Showing posts with label physics. Show all posts
Showing posts with label physics. Show all posts

Friday, October 16, 2009

empty thoughts X

I perceive evolution of knowledge not as continually growing and expanding, but as serially destroyed and recreated.

Expansion is a popular chimera of growth. We think of the universe in terms of ever-orbiting away from those centers that we have identified. We think of political change as manifestation of new direction. We think of steps forward in technology as bursting revelations. But are all of these things not brought about by reconfiguring previous conceptions?

Matter is never either created or destroyed, but recycled. On a quantum level, that's almost always true. On a grossly observable level - the level of content - it is created and destroyed all the time. Not a thing has been brought to my attention that would suggest the growth of knowledge proceeding any differently.

Tuesday, September 9, 2008

LHC and the God Particle

First of all, I am way, way too excited for Wednesday.

Murray Gell-Mann simplified the zoo of fundamental physical particles in the 1960's by identifying their similarities in their symmetries. All 80 (or something) types were made up of three quarks. In the late 60's, the first electron micrographs of protons were taken, finding within this fundamental particle three smaller particles of the correct charges, but of indiscernible structure. These quarks, together with the electron and electron neutrino are capable of explaining everything in the actual world. Among the things that remain unexplained is why there are three families of each of the aforementioned, which are identical in every respect except that they are of three different masses. How is it possible that there are, in perceivable existence, three versions of the exact same fundamental particle which perform the exact same function and have what appears to be the exact same structure?

There is another particle, called a Higgs boson, which - should it actually exist - answers the profound question of why and how things acquire different masses, why so many distinct fundamental particles can arise from the same three quarks, why unique particle interactions occur in particular fashions, and exactly which roles those forces play in our universe.

Particles gain different masses because of the different ways in which they interact with Higgs bosons. Essentially (and I'm not going to try to tackle the actual equations because my mind is feabile and my brain is exhausted), Higgs particles are dark matter. They fill every "empty" space in the universe, and as fundamental particles stream through the universe, those that are said to acquire mass are bombarded with Higgs bosons which slow down their streamline. Those particles which do not acquire mass (photons, etc.) are not impeded by Higgs particles... hence, nothing travels faster than the speed of light :)

The Large Hadron Collider at CERN has been designed (and under construction and legal debate since 2003) to see if the Higgs boson can be revealed. The problem with the Higgs boson theory right now is that it is just mathematical theory - there is no physical observation. The idea behind the LHC is that, as it is a particle accelerator, the collision of protons accelerated within it can result in the creation of a new particle. The energy created by the collision is proportional to a mass (this is the real meaning of E=mc^2), and so a new particle with a new mass can result.

This is why tomorrow is so fucking sweet. Tomorrow... Sept. 10, 2008... and more importantly, Wednesday... the LHC will be "turned on," and the first proton beam will be circulated through the tunnel. The Tevatron particle collider in the Fermi Lab outside Chicago is almost as powerful as CERN's LHC, and may have already shown the existence of the Higgs boson, but have not produced any data, as such. The idea of the LHC is to recreate the conditions up to milli-seconds following the Big Bang, and hopefully make strong suggestions about the nature of this minor event in history.

The identification of the Higgs boson would mean remarkable things for the entire world of physics, beginning with the completion of the Standard Model of particle physics. Specifically, the Higgs boson would give a distinct variable to the differences between massive and massless particles, thus making possible concrete suggestions (as opposed to theoretical) about the nature of the relationship between the four fundamental forces (electromagnetism, gravitation, weak and strong nuclear forces).

Ergo... more redefinition and tweaked theory of the Big Bang.

Boom.

Sunday, August 3, 2008

electron tunneling

In case you were wondering what gets me off...

" By comparison of the measured IETS (*inelastic electron tunneling spectroscopy) spectrum of this molecule with the computed one, it is possible to examine the relative intensities of the different vibrational normal modes, thereby to deduce the pathway for transport. We find that the electrons are injected through the terminal methyl group, tunnel through the sigma bridge to the etheric linkage, mix with the pi electrons, pi tunnel through the aromatic, and switch back to the sigma tunneling, through the thiol and out onto the counter electrode (Galperin and Ratner)."


Bit of background... this was a studying looking at molecular transport junctions wherein a molecule is placed between two electrodes and subjected to applied voltage. This kind of analysis shows particular modes of transport pathways for electrons across the molecule by way of interpreting the molecular junction geometry. This is hot shit because delocalization of electrons across molecules - and in particular, proteins - has the potential to give a great deal of information about protein folding mechanisms...



Protein folding is a fairly simple concept: when DNA copies, it translates its code into a sequence of amino acids. The aa sequence comprises what is called the primary protein structure. AA then fold, through several types of electromagnetic interaction, into secondary structure which begins to take on 3D characteristics. Secondary structure can then fold into several different types of final form, depending on the protein's destined function. But for the purpose of where I'm going with this, I'm going to refer only to primary and secondary structure.

there's a reason that computer modeling has trouble accurately replicating the speed in which proteins fold into their final conformation. that reason is electron tunneling.

in proteins there have been found to exist very significant long-distance tunneling currents of superposed paths over which electrons can delocalize across an entire structure - not just between neighboring atoms which was the conventional assumption.

what this means is that an electron localized to... atom A... can enter into a more delocalized, higher energy superposition between atoms A and B. when it yields back this high energy state, the electron can then relocalize to B rather than back to A, if this is energetically favorable. sound familiar? this is basic electron transfer. now imagine the same mechanism occurring between amino acids of primary and secondary protein structures. because the distance between aa is so much greater than between individual atoms, electron coupling falls away and electrons must delocalize via tunneling currents, connected by "bridges" which enhance tunneling along multiple superposed paths within the molecule.

for instance, in the tubulin protein alpha and beta dimers that make of microtubules (previous post) contain a somewhat patterned arrangement of tryptophan amino acids, arranged all within 2 nanometers of each other. because tryptophan aa contain not only an aromatic ring, but a double aromatic ring (an indole), they provide a tremendously stable delocalization site for electron density, and are thought to be key players in the tunneling current in and between tubulin dimers [this is the tunneling that causes the conformational change in alpha and beta monomers that result in the propagation of an electrical signal down their lattice in the microtubule].

the signal is not just propagated by means of the tryptophan current network; there is also a lattice composes of the aromatic substituents of histidine and phenylalanine amino acids, which correspond to an additional three tunneling possible tunneling patterns. this current-strengthening effect is responsible for the nature of the electromagnetic signal as it is transfered down a microtubule, and from one microtubule to another.

it works as such: the transfer of an electron from one space in a primary structure to another space causes a conformational shift which directs the primary structure to take on secondary characteristics. cysteine amino acids will be reoriented such that they are within few enough angstroms of one another to be reduced to form disulfide bridges... hydrogen bonding will cause proline rings to the outer surface of the molecule such that a helix is left handed as opposed to right, etc. the reason protein folding can occur so rapidly is that this works the other way as well: conformational change of the protein as it folds influences changes in the tunneling current pattern so that the tunneling options electrons have are altered (Balabin and Onuchic 1998).

the remaining question, then, is what controls the dynamics of tunneling electrons? something to do with phonons (vibrational degrees of freedom) as produced by tunneling effects, which then enhance feedback between tunneling current and conformational changes. my understanding of electron-phonon interaction, however, is excruciatingly limited.

i must find someone to educate me on this one... quite frankly, i'm tired of staring at primary literature trying to navigate my way around equations for this shit. where is my on hand physicist?... i can't fit this into my theory of conscious DNA until phonon emission finds its place! gr. grumble. pass out.

Sunday, July 6, 2008

meat machines

"we are automata entirely controlled by the forces of the medium, being tossed about like corks on the surface of the water, but mistaking the resultant of the impulses from the outside for free will" - Nikola Tesla

i'm about to disagree with my hero - my high school english teacher would shit himself in exaltation right now.

i agree that we are - because we are meat machines built of subatomic wave-particles - automata in the mechanical sense, our medium being the zero point field, i will also agree that we are tossed around on it like corks. however. i will firmly stand that this does not eradicate free will.

so here's why this works. and it only works under the pretenses of a monist world - one in which there is only one substance that makes up reality, which is to say, mind substance and matter substance are really both one energy substance [and yes, in terms of being corks, monism requires Bohm's gnosis: in order to bobble on the surface of the implicate zero point field, our meat machines need be explicate... elsewise, gamush] . this eliminates the fragmented and confused amalgam of the Western worldview. which is fine with me, because on the quantum level the monist view is the only one that really makes sense anyway. matter is wavelike; it is waves of possibility which can be in two or more places at once as it emerges from the superposition of quantum possibilities.

quantum objects, then, exist as the superposition of these possibilities until our observation collapses them into an actuality, or a single localized event. this is to say that observation alone transforms existent possibility into an actual event - causation. this is how the mind exercises free will.

Newtonianly speaking (muddled laugh...), the theory of causation is an upward theory: causal interaction moves from the micro-level quantum particles up to the macro-level brain and consciousness. this ordains causal power to none other than interaction between quantum waves. the problem here [keeping in mind the monist idea that matter and consciousness are both comprised of wavelike possibilities] is that if there were only upward causation in the world, our persons, as nothing more than material possibility, would not feasibly be able to cause the collapse of other waves of possibility into actuality.

ergo, downward causation gives consciousness the power to choose between material waves of possibility provided by quantum objects.

there is, of course, a paradox here. downward causation is discontinuous... mostly in the sense that it is circular: the observer is essential for the collapse of possibility into actuality, however, the observer in itself is merely a possibility before the collapse has taken place. so... there's something that needs to be algorithmically defined in the distinction of a monist world...

nonetheless, monism is how i've rationalized free will. sorry Tesla.

we are all of he same electromagnetic field energy (which arises from zero point). it is the fuel on which everything physical - animate and inanimate - runs. in the body, the field moves through subatomic processes, molecular reactivity, tissue function and organ cooperation. as it moves... as it interacts with the meat machine, two things occur (obviously more than two things occur, but for the sake of coherency...). first, the matter itself is altered with each interaction - this is upward causation. as in the brain, when you learn something new the biochemical feedback cascade mechanisms in the synapses at work are changed such that the next time the learned issue is encountered, the brain responds with increased sensitivity, or biochemical familiarity. second, as the field moves through the meat machine, the wavelengths produced in the zero point field interact with each other to produce interference patterns which (along with Gibbs free energy which i haven't fully reasoned yet but have insisted is involved) produce consciousness. mind is, then, a byproduct.

this is why free will still works. if mind is an emergent property, then we can all be explicately run by the same electromagnetic field, but as it interacts differently over space/time with our differently sensitive meat machines, different minds are produced. and because mind then has some control over the guiding of subsequent energy through the machine - downward causation - there develops a level of free control over the ultimate behavior.

i'm still working this out... it's entirely fractured thought at this point.

Monday, June 23, 2008

fragmentation

David Bohm is a deity.

i am completely and utterly overwhelmed by this tidal wave of a theory into which i've recently dove.

Bohm's premise for the ideology of a new order of physics is that we - as humanity and as scientists - define the universe in terms of the Cartesian definitions of matter. that is to say, our perceived reality exists as a one-to-one correlation between the space/time coordinates of all matter. what Bohm suggests (and this is from 1980 so it's by no means a hot new thing) is that our reality is skewed by the fact that we perceive it in terms of fragments, or individual chunks of matter. namely, individual objects are the primary products of existence, and their continuity is secondary if regarded as important at all. to remove this fragmentation - which is implicated as paramount to reality being an illusion instead of, well, a reality - Bohm introduces the idea of Implicate and Explicate order.


Assumptions:
1. quantum particles are amplifiers of information contained in the quantum wave
2. two subatomic particles once interacted can respond to each others' motions thousands of years later, light years apart
3. space and time are derived from the Implicate Order; everything is connected such that any individual element can reveal information about any other element in the universe


The Holomovement:
a hologram is created when two interfering wavelengths collide, id est, information about the entire holograph is revealed by a single frequency of the film because every point is completely determined by the overall configuration of the interference patterns. the whole is implicit in each part. the holomovement, then, is essentially the feedback mechanisms between implicate and explicate orders.

Consciousness:
one moment gives rise to another in which the context that was previously implicate is now explicate, and explicate context has reverted to being implicate. is consciousness an interchanging feedback where implicate information forms the explicate world which then reverts to the implicate world and portrays to it new information? can we accumulate perception in such a way as to develop a self in this kind of fashion? what explains the exchange of information between implicate and explicate worlds? well, subalgebra. the superposition of series such that one enfolds into a transformation of the former. so an element undergoes a set of Euclidean metamorphic operations which can be used to describe the quantum content of an object. if two elements are similar in a set of operations, then there are a superimposed set of elements that describe the metamorphoses in a similar way. namely, Euclidean systems exercise superposition such that there will always be a system, E', enfolded relative to a previous system E. how the subsequent unfolding occurs such that E is mapped back onto E'... i have no idea. i'm getting there. for now i'm just blown away. phoosh.

But as an introduction to what i'm sure will be a series of flabbergasted nonsense regarding, i feel that i should state that my primary interest at this point relative to the Implicate Order is that each individual participates in the content of the explicate world as points in a holograph... without one, the explicate world is incomplete. we are fragmented by individual avoidance of dissonance and cultural memes. and we are whole as the exchange of implicit and perceived waveforms and interference patterns.

Wednesday, November 7, 2007

supervenience of subconsciousness

“It is clear that there is no more of a conceptual entailment from biochemistry to consciousness than there is from silicon of from a group of homunculi…. So consciousness fails to logically supervene on the physical.”

Chalmers is suggesting that consciousness can't be reduced to a physical structure or property because the silicon model of neural circuitry is functionally identical to biochemical neural circuitry, yet the silicon model can't exhibit consciousness. This is an assumption that silicon and neural circuits are identical... but I would contend that there is a “conceptual entailment from biochemistry” that provides a physical property on which consciousness may very well supervene.

The difference between a silicon and neural circuit is plainly that the former is closed and the latter is open... such that the electrical flow of messages through each respective circuit may occur in the same phenomenological fashion, but not the same physical fashion. Namely, when circulating an electrical signal, a closed circuit releases energy only in the form of heat, whereas an open circuit releases energy as mostly Gibbs free energy with the ability to do work, and very little heat. A silicon circuit is not self propagating, namely, through its path it meets only with resistors and inductors which cause it to dissipate heat. However, a neuronal signal is self propagating, and free energy in its environment is both consumed and produced by that process. This, of course, is assuming that energy and heat are physical properties on which consciousness might supervene. Since the free energy has the capacity to perform work, and heat does not, the neural circuit is the one with the ability to support consciousness.
Because free energy is undefined aside from its ability to do work, it is possible that this particular physical property is the medium through which neural structure and consciousness are connected. Therefore, I propose that the changes in free energy that occur during electrical signal propagation in a neural circuit may be the physical cause of consciousness. Free energy, being the physical difference between a neural and silicon circuit, would explain consciousness arising in one and not the other, and provide a physical property to which consciousness might be reduced.

But all this... is written out of fear. If humans manage during my lifetime to find the physical matter of consciousness such that we can replicate it... my soul will crumble, and my fascination with the human condition will suffer a dreadful, murderous demise. As a neurochemist, I need for there to be some manner of correlation between biochemistry and consciousness. As a mind, I need for that matter to be untouchable, and irreplicable.