The Dawning of a (not so) New Kind of Science

I nearly forgot that I had this blog. I wish I could blame my absence on productivity elsewhere, but I have nothing to show for that. So instead, I will blame my absence on pure laziness.

I have decided to change the title of the blog to reflect a change in my passions. I am still a chemical physicist[1]. However, I have a new trajectory in my studies: biology.

The material that comprises a cell is spectacular on a chemical level. And though some people have taken the awe of the environment and ascribed to some fluffy nonsense, it is this very aspect of biology that has me intrigued. So I decided to stop staring at simple molecules and instead focus on the problems that seem to plague modern biophysics.

Every century has brought new insights into the nature of reality. The nineteenth century brought about Charles Darwin's theory of evolution, the discovery of vehicles of trait inheritance (genes) by Mendel , Maxwell's equations for electrodynamics, and the birth of statistical thermodynamics from the mind of Boltzmann. The twentieth century gave us complete understanding of the atom and allowed us to probe further the nature of molecules and the phases of matter. From this we were able to find the molecular basis of genes (DNA molecule) and the molecular composition of life (eg. proteins and cell membranes). So what will this century bring us? What exciting new discoveries could possibly arise?

This is an exciting time for this field of study. Computational power is now relatively cheap. We can run near pico-second simulations of common cellular processes. We are extending the capacities of abstract mathematics to link quantum processes with classical calculations to allow simulations of enzyme activity. Life is being explored at the atomic and molecular level, and it is at this level I feel that we can gather appreciation and understanding of our evolutionary past.

This isn't "new" for many people. Biophysics is a field older than me. But it is an ever-expanding field with high strung investigators desiring to change the landscape before them. And to this, I tell the Rabbit I will follow him down the hole and see where this takes Us.

This blog will continue (i.e. start) to talk about chemical physics, but there will be larger emphasis on biological processes. I decided to change the title to Scienctific Elucidations to better reflect the unification of biology, chemistry, and physics [2]. The URL has changed as well to reflect this. Happy journeys to my fellow travellers!
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[1] That's a fancy way of saying "I'm still a physicist imprisoned in the chemistry building".
[2] Plus, "bio-chymico-physico elucidations" seemed too much like a toungue twister

Necker Cube Redux

Looking at the necker cube again, I noticed something cool. There is actually a plausible 3D shape in the drawing; a kind of trapezoial looking structure. Treat the middle rectangle as the top (blackened in the image attached). Treat the trapezoids which share the sides of the center rectangle as side of the 3D figure. Do the same to the triangles which meet at top-left and bottom-right corners.

What do you see?

Maybe I'm juts making this up though...I need to stop staring at this thing and actually study for my finals...

This Spinning Ballerina and Other Curiosities About Our Perception

This is an old optical illusion, which had been erroneously associated with a right brain vs. left brain test. But for the past few days I can't help but constantly think about it and the implications the results have. Here is the image of the spinning dancer:

Of course, the phenomena involved is the same as that of the Necker Cube:

The astute observer notes that our brain is attempting to make sense of visual information before us that is lacking in very crucuial information. In this case, both the cube and the dancer are two-dimensional objects with no real cues on the depth of the object being presented. However, our brains process the given image three-dimensionally since they seem very familiar to us already.

We have all seen cubes before. We expect cubes to have a specific length, width, and height that are equivalent. The necker cube seemingly has such proportions, but it has no means of biasing our interpretation of the three-dimensionality. The front of the cube cube can be either the lower-left square or the upper-right square. Instead of viewing the image for what it is, several rectangles that either share sides or bisect one another, our brain interprets the shape into something familiar.

This is what is happening with the dancer. the dancer does not exist. It is a two-dimensional piece of art that moves. It is really an assimulation of pixels of various shades of grey and black changing with time. You can literally sit here and determine the trajectory of various pixels over time, and consider the motion as oscillatory.

But our brains aren't programed to initial think of the dancer as a collection of composite pixels. We see an image. The initial guess is that of a dancer, and the collective motion of the pixels gives rise to a spinning dancer. But which way is the dancer truly spinning? Due to the lack of specific cues in the image, the dancer can spin either way for an observer. The image possesses an instability due to lack of information, and our brain simply choses a direction of spin.

You can stare at the image and get the spinner to spin either clockwise or counter-clockwise. That is a fun feat. But the real power comes from seeing the motion of the pixels themselves. That is, instead of seeing a dancer that is spinning, you are observing instead the oscillatory motion of the collection of pixels. To do this, you need to consciously trick your brain.

First, stare at the extended foot. When it reaches the extremum on one side of the image, try and follow the foot as if it is returning the way you saw it spin. You may not be successful at first, but keep trying. You should be able to finally achieve the interesting feat of seeing the image for what it truly is.

All images that possess the multistable perceptual phenomena have a real shape and then the percieved shape. The Necker cube is really a collection of two-dimensional shapes. The dancer is really pixels in motion across a screen. But our minds didn't evolve under conditions of being astute geometrists or graphic designers. It evolved under the necessity to process information and to make assumptions. In real environments, such assumptions have utility, such as maintaining survival. In highly contrived environments, such as those available to us through the means of technology, we can manipulate these perceptions and see where the assumptions are created.

This is what has amused me for the past few days. What do you think?

An Update

I almost forgot I had this blog.

A little background story for those unfamiliar with who I am. I am a first year graduate student at the University of Illinois in Urbana-Champaign. As a first-year, your goals are to (1) pass classes, (2) teach undergraduates, and (3) find a research group. Actually, the most important one is the last one, but the others need to be accomplished as well.

Objectives (1) and (2) are easy to do, especially when the course you teach is general chemistry and the courses you are enrolled in you have taken as an undergraduate before. In my case, I just had to brush up some more on chemical equilibria[1] and with being a physics undergraduate I have already suffered through enough mechanics (classical, quantum, and statistical) to last me awhile. It is that pesky (3) that is seemingly difficult.

This is the step/level I am stuck on. I came here for several specific reasons, most of which seem to have gone by the wayside due to circumstances beyond my control. I have a couple of options left for me, but they are closing fast. Objective (3) has kept me the busiest. I don't burn the midnight oil on my homework or on grading quizzes. I've been burning it to try and figure out what my next move is.

I came here to do chemistry, but if push comes to shove, I may have to defect to another department/program altogether. Perhaps a masters in mathematical physics would open more doors for me? The future is a blank slate ready to be written on.

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Notes:
[1] Actually, the correct term would be to "dumb down". Apparently, chemical activities are not taught on the freshmen level...

Chemists have a sense of humor

Science is a human endeavor, and so humor tends to be intertwined amongst the seriousness. This webpage with various silly-named compounds is a prime example. I might buy the book for my desk to keep me smiling throughout the day.

Now that the politicking is done...

We should be amused by some weird ads.

My all-time favorite: Chuck Norris supporting Mike Huckabee. Only for the weird punch-ending:



Okay. Giant man in a business releasing some sort of strange liquid on a crowd of peons below while maniacally laughing. Fucking brilliant! Sure, it's "gasoline"...




"San Francisco values" is a keyword amongst conservatives that means "things I ought to hate". But that isn't what's funny about this ad. What's funny is the awkward three dancers that appear at 0:13. Are they supposed to represent the debauchery that happens at San Francisco? Oh well, judge for yourselves the oddity of the three random disco boppers:



This is a really odd collection of stock film that is reminiscent of 1940s French surrealism. But the most hilarious part comes at 0:10. i recommend people to stop the film there to bask in the glory of apparently proverbial butt rape.



This next one should win over voters. Yay, puppies! Oh, wait. Weird close-up of dog feces, and an even more bizare subtitle "Experience" while the candidate cleans the fecal matter off the ground. Gah, no wonder this one lost the primaries:



This is one way to try to get the young vote: remake Johnny Cash's "I've Been Everywhere" with a side-reference to a Bob Dylan classic, "Subterranean Homesick Blues". My only criticism: he obviously didn't hep make the song, since he didn't even strum a real chord in the beginning of his ad.



This is just a very weird ad showing paranoia. Funny historically, because he didn't get this out in time to head-off his associations with oil executives being in ads from independent groups and Al Franken, his opponent:



Very Mac vs. PC like commercial concerning the "Prop 8" in California. I think I will take hints from this commercial on how to pick up progressive, liberal ladies:




Okay, I love Nader. I voted Nader, and I've supported Nader since 2000. But this is a really strange soliloquy to Cardozo the parrot where Nader is addressing his angst about the apathy of America toward the corporate chains latched onto her and whether he should dress up like a Panda. I think he should have skipped this strange video with the cute parrot and just dressed up like a panda.

A pitiful attempt to defend Palin's understanding of the Office she seeks

Already our favorite dipshit is echoing the talking points of the Palin apologists. She "watered down" the explanation since the question was asked by a third grader. To wit, any reasonable person would respond, where was the third grader in the room?

And his deflection to typical rabble is funny. Yes, the Vice President presides over the Senate, as stated in the Constitution. The Pope also shits in the woods, so tell me something I don't know already.

Presiding over the parliamentary procedures as a means to exert power is a dangerous game. To wit, the example of John Adams, who was perhaps the most active Vice President toward his Senate duties in history, but his activity nearly cost him his political career. Since there has been a longstanding tradition of VPs running for head cheese, they tend to relgate their formal duties to the President pro tempore.

Now, onto what Palin actually said:

That’s something that Piper would ask me! … [T]hey’re in charge of the U.S. Senate so if they want to they can really get in there with the senators and make a lot of good policy changes that will make life better for Brandon and his family and his classroom.

Err... no, not really. The President of the Senate can make judgments on point of order and other typical rules of order, but they don't "get in there with the senators". Silly gibberish coming from someone who seems to have never been bothered to read the Constitution at least once.

But I expect nothing less from my favorite little dipshit. Keep on defending the worst vice presidential candidate ever.

The GOP is having a cow over ACORN

But something tells me that the same nitwits who clamor on about ACORN will give the same condemnation to Young Political Majors.

Funny how the mind works in crank land.

Irony makes the world go round

While we have some anonymous election lawyer stirring the moonbats into a frenzy over a possibly legitimate case, the FBI is investigating ACORN on potentially aiding in voter registration fraud.

Unbelievable. Something tells me that those self-proclaimed "intellectually honest" GOP loyalists are cheering on the FBI, while the more sane GOP members are bashing them. Say, former US Attorney David Iglesias, one of the attorneys who was fired for not kowtowing to the ridiculous demands of the GOP to prosecute ACORN and other similar programs for voter fraud back in 2006.

Irony makes the world go round, it seems.

I question this anonymous source

PajamasMedia has posted a story from an anonymous election lawyer about the Tan Nguyen indictment. However, I think this anonymous lawyer needs to relook at the history of the case.

For Spanish readers, here is the original letter. For those who lack the education in Spanish, the "damning" portion translates as follows:

You are being sent this letter because you were recently registered to vote. If
you are a citizen of the United States, we ask that you participate in the
democratic process of voting. You are advised that if your residence in this
country is illegal or you are an immigrant, voting in a federal election is a
crime that could result in imprisonment, and you will be deported for voting
without having the right to do so.

The backstory, according to the LA Times article previously linked, was that the original letter in English had "green-card holders", which was translated into Spanish as "emigrados", which translates back into English as "immigrants".

Of course, green card holders cannot vote, so the original English draft was correct. However, immigrants can, so long as they are U.S. citizens. It is important to make such a syntactical distinction. An immigrant is anyone whose country of origin is different than the one they currently reside. An illegal immigrant is one who resides illegally in a country not of their origin. A legal immigrant is one who resides legally in a country not of their origin. Legal imigrants include not only people who have green-cards and similar documentation, but also people who have become citizens through the naturalization process. Therefore, the bolded is vague and confusing to someone who has earned citizenship but may have been an immigrant to the country. Therefore, the letter was intimidating to some Latino voters.

It is true that no criminal intent was discovered (archived LA Times article). However, this current GOP case is about whether Nguyen obstructed the investigations. I won't comment on this, as I am neither interested in that allegation nor does it affect me in my current geographical location.

However, what i do find entertaining is the overall conspiracy tone of the article. I note that if it weren't for our favorite knight in tin-foil armor, I probably would not have even noticed it. How much of reality do these sycophants have to do in order to justify their nuttery?

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