Songs without Words

The most familiar solution to the oxygen-transport problem in larger organisms is hemoglobin, a collection of four-subunit (usually two pairs of polypeptides) proteins which utilize porphyrin heme rings containing a single iron atom.  However, the use of hemoglobin, carried within cell carriers (erythrocytes), is limited to vertebrates.  Invertebrates have independently developed different oxygen-transporting proteins.

Hemocyanin

Mollusks (e.g. octopus, horseshoe crabs, etc.) use copper rather than iron to carry oxygen, incorporated into a protein of the hemocyanin family.  Hemocyanin, which uses two copper atoms to bind each O2 molecule, is dissolved in the hemolymph (blood analogue).  Hemocyanin is translucent gray when deoxygenated and sky blue when oxygenated.  Although hemocyanin is generally less efficient than hemoglobin, it is advantageous in certain environments unique to the underwater milieu.  Hemocyanin, unlike hemoglobin, is designed to aggregate.  When hemoglobin subunits aggregate, for instance in the thalassemias, it is disastrous because the erythrocytes containing the aggregates are destroyed.  However, hemocyanin (MW ~400kDa) can form aggregates in the millions of daltons (see the Keyhole Limpet Hemocyanin (KLH) article on Wikipedia).

Erythrocruorin

Annelids such as earthworms present another solution, which is erythrocruorin, which like hemoglobin contains heme and a single iron atom carrier.  Although erythrocruorin is also not bound in cells, it is notable for forming exquisite protein structures composed of 180 subunits, with a macrostructure consisting of two stacked hexagonal rings (see http://www.uta.edu/biology/arnott/classnotes/5365/Erythrocruorin%20micrograph.jpg).  The total molecular weight of each dodecameric complex is 3.5 megadaltons, which includes 144 “hemoglobin” subunits and 36 linker subunits.  The PNAS paper publishing the structure posits that the giant size is a way of maintaining high oxygen tension and harnessing cooperativity while incurring minimal osmotic cost.  What is amazing in this case is the fidelity of protein assembly on such a grand scale.

Hemerythrin

Hemerythrin uses iron to carry oxygen, like hemoglobin, but uses two irons per oxygen and does not contain a heme ring.  Used by various marine invertebrates, hemerythrin is colorless when deoxygenated and violet-pink when oxygenated.  Each hemerythrin subunit is composed of four alpha helices, and the subunits join in trimers.  While hemerythrin does not exhibit cooperativity, it does exhibit a greater affinity for oxygen than for carbon monoxide.

Beyond nature

A recent Nature article from earlier this year detailed a UPenn group’s bioengineering feat of devising a new oxygen-carrying protein based on design principles.  Apart from heme groups, the rest of the protein was invented through rational design.  The resulting molecule, which is advantageous for being able to deliver oxygen faithfully in the presence of CO (unlike human hemoglobin), shows that the “hemoglobin fold” is far from mandatory.

After struggling with lighting 3D models, I finally came across a nice and simple tutorial that explained how to set up a basic three-point lighting scheme.  What a difference it makes … .  Eyes are still creepy though.

Swift 3D v6.  Temporary eye texture from renderosity tutorials (by nezbitten)

The main exercise was the head, so here are side and front views in wire and flat shading:

The back of the head is deformed because once I drew in the hair, it was no longer a priority.  Swift 3D is somewhat more difficult to use for this purpose because it is difficult to “grow” a mesh bit by bit, and the polygons are strictly triangle-based, as opposed to quadrilaterals as seen in other programs.  Large arrays of triangles are just conceptually much harder to visualize in 3D.

I fashioned this head out of a box which was 4h x 2w, duplicated across the midline.

Life is, in simplest terms, a temporal string of choices.  At any given moment, the agent may act or not act; or, formulated differently, the agent may act offensively or defensively.

Imagine a game where there is one die, with each face painted a different color from the rainbow (indigo not included).  If the green face is up, then you are happy, and otherwise, you are unhappy.  A man asks you every hour whether he should roll the die or not, and you can reply “yes” or “no.”

The expected outcome of this simple game is that the idealized agent replies “yes” until the die turns green-side up, then replies “no” thereafter  This pattern of behavior not only represents political spectra, where rebellious youths turn into conservative adults, but also romance, economics, academic policy, sports games, and so on.

The nuances to the game enter when there are multiple people playing, who want different colors and who may also influence the man’s eventual action – to roll or not to roll.  Human behavior deviates in several cases (e.g. the rural poor, academic elite) because of additional layers of superimposed concepts.   For instance, we could imagine that another player convinces you that you desire another color than that which suits you, or that another player believes in a “global happiness” and thus seeks to maximize the happiness of the most people in the group, rather than for him or herself.

There is not much difference between the game that is played by all living creatures and the game played by humans, but humans have simply added so many rules and strategies that they often do not realize that they are still playing the same game.  The most intense dualities stem from this ebb and flow: desire and satisfaction, searching and finding, shifting and settling, working and resting.  The subtlety is that inaction is not a null in this game but a nearly equal force and choice as action itself.  There is an energy behind both action and inaction, and that is what creates the conflicts that characterize life.

… hug everyone who helped to make something this spectacular … for a free product.  Ten years ago, I would never have believed that a map could look like this.  This is a view of Beacon Hill and the Commons, which I walk over whenever I get off the T at Park Street to get to lab in the morning.

This time it’s bears!

People who live with their pasts can write memoirs and autobiographies. I only live with the present and the future, the past lingering as a volume of knowledge in the living moment. That’s why I think my equivalent of a memoir is more like a simple present introspection, although the difference is that the introspection is more ‘closed’ from outside characters.  When I hear the wash and noise of silence, or when I am sleeping, that is when this inner world is most apparent, and that is what I’m depicting here.  Since I am so young, this short and simple diary-style introspection should suffice.

This five-page illustrated diary entry sums up my life, which is on a cycle of obligation and fulfillment. During the obligation segment, a large clump of things I need to do but that I can’t seem to commit to build up, and during the frenzied fulfillment stage, I finish them one by one (or release the ones that have expired). While the obligation stage is full of stress and a looming shadow, it is also a period during which I flit from one thing to another, learning as much as I can. Fulfillment is made possible by the disjoint skills I hone while distracted by other things. It can take months or years for me to understand how something I’ve learned how to do is relevant to fulfilling my promises. But at some point, everything just comes together. I just have to have faith that my instinctive investments will culminate in a grander art in the end.

At a gift store a few weeks ago, I saw a nice set of matching wrapping papers which were sold as a set.  The first was a floral black and white print, white-dominant, and the second was a polka-dotted print, black-dominant.  Even though I didn’t buy it, the concept lingered and I wanted to try applying the concept to a dress fabric because it seemed like a rather nice combination.  I freehanded the dress pattern without reference and transformed the polka-dots into a sinusoidal pattern, but the rest of the body is actually traced from a photograph, so I wouldn’t really consider this art.  Although by virtue of what photograph I traced this from, perhaps this conveys more ideas and emotions than other works that I would consider “art” …