Archive for November, 2006

I sit and ponder over a great many things. Physics, chemistry, biology, health care…these are only some of the things I tend to sit and think about. They’ve taken the center stage as of late, but not because they are the most important. Their application deals with the human condition, and so I consider them of value. There are other things that deal *more* directly with the human condition.

This year’s mid-term elections were, for me, a let down. The fact that the democrats stole back the house and senate was somewhat nice, in so much as I tend to agree more with the democrats than the republicans. But really, neither party suits me *well*, just the democrats suit me passably. What was really my problem with the mid-term elections was the number of states that passed constitutional referendums outlawing gay/lesbian marriages.

The history of society, from the dawn of recorded history until today, has been a story of evolution. All throughout history, we have oppressed, raped, murdered, stole, cheated, and otherwise destroyed human beings. Always, there was one or two issues that were the most horrific at the time. Genocide (multiple times, the jews in Germany, Aztec and Incan civilizations), enslavement of an entire race (multiple times, Israelites, Egyptians, African Americans), improper executions and killings (again, multiple times, the penal system in the dark ages, the inquisition, the crusades, the Salem Witch Trials, our civil war and our treatment of slaves). As we have evolved as a society, we have shed ourselves of these inhumane acts time and again. We have slowly, almost painfully slowly, loosened the grip of our fear and instinct that drives us to these horrors and instead embraced tolerance and understanding. Never has it happened without a fight though. The people being mistreated must always show the people doing the mistreating that their acts are wrong, and the people committing the crime never believe them. So the cycle continues.

I prefer to think that a person could graph this cycle in the form of a spiral, like a seashell. In the center, the earliest and most atrocious crimes against humanity. Then, as we progress as a society, the spiral moves outward, and the crimes become lesser, and society better.

Today, we still have atrocities in our society. If you look at it on a global scale, there are very horrendous things taking place. But, if you pull back to just our nation, the picture is brighter. And this is why gay/lesbian rights are now in our minds. In the 1500s, if you were a gay man, working for a lord, barely surviving on the small amount of food you were allowed to keep while working 16 hour days, you didn’t complain about the fact that society didn’t accept your sexuality. In the context of your indentured servitude, that was a minor thing to complain about. You hid it, you maybe got lucky and found someone to surreptitiously share it with, but you didn’t complain about it or ask for it to be changed. Today though, that has changed. The core layers of the seashell, the right to life itself, the right to liberty and self determination and freedom from slavery, these things are now well settled here in America. Once a person has the right to their own life, and the right to their own self determination, the single most important thing next on the list of things that contributes to an overall happy life is the choice of person that you spend that life with. Of course, the majority thinks that life is good as it is and nothing should change, but that’s only because they are already free to choose the best mate to spend their lives with. None of them have had to make a choice between spending their life with the person they both love and are attracted to, or having access to membership in an exclusive club known as society. The majority has nothing to gain by allowing gay/lesbian marriages, but they fear they have something to loose (and in truth, slave owners had something to loose by granting slaves freedom, whites had something to loose by granting minorities equal standing, the majority almost always stands to loose something when they quit oppressing another group, but the real issue isn’t whether the majority stands to loose something they value, but whether they ever had a *right* to what they stand to loose in the first place). And so the fight goes on, and the seashell gains yet another section.

But the gay/lesbian community WILL win. There is no doubt of that. One need only read our own Declaration of Independence to know why. There are three things that the Declaration of Independence claimed we all had an inalienable right to: life, liberty, and the pursuit of happiness. For all that the anti-gay community screams at the top of their lungs that the gay lifestyle is a choice and that they shouldn’t be choosing it, they miss the most important fact of all. The gay/lesbian community *DOES* choose it (no, I’m not saying it’s a choice to be gay or lesbian, I personally think that’s the way they are born, I’m just pointing out that it’s *irrelevant* whether they choose to be that way or born that way, because in the end, they are *free* to choose that lifestyle if they wish, or so our Declaration of Independence would teach us), even in the face of hate mongering teenagers that use baseball bats to beat a high school student to death for his effeminate attributes. What this means is that it is *MORE IMPORTANT* to a gay/lesbian person’s happiness that they be who they are than it is to have all the things that society currently takes away from them once their preference is known. For a person to sacrifice so many aspects of their life that contribute to happiness, to deal with ostracism and being an outcast, to willingly mark themselves a target for the scorn, ridicule, and derision of our society, all in order to be able to be with the person that suits them best as a companion, mate, life long friend, and the person that shares the ups and downs of their life, is prima facia evidence that their choice is no choice at all, but a prerequisite to their attempt to fulfill one of their three inalienable rights: the pursuit of happiness.

It is for this reason alone that I *KNOW* that gay/lesbian rights are the next thing to come on the seashell of the evolution of our society. We’ve already covered self determination for Native Americans, freedom from slavery for African Americans, civil rights for women, and civil rights for minorities. The next item on that list has now popped it’s head up and said “I’m here…let’s start dealing with me.” Of course, as is always the case, the majority doesn’t want to change. They have no need to. But that’s irrelevant. The majority *NEVER* wants to change. It is always the downtrodden that force the issue. The only question then is whether or not people in the majority have the vision, the clarity of mind, to see the movement for what it is, simply another step in the evolution of our society as we continue to wring out the injustices that live farther out on the seashell and do the right thing even though it doesn’t benefit them, or whether the people in the majority are so callous and unsympathetic to their fellow human being that they would willingly overlook their fellow human’s pursuit of happiness simply because they choose to remain blind and ignorant.

I am neither blind, nor ignorant. The time has come, it *WILL* happen. Now we need only make it come to pass.

I know I said in my letter to Discover that the primary cause of turbulence was electron orbital period difference between the two surface areas. But, there’s more to it than just that when it comes to bonds between molecules that allow for liquid (or solid for that matter) state. For any two given molecules to successfully bond into a liquid state, there must also be a geometric compatibility. If the molecules are shaped right (such as two water molecules), there is room for the molecules to “buddy up” to each other. Think of it like two humans on a couch, spooning. Even though in ice form the water molecules strive for an oreintation through the entire crystalline structure that achieves (as closely as possible) symmetry in the positioning of oxygen and hydrogen molecules, in liquid form that symmetry is violated for temporary positions between molecules that are, as the analogy goes, spooning. This position isn’t something that the entire substance can do at one time because it’s lack of symmetry would eventually cause molecules to be in an unsustainable position as you add more to the overall make up. However, short lived positioning of this sort would be expected as molecules are jostled around by intertia. This also explains why water is denser than ice. The number of molecules at any given point in time in this “spoon position” is going to be fairly constant as a percentage of the total molecules, and it is going to be capped to a maximum position by the need to keep an overly large group of “spooned” molecules from coming into contact with non-spooned molecules in an unfavorable way. This would also explain why water isn’t compressible.

The same can be said for more complex molecules such as octane. But, hydrocarbons, especially longer ones, don’t have a molecular shape conducive to forming a stable crystalline matrix, which is why as most hydrocarbons freeze you get wax instead of something ice like. Complex molecules, without a good geometric shape that can be positioned into a stable matrix, will always form poor solids like this. Amongst other things, an octane molecule might be able to buddy up along side another octane molecule fairly well, but the ends have a hydrogen in the way that keeps two ends from buddying up well. This, BTW, also explains why long chain hydrocarbons, especially ones where the ending hydrogen have been ripped off, can for much more solid forms instead of way, such as polypropylene or high density polyethylene, two of the most common and most durable and most chemically resistant plastics known to man.

For the case of most metals, the situation is actually easier. Since the metals aren’t molecules, but atoms, at the time of crystallization, they have a simple shape that’s easy to make geometrically symmetrical, a spere. Also, atoms of the same type will always have the same electron orbital periods, so that’s not an issue. The only thing that will keep a stable atom from forming a solid with atoms of the same type is interference from other atoms. For example, while iron doesn’t like to bond with many things, it *does* like to bond with oxygen. Once it does, it’s geometric shape is no longer well suited for making a solid crystalline structure. Hence why iron metal is strong, and rust is structurally weak. The concept of stainless steel can be explained in that the presence of other metals in the crystalline structure (aka, nickel) provide the surrounding iron molecules with what they need to resist the chemical “urge” to combine with oxygen (in other words, the nickel donates or borrows some electrons from the iron in order to stabalize the iron to the point that it is no longer interested in an ironoxygen bond, without looking at my period chart I think the nickel is borrowing from the iron since oxygen likes to borrow from other elements itself, and also if you expose stainless steel to hydrochloric acid, something that has the ability to provide spare electrons to the nickel instead of the nickel using up the iron’s electrons, then the steel will rust regardless of it being stainless steel).

Anyway, that’s all for this post, just a little refinement of the whole gas->liquid->solid state properties of atoms/molecules.

Super Computing ‘06 was this last week. I didn’t go to the whole thing, just the last two days as part of an InfiniBand/iWARP specific working group meeting. Tampa was nice, even if the downtown area did have little to over in the way of exploration and discovery. My hotel, on the other hand, was a $100 per night travesty that I wouldn’t wish on people that were happy with Motel 6 (note: it was the only damn hotel with rooms left 1 week prior to the convention…I hadn’t originally planned on going).

I arrived at the hotel about 10am Thursday. I went to the desk. I asked to check in. They said they couldn’t check me in because the hotel was full and they hadn’t checked anyone out yet, so the system simply wouldn’t allow it. I asked them if I went on to the convention, from which I wouldn’t get back until 9pm or later, would things be OK? They said yes, I was prepaid and my room held. So, I gave them my one bag and proceeded to the convention center. I ended up getting back at 9:30pm. I went to check in again. Lo and behold, they have no rooms available. I wasn’t really all that surprised :-/ So, I told them to try and find me something. About 30 minutes later, they announce that they’ve found me a room, give me keys, and I’m on my way. I go up, put my key in the door, open the door, and the room is all dark except for the TV and some guy obviously laying in bed says “Hello?”. So, I head back downstairs and say to the front desk “Houston, we have a problem.” I tell them what happened, and the guy goes back to work on finding me a room. After about 5 minutes, he says he can’t and there’s nothing he can do. At which point I said (rather nicely mind you, I was even complimented by a girl at the counter for not being mad “Dude, I was here at 10am, you’ve got my bag in your storage area to prove it, I’m prepaid, and they said my room was held. So, I understand if you don’t have any rooms, so just hook me up. If you gotta buy me a room elsewhere, buy me a cab ride there, and a cab ride to the convention center in the morning, doesn’t matter to me, just take care of it.” He wasn’t mad, but I could tell he was in a bind and not sure what to do. It probably would be easier if I *had* been mad and he could kick me out or something, but I was nice, and laughing while still resolute, and told them I was gonna go have a smoke outside then sit at the bar until they get things figured out. So, another 30 minutes later he says he found me a room, but they’ve gotta clean it first (I wonder if some party with multiple rooms agreed to double up or something to open up a room?) A little while later, I finally had my room on the 14th floor, where all the rooms had “Executive Club” tags on the door (14th floor is the top floor of this hotel). After having seen the room, if this is the “Executive Club”, I’m now deathly afraid of the regular rooms :-/ When a Motel 6 room is the best they got, that ain’t much.

Anyway, aside from that everything went well, had lots of good conversations between myself and other developers, that sort of thing. The next two InfiniBand working group conferences are Sonoma (in the Lodge at Sonoma resort) in mid-March and in Dresden (sp?) Germany in July-ish, then at SC07 next year. I’d like to go to all three. We’ll see how that works out.

As an additional data point, the fact that a water based mucous should
have basically an identical electron orbital period to seawater
(assuming whatever is dissolved in the water to turn it into a mucous
doesn’t alter the base water’s orbital period), coating either the
submarine or the dolphin in that mucous would result in a reduction in
turbulence simply because the two layers of material would have
identical orbital periods resulting in a much reduced opportunity for
inertia and other factors to force the two material faces into an overly
close proximity of each other, reducing the possibly of a rebound
reaction. I would check the dolphin to see if its skin secretes a
mucous, and you could try replicating that mucous if it exists and put
in on a steel hull to see if it works.

I didn’t want to just point Discover Magazine at my livejournal page (well, ryeth told me not to), so this is the actual email I sent in about the question they asked. It contains more than my post did because I needed to explain a bit about my theory of gravity and electrochemical bonds in sympathetic molecules in order for the turbulence answer to make sense. However, for anyone who’s actually been reading my posts, there is new information in this letter that hasn’t been in a post yet, so you may want to read it.

The email…

So, I got this month’s Discover Magazine on Friday. The article about the Scientist of the Year is what prompted all of these posts I’ve been making. But, there was another article that I’m going to respond to here. The article is titled Million Dollar Math with a byline that reads “If you can solve the world’s most daunting methematical challenges, fame awaits. Fortune, too, if you want it.” There are 7 mathematical problems identified in the article. One of them is labeled The Navier-Stokes Equations. This one basically wants an explanation for turbulence in fluid and gas dynamics. They already have pretty good models that mimic the turbulence, but they don’t yet have an answer as to why it exists. They think the answer can be found by looking into these equations. I disagree. I think the answer to the “why” of turbulence is in my last post.

Let me give an example to illustrate my point. I’ll use the case of a submarine in seawater. Electrochemical attraction creates a net pull that we call gravity. Electrochemical repulsion of atoms/molecules in atomically significant proximity of each other balances that force out. The two surfaces in this case, the steel hull of the submarine and the liquid form of water which is not solid, but in some ways behaves like a solid due to the constant formation of inter-molecular bonds between the water molecules as described in my Chemistry as physics post, will reach a state of equilibrium in regards to the opposing forces of attraction and repulsion. This equilibrium is maintained as long as the water and submarine are at rest relative to each other. However, once you start forcing the submarine to move through the water, you disturb that equilibrium. Random chance would indicate that at various points in time you are going to shove the electrons of a water molecule and a steel molecule close enough together that the resulting repulsive force will be quite violent. The random violent repulsion will result in a water molecule bounding away from the hull of the submarine with extreme inertia. Inter-molecular pull between water molecules will slow down the rebounding molecule and simultaneously accelerate other water molecules. If you get enough simultaneous rebounds, which is bound to happen just due to random chance, you end up creating a whorl of turbulence. This rebounding force is matched in the hull of the submarine…it’s called drag. And the harder you shove the submarine through the water, the more often you are going to force electrons into too close of a proximity, increasing the turbulence and the drag both.

When the force of shoving the steel through the water is high enough, the various rebound forces may actually get so violent that they momentarily cause the water to break it’s normal liquid state bonds and vaporize, causing cavitation. In fact, I think this is the reason why, if you are a chemist trying to vacuum distill a mixture, having a stir bar in the flask that causes cavitation helps with the distillation process. If you don’t have to actually reach the point where you are providing enough heat for heat alone to result in vaporization, then you can get very close and let the stir bar break the liquid bonds for you. All you have to do is have enough heat and vacuum so that the liquid bonds don’t reform once they’ve been broken. This is a much more orderly means of distillation than a purely heat induced distillation, which can result in sudden and violent boiling that runs out of the heating flask, down the condensor, and spoils the collection flask.

So, that’s my theory on the cause of turbulence. It’s bound to happen any time you disturb the equilibrium of two disparate (aka, non chemically reactive) surfaces in contact with each other. The exact location and appearance of any given electrochemical rebound is random due to things like the current orbit of electrons.

Now, this leads to a possible theory for minimizing turbulence. Since it’s the juxtaposition of electrons that is the source of the rebound effect, if you could create even just a minor buffer zone between the electrons in the steel hull and the electrons in the water, then you might be able to minimize the force of the turbulence. I’m not certain that water molecules will respond to this, but if you could create a net negative electrical or electromagnetic field around the hull of the submarine, it might keep the water molecules far enough away (from a molecular standpoint) to reduce the turbulence of moving the submarine through the water. Think of it like turning the hull of the submarine into a Star Trek’esque deflector shield meant to keep the outer shell of electrons in the water just a little further away from the submarine then they stay naturally.

In fact, there was an article discussing just *how* dolphins can swim as fast as they do. Maybe you should start your investigations there. For all we know, the skin of the dolphin may generate a small electromagnetic field that helps to keep water from getting quite as close as it might, reducing turbulence.

Here’s my theory. The typical atom has a nucleus and some number of electrons orbiting that nucleus. The attraction of electrons to protons, as well as the repulsion of protons to other protons and electrons to other electrons is the electrochemical force. Like magnetism, this force is greatly amplified by proximity. If you can imagine an atom the size of the state of North Carolina, the nucleus may only be as big as a car in the city of Raleigh while the electron is a little bird buzzing around the entire state. Now imagine another atom is centered in the state of South Carolina with similar properties. Let’s assume for the sake of this illustration that these two atoms are not compatible when it comes to making a molecule. This implies that the electrons in their orbits can not find a suitable way for the two atoms to join such that the electrons maintain an acceptable distance from each other. If the electrons get too close, then the fact that the nucleus of each atom is so far away results in the greatly amplified repulsive force of the electrons being too strong for the mutual attractive force that each nucleus exerts on the electrons to overcome. If, on the other hand, the South Carolina atom is instead over at Australia, then my theory is that over long distances such as this that the strong repulsive force of the electrons is mitigated and the net attraction of the atoms to each other outweighs the net repulsion, giving rise to gravity.

So, either because of mass reasons, or because the attractive force between electrons and protons is stronger than the repulsive force between electrons and electrons and protons and protons, the result is that electrochemical forces over an atomically significant distance is a net positive attractive force.

Once the atoms or molecules are within sufficient proximity that electron repulision starts to overpower the net attractive force, the molecules may settle into positions that allow for molecular bonding to take place, giving rise to liquids and solids. Or, they may be of such a shape and composition that this sort of positioning isn’t possible, leaving the mixture in a gaseous state.

What they will all do though is reach a point of equilibrium where the net attractive force is offset equally by the occasional repulsive force (or lack thereof). The more matter there is involved in this equilibrium (aka the higher the mass), the more the net attractive force will try to overcome the elevated repulsive force. At a certain point, the attraction becomes high enough that you get chemical alterations, followed my atomic alterations (aka, fusion), followed by complete collapse (black hole).

BTW, this explanation of gravity is part of my Physics as chemistry post that I haven’t even gotten to yet.

Could you imagine how cool it would be if someone built a device that is able to detect the 60Hz electromagnetic radiation given off by your typical electrical wiring in your house, and converted that detection into a visible display that allowed you to wander through your home using a camera and the now visible wiring in your walls to guide your steps?

Photons don’t exist. I’m probably going to take a lot of flak for saying that, but I believe it. Photons are something we created to explain the fact that visible light can effect movement over distance, therefore we surmised that it must have mass of some sort and that a particle hitting the target was the source of the movement. That simply isn’t true. Light is an electromagnetic wave, no more, no less. If you want to see the proof of the idea that an electromagnetic wave can create movement over a distance without the use of particles to explain it away, look no further than your microwave oven, or the antennae on a radio.

The best analogy I have thought up so far is that electromagnetic waves and their effect on distant objects can be thought of like a surfboard, a row boat, and a cruise ship on the ocean. Even a modest wave on the ocean can cause a surf board to do what it’s supposed to do and ride the wave. But, that same wave will only just rock a row boat, and it will have no effect what so ever on the cruise ship. Matter and electromagnetic radiation interact on the same basic principle. The amplitude and frequency of an electromagnetic wave front determines whether it effects the surf board, the row boat, or the cruise ships of our universe. In the case of a microwave, it creates a not so gentle rocking of the water molecules (and other similar molecules), thereby imparting inertia to the molecules which we perceive as heat.

If light *did* have a photon, then we’ve got some explaining to do. Astrophysicists have shown that light from far away binary star clusters undergoes a doppler shift as the stars rotate around each other (this is how they measure the speed at which the stars are orbiting each other). Any given star has a unique light signature when the light is analyzed through spectrographic means. That signature will shift up and down the scale depending on whether the star is moving toward or away from us. The implication here is that if you were moving towards the star at a high enough velocity, the doppler shift would cause the visible light to shift upward to the point that it was completely out of our visible spectrum. With enough velocity, things like normal radio wave signals would shift all the way up to the visible spectrum (how would you like to be able to *see* your favorite FM radio broadcast instead of hear it?) Now, to date I’ve not heard a single scientist suggest that FM radio transmission are based on photons, yet if we believe that photons are the source of light, and we can doppler shift FM radio transmissions into the visible spectrum, then just at what point along that doppler shift did our FM radio transmissions gain photons?

So, here’s my theory of what light (and all electromagnetic radiation) is. There is a constant force in the universe that causes all objects with discernible mass to exert a pull on other objects with discernible mass, gravity. My theory is that by causing individual atoms or molecules in one place in the universe to vibrate, it creates a vibration in the gravitational pull between that object and all other objects in the universe. Think of gravity like a tight string between each and every object in the universe, and when you cause an object in the universe to move, it sends waves down that string. We then detect those waves through sympathetic movements in tuned receptors either as part of our body or that we have created specifically to detect those vibrations. We initiate movement of electrons inside the wiring of an FM radio transmitter tower, that movement creates vibrations in the gravitational pull between the molecules of the wiring in the tower and the molecules in the antenna on our car, that sets up sympathetic movement of electrons in the antenna, which we then detect in order to receive the FM broadcast. Similarly, light works the same way, except that the frequencies are *much* higher and we have molecules in the rod and cone cells of our eyes that are tuned to be sympathetic to those higher frequencies.

When you start to think of electromagnetism in this way, it gives rise to some interesting theories about what we could do with this property of nature. Going back to the ocean wave analogy, if we start to classify what frequency and amplitude of radiation effects what atoms, or electrons on atoms, or whole molecule groups, then you start to think that maybe you could create an airplane that uses a jet engine not based on mechanics, but based on electromagnetic radiation tailored to the right amplitude and frequency necessary to shoot nitrogen molecules out the back end. Or maybe we could create a microwave oven that actually tested the sympathetic frequencies of the food being heated and then tailored it’s output to match the best frequency for the creation of sympathetic movement in that particular food, thereby increasing the overall efficiency of the design. Or maybe we could use targeted electromagnetic radiation in fields like synthetic organic chemistry to allow us to selectively chop off the particular portion of a molecule we want to get rid off with surgical accuracy (people are already experimenting with using microwaves for this exact purpose, but I would classify the current state of this research as “Gee, look at what that did” as oppossed to “OK, tune the radiation to this frequency and amplitude and that will exactly excise this component of the base chemical”).

I actually think this explanation of electromagnetism will be an important part of the whole Chemistry as physics class of science I posted about earlier. Without understanding the sympathetic movement of matter as a result of exposure to electromagnetic radiation, you won’t be able to accurately describe chemistry in terms of force/movement. This is a force that must be factored into those equations.

So, the current debate in astrophysics is around this theory of dark matter. You see, we noticed that large galaxies seem not to follow Newton’s laws of motion once you get far enough from the center of the galaxy. Newton’s laws would state that the further an object is from the center of the galaxy, the slower its orbit should be due to the balance between the reduced gravitional force and the inertial forces attempting to fling the solar system out of the galaxy and into deep space. The theory is that there is dark matter in the galaxy that adds additional gravitational force to the overall gravity of the galaxy, but which is not detectable by us far flung human beings. While this theory may be correct, there is another theory that hasn’t gotten nearly as much play time, but which I find very intriguing due to a couple follow on theories it creates.

The alternate theory is that gravity itself does not dimish with distance infinitely, but instead once you reach a certain distance from an object, the gravity tails off to a constant. This theory was just a theory and had nothing to support it until recently. Then another scientist created a system of math called TeVeS (for Tensor/Vector/Scalar) that suppossedly explains this phenomena in galaxies without the need of dark matter from a mathematical perspective (the original theory just said gravity tails off to a constant at distance, TeVeS gives the reason *why* gravity might tail off at a distance).

So, why do I like this theory (which, after reading up on dark matter, I have to admit that dark matter certainly sounds more likely, but for the sake of argument I’m going to outline what I came up with anyway)? Because the basic idea that a force in our universe might exert a diminishing force over distance, and then settle in to a not so dimishing force once a certain threshold in distance has been reached caused me to muse over the possibility that all the forces in our universe are actually the same force tailing off multiple times. That quantum force would tail off and become strong nuclear force, strong nuclear force would tail off and become weak nuclear force, that weak nuclear force would tail off to electromagnetic force, which would then tail off to gravity, which would then tail off to something else (I’ll get to that in a minute). Think of this kind of like those Russian dolls where as you take apart one doll, there’s another doll inside. You take that apart and there’s another underneath that. This sort of explanation for all the forces in our universe has a certain elegance that makes it hard to just throw away

This then lead me to a different theory entirely. One that’s sure to hackle more than a few feathers. It’s a theory for *why* the big bang happened. To be succinct about it, the big bang is the result of a scientist in a white lab coat performing an experiment in a particle accelerator in a universe that we couldn’t begin to understand nor interact with because the basic particles in that universe are all massive point singularities that result from a universe such as ours collapsing. Their electrons and protons are entire collapsed universes to us. Our gravitational force would tail off to their equivelant of quantum force. Our largest galaxy clusters would be seen as quantum particles. A single solar system would be so insignificant to that scientist as to be undetectable. A single person on a single planet in a single solar system saying “Hi” would never result in any sort of detectable phenomena that they could observe. It would explain why we can’t see anything outside of our universe (and in fact would have an impact on dark matter theory since our universe would no doubt be impacted by the presence of universe sized electrons and protons around our exploding electron or proton). It would explain why there was nothing then a big bang. It would explain why we can’t prove God (because we can’t interact with God, we are on different time scales, what we see as billions of years happens so quickly in His universe that the majority of what our universe does is totally undetectable by Him). It also raised the interesting question of whether or not we are creating entire universes with every particle collision experiment we perform. Are we in fact creating life at a smaller than quantum scale that we can’t even detect? Are we creating the same sorts of “where do I come from, and why do I exist?” questions in sentient beings that develop from our experiments? How many layers down might we be? Could our God in fact be another God’s experiment? Could we be 10, or 100 layers down? When we do a particle experiment, could sentient life develop, and over millions of years in their time (and less than a millionth of a second our time) perform their own super collider experiments, and create more layers of life below them?

Bake your noodle on that possibility for a while…

One of the things that needs to happen in order for scientist to be able to map out the chemical process in a cell is that we need to revamp our understanding of chemistry in general. Right now, chemistry is mainly a collection of knowledge, a database of known reactions and reactants if you will. We need to be able to predict what unknown chemicals will do when put together in a cell. This is highlighted by some research scientists did on a particular wine and its relation to longevity (I think the particular wine was Pinot Noir or Pinot Grigio, I can’t remember which). In that research, scientists found that by feeding geese a small amount of the wine each day, the geese experienced a 50% increase in their average life spans. When they went to examine why this happened by looking at the chemical makeup of the wine, they originally thought they only had to examine maybe 100 unique chemicals in the wine. It turns out that there were in excess of 10,000 individual chemicals present in the wine. Trying to isolate which one or what combination of a few chemicals[1] were responsible for the lengthening of the geese life spans is a next to impossible task. But this is just one problem out of millions where if you try to look at the complete chemical makeup of any biological organism or its products, you are overwhelmed with a plethera of chemicals, many of which may be totally unknown to chemistry right now.

What’s worse is that biological entities are based in part upon a balance between primary and secondary chemical reactions[2]. So any attempt to control or alter the chemicals in a cell need to account for these different reactions and the progress of chemistry when the primary and secondary ingredients are at different concentrations.

So I propose we start working on a new project to reclassify chemistry in terms of physics. We already know that individual atoms bond with each other to make molecules. We need to quantify the characteristics of individual atoms that contribute to whether or not this bond happens between any two atoms. Things like electron orbits, protonelectron attraction, electron shell mechanics, etc. all have to be accounted for in the equations. Eventually, the math should be able to predict whether or not any two (or more) atoms would combine into a molecule and what level of affinity they would have towards the combination.

Next we need to think about molecule to molecule bonding. The whole issue of state transition from solid to liquid to gas is a balance between heat (which is nothing more than molecular inertia[3]) and inter-molecular bond strengths. In addition, there is the issue of heterogenous molecular bond strength which gives rise to the concept of disolving solids in liquids. The math would need to be able to predict how strong the inter-molecular bonds would be, and also the elasticity of those bonds (if the bonds weren’t elastic there would be no liquid state, you would go straight from solid to gas). Then the math also needs to predict whether or not a molecule of a particular type would accept or reject a contaminate molecule, and the degree to which it would do so.

Once you have all this math in place, you should be able to predict the melting point and boiling point of any chemical compound, the possible primary and secondary reactions of any combination of atoms and molecules, the heat necessary to produce specific chemical reactions that require force to take place[4], the soluability of any given solid in any given liquid, and the heat of liquification and vaporization of any given chemical either pure or with other chemicals mixed in, and the type of solid or liquid the chemical would naturally become when allowed to do so[5]. With that information at your disposal, it then becomes possible to start modeling a human cell on a computer, start it off with all the known components of a cell, the DNA of a cell, and the starting chemical inputs that the cell would normally have in the human body, then allow the computer program to predict all the chemical reactions that would take place in the cell both as a result of chemical compounds in proximity to each other and as a result of DNA markers triggering specific protien sythesis in the cell. From that, you can then find out what the output of the cell would look like. It’s this output that is necessary to begin to be able to isolate the chemical markers that are out of range in humans with autoimmune diseases or to predict accurately whether an organ donor’s DNA is a close enough match to the recipient for the transplant to not be rejected.

When you then expand this model from a single cell to a model that simultaneously models all the cell types in the human body, and also models the osmotic flow of chemicals and markers from one part of the body to another, then you can finally model the effects of individual gene splicing or even just individual protien sequence splicing in a single gene so that you can predict the results of genetic engineering without just having to resort to trial and error tests to see what will happen. It’s this sort of model that will tell you when you splice in a gene for blue eyes, just what effect that will have on the cells in your big toe. This, in my opinion, is the eventual future of bioinformatics.

Now, where this REALLY starts to get interesting is when the model of the cell is sophisticated enough that you could plug in a specific person’s exact DNA sequence, start the model as embryonic stem cells, and allow the model to progress through growth into a human being. If the model is accurate enough and you plug in the DNA of a person with a genetic abnormality, such as sickle cell anemia, the model should predict that the red blood cells will be deformed when they are created by the bone marrow. If you can get to that point, then medicine could be revolutionized by allowing doctors to plug a patient’s exact DNA into a computer model, run the model, and isolate specific genetic problems, and model custom chemical treatments that could compensate for the genetic abnormality. An industry around custom tailored chemical treatments could be born. What’s even better, is that with the chemistry as physics mathematical system, you don’t have to know about the chemical or how to produce the chemical before hand. The same mathematical system that allows you to model the chemistry of cells would allow you to predict the most efficient methods of production for any given chemical, known or not. And if you can’t readily make it using sythetic organic chemistry[6], then you can allow the computer system to custom design a bioengineering blueprint for you instead[7].

The two biggest hurdles to this are A) creating the mathematical representation of chemistry (it’s going to be a big job) and B) finding sufficient computing horsepower for the model. For A, someone just needs to get started on it. We have a big enough database of chemical reactions that we should be able to start reverse engineering that data into a mathematical model. For B, advances in high performance computing clusters, advances in both processor power and cluster interconnect speeds, and advances in software that help you split big problems into managable chunks will all help. But, a cluster large enough to do this sort of modeling would be prohibitive today. It will be a while still yet before we get high enough processing speeds to implement the model.

1. Modern medicine, aka isolated chemical medicine, is based upon the concept that we can achieve most of the desired results by using isolated chemicals or just a few chemicals. In terms of cellular biology though, sometimes it’s not a chemical, but the relative concetration of lots of chemicals that makes the difference in what particular reactions occur in a cell. This is why it is sometimes difficult if not impossible to isolate a single chemical responsible for the effects of natural/herbal concoctions (the ones that work anyway, a lot of those concoctions are hooey).

2. In any given mixture of chemicals, you will often find that more than just a single, desired chemical reaction takes place. In fact, cell life in human cells is a perfect example of this. As long as a human cell has sufficient oxygen to be used in the chemical reactions in the cell, it remains a live and viable cell. If this oxygen is ever removed while the cell is still at operating tempurature, a secondary reaction takes place. That secondary reaction, in some way (which I haven’t researched, so I can’t name), destroys a necessary part of the cell. As a result, if you then re-oxygenate the cell, the chemical reactions that comprise life do not return with the oxygen. It is therefore necessary to be aware of possible secondary reactions because they usually happen in minute amounts even when the primary reaction is busy taking place, and these secondary reactions are going to create anomolies in the outcome of reaction predictions if not accounted for.

3. The state of any given chemical: liquid, solid, gas; is determined by the inertia of the individual molecules (mass times speed squared) and the strength and elasticity of the inter-molecular bond. For example, a solid at 0 degrees Kelvin has no inertia what so ever. Above that temperature, the molecules have some intertia. However, the inter-molecular bond stretches somewhat to allow for small amounts of movement, but it doesn’t break. At the point the solid becomes a liquid, you have a transition where the molecules finally have enough inertia to break the inter-molecular bonds, but not enough to escape the other closely positioned molecules and their bonds, so the molecules essentially bounce around breaking and reforming bonds continuously. It’s at this point that the molecules can exert a bond force on disparate molecules (such as a salt molecule in water) and the inertia and bond of the two molecules will rip the other molecule out of its solid state, breaking it apart, resulting in the solid dissolving in the liquid. As you add more heat, the inertia gets higher until you finally reach the point that the molecules have enough inertia to completely break free of the other molecules, and you get the transition from liquid to gas.

4. Certain chemical reactions only take place in the presence of a catalyst. Generally speaking, the role of the catalyst is to selectively destroy part of one of the starting chemicals. For example, you may need a molecule of a specific weight and with a specific inertia so that the molecule will have precisely the energy needed to essentially break off part of a stable molecule to make room for a different molecular component to attach itself where you just broke off the item you didn’t want there. The model of chemistry would need to account for this type of selectively forced molecular destruction based upon the weight and speed of atoms/molecules at a given temperature and a given chemical makeup.

5. Most liquids will crystalize as they become a solid, aka water becomes ice. There are exceptions. For instance, glass. The transition from liquid to solid happens so quickly with glass that the molecules don’t have a chance to rearrage themselves into crystals. Knowing the inter-molecular bond strength of a given molecule and the elasticity of that bond should allow you to predict which compounds will crystalize and which won’t. Of particular interest in this respect is whether or not we could find a biologically compatible/inert liquid that transitions to a solid without crystalizing. If we could, then it would be possible to actually make cryogenic freezing and preservation of live humans a reality. Without crystallization, the cells would not be destroyed in the freezing process (yes, this involves removing the water from the human body and replacing it with the other compound, but that would be done after the body is already cooled to a low enough temperature that cellular activity has all but stopped, you then replace the blood/water with this other compound, then freeze the body, then later thaw it out, replace the compound back with blood/water while still too cold for the cells to operate, then warm the body, at which point it picks up right where it left off). This could be used for long duration space travel, or even for such unthinkable things as freezing yourself for 100 years just to see what the future holds, or freezing yourself long enough for medicine to be able to cure your currently incurable disease.

6. Synthetic organic chemistry is a term used to denote the typical beaker and test tube variety of chemistry where you try to produce desired end result chemicals from one or more controlled chemical reactions.

7. Bioengineering is the science around inserting DNA into simple cellular organisms (bateria, yeast, etc.) that cause the organism to produce complex chemicals for you that would be impossible or cost prohibitive to try and produce with synthetic organic chemistry. Since DNA can be used to create protiens that bond to and work on specific molecules, it is actually far more precise than putting a bunch of chemicals together in a glass jar and hoping that the reactions you want will take place instead of ones you don’t want. It’s also far more controllable than the alternative, and not nearly so prone to runaway chemical reactions, explosions, etc.

So, we all use computers. If you don’t, you aren’t reading this now. The next big thing in computers, I predict, is the truly voice interface based computer. It’s slow and clumsy to type into a computer. Today, we already have voice recognition software that uses grammatical cues to enable the software to recognize what you are saying without being trained to your voice. The next step is to reorganize the human-computer interface to change the structure and typical interaction to make more sense with voice commands. Let’s face it, icons and double clicking do not easily translate to voice commands. We need a whole new paradigm to represent how you interact with a computer when it’s listening to what you have to say instead of responding to what you do with your hands. There won’t be an easy translation here, it’s going to require a whole new way of doing things to be optimal. So, I suggest we get off our asses now and start working on a whole new interaction methodology that makes sense to people but isn’t related to the past. Don’t let the bagage of Windows or Mac OS X or Linux limit our future progess. Let’s do it right. The company that does that first, is the future. Period.

I originally had a theory based upon my theory ofPosition Relative Cellular Differentiation that if you could get an embryonic stem cell from a human adult, that you could then place that stem cell in a bath that resembled the nutrient complex of the zygote at very early stages of conception, then add constant stirring to that bath to prevent clumps of cells from forming, then maintain a steady flow of incoming fresh fluid that matches the nutrient rich influx of fluid into a zygote, and that would cause the stem cells to continue dividing indefinitely without differentiating. You could then bleed off the excess bath from the container and that bath would contain some waste chemicals and a steady flow of stem cells. I then read that the embryonic stem cells were separated from the nutrient rich bath by a layer of cells called the blastocyst. I thought that shot my theory to hell. Then I realized that all you had to do was compensate for the changes in chemical markers and nutrients that the stem cells see because of the blastocyst cells and as a result the bath would promote stem cell growth. This mirrors the fact that current stem cell growth methods include a layer of feeder cells on the actual nutrient substrate between the stem cells and the nutrients. So, once again, we need to map out the chemical marker production of cells relative to DNA so we can duplicate the effects of these blastocyst or feeder cells in the base bath mixture so that we can eliminate them from the growth process and get on with the mass production of genetically keyed stem cells that are necessary to correct things like the need for bone marrow transplants, cures for adult onset diabetes, etc.

Carbon nanotubes are sure to become a very important part of our technology over the next 50 years or so. I recall someone bringing up carbon nanotubes as a superior material for the creation of capacitors due to the extreme surface area that is necessary for a good capacitor. There is a similar eletrical principle that electricity (or more appropriately the electrons that move in an electrical wire) are all located on the surface of the wire, and that the center of the wire plays a relatively negligible role in the overall capacity of the wire. That got me to thinking that if you could plate carbon nanotubes with a highly conductive material, such as copper, prior to forming the nanotubes into any sort of shape, that you could then form the nanotubes into a wire form and the extreme amount of surface area to conduct electricity along with the absolutely insane strength of carbon nanotube based materials might make for seemingly superconductive wiring that is able to handle more current in a wire the size of a human hair than you can today in wiring 1000 times larger. In addition, for high voltage wiring that runs from power plants to cities, the extremely small diameter and amazingly high strength of the carbon nanotube based wiring would mean that high voltage power lines would be A) able to carry a much higher capacity than before and B) be immune to things like ice buildup causing power lines to snap in winter. In addition, the amperage carrying capacity of the extremely small wires would totally revolutionize the state of electric motors, enabling nano-sized electric motors and increasing the power output of normal electric motors to entirely new levels of power output. Think of a 100 horsepower electric motor that is the size of an alternator and weighs about 3 pounds and the impact that would have on the feasibility of electric vehicles. A motor’s power is mostly limited by the amperage you can put through the windings in the electric motor and the number of windings in the electric motor. By making super high capacity wiring that is extremely small, the amperage and number of windings in a motor increases exponentially and so does the resulting power.

A group of scientists have learned how to cause a normal human partially differentiate adult stem cell[1] to revert to an embryonic stem cell. By exposing the adult stem cell to a certain chemical concoction, it reverts to an embryonic state. However, it only works on certain lines of adult stem cells. My previous theory about the variance in chemical markers based upon DNA explains this behavior. Instead of using a “one size fits most” chemical marker concoction and mapped out the specific cell’s DNA, you could get 100% of adult stem cells to revert to their embryonic state.

1. Adult stem cells are found in normal adult bodies, but they are partially differentiated already and a predisposed to only form certain type of final cells. For example, all adults have stem cells in their blood, but those stem cells are predisposed to only form blood, bone, and a few other types of cells. By reverting a stem cell to the embryonic state, it is then possible to trigger it to become any cell that the body needs, not just a few types.