Category Archives: Science

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

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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!

Film Review: A Wrinkle in Time

The book by Madeleine L’Engle on which this movie was based was one of my childhood favorites. I looked forward to the film eagerly because I wanted to see a gifted director do justice to the material. I thought that many of the changes were promising updates for modern audiences, able to bring the book’s uplifting message of love to more people.

On an even more personal note, my still-unfinished novel, Hallie’s Cache, was inspired by A Wrinkle in Time. In both stories, a misfit young teen girl looks for her missing father and grows into herself in the process. A Wrinkle in Time was rejected from 26 publishers before going on to win the Newberry Medal and become one of the most beloved children’s books of the 20th century. There has been a previous attempt at making a movie out of this material in 2003, with mixed success. It has always defied categorization: is it for adults or children? Is it fantasy or science fiction? Is it too Christian or not Christian enough?

After watching the current version, I’m not convinced that it’s possible to make a good movie out of this book. The director, Ava Duvernay, did everything right: she assembled a great cast and approached the project with care, respect, and a wide open vision. And I enjoyed it on its own terms; I identified with Meg and her teenage problems. I found Storm Reid to be an appealing and relatable actress. I rooted for her and her friends to save her father. I loved the trippy visuals, the costumes, the animations. I even cried for the brokenness in the world, as gently as it was portrayed, and cheered for the family’s reunion. But it wasn’t the story that packed the emotional punch that I remembered and loved all these years. Opening to mixed reviews and eclipsed at the box office, it is likely to remembered, if at all, as a footnote to Duvernay’s career.

As much as I hate to admit this about a childhood favorite book, the problem is likely not with the filmmakers, but with the source material. Written in 1962, A Wrinkle in Time is of a particular time and place. The book’s characters are all European-Americans, redheads or mousy-brown-haired with Anglo-sounding names like Charles Wallace and Dennys (who, with his twin brother, is wholly absent from this movie). It famously opens with the Bulwer-Lytton cliche: “It was a dark and stormy night,” as Meg watches a thunderstorm from her lonely, cluttered attic room. For these reasons, and because of the three witches, the gossip about Mr Murry’s disappearance, and the neighbor’s sheets drying on the line, I had always pictured it taking place in an eccentric, secretive New England small town–a small town with a dark side like the ones that L’Engle herself, and her contemporary Shirley Jackson, lived in and raised their families.

Bringing this story out into the bright Southern California sunshine as this movie did took too much of the edge off. Certainly there are edgy areas of Southern California too, but we didn’t see those. The Murrys’ home is gorgeous and spacious. The middle school Meg attends is a well-resourced model of ethnic diversity headed by principal of color who is a three-time science teacher of the year award winner. This muddies the rationale for why Meg is bullied by the other students. In the book, Charles Wallace is an odd prodigy, perhaps a savant on the autism spectrum although that was not understood at the time the book was written, and Meg gets in trouble at school for defending him from bullies. She is thereby always his protector, and her actions at the end of the book, when her fierce love saves Charles Wallace from IT’s clutches, are perfectly in character and make emotional sense.

In the movie on the other hand, Charles Wallace is still a prodigy, but he appears quite well tolerated, happy, and self-contained, and he doesn’t need Meg to protect him. If anything, he is the one protecting Meg. Meg’s outcast status is instead attributed to her father’s disappearance. But in present day California, with so many children being raised by single parents and blended families, her father’s disappearance would not be the scandal it was in 1962. Her loneliness can and does lead her to act out further, but it is a feeble justification for her school situation as depicted here.

Details of what happened on Camazotz are also compressed in the movie. The book’s depiction of Camazotz, the planet that has given in to evil, gives off a sort of Kafkaesque bureaucratic banality. Complete conformity to a 1950s suburban nuclear family ideal is expected, and outsiders’ food turns to dust in their mouths. “IT,” the master controller, appears in the book as a disembodied brain on a dais. IT appeals to Charles Wallace and seduces him to ITs side because of ITs ability to control and impose order on messy human impulses. IT was a metaphor for the tyranny of a society that values and runs on brains and intellect alone and disregards love. That in the book there are two battles against IT and that Meg must make the decision on her own to return to Camazotz and rescue Charles Wallace compound the sense of foreboding and dread, as well as making Meg’s triumph sweeter and more meaningful when she does ultimately rescue him.

The movie, however, shows little of Camazotz; the scene with the kids bouncing balls in unison seems like a confusing non-sequitur rather than a Potemkin village masking the fear and desperation of the populace. After her father and Calvin are defeated, Meg is forced immediately into lonely battle with IT. This battle scene was disappointing. Some of the creepy tree-like things with branches might have supposed to have been neurons with dendritic trees, but the overall connection of the movie’s IT to an emotionless, loveless, disembodied brain capable of the ultimate in mind control was weak.

The rescue scene itself focused too much on whether Meg herself was lovable in spite of her faults and not enough on the transforming power of Meg’s sacrificial love for Charles Wallace. The book is unapologetically Christian in outlook, reflecting L’Engle’s own Christian faith and naming Jesus as one of the warriors against the darkness that enveloped Camazotz. I believe that L’Engle intended Meg’s love for Charles Wallace here to be selfless and Christlike, yet her Christian imagery and references have been dropped from the movie, to its detriment. Mrs. Who quotes and references many world religions; Christianity could have been included there. And why not acknowledge Jesus’ role, and the role of faith for many Christians, in fighting evil? True to her character, the scientist Meg would likely remain skeptical, and that would be okay too. Warriors can come from all faith traditions, and from no faith tradition.

The other big problem with this story is the science, the so-called “Wrinkle in Time” itself, known in both the movie and the book as a tesseract. Back in 1962 at the dawning of the Age of Aquarius, when the theory of relativity was new and humans hadn’t yet gone to the moon, the idea that you could bend space-time with your mind by “tuning” it to the right frequency might have been a little more believable than it is now. There is a scene in the movie in which Dr. Murry is shown giving a seminar about how tessering works. Jeers and guffaws of disbelief come from the audience; as well they would in real life. He sounds like a New Age motivational speaker in the tradition of Werner Erhard, or a trickster like Uri Geller.

I still remember when an annoying boy in my physics class explained to me what a tesseract “really” was: a cube within a cube, a projection of 4-dimensional space into 3 dimensions the way the drawing of a cube on paper as a square within a square was a projection of 3-dimensional space onto 2. There was nothing about wormholes or traveling 93 million miles with just your mind. Talk about disappointing! It wouldn’t have taken much to give Dr. Murry in the film a high-tech device that would make tessering possible, or some novel psi powers based on his and his wife’s research. These would have to be hand-wavey and entirely fictional of course, but good shows have been based on less. What doesn’t work is asking us to accept that New Age mumbo-jumbo somehow became true for this family because they “believed in themselves.”

As a smart girl who was interested in science, I believed too long in this book’s oversimplified and inaccurate version of how science works. Meg’s parents worked together in a homemade lab; when her father disappeared, her mother continued her experiments in the kitchen, bunsen burner on one counter, soup on the other. There was no mention of grants, funding, students, safety regulations, collaboration outside the family unit, or even publication. It’s a more romantic and family-friendly vision of doing science than has ever actually existed. Perhaps this vision was inspired by the real-life Curies, French Nobel Laureates Marie and Pierre and their children, who discovered radioactivity; yet their work had a visible dark side. Modern science is safer for its practitioners, and it is more open and collaborative than either what the Curies experienced or L’Engle’s vision. It is also more expensive and more technical, and requires more energy and perseverance than romantic genius for success. A film that wants to inspire young people in science in the 21st century would do well to tell a more accurate story about the scientific process. This film drops that ball completely.

I hope this movie inspires its young audience, but sadly, I don’t believe it’s memorable enough for that.

Already? Why I don’t like Daylight Saving Time anymore

I haven’t blogged yet this month and suddenly it’s mid-March already. Tonight we set the clocks ahead one hour. This time of year brings out a predictable spate of articles about the history of Daylight Saving Time (not “Savings” Time) and partisans on both sides weigh in.

The one thing everyone seems to agree on is that they hate changing the clocks. I used to not mind it as much as I do now, but that was before it was so G-d-awful early in the year. Daylight saving time started in the USA in 1918 with the idea of saving energy. That means it is 100 years old this year. I actually remember the biennial clock ritual as a child with a little fondness. Thinking it through helped me understand clocks, timekeeping, time zones, circadian rhythms, and jet lag a little better. And somehow the stakes were lower for sleeping in.

But we don’t currently observe your grandfather’s Daylight Saving Time. The first federal standards established that DST would start on the last Sunday in April and end the last Sunday in October. But in 2007 and 2008, DST was extended by another month, into March and November. This extension was politically motivated and driven by candy and golf industry lobbying. The hoped-for energy savings have not materialized.

This is when I started to get angry about this issue. Nobody asked us: there was no popular vote on this change, and no consideration for what the time shift does to the human body clock.

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Daylight Saving Time doesn’t actually save anything. It just shifts light from the morning, when it is needed to entrain the body’s internal clock, to the evening, when it contributes to insomnia. Especially when instituted so early in the year, before the equinox (before the day is even as long as the night) it puts everyone in a state of perpetual eastward-going jet lag.

The body’s clock never actually adjusts to daylight time. The spring forward clock change is associated with a 25% increase in the risk of heart attacks  and an increase in traffic accidents on the Monday following the time change (Be careful out there!) And it’s in exactly the wrong direction to help sleep-deprived teens be able to get up for school. Daylight Saving Time is one of many factors that disconnect humans from the natural world.

I think we should just end this 100-year-old experiment altogether, and live on standard time all year round. But I’d settle for a return to the standards of the 1960s and early 1970s, when turning the clocks ahead really meant the coming of spring.

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Super Blue Blood Moon Eclipse 2018

Live Webcasts! How to Watch the Super Blue Blood Moon Online from Space.com

The coverage is a little breathless, but I’m still glad I got up to see it.

Why is it “super”?

Because the moon is close to the Earth in its orbit this month, and appears larger and brighter than usual.

Why is it “blue”?

Because it is the second full moon in the month of January. There actually won’t be one in February at all this year.

What’s the “blood” about?

When the Earth’s shadow passes between the sun and the moon, the moon no longer reflects the sun’s light, but it does reflect a bit of light from the Earth, which appears reddish. The red color has historically been called a “blood moon.”

And the eclipse? Didn’t we just have one of those last summer? (And I didn’t keep the glasses)

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Yes, we had a total solar eclipse last summer, which I wrote about here and here. This month we had a total lunar eclipse. A solar eclipse happens when the moon comes between the Earth and the sun, covering the sun for a few minutes. A lunar eclipse happens when the Earth comes between the moon and the sun, and the Earth’s shadow covers the moon. Lunar eclipses last for several hours, and you don’t need glasses to see them. The downside is that you have to get up in the middle of the night.

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I got up just before totality started, and I took some pictures with my iphone camera attached to binoculars. I also have a small telescope, but wasn’t able to attach the phone effectively there. I could see the moon very well through the west-facing glass sliding door that leads out onto our back deck. I opened and shut the door multiple times to keep from getting too cold and to keep the cat from escaping!

Individually the pictures are kind of small and grainy, but together they make a nice collage:

Lunar Eclipse Jan 31 2018

You see how the path of the Earth’s shadow travelled from the upper left to the lower right, how long totality lasted (in comparison to last year’s solar eclipse), and just how bright the reflected sunlight is, relative to the reddish light reflected from the Earth. I stopped watching as the moon set behind some trees and the sun rose.

For more information, viewing, and pictures, check out the article above, this National Geographic article, Rare ‘Super Blue Blood Moon’ Coming–First in 35 Years and these photos submitted to Newsweek from all over the world: Here are the Best Pictures of the Lunar Eclipse Super Moon. 

The Ozone Hole is Healing!

Remember the Ozone Hole? It was one of the big environmental problems of the 20th century that seemed to go along with all the other reasons that our planet was in trouble. It was a reason all we light-skinned people, especially the Aussies, were going to get skin cancer and cataracts. According to the Ozone Hole website, the ozone hole of 2006, over Antarctica, was the biggest ever:

The 2006 ozone hole over Antarctica (Photo credit: NASA)
The 2006 ozone hole: big, blue, and scary (Photo credit: NASA)

So what is ozone and why is a hole in it bad?

Ozone is a gas made up of three oxygen atoms, with the chemical formula O3. (The normal oxygen we need to breathe is O2). It occurs naturally in small amounts in the upper atmosphere (also known as the stratosphere) and forms a thin layer covering the entire planet. This stratospheric ozone layer (“good ozone”) protects life on Earth from the Sun’s ultraviolet (UV) rays. Near the Earth’s surface, however, ozone is created locally by chemical reactions between air pollutants. High concentrations of ozone down here on the ground are toxic (“bad ozone”). The Ozone Hole is a thinning of the layer of protective “good ozone” that allows too much UV radiation to reach Earth’s surface.

Why did the layer get thinner?

Some chemicals that were used in spray cans and in air conditioners and refrigerators contain chlorine and bromine atoms, and these atoms are released when the chemicals come into contact with UV light. Then, when these chlorine and bromine atoms drift up into the stratosphere and encounter the ozone layer, they destroy it. A single chlorine atom can destroy over 100,000 ozone molecules. The most common of these ozone-depleting chemicals are called CFCs.

In 1985, the Montreal Protocol regulating CFCs was introduced. This is an international commitment to phase out ozone-depleting chemicals that was ratified by all UN countries. On January 4 of 2018, the first study was published that used measurements of the chemical composition inside the ozone hole to confirm that not only is ozone depletion decreasing, but that the decrease is caused by the reduction in CFCs. In other words, the Montreal Protocol is working! NASA Study: First Direct Proof of Ozone Hole Recovery Due to Chemicals Ban.

This is only a first step and more needs to be done, because CFCs last a long time and the CFCs made in the last century are still around causing trouble in this one. But it is still a good example of how science can influence governments’ decision-making, and how the nations of the world can work together to solve big environmental problems. May our leaders learn from this example!

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This post is part of the We Are the World Blogfest, a monthly event created by Damyanti Biswas and Belinda Witzenhausen to showcase stories of hope and light. The #WATWB cohosts for this month are:  Shilpa GargSimon FalkLynn HallbrooksEric LahtiDamyanti Biswas and Guilie CastilloPlease link to them in your #WATWB posts and go say hi!

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