Category Archives: Science

High School, Again

It’s 6:45 am but it might as well by 1:45 am. Or 2:45. It’s dark as night out and i have to go to work.

I started a new job in January. I am a teaching fellow in a highly academic, STEM-focused school, training to become a Biology teacher. I’ve spent the last 5 years teaching science part-time with a small educational non-profit. While this was good for my family life and my music-making, it was time to go back to work full-time again. My daughter is in college and my son is in high school. They are both pretty self-sufficient now.

As I walk through the noisy hallways of the school, which is located in a converted office building, I am surprised and a little dismayed by a feeling of deja vu. This is a private independent school (which means I can teach here without a teaching credential) whereas I went to a public school in a more typical public school building. But it’s no secret that I didn’t enjoy high school very much the first time around. I was 2 years younger than my peers and a social late bloomer. I have realized in retrospect that I was suffering from at least social anxiety, math anxiety, and their granddaddy, performance anxiety. Awareness of all of these, as with many mental health issues, is much better nowadays, as is treatment. But this time of life can still be fraught for many teens, especially here in hyper-achievement-oriented Silicon Valley.

Some folks have even asked me, why do this at all? I have a PhD, so perhaps I could get another biotech or project management job. Perhaps. But when I did work in those fields I felt like there was something missing: a human connection, a child-like joy in learning new things. I felt that joy intermittently in music, and with my kids, but rarely at work. I was stuck forever looking for my “passion” in all the wrong places.

Teaching, though, makes sense. In a weird way, it’s like coming home. There is something very primal, and comforting about having a bell schedule and class periods that are the same every day. The subjects are familiar too. While cutting-edge science has marched ahead, high school physics and math remain much the same. They are learned at younger and younger ages though; the AP Calculus I learned as a senior is taken here by sophomores and juniors. And, as Christa McAuliffe said, it touches the future. I’m here now as a teacher in midlife because I wasn’t ready before. I only came to like teaching after I became a parent and taught in a number of informal, non-school settings like church and Girl Scouts. It’s time, after all those years, to face down that anxiety and defang it.

Tomorrow is another day. The alarm rings at 5:45.

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Motion

December 20th 2018 was my last day at my old job. I worked as an instructor at the educational non-profit, Science from Scientists, for over 5 years. Fittingly, my last day took place at Lipman Middle School, the same school I started in when I moved to CA in 2015.

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View from the Lipman parking lot, my first day, in 2015

Nestled on the side of San Bruno Mountain in Brisbane CA (pronounced “Briz-bane,” not like the “BRIS-bin” in Australia), Lipman is in an idyllic environment. Like many public schools in CA, it comprises a collection of smaller buildings, which students walk between and among to get to classes. (One aspect of school I always disliked when I was a student was the “closed campus” rule that students couldn’t leave the grounds during school hours. If they did, even to go to, say, the pizza place across the street for lunch, they faced severe consequences. Suspension for getting a slice of pizza—a strange prison-like mentality.)

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Almost the same view, a year later

Lipman, though, has an outdoor classroom the woods, and we were able to do some of our SciSci lessons outside. Beanbag tossing with prism goggles could get a little rowdier than usual outside, and no one would mind.

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Tossing beanbags at a target while wearing prism goggles. “Altered Reality”

Other days, we fished, we looked at the moon, we made DNA origami, and we built models of brains.

Our last class before Christmas break was a lesson called “Rover Restraint.” Many schools do this: students have to build a contraption to keep a raw egg from breaking when dropped from a height of around 8 feet. In our version, we compare it to landing a Mars rover like Curiosity.

And to keep expectations in check and the playing field level for everyone, we limit the planning and building to one class period, using only the materials we bring with us from SciSci. I stand on a stool and drop each entrant from the same height. This procedure usually leads to a nice mix of some eggs cracking and some surviving, and a range of designs and budgets, making it relatively straightforward to pick a winner. (The winning group gets a nice set of SciSci pencils!)

Onward and upward! I’m going to miss Lipman, and Rover Restraint. This post is 2 weeks late for Dr. KO’s Mundane Monday prompt, Motion.

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View from the parking lot in 2018 during the devastating Camp Fire, 180 miles away

 

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

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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Mundane Monday: Skies

Dr. K Ottaway, host of the Mundane Monday challenge, asks us to post this week about skies. But not blue skies, “skies that worry me” (although if you would like to see a really blue sky, check out this post over the White Cliffs of Dover). She posted a fire sky, which inspired me to post one too.

Sunset over Los Angeles made more colorful by haze from California wildfires
Sunset over Los Angeles made more colorful by haze from California wildfires

This picture was taken last year, 2017, from Griffith Observatory in Los Angeles. As with Dr. KO’s picture, the smoke from the fires makes the sunset eerily beautiful.

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Blood moon eclipse

The sky has often been a source of worry. In the past, people looked to the heavens for signs. Eclipses, especially, were thought to portend major events.

We’ve had a few of these in the past year. I hope that instead of the primal response that such events have historically evoked, we humans can use them as signals to come together instead.

 How to Help Victims of The California Wildfires, Refinery 29, by Alejandra Salazar, August 11, 2018

 

Brain discovery could block aging’s terrible toll on the mind

My first instinct on reading this is that the findings are a bit over-hyped. A cure for Alzheimer’s? Really? Of course everyone and their brother wants to prevent brain aging and disease and everyone and their brother has something to sell you to do that–computer programs, supplements, oils, or the next Silicon Valley biotech startup IPO. But as a neuroscientist, I think that even if it is over-hyped and not a panacea it is still very worth pursuing medically. It’s a fresh approach and is likely to be an important missing piece of the puzzle. The brain is a hard organ to study, and neuroscience research has progressed slowly–and not for want of trying!

author david wolf

Faulty brain plumbing to blame in Alzheimer’s, age-related memory loss — and can be fixed

NOTE: this article not written by David T. Wolf, but selected by him from Science Digest

Date:July 26, 2018

Source:University of Virginia Health System

Summary:  Aging vessels connecting the brain and the immune system play critical roles in both Alzheimer’s disease and the decline in cognitive ability that comes with time, new research reveals. By improving the function of the lymphatic vessels, scientists have dramatically enhanced aged mice’s ability to learn and improved their memories. The work may provide doctors an entirely new path to treat or prevent Alzheimer’s disease, age-related memory loss and other neurodegenerative diseases.

Obstructing lymphatic vessels (in green) in a mouse model of Alzheimer’s disease significantly increased the accumulation of harmful plaques in the brain. “What was really interesting is that with the worsening pathology, it actually looks very 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

 

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