Wednesday, June 26, 2019

A poem, annotated

For the class I taught this past quarter, my practice was to do any assignment myself that I have assigned to my students. It allowed me to be in their shoes and also gain what I hope they gain from the exercises.

Their second paper assignment was a multimodal paper. For this project, I annotated the poem, Death and The Pretense of Youth, by Chicago poet Edwin Alvarez, for anything related to scientific concepts or phenomena. This poem is aesthetically beautiful and symbolically rich, and in this assignment, as it is for a biology class, I concentrated on explaining the many scientific references and allusions the poet makes. It is one of several poems I shared in my class for students to read. The passages I annotated are indicated below in bold. Some of these are hyperlinked to supplemental information, and bracketed numbers indicate footnotes with brief explanations or observations.

Death and The Pretense of Youth

When I was a child
My Mother once told me
“Que Cera, Cera”
What will be will be?
This small ditty would hold my hands together in Church
Little would I know that decades would flow
Of colonialism, segregation, and language divisions
The Religious right, Austerity, and Entitlement.
The selfish gene[1] persists
with its mind of its own
Its root knows no cause just existence
Yet the cells just kill themselves[2]
Cells kill themselves because of stress
or kill themselves because their neighbors experience that stress
A death induced signaling complex[3]
One of multiple factors
heat, radiation, nutrition, oxygen deprivation
and others
When a cell isn’t recognized by “itself”[4]
Another one does the dirty job
Recognized as “other” the cell is
marked for a kill.[5]
A dead cell becomes cellular debris
to be washed up on a lymphatic shore.[6]
New growth, that which replaces
what was lost
all depends on
a new generation
a doubling replication[7]
where once was is and will be again
The copy to copy of stem to branch to stem[8]
a veracity of verisimilitude
to age but yet remain forever young
The voracious act to live intensifies a spontaneity
to begin again
as is
better or worse
Simultaneity expressed as natures remedy-
The organization of bees?[9]
Velvet Deer Horns?[10]
Wandering Swallowtail moths?[11]
Clustered post work traffic?[12]
Dried peanut butter protein?[13]
Natural facts of aggregation?[14]
Strange quarks[15]or Charmed?
A spooky action at a distance, no doubt?
The anthropomorphic quark speaks of No Higgs[16]
It sees the feather and then the whole flock
It is born unto
an ancestry of desire[17]
What mothers and fathers regret
born unto
an unceasing chain

[1] The selfish gene
The theory of the “selfish gene” postulates that genes promote their own survival without regard to the survival of the organism or species.  It is an expression of the gene-centered view of evolution (as opposed to the views focused on the organism and the group). According to a gene-centered view of evolution, the more two individuals are genetically related, the more sense (at the level of the genes) it makes for them to behave selflessly with each other. This idea has emerged from early 20th century thought, but popularize by Richard Dawkins in his 1976 book of the same name.

[2] Apoptosis
Apoptosis, or programmed cell death, is a specific process whereby a cell kills itself. It is a normal process in development and certain immune responses.

[3] Apoptosis signalling
There are several stimuli that can induce apoptosis, and the nature of the stimuli will determine what signaling pathways are activated to enact cell death. One pathway, known as the “extrinsic” or “death receptor” pathway, is activated when a protein called the “death ligand” binds a specific cell surface receptor which in turns sets of a signaling cascade inside the receptive cell, including the formation of a complex of proteins that bind to form what is known as a death-inducing signaling complex (DISC).

[4] Self-recognition by immune system
The immune system is able to defend us by recognizing and acting against foreign elements without reacting to or harming our normal cells. To do so, it needs mechanism by which immune cells recognize something as “self” and “non-self”. Cancer cells have been known to harness this “anti-immunity” property to evade destruction by the immune system.

[5] Killer T Cells
These are specific immune cells that can detect infected cells and directly kill them to protect uninfected cells.

[6] Lymph
The lymph system is a major part of the immune system. It carries in its fluid, called lymph, immune cells to parts of the body, and the fluid is filtered to remove harmful cells such as bacteria and cancer cells. During infection, central areas of the lymph system, called nodes, can swell, especially in the neck, arm pits and groin areas.

[7] Cell division
Organisms grow by cell division, where in 2 daughter cells are produced from 1 parent cell, each with a copy of the DNA from the parent cell. In the case of organisms like plants and humans, each of these cells maintains two copies of each DNA molecule (chromosome). A specialized form of cell division, called meiosis, results in haploid cells that contain only one copy of each chromosomes. These daughter cells are destined to become reproductive cells (eggs and sperm).

[8] Stem cells and tree of life
Here the poet may be making allusions to two biological terms, stem cells, and the tree of life (along with its branches). Most cells in our body are very specialized. Skin cells have very different form and function from liver cells, for example. But they all emerge from undifferentiated cells called stem cells, which are not specialized but have the potential to grow into specialized cells such as heart cells, brain cells, and blood cells.

The stem and branches of the tree of life is a visual representation of how Charles Darwin first envisioned the evolution of life’s diversity, one branch of life yielding many other branches as species evolve. Recent advances in DNA sequencing have revealed that life’s evolution is a little more complicated than that, with some “branches” grafting themselves on to others (apologies for extending this metaphor to its limits here).

[9] Emergent properties in bees
Bees, and other social insects such as termites and ants, act as individuals in ways that they collectively outstanding macroscopic structures and complex behaviors. Scientists enjoy studying these insects to understand how such individual behaviors can collectively perform and enact complex patterns, structures (like a beehive or ant colony) and behaviors.

[10] Deer antler velvet
Deer antlers grow when seasonal tissue, rich in blood vessels and nerves, grow over the antlers and deposit proteins and minerals that form the antlers. This “velvet” is shed seasonally, and humans use this in folk medicine. It may be that the high level of hormones in deer antler velvet may underlie folk medicine effects on humans.

[11] Swallowtail butterfly and moth
The swallowtail butterfly include over 500 species of large and beautiful butterflies, so named because of the extensions on their hindwings. The black swallowtail can be spotted in Chicago, where it lays eggs for its larvae to much on such plants as Queen Anne’s lace and their garden relatives, carrots, parsley, fennel and dill.

The swallowtail moth is not at all closely related to the butterfly, but shares the distinctive hindwing extensions. It is native Europe and the Near East, where it is common.

[12] The science of traffic patterns
Automobile traffic may sometimes seem chaotic, but scientists love studying order in this chaos. Understanding how patterns of traffic congestion emerge can not only help improve traffic forecasting and road design, but also lend understanding to other processes prone to traffic jams, both in nature and in human-made environments.

[13] Peanut protein allergy
The cause of peanut allergy is unclear and at least 11 peanut protein allergens have been described. Peanut allergies are uncommon in children of undeveloped countries. The hygiene hypothesis proposes that the relatively low incidence of childhood peanut allergies in undeveloped countries is a result of exposure to diverse food sources as well as non-food antigens early in life, increasing immune capability, whereas food selection by children in developed countries is more limited, reducing immune capability.

[14] Protein aggregation
Proteins have sticky parts that are usually hidden inside a well-folded protein. But when proteins unfold abnormally, those once hidden sticky parts can stick to each other, resulting in large clumps of abnormally functioning protein. Such aggregations have been associated with several human diseases, such as Alzheimer’s and Parkinson’s diseases.

[15] Quarks
Most of us grew up learning that atoms were the fundamental units of the universe. But we also know that atoms have parts, called protons, neutrons and electrons. And yet these sub-atomic parts have parts of their own, called quarks. They are so small, and have strange properties, that have prevented us from actually observing them. We only know of their existence through experimental evidence, though they had been proposed to exist in theories dating as far back as the 1960s.

[16] Higgs boson
It’s challenging to describe the Higgs boson in a few words, but in one sentence, the Higgs boson is “the visible manifestation of the Higgs field, rather like a wave at the surface of the sea.” And what is the Higgs field? It is a field (much as we have electromagnetic or gravitational fields) thought to exist in every region of the universe with which particles, such as electrons, interact and as a consequence, have mass. Without the Higgs field, these particles would have no mass. And the Higgs boson is the unit of the field with with the particles interact with. Like the wave in the sea.

[17] Epigenetics
We know we can inherit traits from our parents through genes. Specific changes in the DNA of one parent are inherited in the DNA of the offspring. But there are traits that can be inherited without permanent changes in the DNA. Rather, there are temporary changes that alter the way DNA is expressed, how on or off a gene will be determined by special chemical tags that can be removed. How temporary they are can determine whether they can be passed on to a next generation.

Monday, February 19, 2018

The android is us, maybe?

I’ve been reading Blade Runner (in French) and it’s gotten me to think a lot about human programming. Androids like those in Blade Runner are now a common feature in today’s literature, cinema and television. They provide an instrument to interrogate a number of things, one being how technology can affect us as humans. But a more interesting thing to me is the interrogation of what it means to be human at all. In fictions such as Westworld, Her, and Blade Runner, the robotic “fake” humans reach a level of sentience and that makes the reader or viewer wonder at what point can these creatures still be considered not human? Can they ever be considered human? All their behaviors and memories can be ascribed to programming. They are thus not natural sentient beings. But these fictions also make rethink about my own humanity and how much programming determines my own behaviors, thoughts, emotions and memories as well. Yes, programming of humans. We have within us free will to choose to respond to a situation in very different ways. If I drop a cup and shatter it, I can: get angry, get frustrated, get sad, or I can laugh. What determines which reaction it will be? Perhaps how my day went before the incident. But where’s the free will? Perhaps a bad day at work will “program” me to be grumpy. But can I not re-program myself out of a bad mood so I can react to the broken cup with laughter instead? I think so. I think somewhere in there is some Buddhist thinking too, about the nature of the mind. There might be some science here as well. In research on things like stereotype threat, we see how societal biases and stereotypes can program us to underperform. But that these programs can be buffered by interventions such as value affirmation writing exercises. The documented positive results of these interventions are pretty impressive, all from a 5 minute writing exercise that ends up short circuiting the otherwise negative programming that comes with stereotype threat. So in a way, androids in fiction are a thought experiment of a simplified human that allows us to think about the nature of what it is to be human. Though we are now on track to see androids and artificial intelligences reach a state close to sentience pretty soon. Perhaps all the fiction that has been written on this topic may allow us to be better prepared, ethically and emotionally, to the advent of such new creatures on this planet.

Friday, February 16, 2018

I work at an art school now!

It's been a long time since I've posted here, and no better time that this new lunar year in my new home in Chicago, where I am currently a lecturer at the School of the Art Institute of Chicago (SAIC). This place is amazing in so many ways, and especially for a scientist that appreciates art as much as I do, it's kind of dreamy. SAIC has a science requirement for its students, so there are loads of science classes offered and lots of scientists teaching here. I am currently teaching a course called the Science of Food. Yum. There is a Scientist in Residence Program, and just last week I got to see the coolest talk on the complicated nature of light from a physicist's (SAIC professor Kathryn Schaffer's) perspective. It was an amazing talk, well illustrated in both words and pictures on a topic that challenges our ability to communicate. How does one draw or describe something like light, which takes up space but is not a material thing, behaves both like a particle and like a wave, is invisible and yet allows us to see? That's where math comes in. But how to talk about the wave function in the equations? It's a challenge that stirs up all we take for granted in describing the physical world around us. And as a science educator, the talk made me think more carefully of how I used illustrations to convey nature to my students. If one is not careful, illustrations may give students the wrong impression about science and the nature of the universe.

The images used in the above poster for the talk, for example, are three different ways to represent light. Light propagates through space as a disturbance in the electric field. An electric field has both a strength and a direction, and the convention has been to indicate direction with an arrow, and strength with an amplitude or height of an arrow, hence the wave shape of how light is normally illustrated. But that can be a deceiving depiction, leading many to think that light actually moves that way in a sinusoidal fashion. It does not! Professor Schaffer prefers the bottom depiction, that conveys strength of the field by the thickness of the arrows, rather than by their length. It still conveys the same information as the top diagram of light, showing how the strength and direction of the fields alter as light moves through.

Now that I'm in a milieu where all sorts of things science and art are explored and discussed, I hope to get back to writing here. More soon to come!

Sunday, December 8, 2013

Better Living Through Charts and Graphs

Back in March 2013, I decided I'd lose some unwanted 10 pounds I had gained and go back to what I considered my ideal weight and waist size so that I can fit into my favorite pants and shirts I simply refused to give away or replace. I managed to reach my goals in 6 months, with the help of a couple of smartphone apps that allowed me to monitor my caloric intake and expenditure through diet and exercise, respectively. But just as important, if not more, was simply measuring on an almost daily basis my weight and waist size. It gave me a solid and immediate readout to how well I was eating and working out. Ultimately, it was trying on those clothes and not feeling them too tight to button that showed it had all worked.

But suddenly, things started fitting tight again. What happened?

I looked back at the chart of the numbers I had been tracking all these months and saw that I had suddenly gained both weight and inches. But why then all of a sudden? The graph of my data gave me some clues.

As I've indicated by the two icons, my sudden gain in pounds and inches coincided with two things: the autumnal equinox (September 23), after which the days get progressively shorter, and Halloween (October 31), around which candies become excessively and too easily available.

Click on graph for larger view.

Every year, around this time of year, my body and my spirits slow down. I start to eat more and move less. I feel less motivated to do anything and I sleep more. So this, coupled with very easy access to large amounts of sugary candy, probably combine to explain my sudden gains.

Knowing this now motivates me to crank up my exercise routine, something I should have done earlier in the fall in anticipation for my annual slow down. And also keeps me from munching on the leftover Halloween candy in my office.

Many people track fitness and other progress by taking pictures, which is great. But there's nothing like a graph, a picture of the actual numbers that measure what matters, to tell you what's going on, and how you're progressing, as well as offer you a handle on unexpected changes in course.

Sunday, December 1, 2013

Monthly music video: Chartsengrafs by Grandaddy

Chartsengrafs by Grandaddy
No video. Just the song, and a graph.

From the album "The Sophtware Slump" (2000)

"birds come...and then they go"
i traded laughs
in for charts & graphs
but all that's only fun
until evening comes
your guess as good as mine
as to just what kind
of trouble i might find
tonight out of my
my mind
my mind
my mind
my mind

Sunday, October 20, 2013

ART and SCIENCE breakthrough contest - DNA, in your face!

The PAX3 gene is involved in the development of the face. Toronto based scientist Dennis McCormac had his PAX3 gene sequenced, and in collaboration with an artist, had his particular sequenced of A, C, T and Gs compose a portrait of his face. Edward Tufte, are you seeing this? Talk about making a visual connection between genotype and phenotype, between DNA and the trait it determines! This is gold to me.

This collaborative art and science work is in the running in a science visualization contest. If you like this as much as I do, please VOTE HERE for this piece by scientist Dennis McCormac and artist James Fowler!