The Earth is far more nuanced than the naked eye can appreciate.

The true nature of the universe spoke about 50,000 years ago in our galactic neighborhood. We heard its echoes on December 27, 2004, and we had heard nothing like it before. Mankind truly is fragile. I think we overestimate our durability in the face of the vastness of the universe. That this amount of destructive energy could be so concentrated really boggles my mind, and yet we were over 50,000 lightyears away when it happened. Can you imagine what this would do at closer distances?!

Sorry about the lack of posts the last few days. I was in charge of planning the Chemistry Club’s trip to Sacramento for the ACS(American Chemical Society) Regional Meeting there, which happened somewhat last minute Thursday and Friday. We only had the opportunity to attend the undergraduate day, and found some of the presentations very enlightening (as with the green chemistry seminar given by University of Oregon’s “James Hutchison”:http://darkwing.uoregon.edu/~chem/hutchison.html) and some of them not so enlightening (my lips are sealed).

Overall, a very short trip, but something fun and different to do with the Chemistry Club, which has not done much in past years. As a new officer this year, I have worked with the rest of the officers to conjure up new goals to tackle in order to gather the interest of undergraduates _vis-à-vis_ Chemistry and involve current Chemistry majors more so than in the past. I believe this trip to be an excellent first start in that direction. Our next step will include some fundraising in order to give us the financial freedom to envision even larger goals (Scholarship, National ACS Meeting trip, et cetera).

!(alignright)http://www.sensoryoutput.com/wp-images/postings/psi_large.jpg(Greek letter psi)! Friday in my advanced physical chemistry lecture, we stumbled upon the bizarre reality of the universe in which we reside: collapse of the wavefunction. Before today, I was familiar with such notions, but did not know the explicit name for the phenomenon that many of the great minds of quantum mechanics and physics in the early twentieth century found unsettling. Before I get more into what collapse of the wavefunction is, I would like to say that this discussion starts to cross philosophical bounds that many people have wrestled with for some time. Many scientists find the results a bit uncomfortable (as anyone should who understands what I am about to present).

I have not read the parts of my textbook that cover this, so my explanation and word usage may not be consistent with literature. I will do my best to present the idea. First a definition. A “wavefunction”:http://en.wikipedia.org/wiki/Wavefunction that is a solution to “Schrödinger’s Equation”:http://en.wikipedia.org/wiki/Schroedinger%27s_equation contains the probability of configuration in space and time. Because the configuration of a particle in space can give us certain physical information about the particle (energy, momentum, angular momentum, et cetera), the wavefunction allows for extraction of those physical quantities. (There are some restrictions on what one can and cannot know from a wavefunction modeling a system, but I will not get into those gory details here.)

So, collapse of the wavefunction means that when a physical measurement of a system is taken, the wavefunction (being a probability of many states linearly combined to form a superposition state) collapses to the value measured physically. This may not initially strike you as bizarre or shocking simply because you do not understand the scope of this fact. Here is an interesting example of this phenomenon at work.

Figure 1 shows that a vertically-oriented polarizer (90 degrees) produces vertically polarized light when randomly-oriented incident light passes through it.

!(aligncenter)http://www.sensoryoutput.com/wp-images/postings/pol_fig1.jpg(Figure 1. A vertically-oriented polarizer produces vertically-polarized light.)!

Figure 2 shows what happens when a second polarizer is introduced at forty-five degrees to the first. The first gives vertically-polarized light and the second, produces one-half the intensity of the light produced by the first. Why? The second polarizer is oriented to select only half of the same number of vertically-polarized photons. So far so good.

!(aligncenter)http://www.sensoryoutput.com/wp-images/postings/pol_fig2.jpg(Figure 2. A linear polarizer at 45 degrees will produce one half the intensity of light when vertically polarized light passes through it.)!

Building on the concept presented in Figure 2, we see that two polarizers that are oriented perpendicular to one another in Figure 3 and allow no light through. These are often termed cross-polarizers.

!(aligncenter)http://www.sensoryoutput.com/wp-images/postings/pol_fig3.jpg(Figure 3. Two polarizers perpendicular to one another produce no light.)!

Now for the weirdness of the universe that is collapse of the wavefunction. In figure 4, if we introduce a third polarizer at forty-five degrees between the two crossed polarizers, we expect that the light coming out the end to be of zero intensity. Why? The second polarizer selects half the light (3) coming out of the first (2). When this light passes through the last polarizer, we expect it to block all light given that it should block all vertically-polarized light. But, as it turns out, the light is no longer vertically polarized. Upon making the measurement of the polarization, we have caused the wavefunction that defines the orientation of the light to collapse to the measured value as it emerges from the second polarizer. So, the next polarizer selects only the horizontally-polarized light, producing half the intensity of (3). Bizarre huh?

!(aligncenter)http://www.sensoryoutput.com/wp-images/postings/pol_fig4.jpg(Figure 4. We introduce a third polarizer and expect no light at the end, but this is not the true result.)!

For the longest time, I was perplexed about the nature of polarizers in my research. The activity of one polarizer is not that bizarre and neither is two, but when a third is introduced, these contradictory behaviors emerge that defy the logic that drive the activities of the one- and two-polarizer setups. I am still perplexed by this result, but at least I can now attribute the behavior to some phenomenon. I’ll post another example about this another day.

When I began pondering this more on Friday, I was inclined to ask what is happening physically that causes such a result. That is difficult to answer, but as it was explained to me, the act of measuring disturbs the wavefunction, altering it and causing it to take on the form that gives the value extracted. I am not sure if I have explained this well enough, but if you have questions, please post them!

Tonight, I decided to complete my advanced physical chemistry problem set far ahead of Friday’s due date. One of the problems asked for a reason why nuclear fusion in stars is possible given that the hydrogen nuclei do not possess enough kinetic energy to overcome the coulombic repulsions of neighboring nuclei (thus preventing fusion). Classically, the law of conservation of energy would say that nuclear fusion within stars in not even possible, but we all know this to be true, so what is going on?

Well, in short, by confining the hydrogen nuclei in a well of sorts, the energies are quantized and the wavefunction solutions to the Schrödinger equation the of those nuclei give that there exists a probability that the nuclei will exist outside the well—where other nuclei live. (Think tunneling.) If two nuclei are close enough, then fusion occurs. Cool!

!http://www.sensoryoutput.com/wp-images/postings/pchem.gif(Wavefunctions of a particle in a one dimensional asymmetric square well)!

“SpaceDaily.com”:http://www.spacedaily.com/ recently published an article entitled “Vast New Energy Source Almost Here”:http://www.spacedaily.com/news/energy-tech-04zze.html. The new source? Hydrogen. You are probably wondering why hydrogen is being called a new energy source, as we already know it can be harnessed for use in fuel cells. The big deal here is the collection of hydrogen in a environmentally clean and green manner. Generally, the creation of one energy source requires some use of another. For example, many car manufacturers in the 90s touted their all-electric vehicles as green, yet in order to recharge them, they were plugged in at home and pulled energy from the grid—energy created from fossil fuels. So much for clean power! The same principles apply to hydrogen: some energy is required to evolve the gas from water, but if that initial energy is renewable, the hydrogen economy of the future can truly be green.

Enter solar power. Using a combination of solar power and catalysts, scientists have created a viable system to splitting water into hydrogen and oxygen gases in a clean manner. I have often spoke to my friends about a future energy supply that is completely renewable, the idea stemming from the use of solar energy to produce hydrogen, which can be stored for later use. Certainly there still exist some caveats to a hydrogen economy such as distribution, storage, and safety, but cost and ease of production is hardly an issue with this and other new innovations.

Imagine a distributed hydrogen economy where every household produces its own solar hydrogen for use in a small fuel cell generator. There would be fewer issues with distribution, far greater efficiencies as power would not be lost as heat over long-distance electricity grids, and cost would really only include the initial outlay for the generator/solar system and maintenance.

Still, this is all years out, but with the research surrounding fuel cells and the rise in production and use of fuel cell generators, it shouldn’t be long now.

As I usually do, I checked out “Science Daily”:http://www.sciencedaily.com/ yesterday and found an interesting article entitled “New Way Of ‘Seeing’: A ‘Neutron Microscope’”:http://www.sciencedaily.com/releases/2004/08/040804085752.htm. Certainly, upon reading the title, it makes perfect sense that one can use any subatomic particle as an imaging medium so long as: 1. it interacts with the subject intended to be imaged, and 2. is capable of being detected (and focused) easily. (Actually, the two requirements are really just one, as one cannot detect a particle without interaction.) For example, neutrinos, which are almost-massless particles that are emitted from suns by the billions of billions, pass through our bodies every second, but rarely interact with our matter. As such, neutrinos will fail to serve as the probe in a diagnostic imaging device.

The most pervasive particle/wave used for imaging is the photon. Varied energy photons give information about matter with which they interact. For example, infrared photons equate to the vibrational energy levels between atoms in a molecule and microwaves correspond to the rotational degrees of freedom in a molecule. Another particle used to image is the electron (as in a SEM(Scanning electron microscope)).

The article discusses some of the details about the device and what it was tested on (a rat). The press release, however, fails to mention the effects of neutrons on living tissue. Neutrons do interact most heavily with hydrogen (of which our bodies have a lot), but does this interaction involve radioactive decay? I would imagine not simply because such activity would require high energy neutrons impacting a nucleus: the neutron source in this microscope probably emits low-energy neutrons just strong enough to pass through dense tissues like bone. Of course, this is just a supposition, so anyone with more knowledge in the area of particle physics better speak up.

I know I promised something yesterday, but a 42.9 mi (69.0 km) bike ride averaging 19.7 mi/hr (31.7 km/hr) and climbing over 2700 ft (823 m) really drained me for the day. I did another 30 mi today at a killer pace thanks to the same group really pushing my current limits, but I feel great and ready to start another week. Here is a post as promised.

Although this story was released last week, it is the “Nature Medicine”:http://www.nature.com/nm/ August cover story: “Scientists Finger Surprise Culprit In Spinal Cord Injury”:http://www.sciencedaily.com/releases/2004/07/040729092834.htm. Well, what wrecks havoc at the site of a spinal cord injury, often resulting in debilitating, permanent paralysis? ATP(Adenosine Triphosphate), a versatile molecule that powers events ranging from protein folding and processing to intra- and inter-cellular signaling. Clearly, ATP’s high-energy phosphate groups also serve a negative function, turning this life-giving molecule into a killing machine:

bq. The finding that ATP is a culprit in causing the devastating damage of spinal cord injury is unexpected. Doctors have known that initial trauma to the spinal cord is exacerbated by a cascade of molecular events over the first few hours that permanently worsen the paralysis for patients. But the finding that high levels of ATP kill healthy cells in nearby regions of the spinal cord that were otherwise uninjured is surprising and marks one of the first times that high levels of ATP have been identified as a cause of injury in the body.

Using mouse models, the study shows that by inhibiting the effects of ATP neurons, mice who suffered spinal cord injuries recovered much of their original function. This provides great hope that people who suffer such injuries may one day be treated within minutes, preventing the hazardous effects of ATP.

I do not have access to the original article, but the press release touches briefly on the origin of ATP in the spinal cord. Interestingly, astrocytes, a type of support neuron, produce ATP in high quantities. In addition, neurons in the spinal cord have a so-called “death receptor” to which can ATP bind that activates a internal signaling pathway triggering death. The rupture of these astrocytes may well release the ATP, leaving it to cause the death of neurons and further harm the accident victim. This sort of activity is very similar to activity found on the cellular level around a cut or scratch. When cells around a wound rupture, they release their contents including various enzymes and ATP, damaging other nearby cells and causing a cascade of events resulting in a clot and arrival of immune cells to ward off infection.

This analogous activity in the spinal cord is somewhat puzzling from an evolutionary standpoint. Clearly, scientists have not yet learned of any function ATP serves in healthy individuals _vis-à-vis_ these death receptors (or this study would not have been as surprising), so now attention must turn to understanding what “normal” purpose this receptor serves during the lifetime of a neuron. I might hypothesize that this may exist simply for programmed cell death upon reaching a certain age. Then again, I might be proven wrong and the real result may be just as unexpected as this discovery here today.

Disorders of the mind are particularly complex given we understand relatively little about the physiology of neurons in the brain. Recently, there have been several developments on this front. A research team at Cornell University “found evidence to support(Laser Microscopy Technique Settles Long Debate About Brain Chemistry, Could Aid Studies Of Alzheimer’s And Stroke Damage)”:http://www.sciencedaily.com/releases/2004/07/040702093449.htm the Astrocyte-Neuron Lactate Shuttle, a hypothesis surrounding metabolism and how the brain uses energy stores. Specifically, by using a multiphoton laser microscopy technique, the researchers were able to observe two fluorescent—not _fluorscnet_, sorry inside joke—energy states of NADH(nicotinamide adenine dinucleotide). They saw that particular coenzyme undergo specific changes that supports both theories that the brain burns glucose completely to oxygen and water while also using lactate from astrocyte cells as an extra energy store approximately ten seconds after a neuron is activated.

By more fully understanding how the brain uses energy upon activation, the study’s authors point out that research into diseases of the brain should be better able to understand why neurons go haywire (either by dying, losing functionality, or stop producing a particular neurotransmitter) and cause such diseases.

In other related news, researchers at believe they have found a “brain serotonin enzyme that might explain psychiatric disorders”:http://www.sciencedaily.com/releases/2004/07/040709085406.htm. Although this enzyme was found in mice, human beings have a great deal of genetic material in common with these creatures. As such, researchers posit that human being most likely carry the same enzyme or an analog that closely resembles it.

Why is it important to have found such an enzyme? Serotonin is a neurotransmitter, levels of which have been shown to drastically affect mood, appetite, personality, etc. Low serotonin is believed responsible for psychiatric disorders like depression, PTSD(post traumatic stress disorder), and sleep-related illnesses. Clearly, by understanding what processes in the brain cause serotonin mRNAs to be transcribed, drugs can be altered to either mimic the effect of this enzyme if it is indeed misfolded or not present due to a mutation or increase its effectiveness in causing transcription of the RNA precursors to serotonin.

Of course, do not expect practical applications anytime soon, but this discovery bodes well for those suffering from related disorders.

(BTW, I’m posting a trackback to “NSLog();”:http://nslog.com/, as he is testing trackbacks. I know this is totally unrelated to the content of this post, but I don’t really feel like posting another just for this purpose.)