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
FEBRUARY 22, 2019 ~ EOALVAREZ

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.
https://www.nature.com/articles/529462a

[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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2117903/

[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).
https://en.wikipedia.org/wiki/Death-inducing_signaling_complex

[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.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4836822/

[5] Killer T Cells
These are specific immune cells that can detect infected cells and directly kill them to protect uninfected cells.
http://www.tcells.org/scientific/killer/

[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.
https://medlineplus.gov/ency/article/002247.htm

[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).
https://ghr.nlm.nih.gov/primer/howgeneswork/cellsdivide

[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.
https://www.mayoclinic.org/tests-procedures/bone-marrow-transplant/in-depth/stem-cells/art-20048117

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).
https://www.theguardian.com/science/2009/jan/21/charles-darwin-evolution-species-tree-life

[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.
https://www.tandfonline.com/doi/abs/10.1080/0005772X.2017.1290893?journalCode=tbee20

[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.
https://sciencing.com/do-deer-velvet-horns-6690259.html

[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.
http://www.naturemuseum.org/the-museum/blog/6-common-butterflies-you-ll-see-in-chicago-parks-and-gardens

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.
https://butterfly-conservation.org/moths/swallow-tailed-moth

[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.
http://www.washingtonpost.com/wp-srv/national/daily/aug99/traffic05.htm

[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.
https://en.wikipedia.org/wiki/Peanut_allergy

[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.
https://www.sciencedirect.com/topics/neuroscience/protein-aggregation

[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.
https://www.forbes.com/sites/startswithabang/2019/04/18/quarks-dont-actually-have-colors/#5c9776701fe5

[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.
https://home.cern/science/physics/higgs-boson

[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.
https://learn.genetics.utah.edu/content/epigenetics/inheritance/

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!

Science in several languages

There are different versions of this old joke (the one with "butterfly" is the most common), but as this one is about science, and foreign languages is another love of mine, I thought I'd post this one.

Learning through Research workshop: Day 1

This conference has been amazing! Though I have been taking much notes, the rest of my time has been spent talking to such an interesting and enthusiastic collection of people here while I have the chance, so not much time to updating the blog promptly. Here is the summary of Day 1. I have long detailed notes which I would be very happy to share with anyone. If you want those, just email me at mdvinces at gmail.com.

SUMMARY of today’s session:

Opening remarks - by François Taddei, Frédéric Dardel, Claudie Haignere, Ariel Lindner

Lee Hartwell – Teaching the teachers in a new information era 

Having received a Nobel Prize for his work on cell cycle checkpoints, Lee has been an early advocate for personalized medicine and at Arizona State University is pioneering science teacher training. Three steps for teaching science to non-science majors (whether students or teachers of students):

            INTEREST -> MOTIVATON ->SKILLS

Too often traditional education focuses on the Skills part, at the cost of Interest and Motivation, which in the end undermines acquisition of Skills.

Nathalie Kuldell– Teaching and Learning with imperfect learning machines: Using synthetic biology for teaching students and teaching teacher.  

Nathalie has been using Synthetic Biology to engage students in biological engineering, and now is using the same techniques, through the online BioBuilder.org platform, for teaching teachers. The platform has three main elements: 1. Online content, including explanatory animations. 2. Activities for both the lab and the classroom. 3. A space for sharing data, results, practices, ideas.

This approach brings the exciting engineering aspects of hands-on design and building into biology education.

Stephen Friend – Democratization of biomedicine.

 

Expertise in medicine has been the closely guarded domain of the medical experts. But the time is now for democratizing biomedicine, empowering patients to control how their data is used, empowering physicians and drug companies with unparalleled power or personal patient data, and moving medicine into a commons space where real advances in predictive medicine can be accomplished. Stephen is founder and president of Sage Bionetworks, which aims at providing the necessary commons for biomedical information.

François Taddei – From individual questioning to collective exploration – the education revolution. 

Education is today a conservative affair done much as it has been done for hundreds of years. While technology progresses ever more rapidly, education has fallen behind, to the detriment of societies where more people are left out of understanding and engagement of science. Goal is to reform university education so it is open source and accessible to more people and not limited to elite campuses, hand in hand with opensource software and hardware movements, and to allow learning by playing. Some of this is being done at the CRI already, but ultimately want to establish a model for Open FIESTA (Faculty for Innovation in Education, Science, Technology and Arts).

Live from Paris: Learning through Research workshop

It's been far too long since I've written here, as counting the number of Science Videos of the Month missing will attest. But with some projects out of the way, I will have more time to devote here.

I am writing this from Paris, France, where I am attending the "Learning through Research" workshop, hosted by the Center for Research and Interdisciplinarity (CRI). The 3 day workshop has an extraordinary cast of individuals ranging from the 20 year old creator of UnCollege, on to Nobel Laureate, all with a mission in common: to re-think the way science is taught and conducted to make both more democratic, accessible and innovative. Titles of the sessions include: Innovative science teaching, Promoting innovation, Citizen science, Quick talks for emerging innovations, Scientific games, Building innovative tools for science & education, Empowering communities, and Creative learning.

I'll be writing about my experience here in the days to come. In the meantime, you should be able to follow the workshop live at this site: http://www.nightscience.org/#!live-the-event!

My 20 minutes of fame at NerdNiteDC: Loving your inner germs

I'll be presenting tonight at NerdNiteDC at the DC9 club. It's a night of music, drinks and science. I will be presenting a fun and informal 20 minute talk about why we should love the good nerd germs and not give all of our undivided attention at the bad boys of the microbial world, using Molly Ringwald, Judd Nelson and Anthony Michael Hall in an extended metaphor all the kids are sure to get.

Beyond the edge of the sea: art and science from the ocean's deep

The National Science Foundation is the main source of basic research funding for science and engineering in the United States. But on the third floor of the NSF one can find a fascinating interface between science and art. Until the end of this month, the Art of Science, a committee of volunteers interested in the meeting of the worlds of science and art, hosts a traveling exhibit called Beyond the Edge of the Sea, a collection of watercolor illustrations of the fantastical marine life found around deep-sea hydrothermal vents during expeditions in the deep-ocean submersible, Alvin. The exhibit is the product of a partnership between illustrator Karen Jacobsen and oceanographer Dr. Cindy Lee Van Dover. Both were at the NSF this week to talk about their work in Alvin and the process of observing and collecting samples at great depths, a few thousand meters below sea level, and the process of capturing the images by watercolor.

The scientist (back to us).

The artist.

Some of my favorite drawings are one with notes from the artist, most of which are technical notes, but there is a tone of excitement, curiosity and fascination which combined with the beautiful illustrations make this exhibit so compelling.

As magical as the visual aspects of the sea-life around ocean vents are, equally awe-inspiring is the fact that this life exists without the need for the sun. Even organisms in caves derive energy from the sun, since their food sources are ultimately derived from life above ground. Sea vent organisms derive energy from the chemicals that emerge from the hot vents, and the bacteria that live there that are able to produce organic matter with them through a process called chemosynthesis.

Next stop for the exhibit: Madison, Wisconsin. Be on the look out for this magic visit from the ocean's deeps. You can get a preview of the images here.  For more detailed information on the biology and geology and chemistry of the vents, refer to this easy-to-read guide (PDF).

UPDATE: A recent story on NPR on "The Deep-sea Find That Changed Biology".

A music video to launch SOSCIENCE

This is the first post in a blog devoted to science and society: SOSCIENCE!

Thomas Dolby - She blinded me with science