state. What I am trying to show here is that is no one size does fits all when it come to the instincts. This is usually a green zone. But there is also a yelloow buffer zone for each instinct. The buffer zone may not be the optimum green zone of the bright green bulls-eye, but it lies within the range of instinctive adaptation. Maybe culture could benefit by defining the optimum for all the various instincts and then define the buffer that allows for choice within the adaptiverange of that instinct. Maybe other forum members would like to propose what they see as the the green, yellow and red zones of say the hunger instinct. After we set the outline for each instinct we can go back and argue the details. Let us start at the green zone.
  24. I didn't mean 100,000 cases of AIDS but 100,000 deaths from AIDS. I was around when the first confirmed case was reported. It was postuated to come from monkeys. The media began keeping a running tally like bird flu. It sells soap. The gay population was the initial focus. As the number of Gay AIDS cases rose quickly the numbers then spread to the bi-sexual population, then the IV drugs users. This last spread was assumed spread because of contact between prostitutes and bisexuals. The numbers then began to spread to the straight population and then even to children. Then it was everywhere in all walks of life. The gays were hit so hard near the very beginning, that they organized and took precautions causing the number of new cases to quickly decrease. This tricked down to the rest of the population until the current steady state. There are few new cases in USA, mostly existing cases. It spread internationally to poor countries.
  25. I was being a litle silly to lighten things up. I was also trying to discuss the possiblity of nervous tissue and cellular differentiation control. I have no direct data because it is new and not a big area of study. The choice is wait until then, or logically continue along this line of reason. One of the practical problems of this hypothesis is that there are not enough chemicals given off by local nervous tissue to cells to explain such an important role. The blood supply is very obvious. Even the surface charge of sodium cations is sort of stuck to the nervous tissue and is not being trinkled in a steady stream to the cells. If it does flow it probally ends in the blood for recycle. There is a way for the potential to conduct. This is connected the hydrogen bonding within the local water. If we look at the surface of nervous tissue, the external positive surface is in contact with water. The hydrogen of water needs to compete with all these sodium cations, creating a hydrogen bonding potential. The hydrogen proton is the fastest thing in water. This will conduct outward from the nervous tissue, through the water, as the protons bump the next guy. When the signal reaches a cell surface, the hydrogen bonding potential will be made higher on that surface than what is being created by the local surface charge. This will increase the effective outside potential of the cell or a side of the cell. If we look at the nervous tissue, its outside positive charge is not static. The neurons needs to constantly use ATP energy to maintain the potential, up to 90% of metabolic ouptut. There is always leakage, much of it to drive the active membrane transport. There are also cationic current flows, including hydrogen proton flows, along the surface due to neuron firing. The sodium pumps are pumping, sending out signals at the level of the hydrogen bonding. The hydrogen bonding gradient from the nervous tissue to the control cell is being expressed by pulse patterns connected to what the local nervous surface is doing. If we look at the outside positive surface of any cell, being positive means electron deficient. This is loosely analogous to the potential of metabolic oxidation, where molecular oxygen is electron deficit. This is the cellular trick or lure that draws reduced foods materials to the cell. It creates the scent of an oxidation potential which can lower the reduction potential of biomaterials. The food travels up the projected aqueous hydrogen bonding potential gradient stemming from the outer cell surface. The cells in the body lure food from the blood in this way.
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