Category Archives: Education

Thursday Doors: Mural

I started a new full-time job last week. I’ve been too busy with it to blog about it in detail–too busy to blog at all, in fact. But I wanted to get started again with this week’s Thursday Doors.

Behind the school where I work, there is an astroturf “lawn” and a basketball court. There are also some picnic tables for the students to eat lunch. And a door.

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Students painted this mural, with names of famous cultural figures, next to the back door last year. I like how they included two genders and several nationalities. I spend a lot of time looking at this mural when I’m supervising student lunch.

I have showed a school, with murals, in Thursday Doors before. That school was a more typical California public school, with a lot of separate buildings.

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My new school is different. It is located in a former office building in San Jose. Architecturally it is unusual for a school too, with a lot of windows but not much in the way of athletic facilities. These students are more interested in science than sports anyway.

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Thursday Doors is a weekly feature allowing door lovers to come together to admire and share their favorite door photos from around the world. Feel free to join in on the fun by creating your own Thursday Doors post and then sharing it, between Thursday morning and Saturday noon (North American Eastern Time), on the linky list at Norm 2.0’s blog

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Thursday Doors: Birthday Library

For my birthday this year, I got my own Little Free Library. I’ve wanted one for almost as long as I knew that they existed, but I had been a little intimidated by the cost or by the thought of having to build one myself. Then I was also not sure about how to put it up in the yard. It seemed like a lot of effort.

But I really like these little libraries, and I’ve included a few in past Thursday Doors posts, for example here.

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This library sits outside the UU church of Palo Alto, which I have attended a few times. There is another outside Brewer Island Elementary School (where I taught about photosynthesis this morning), painted blue like the school.

And I recently found a geocache in this Little Free Library in Redwood City, in a neighborhood near Roy Cloud Elementary, where I am teaching tomorrow. It kind of looks like an elf lives there.

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I wish I’d been more systematic about taking pictures of all the libraries I’ve found, especially the ones where I’ve found geocaches.

Because finally, I am going to have my own! I got an unfinished one for my birthday. Right now it is still sitting on the floor in the front entryway, next to the shoe rack.

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But it is pretty close to being ready to go. And, because this is Thursday Doors, notice the nice doors on it! My husband ordered it from LittleFreeLibrary.org. The post came the next day. It is extremely tall (I include some of the room furnishings for scale):

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I’d like to paint it with some kind of music theme, or space/sci-fi theme. But the picture hasn’t quite crystallized yet. And it looks like I will have to dig quite a deep hole for that post!

Thursday Doors is a weekly feature allowing door lovers to come together to admire and share their favorite door photos from around the world. Feel free to join in on the fun by creating your own Thursday Doors post and then sharing it, between Thursday morning and Saturday noon (North American Eastern Time), on the linky list at Norm 2.0’s blog

Mundane Monday: Assembling the Bones

This week’s Mundane Monday theme is “bones.” For this theme, Dr. KO has a nice picture of an alligator snapping turtle skeleton, which you should definitely check out (also, raise your hand if you knew before this that there was a such thing as an “alligator snapping turtle.” My hand is not up). At first I was concerned I wouldn’t have anything for this week, and then I remembered. This is a great lead-in to the topic that’s been on my mind recently: Back to School!

I have not had much time for blogging lately because my teaching job has started up again. I teach middle-grade science with a non-profit organization called Science from Scientists. Regular school, including my kids’ high school and college, started already a while ago, but SciSci gives the teachers and students a week or two to get settled in before we start our visits. This year I have two completely new schools and two new co-Instructors to work with. I’m also going back to two schools I worked with last year and liked.

One of our most popular lessons at SciSci includes the dissection of an owl pellet. Most of my prior exposure to owls has been via children’s fiction, and I first learned about the pellets as an adult when I taught this lesson.

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Mr Rogers’ neighborhood had an owl in it!

Owls don’t poop. They eat their prey whole and digest it in the gizzard, a second stomach. They absorb nutrients like we do from the soft parts of the prey, and eventually regurgitate a pellet containing the indigestible bits (mainly fur and/or feathers and bones). This is a YouTube video of the process that we show our students. It was taken in Ontario in 2014:

Will you ever look at Hedwig quite the same way again?

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One of the many cool things about owl pellets is that you can dissect them and find out what the owl has eaten. If you buy the pellets from Carolina Biological Supply like we do, you usually find a mouse skeleton, maybe two, in the pellet. Occasionally you might find a bird. The prey animals can be identified by the skulls, and sometimes a large portion of the skeleton can be reconstructed.

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Students dissecting an owl pellet and reconstructing a skeleton

These bones are quite small, but very interesting!

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Amazing New Brain Map of Every Synapse Points to the Roots of Thinking

Dave Wolf is on a roll this month with posting cool neuroscience articles! This study, from a team at the University of Edinburgh, is a real tour de force that takes advantage of modern technology in neuroscience. I can imagine that some day that we will be able to map the human synaptome, non-invasively, and in real time. Then we would finally have the tools to address more fruitfully questions such as the nature/nurture debate, how mindfulness changes the brain, even the nature of consciousness and transcendent experiences. Check out author Shelly Fan’s other work too!

author david wolf

By Shelly Fan – Aug 14, 2018*

Imagine a map of every single star in an entire galaxy. A map so detailed that it lays out what each star looks like, what they’re made of, and how each star is connected to another through the grand physical laws of the cosmos.

While we don’t yet have such an astronomical map of the heavens, thanks to a momentous study published last week in Neuron, there is now one for the brain.

If every neuron were a galaxy, then synapses—small structures dotted along the serpentine extensions of neurons—are its stars. In a technical tour-de-force, a team from the University of Edinburgh in the UK constructed the first detailed map of every single synapse in the mouse brain.

Using genetically modified mice, the team literally made each synapse light up under fluorescent light throughout the brain like the starry night. And similar to…

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Film Review: Fallen Kingdom, The New Modern Prometheus

This year, 2018, marks the 200th anniversary of the publication of Frankenstein; or, The Modern Prometheus. The classic novel was written as a parlor game in 1816, the year without a summer, by the teenage Mary Wollstonecraft Godwin (later Mary Shelley).

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Wordsworth Classic Edition

The Governing Myth

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HRW Edition

Her story of Dr. Victor Frankenstein and his monster casts a long shadow. Its adaptations in popular culture have become what author Jon Turney calls “the governing myth of modern biology“: a cautionary tale of overreaching by a scientist that ends in tragedy and death.

A central tenet of this myth is that the monster, cobbled together from dead body parts and animated by electricity–created by man not God–is against the natural order of life. The story’s horror comes not just from fear of dying at the monster’s hand, but from a more primal sense that the universe itself will not abide this creation or those that created it. In the words of Ian Malcom, “Life finds a way.”

The Myth Updated

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Richard Attenborough in Miracle on 34th Street. Image: Jurassic Park wiki

The original Jurassic Park updated this governing myth for the 20th century. Instead of electricity and magnetism, the sexy new science to be harnessed is genetic engineering. And instead of a humanoid monster killing everything its creator loves, we have dinosaurs. But the same hubris, greed, and willful ignorance remain–along with the same sense of wonder and naive good intentions.

In a humanizing scene, John Hammond (played by Santa Claus from the remake of Miracle on 34th Street) explains to Dr. Sattler that he wanted to bring magic to children with Jurassic park, just as he did years ago with a flea circus. But his park is collapsing, melting all around him, along with his ice cream and his dreams.

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Jurassic Park Ice Cream. Image: Popcorn Cowboy

John Hammond, like Dr. Frankenstein before him, gets his comeuppance by the end of the book (although it takes a few movies to finish him off). And, the other craven greedy villains such as Donald Gennaro and Dennis Nedry become dinosaur food quickly and spectacularly. While of course the cute kids, Hammond’s grandchildren, survive.

Leaving the island of the dinosaurs after his misadventures, protagonist and good guy Dr. Alan Grant looks out of the helicopter to see modern pelicans flying as they should. His theory of dinosaur-to-bird evolution has been validated. His skepticism about Jurassic park itself has been vindicated, too, at great cost, and all is back in balance.

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Image: GIPHY

Life found a way to put humans in their place.

Science, not Myth

The original Jurassic Park had unforgettable characters, amazing effects, an awesome music score, and was thematically resonant with Frankenstein, a timeless classic of English literature.

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Image: Jurassic Park wiki

Jurassic Park also, almost unique among modern science fiction movies, contained a testable scientific hypothesis. The story spawned a virtual cottage industry of scientists looking for ancient DNA in amber until the half-life of DNA molecules was calculated several years ago. These results showed definitively that Jurassic-era DNA could not have survived long enough to be reconstructed to clone dinosaurs. Real-life Henry Wu wannabees will have to make do with trying to bring back animals more recently extinct.

The Myth Transformed

Jurassic World: Fallen Kingdom is like Jurassic Park‘s ugly stepsister, a monster cobbled together crooked from all the shiny parts of the original. Its dinosaurs are bigger, badder, and uglier. The heroes are hiding out in remote cabins and ineffective non-profit organizations. The benevolent-ish grandpa, this time named Ben Lockwood, isn’t Santa Claus. He’s an invalid who is being taken advantage of by his underlings.

And the cute grandchild, Maisie? There’s something otherworldly about her too. She lives by herself, except for an elderly governess, in a creaky old mansion above a museum, and looks and talks like English musical child prodigy Alma Deutscher.

Most of the plot of Fallen Kingdom will surprise no one. People stand there, mouths open, until they get lunched by dinosaurs. Greed and hubris are again on display in ever-uglier forms. A plucky child escapes death by dinosaur and makes a fateful decision. The audience will probably cheer when a particularly horrible example of humanity tries to take a trophy from a dinosaur he thinks is asleep and then loses his arm, and his life, in the process.

What is different in Fallen Kingdom is that while the body counts pile up, balance is no longer restored to the movie’s universe. The otherworldly Maisie turns out not to be Ben Lockwood’s granddaughter at all, but a clone of his deceased daughter. The flying creatures Owen sees at the end of Fallen Kingdom aren’t Dr. Grant’s friendly pelicans. They’re pteranodons.

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Image: Jurassic World Universe

In their race to save and weaponize the most clever and aggressive dinosaurs, the humans of Jurassic World: Fallen Kingdom abandon another of their creations, the gentle plant-eating brachiosaurus. This is the same species that first evoked awe and wonder in the original Jurassic Park. The scene where a brachiosaurus calls to the retreating human ship as it awaits its own death on the island has become an audience tear-jerker. “That scene represents the ending of a dream that started 25 years ago,” says director J.A. Bayona.

I think this scene represents a new reading of the Frankenstein myth for modern scientists. Frankenstein’s creation does not start out cruel and murderous. He only becomes that way when he is abandoned by his creator. Hank van den Belt, a Dutch professor of philosophy, writes in Science magazine that Dr. Frankenstein’s greatest moral shortcoming was that he did not assume responsibility for his own creature and failed to give him the care he needed. Owen’s conscience is similarly pricked when he realizes how he may have failed to give Blue the care she needed.

Modern audiences for Frankenstein sometimes confuse the name of the scientist with the name of the monster. This confusion mirrors the increasingly monstrous behavior of the scientist. Dr. MG Bishop of King’s College Hospital in London is quoted in the same issue of Science:

Read the book and weep for those we have rejected, and fear for what revenge they will exact, but shed no tears for Frankenstein. Those who think, in ignorance of the book, that his is the name of the Monster are in reality more correct than not.

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A sad brachiosaurus awaits its death on Isla Nublar as the last rescue boat leaves

In Fallen Kingdom, life as we know it no longer finds a way back. Instead, the worst impulses of human nature have found a way to transform nature itself.

This review also appears in slightly edited form on Movie Babble

 

Book Review: The Hate U Give by Angie Thomas

The Hate U GiveThe Hate U Give by Angie Thomas

My rating: 5 of 5 stars

I will start by thanking PJ Lazos at Green Life Blue Water, who introduced me to this book, The Hate U Give, a debut novel by Angie Thomas. I might not have read it without her excellent review; I was initially turned off by the word “hate” in the title and by the prospect of YA fiction preachiness. Those concerns were completely unfounded. This novel is a great read: sad, funny, forgiving, and wise. And Starr, the viewpoint character, is a strong and relatable voice.

The novel’s plot comes straight from tragic headlines. Starr is the only eyewitness to her black friend Khalil’s shooting at the hands of a white police officer. She tells the story to the media and eventually testifies before a grand jury. The officer who killed Khalil is not indicted. But those are only the bare bones. The meat of the story is about Starr’s conflicts due to straddling two worlds: the inner city ‘hood where she grew up and still lives, and the wealthy, mostly white, suburb where she goes to private school.

I am not qualified to speak to its authenticity regarding African-American culture, but because of Thomas’ skill at writing vivid characters and dialog, I found most of the book very easy to understand and relate to. I especially appreciated the way the author was able to walk the reader through Starr’s thought processes as she moves from being a terrified, silent teenager to a more mature activist, ready to speak her mind and shine a light on injustice. At first I was a little impatient with her reticence; it seemed self-defeating to me and I wondered where it came from in such an otherwise bold and self-aware character. But then even Starr herself shared the same impatience, and she was a self-aware enough narrator to figure out and explain the effects that fear, conditioning, and loyalty had on her. These insights are not something one can understand merely from reading headlines on the news.

After I finished the book I realized that it contained characters that touched on almost every point of view, and that those choices must have been deliberate. There was a heroin-addicted parent, a clueless and mean white girl, an abusive drug kingpin, an activist female attorney, a set of fiercely protective parents, an upper middle class black family jokingly referred to as the Huxtables, a well-meaning white boyfriend, an Asian friend and ally, and a strict family matriarch. In fact, if you watch the TV show “Black-ish,” you may recognize the broad outlines of many of these characters, or at least their quirks. But at the same time each character had his or her own unique voice that made the novel fresh and original. The author has a wonderful ear for dialogue that never sounds forced or confusing, in spite of the liberal use of slang. Reading this book is like being a part of Starr’s extended family.

I was also initially a bit wary of this book because I was afraid it would be a downer, something to feed despair and hopelessness about the brokenness of our world. Nothing could be further from the truth. Young people like the author and the real communities represented by Starr and her friends can point the way forward and give us all hope for the future.

View all my reviews

Thursday “Tors”: Brandenburg

So I am here in Berlin, and I have wifi. Woot!

“Tor,” which sounds a lot like “door,” is the German word for gate. (It’s also the German word for “goal,” which you’ll be hearing a lot of with the World Cup about to start). The most famous Tor in Berlin, and perhaps in all of Europe, is the Brandenburger Tor. According to wikipedia, “the Brandenburg Gate was often a site for major historical events and is today considered not only as a symbol of the tumultuous history of Europe and Germany, but also of European unity and peace.”

I lived in Germany for 8 months in 1983. I graduated from high school young and took a gap year between high school and college, living with my family while my professor father took a sabbatical at the Freie Universitaet in Berlin.

This is what the Brandenburger Tor looked like back then, in a picture I took with a Kodak Instamatic. You could only see the back of the chariot on top, from a distance, behind the Berlin Wall, and the whole structure was pretty dirty.

“Achtung! Sie verlassen West-Berlin”

“Attention! You are leaving West Berlin,” the sign informs you, in case you were confused about the concrete wall, the no-man’s land, and the guard towers nearby.

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Brandenburg Gate from the West, May 1983

(Admittedly, the faded color printing doesn’t help, but it’s held up surprisingly well for 35 years.)

This is what it looks like today, from the other side, on the famous avenue, “Unter den Linden.” The gate itself has been cleaned up, the wall is gone, and there are tourists everywhere.

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This souvenir shop now hangs the opposite sign over its door: “ACHTUNG Sie verlassen jetzt Ost-Berlin” (Attention you are now leaving East Berlin). Our kids, who weren’t yet born when the wall fell, don’t remember anything different. To them, Berlin’s Tor has always been open.

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Thursday Doors is a weekly feature allowing door lovers to come together to admire and share their favorite door photos from around the world. Feel free to join in on the fun by creating your own Thursday Doors post each week and then sharing it, between Thursday morning and Saturday noon (North American eastern time) at Norm 2.0’s blog here.

 

Mundane Monday: Fingerprints

This week’s Mundane Monday theme #164 is “A Use for Hands.” I am posting it on Tuesday because of European hotel wifi bandwidth failure.

Last week my hands were used in a fingerprint forensics STEM outreach activity.

There are 3 classes of fingerprints: arch, loop, and whorl. Arch is the least common, with only 5% of fingers in the USA exhibiting an arch print. My right index finger happens to have a good arch.

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So, I made a bunch of examples.

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They were used in an outreach activity at a STEM festival last weekend. Kids who came to the booth had to figure out who stole the candy, based on fingerprint, hair, and cryptology evidence.

Here’s one of the suspects. (My hair is not really pink: it’s an app!)

IMG_3494Mug shot of the Strawberry Snatcher

Memories of Memorizing

When I said I had decided to perform the Telemann viola concerto from memory I was met with some skepticism.

2ndmovementaskew.jpg“You don’t *have* to, you know.”

“I don’t think I could do that.”

“A lot of soloists nowadays are using the sheet music.”

“I’d want the sheet music there just as a security blanket.”

There’s a lot of overlap between shared experience and advice. It’s a general human tendency to believe that the lessons of one’s own experience are relevant for others too. But, as I’ve learned (from—ha—experience), it’s better to let the recipient decide how and why that is true. This blog is intended in that spirit.

In my case, I need to memorize.

In my day job, I am a neuroscientist. I worked for several years in biotech, then in academia as a project manager, and now in STEM education and outreach. I could go on, comparing different aspects of scientific and musical careers, but for now, this concerto performance is taking me back to my PhD thesis defense. At Stanford where I was a student, as at other major research universities, PhD candidates have to write a thesis, present their work in a departmental seminar, and then answer questions from their committee, which comprises several professors in the student’s field of research.

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Cultured neurons, from a figure in my PhD thesis

My thesis committee members were intelligent and kind, and my thesis consisted largely of putting together three already-published papers and two manuscripts in preparation. I didn’t expect to fail based on my scientific work. But I did have these nagging thoughts that I could fail based on my presentation of that work. I had a history of performance anxiety and self-sabotage. There were the points lost from school reports because I read them verbatim from note cards. And the speech I gave for my failed run for student council. An All-State audition in which Mozart’s Violin Concerto #5 reduced me to tears wasn’t any better. And then came the worst one of all: the disastrous audition for the University Orchestra my freshman year in college that started me down the road to quitting the violin.

But there was a glimmer of hope in grad school, and it lay in the results of memorization. A few years before my thesis defense, I gave my first talk at a major scientific meeting, the Society for Neuroscience meeting in Phoenix AZ. My 10-minute talk was scheduled, along with two others from my lab, in a session starting at 9 am on Monday morning. The night before, I paced an empty hotel conference room, memorizing my talk word for word. One of my lab-mates had suggested I do this. She was older than I, a postdoc and a rising star in the field, known for giving good talks. And she let me in on a secret: she still got nervous. Like, really, really nervous. But these talks were only 10 minutes, short enough to memorize, and that helped her. It might help me too.

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Cajal’s drawing of the hippocampus, a brain structure important for memory. Public Domain, https://commons.wikimedia.org/w/index.php?curid=612536

I had about 10 slides and so first I memorized the order of the slides, then I chose a visual cue on each that would remind me of the slide to come. When I changed to the next slide I oriented the audience to what they were seeing and then gave the slide’s important message. Then it was time for the transition to the next one. This mental map of order of slides/visual cues/transitions/important message was something for me to hang onto and think about, even as the storms of anxiety raged.

The next morning busses from the hotels were crowded and we almost didn’t make it to the convention center in time. With over 25,000 neuroscientists in attendance from all over the world, this conference is so big that only a few convention centers in the country can handle it, and this particular meeting took place before the Society figured out that Phoenix wasn’t one of them.

The logistics were in disarray; attendees were packed into the ballroom like sardines without enough chairs and the podium lights weren’t working properly. My mentor was first from our lab to give her talk. I watched as the podium light went on and off randomly but she continued to speak calmly. The projector functioned, but there was no pointer available, laser or otherwise, and as she stepped back to the screen to point at something on one of her slides, she disappeared entirely. In the dark, she had missed the edge of the podium and fallen off. The audience gasped. She re-emerged, uninjured, climbed back up and finished her talk. Her voice shook but she got it under control. The podium lights came back on sometime near the end. The timing bell rang, people asked questions.

And then I was next. I took the stage wondering what fresh hell awaited.

My own talk went off without incident. The lights, and the laser pointer, and everything else were up and running by then thanks to the hardworking convention staff. I was hyper-aware of where the edge of the podium was. I knew my talk well. I’d just witnessed one of the worst things that could possibly happen during a talk, and I knew it was survivable. My friend’s preparation, the fact that she knew her talk backwards and forwards, had made the difference.

Several years later, when I was giving my thesis seminar, I had this experience to think back to. My seminar was about 5 times longer than the little 10-minute meeting talk, but I still approached it the same way: slides/visual cues/transitions/important messages. I just had more slides. I ran through them mentally, over and over again. The order was comforting; it was the stick I gave the trunk of my elephant brain to hold onto.

I passed.

Concertos don’t use slides or projectors to deliver their message, which is different from a scientific talk. But certain principles still hold true. First of all, having note cards, prompts, or the sheet music “just in case” isn’t going to work for me. If I know it’s available I’ll lean on it. I’ll steal a look and then start reading it verbatim. Instead I need to be prepared to look inward, not outward, even–or perhaps especially–for that cue to keep going when I stumble.

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Elephants and their trunks. Photo by Antoine Plüss on Unsplash

Of central importance is something that Meditation Instructor Eknath Easwaran called the stick for the elephant trunk.

The human mind is rather like the trunk of an elephant. It never rests. It goes here, there, ceaselessly moving through sensations, images, thoughts, hopes, regrets, impulses. Occasionally it does solve a problem or make necessary plans, but most of the time it wanders at large, simply because we do not know how to keep it quiet or profitably engaged.

Easwaran goes on to recommend the mantram, a spiritual formula in the form of a word or short phrase, to steady the mind. This is a subject of study for a lifetime. And I am not naturally a great meditator; sometimes when I try, it puts me to sleep. Furthermore, I find words themselves to be an awkward fit for a steadying mental substrate.

My mind gravitates more towards deeper non-verbal sensory experiences: pictures, kinesthetic feelings, and music. It is those sensations that I string together as another kind of mantra. Not power point slides this time, but bridges, ladders, and lattices. Finger patterns, and arpeggios climbing to the sky before sliding back down the other side of the bow. The deep purple of the C, the forest green of the G, as I put bow to string.

Brain Coral. Photo by Daniel Hjalmarsson on Unsplash
Brain Coral. Photo by Daniel Hjalmarsson on Unsplash

Happy DNA Day!

Today, April 25, is National DNA Day. This is an obscure holiday, ranking somewhere above International Violin Day but probably below the recent pi day, or even the upcoming May the 4th be with you.

It celebrates something important, though. National DNA Day commemorates the successful completion of the Human Genome Project in 2003 and the discovery of DNA’s double helix by James Watson and Francis Crick in 1953.

DNA stands for DeoxyriboNucleic Acid. The “nucleic” part means it is found in the nucleus of all cells. There are many different ways to visualize DNA. These are some of the most common:

Francis Crick's DNA model, Rosalind Franklin's X-ray crystallography, a schematic double helix, a bacterial chromosome, some DNA isolated in the lab
Different views of DNA

The upper left shows Watson and Crick’s original wire model of the DNA double helix. On the lower left, the abstract X is one of Rosalind Franklin’s X-ray crystallograms that were used to help determine the structure. The upper right, looking like a beaded necklace, is a bacterial chromosome viewed under an electron microscope. And the lower right, with what looks like some cloudy snot in a tube, shows some DNA extracted from strawberries with common kitchen materials.

The center picture shows the DNA double helical model that has entered popular culture. A DNA molecule is composed of two complementary strands that wind around each other in a helical shape, a “twisted ladder.”  The rungs of the ladder, in primary colors, are the base pairs, which spell out the genetic code.

This song from “They Might be Giants” explains in 2 and a half catchy minutes how the DNA instructions are translated into making different cell types.

Every year the American Society for Human Genetics sponsors an essay contest for high school students and announces the winners on DNA day. This year’s question was about genetic testing.

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Do you think medical professionals should be required for all genetic testing, or should consumers have direct access to predictive genetic testing? 

Check out some of the winning essays here on their website. Congratulations to all who entered!