A Science Junkie’s Guide to Art

Some of the best things in the world exist at intersections between disciplines. My favorites emerge from the union of art and science. It is at the heart of this intersection that artists and scientists come together in order to make explanations of our world all the more rich through art.

Artistic depictions of constellations help us understand positions of stars over time. (CC)

Artistic depictions of constellations bring us closer to understanding our universe by making the night sky more relatable and navigable. (CC)

Take for example constellations. Through my childhood, I was fascinated with the universe. Instead of bedtime stories, I would ask, “Daddy, tell me about space!” He taught me many things about black holes and moons and life cycles of stars, but more than anything I remember the constellations. We lived in a rural canyon with clear night skies. Moonless nights meant more stars than you could ever hope to count — and indeed more stars than my young mind could recognize without help.

Fortunately, help was close. I had a poster of ‘Constellations of the Northern Hemisphere’ tacked to my bedroom ceiling (complete with glow-in-the-dark stars). With the light on, I could see every character’s name and a portrait overlaying the corresponding stars. With the light off, hundreds of small points glowed back at me, and in the dark I would try to remember the patterns and strange names.

Egyptian hieroglyphs from between 1500 and 1609 BCE represented agricultural growing seasons. (Wikimedia Commons)

Egyptian hieroglyphs from between 1500 and 1609 BCE represented agricultural growing seasons.
(Wikimedia Commons)

Science illustration itself has a long tradition, reaching back millennia from celestial pictograms to agricultural records of the seasons. If you will be in New York before October, the American Museum of Natural History is running an exhibit with 400 years of scientific illustration. If you won’t be in traveling through the Big Apple anytime soon, the AMNH has published a companion book (with a bonus century!) of rare science illustrations from their collection.

It is easy enough to buy a poster, or visit a museum for your science art fix. For some, however, passive viewing is not enough. Last September while hiking near San Francisco, I met a woman with an integrated DNA-circuit board design etched into her back. Literally etched. “Why scars? Why that design?” I asked. “I wanted something other than an ink tattoo. The design is a combination of my interests in bio and tech.” She works at Kaiser improving healthcare technologies.

Still curious, I asked her about the scarification process. “You have to go to an expert and have it done professionally,” she told me seriously. Her scars were made on the East Coast by peeling back several layers of skin, and then scraping away the underlying flesh. The top layer is folded back into place, and after several weeks of healing, delicate white scars begin to form. “Some of the details are beginning to fade,” she added. Eventually, over many years, the curves of the double helix and circuit nodes will sink back into her skin. It is poetic, in a sense, that the regenerative properties of her body will reclaim the homage made to them.

Tattoos themed in science are becoming increasingly popular. (CC)

Tattoos themed in science are becoming increasingly popular. (CC)

 While scarification is perhaps more rare, the world of science tattoos is alive and well. In 2007, well-known science writer Carl Zimmer began compiling images and stories behind various tattoos science enthusiasts have accumulated over the years. The results were splendid and zany enough to fill an entire book, Science Ink, which boasts the best by discipline.

“Art” is an all-encompassing term that embraces many media. So far I have focused on the illustration sides of science. There are several other artistic science scenes, and one of my favorites is sound. You can make any math geek’s day by sending them this catchy a cappella love song laden with higher-order math puns. On the programming side, computer music and audio tech continue to mature, giving us gems like the Re: Sound Bottle and sine wave water.

Bathsheba Grossman's 3D-printed sculptures tie algorithms with aesthetics to create math-inspired art. (CC)

Bathsheba Grossman’s 3D-printed sculptures tie algorithms with aesthetics to create math-inspired art. (CC)

Another venue for science art is in sculpture. Take for example the recent collaboration between MIT and Disney to create awesome character models using multi-material 3D printing. And have you ever seen a cube walk on its own? Cubli is here to cure you of that ‘not yet’.

Science art is also creeping into the digital world. Where once artists relied on paper and pigments, we now have digital cameras and high-resolution touch screens to aid discovery. For example, my favorite author, Simon Winchester, recently collaborated with skull collector Alan Dudley and photographer Nick Mann to produce an iPad app named Skulls. The application harnesses recent developments in 3D visualization and user interactivity, as well as traditional text and narration, to explore new bounds of science education through art.

The Amoeba Network, by Maki Naro, is an example of comic art as an explanatory platform for science (shared with permission from sci-ence.org).

The Amoeba Network, by Maki Naro, is an example of comic art as an explanatory platform for science.
(Shared with permission from sci-ence.org.)

Scientific webcomics are on the rise, as well. There are, of course, the wonderful standards like XKCD, PhD Comics, and The Oatmeal. Fortunately, many of these comics are actually comical. One of my personal favorite artist/authors is Maki Naro. He recently moved from his popular blog, Sci-ənce, to the Popular Science blog, Boxplot, where he continues to operate “at the intersection of art and science in an attempt to act as a mediator between the two.”

It seems this mediation drives many scientists who later turn their creative efforts to the arts. Scientific American illustrator, Jen Christiansen, just wrote about the pull between the disciplines, and how she instead decided to merge art and science. The same seems to be true of trained neuroscientist Greg Dunn, who opted to replace his pipette with the paintbrush, and has carved a corner in many hearts with his shimmery, beautiful, Ramon y Cajal-reminiscent paintings of brain.

The intricate patterns in kolams, traditional Indian chalk drawings, are helping scientists better understand protein folding. (CC)

The intricate patterns in kolams, traditional Indian chalk drawings, are helping scientists better understand protein folding. (CC)

Those who practice science art bridge worlds that are cerebral and theoretical with those that are aesthetic and tactile. We rely on artists to imagine distant worlds for us, or to reanimate scenes that have long since faded back into the soil. Art can help us understand the scientific beauty of a flower (with a little help from that fine man, Mr. Feynman), or even help improve our science.

I have an astronomy artist to thank for one of the great joys in my childhood. Because of that constellation poster, I now recognize Cetus the Whale, the galaxy in Andromeda’s armpit, and how to spell Cassiopeia. I consider this a triumph for science art in educating a young girl who was curious about the cosmos.

Jahlela is a recent graduate of the  cognitive neuroscience program at the  University of California, Berkeley. She is an avid photographer, sings constantly, and loves all things science. Follow her  @jahlela or on tumblr

jahlela AT berkeley.edu

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Happy New Year from the Student Blog!

Image via CC BY 3.0 license

Image via CC BY 3.0 license

Happy New Year! As we say hello to 2014, I want to take a chance to look at some of the fantastic work that from the Student Blog in 2013.

We had a look at diverse opinions about science education. There were passionate calls for making research part of the undergraduate experience: see Rachel Cotton’s advocacy for undergraduate research and Sean Lim explanation of what a student seeks from a research mentor. Deepshikha Mishra rounded-up new opportunities for life science in India. Rebecca Marton encouraged students to stay in STEM, and urged other STEM students to do the same. Jeremy Borniger argued that a gap year was the best choice he made before going to graduate school and Anna Goldstein assured us that it is possible to switch research groups – and live to tell the tale!

Several posts highlighted key debates in the science community. Jane Hu looked at the plight of women in science, and why women may not be staying. Michael Selep discussed the difference between translational research and basic science, and found them not to be that different at all. Tyler Shimko entered the climate change debate, discussing how his scientific background made him an effective activist and encouraging others to get involved.

Science communication itself entered the conversation when Jahlela Hasle wrote about the time a poorly written science article made her cry,  and Chris Holdgraf sparked conversation when his observations about being ‘right’ in science included the controversial mantra “Never hesitate to sacrifice truth for understanding.”

The Student Blog also featured some fabulous science writing. Alex Padron gave us insight on the history of science with his post on Alexis St. Martin’s fistula, Katrina Magno looked at the ways scientists are studying black holes, and Prashant Bhat showed how a beautiful bloom could also prove deadly. And Minjung Kim’s review of Brilliant Blunders showed that it’s okay to mess up time and again.

We also had some excellent commentary about the importance of Open Access. David Carroll and Joe McArthur shared progress on the OA Button, an exciting web tool that launched last November. Sara Lindenfeld advocated using Open Access science to educate the public about climate science. Angelica Tavella detailed the Open Access Initiative at UC Berkeley and how she got involved in the Open Access movement, and high school student Jack Andraka gave a passionate argument for tearing down paywalls to help connect young people to science and inspire a new generation of scientists.

Marvin Gee expressed the opinion of many when he resolutely asserted that research is not a job, but a lifestyle.

On a personal note, it’s been an amazing experience working with all these wonderful bloggers over the last few months. There will be more great stuff in 2014, so I encourage you to add “Read the Student Blog regularly” to your list of New Year’s Resolutions.

So stay tuned! The first official Student Blog post of 2014 will launch this week!

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The Infinite Classroom: An Ode to Student-Led Classes in Science

Science education in schools has a flaw: Large lectures are by definition impersonal, and they often leave out the larger context of the material. You can ask a calculus student “Why, exactly, did you just learn that double integral?” to see what I mean. Students go to lecture, memorize the material, regurgitate during the test, and then promptly forget it. Lather, rinse, repeat.

This seems like a regrettable state of affairs. Retention of information is highest when the relevance of what we are learning is transparent and accessible. My experience with student-led classes is not comprehensive, but I am convinced the model is perfect for cultivating true understanding.

Paul Broca

Paul Broca, the French neuroanatomist who first discovered first functional specialization in the brain. The region he identified, now called Broca’s Area, is critical for speech production. (Wikimedia Commons)

A Class on How to Read Science

 As a budding Cognitive Science major, I heard of a class with a peculiar name straight out of an abnormal psychology textbook: BROCA. The ‘Berkeley Review of Cognitive science Articles’ is one of many student-led classes offered at UC Berkeley, and while I never took the class, I had the honor of teaching it this fall.

Three years ago, BROCA’s founders identified a hole in the undergrad CogSci curriculum. For students interested in pursuing research experience and careers, there were no dedicated research methods or statistics classes. As such, students were entering research positions without the skills they needed.

The solution was simple: Start a class with weekly guest speakers who discuss an exciting research paper in cognitive science.  BROCA was born into this model, and by taking the class, students are exposed to not just the written reports of science, but also the personal stories of the scientists creating the reports.

If you are considering starting a similar class for your school, don’t be afraid to reach out. Our speakers have included professors, PhD candidates, research assistants, and even former researchers who have gone on to work in industry.

Importantly, the students are not simply listening to yet another lecture. During the week leading up to each class, students read the assigned paper, prepare responses, and formulate questions. Before the speaker arrives, the facilitators help begin the discussion by covering the basics, then open the floor for debate and inquiry. As needed, we also  design crash courses in many of the topics — how to compare brain imaging techniques or the differences between various animal models.

Another benefit of small classes is versatility. I interviewed several facilitators in other science-themed classes, and though they all shared that theme, the range of topics is impressive. Here is a sampling:

BSJ

The Berkeley Scientific Journal, an undergraduate publication for original research and interviews. (Image by Hadrien Picq)

A Class on How to Write Science

We all consume science writing at some point in our lives — in newspapers, radio programs, documentaries, textbooks, magazines. The writers have to come from somewhere, and the Berkeley Scientific Journal (founded in 1996) is an undergraduate publication that gives students not only a start, but also gives them university credit.

BSJ offers a platform where students can interact with discoveries in a field in a way that is distinct from reading a textbook or lecture notes. For those without experience in research labs, becoming part of an interview team is the perfect introduction to laboratory sciences. I became involved this semester as an author, editor, and photographer. Incidentally, the BSJ’s editor-in-chief, Prashant Bhat, is also a PLoS student blogger.

A Class on how to Integrate Science

The trend for student-taught classes is not exclusive to Berkeley. Just down the coast in Santa Cruz, the Brain Mind & Consciousness class is the first undergrad-taught science class in years. The class and epynomous BMC Society were c0-founded by Andrew Kornfeld, a student of psychology and neuroscience. For 3.5 hours every week, he and several co-facilitators taught students everything from nuclear physics to brain chemistry to drug policy to how patterns in nature are preserved across many scales of observation.

BMC

The Brain Mind & Consciousness Society teaches UC Santa Cruz’s only science-based class taught by undergraduates.
(Image by Andrew Kornfeld)

The most important feature of the class is contextualization of each level of detail. If the students learned the chemical structure of caffeine, it was going to be in the context of how its structure relates to adenosine, and how caffeine’s blocking of adenosine receptors will affect one’s conscious experience.

Another advantage of small classes is flexibility. Last spring, as the Supreme Court reviewed a case on gene patenting, the class was debating the ethics of genetic ownership while overlooking Monterey Bay.

Teaching a class of course comes with its challenges. Kornfeld spoke of his trepidation about speaking for a solid hour and a half. After the first class, he quickly realized discussion-based class was far more important than one that was lecture-based. Another worry for any instructor is information accuracy. Questions will come up in your class that you won’t know how to answer. This is an opportunity to put the question to your class to discuss.

A Class that is not a Class, but Ought to Be

“My school doesn’t offer student-led class opportunities.” There are alternatives to an official academic space that can do the trick. For example, a few years ago a small group of students at Portland State University began a weekly event called ‘Tea with TED’. The premise: bring students together in order to “develop more complex insights about a world that transcends disciplines.”

TWT

Tea with TED examines the crossroads of art + science, education + technology, culture + industry, language + empathy, literature + psychology, and more. (Image by Stephen F.)

During the first 20-30 minutes, students watch a TED talk or two together, and use the remaining time to discuss the talk. The beauty of TED is its fundamental design for wide audiences. For example, if you know nothing about mycelia, start your Tea with TED by watching Paul Stamets’ talk, ‘6 Ways Mushrooms Can Save the World’. The ensuing discussion could range from using mushrooms as alternate fuel sources to ecosystem creation to terraforming other planets. Ideas not easily conveyed with words bleed onto  butcher paper-covered tables — all of this over tea, of course.

TWT’s founder, Stephen F., describes the result as “a colorful, healthful, and intellectual atmosphere that feels like a book club hacked by RSAnimate.” While not technically a class, the Thursday meetings frequently drew 20-30 people. It sounds like the perfect complement to single-subject classes, which can feel detached from life beyond the classroom.

As we move through our years in college, with hope we have collected enough experience in our major to return the pedagogic favor and begin teaching our own classes. Teaching BROCA was the highlight of my week, and I look forward to seeing the next generation of classes in science.

Jahlela is a senior undergraduate student studying cognitive neuroscience and music at the University of California, Berkeley. She is an avid photographer, sings constantly, and loves all things science. Follow her  @jahlela or on tumblr

jahlela AT berkeley.edu

Category: The Student Blog | Tagged , , | 1 Comment

We need to check our work: Rethinking replication and publishing

The most exciting phrase to hear in science, the one that heralds the most discoveries, is not “Eureka!” (I found it!) but “That’s funny…”
― Isaac Asimov

A popular theoretical framework in my field, developmental psychology, compares children to scientists. Alison Gopnik first championed the view that children, like scientists, have theories about the world, and test and revise those theories through their everyday behavior. “A theory, in science or in everyday life, doesn’t just describe one particular way the world happens to be at the moment,” Gopnik wrote in a 2005 Slate article. “Instead, having a theory tells you about the ways the world could have been in the past or might be in the future.”

Children have been observed experimenting by repeating the same intervention many times – for instance, in many of Gopnik’s studies, children place blocks on a “magical machine” to determine which ones make the machine light up and play music. It seems from these repetitions that children want to be sure what they’re observing isn’t a one-off fluke, but a real causal effect in the world. Children study the results of their interventions, and revise their theories if there’s a new result that contradicts their previous theory. This is, in theory, what scientists do to test our theories as well — except it seems that preschoolers have bested us in the process of repeating interventions to check our work.

Replicating a study seems easy enough, but the time and effort involved in replicating even your own work can be quite costly. In most STEM circles, a research group that finds a significant result would be crazy not to publish it as quickly as possible, lest someone else beats them to the punch. Additionally, there is no incentive to replicate, since journals typically seek out new results for publication. In theory, this is a good thing – we want original findings to make progress in science – but publishing norms have taken this to an extreme. A 2007 study by Daniele Fanelli found that 86% of publications are positive results (up 22% from 1990).

The disincentives for replicating are usually enough for researchers to steer clear of it, but the few who try are in for more hurdles. In order to replicate a study, one needs to know how the original study was done. As journal articles are skewing shorter, methods sections may provide less information, giving the reader only a basic idea of a study’s procedure. In many studies, effects could be due in part to small details, like the exact wording an experimenter uses, or even the color of the walls of the testing room. To probe the strength of an effect, we need to play with these variables to see how they affect the results. In the discussion surrounding the replicability of psychologist John Bargh’s studies, fellow psychologist Daniel Kahneman likened the small details in experiments to “the direction of a theatre performance,” and suggested that perhaps the reason why Bargh’s studies weren’t replicating were because Bargh just “has a knack that not all of us have”.

“The conduct of subtle experiments has much in common with the direction of a theatre performance,” said Daniel Kahneman. If these subtle details are what are driving effects, that’s all the more reason to be thorough in reporting our procedures.

Researchers are humans, and we’re subject to the same biases as everyone else, despite our meticulous training in objectivity. There are many points in the process of publishing a study where human bias can lead to a portrait of the world that is less than accurate. For instance, when psychologists Stéphane Doyen and colleagues tried to replicate John Bargh’s famous result that priming participants with “old” words led to slower walking, they found that the experimenters’ unconscious bias in timing participants’ walking speed could have exaggerated the original findings.

More meticulous reporting of procedures and results will encourage researchers to be more critical of their own work, and will create opportunities for collaboration. In casual conversations with other researchers, I’ve often heard things like, “If only I knew how they did that!” or “I wonder if the researchers looked at X in their results…” The availability of detailed procedures and raw data would allow new life for results, and will allow researchers to do replications or extensions quickly, rather than spending time figuring out the exact procedure that led the original researchers to find an effect.

Replications are also important to safeguard against human fallacy. We hope that our current peer-review process will weed out studies in which experimenter bias or poor study design explain the results, but reviewers, like researchers, are human and subject to biases. One glaring bias is the fact that some journals are not double-blind! We scientists pride ourselves on objectivity and recognition of merit, but it’s hard to say how scientists’ reputation (or lack thereof) influences their publication acceptance rate at journals that reveal the authors’ identities.

Reviewers may also fail to spot errors in research. The Economist reported several studies that indicate reviewers are less familiar with stats and less meticulous than one would hope. Anyone who has served as a peer reviewer can tell you – it is a thankless job. Most reviewers are not paid or recognized in any way for their time and effort, besides the right to add an additional line in the “professional service” section of their CV.

Besides their dedication to the furthering of science, reviewers have little incentive to thoroughly vet the papers they’re assigned to review, especially when this volunteer assignment is competing with other job duties, like research, teaching, and grant-writing. Sometimes, reviewers are assigned to comment on papers that are outside their expertise, which makes them even less motivated or qualified to provide good feedback on manuscripts. A colleague of mine recently waited six months to hear back from the third reviewer of his paper, only to receive an email from that reviewer in which he admitted that he did not feel qualified to comment on the paper because the research was outside his expertise.

Often, reviewers are overworked academics with little incentive to give thoughtful feedback.

Though traditional journals are doing their part to adapt to the shortcomings of the current publishing system, alternative open-source and web-based publishing groups are poised to help address many of these issues with new technologies. For one, replications may be more like to be accepted by and easier to execute in non-traditional journals. Many of these journals or publishing services (PLOS, PeerJ, the Winnower) publish based on the soundness of a study’s methods and conclusions, rather than its perceived impact on its field, which encourages high-quality rather than flashy work. Also, without the word-limit and space constraints that come with printed journals, non-traditional journals could allow researchers to upload detailed procedure instructions, raw data, or even video clips of their procedure.

New publishing systems could also improve the speed of science communications. Cover letters to reviewers were probably useful when correspondence about manuscripts was limited to sending mail through the postal service, but they are now just a relic of an old system. Rather than specifying that you changed a sentence on page 34, paragraph 3, perhaps one day authors and reviewers will be able to submit digital documents highlighting changes, comments, and suggestions, rather than writing formal letters to one another; this would cut down on the amount of time wasted on formatting correspondence between authors and reviewers. Online journal PeerJ allows registered users to comment on papers, creating a community in which feedback can be given instantaneously and less formally.

Online publishing and review also opens up the possibility of more feedback. Why stop at the standard three reviewers? Allowing qualified, registered users to comment on or review articles may also present the incentive for higher-quality feedback. Comments, for better or for worse, could be made public, allowing academics to be recognized for thoughtful feedback. PeerJ, for instance, incentivizes high quality comments by awarding points to users who have written a comment nominated as “insightful” by other users.

Surely, there are other cultural changes that need to occur in the science world before we adopt new publishing systems – for instance, as Berkeley cell biologist and Nobel Prize winner Randy Schekman suggested in an op-ed last week, placing less importance on journals’ impact factors. And even after we adopt new publishing systems, they will not be a panacea for all issues in science world. Still, these recurring discussions about the importance of replication and the need for alternative publishing systems suggest that the time is ripe to refine our scientific values and to rethink the system we have in place to uphold those values.

jane huJane Hu is a PhD candidate in the psychology department at University of California, Berkeley. Her research focuses on social cognition and learning in preschoolers. She is also an editor of the Berkeley Science Review. Follow her on Twitter @jane_c_hu, and check out her science blog: metacogs.tumblr.com

 

 

For more about replicability & replication projects:

Check out these open-source publishing and collaborative tools:

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An Ode to Patch Clamping

I’ve been a graduate student in bioengineering for quite a while now—let’s call it “more than five years”—but I harbor a far more embarrassing secret (for a bio-centric program) than that. I’ve only known how to pipette for four of them. When I entered graduate school my lab experience had been limited to computer work: mostly data analysis in Matlab. I had never actually gathered my own data. Perhaps I should’ve directly mentioned this in my application, though at times computational work is all one does to complete a PhD in bioengineering (the field is diverse).

AllYourBugAreBelongToMeThere were many times as an undergrad that I was so frustrated troubleshooting code in Matlab I actually yelled at whatever living thing was inside the computer and obviously out to get me. But I eventually figured out how to massage the computer into doing what I wanted. And that particular problem was solved.

As a grad student I’ve come to know the pains of experimental work with actual living things. One particular technique deserves the utmost reverence: patch clamping.

Less widely practiced than computer programming, patch clamping is one of the most transformative techniques in neuroscience. It’s a delicate process in which you, the experimenter, first bring the tip of a microscopic glass pipette down to a cell membrane ever-so-gently under a microscope. You then physically apply suction with your own mouth on the other end of the pipette, which is archaically connected though a long rubbery tube. By applying suction you draw the cell membrane so close to the pipette tip that it adheres and forms a seal on the rim of the glass. Then with more powerful suction, you break open the bit of membrane that’s stuck to the pipette opening, all while the cell is still alive.

A microscopic glass pipette (in blue) patched onto a neuron in the hippocampus, a region of the brain that processes memory.

A tiny glass pipette (blue) patched onto a neuron in the hippocampus, a region of the brain that processes memory.

When this happens, you suddenly have all kinds of access to the inside of a cell (in my case, a neuron). The liquid contents in your pipette diffuse into the cytoplasm, and the small electrical signals generated by ion channels in the cell membrane are detectable by an electrode that sits further up in the pipette (a cell membrane usually filters these signals such that they are undetectable from the outside). You are now part of the living neuron and can inject current or perfuse drugs into the 15 um (on average) space that generates action potentials, integrates synaptic signals, produces proteins and transcribes DNA.

Patch clamping is a powerful technique that has no alternative.

But it takes a special kind of person to perform such a technique regularly. When one troubleshoots a computer program, there is complete control of the system (even if it doesn’t feel that way). Bugs in code, once solved, are solved permanently. They possess no quantum phenomenon like randomly changing or disappearing. Bugs occur in experimental protocols as well, except that they are much less well defined. Patch-clamp bugs require a personality with the highest tolerance for frustration I’ve ever encountered. They reappear with very few hints to a reason. It’s a maniacal game.

There are obvious parameters to fiddle with when patch clamping. I can count them on both hands, but beyond that, there are an unknown number of parameters that govern the cell about to be patched. Humans made computers, so we know exactly how every part works, down to the transistor. But humans did not make cells, and we don’t know nearly enough about how they work.

When something common goes wrong during a patch clamp experiment—the cell membrane won’t seal onto the pipette, or the cell dies as soon as you break into the cytoplasm, or the patch fails too soon to measure what you wanted—there’s no quick or permanent fix. One can tweak the shape of the pipette to be more amenable to sealing, one can mix up new internal solution (the liquid that goes inside the pipette), one can grow or harvest new cells, trying to be extra careful so as not to hurt them. Any number of these solutions might fix the problem, and each one takes anywhere from an hour to days to try.

A computer program contained in a stack of punched cards, waiting to be inserted into a machine that can read them. You can see edits in red marking where the programmer has made changes from the last iteration.

A computer program contained in a stack of punched cards. The red markings depict where changes have been made from the last iteration through a central computer.

If you converge on something that works, you patch a bunch of cells that day and celebrate! But when you come back next day, the same problem happens. Or a different problem happens, and the cycle starts again. Perhaps this was the frustration early programmers experienced when they had to wait in line to try out revised code on punched cards in a centralized computing center. I applaud them for sticking it out!

Patch clamping can be incredibly frustrating. In my lab we joke about making sacrificial offerings to the “patch clamp Gods.” The technique is often likened to black magic, but when done by someone with utmost patience, it is a powerful art form. To be able to peer at and control the electrochemical signals that govern neurological processes within single cells was revolutionary over three decades ago and has advanced neuroscience at an incredible rate. We now know that ion channels (the pores in cell membranes that control flow of various chemicals in or out) open in a probabilistic manner. We can study how neurotransmitters like serotonin modulate internal electrical signals, and how a neuron decides whether to fire an action potential (i.e. communicate with other neurons), given the small electrical currents induced when a single synapse relays a message to that neuron.

Patch clamping can be excruciating, but like computer programming it opens up an entire scientific realm that is inaccessible any other way*. I commend those who stick with the technique and accept the frustration in exchange for the rewards it offers.

 

*Though as they improve, optical techniques might one day replace patch clamping.

Category: The Student Blog | 3 Comments

What do PLOS and Lady Gaga have in common?

What do PLOS and Lady Gaga have in common?  Nothing really…unless you count this video parody from some grad students at the University of California, Berkeley.

We tracked down the makers of the video to find out a little more about them. Below is a brief Q&A with director Ross Wilson and star Mary Anne Kidwell.

1.) Why PLOS? Was it principle or were we an easy rhyming mechanism?

Lady Mary Anne strikes a pose

Lady Mary Anne strikes a pose

Ross Wilson: The genesis of the idea certainly lies in the delightful phonetic similarity between “in PLOS” and the original song’s titular “Applause”, but we became much more enthusiastic about it as we considered all the timely themes we could touch on in fun ways. I knew that the idea was meant to be when I realized that Mary Wiese, the star of the Hui Zheng lab’s outstanding “Bad Project” parody and viral hit, has two PLOS ONE papers to her name. This project was contingent on our lab being friendly to open access journals, and I am proud that we have indeed published in PLOS ONE and eLife. Additionally, one perk of being an HHMI lab is that every paper we publish will appear in PubMed Central, delivering open access in a practical sense regardless of journal.

Mary Anne Kidwell: The more we thought about the contrast between Science/Nature/Cell and open access journals, the more appealing it was to invoke a well-known journal like PLOS ONE. When it came to writing the lyrics and making the video, it was important to strike the right balance between the challenges that come with publishing in “hot” journals versus publishing in open access journals.

2.)Describe the team, either as a whole or individually?

RW: The team behind the parody was primarily me and Mary Anne; I contributed a lot behind-the-scenes while she delivered the vocals and star power.

MAK: While Ross and I did most of the work, we couldn’t have done it without our incredibly supportive lab. They provided lot of amazing ideas and help for the video, such as inspiration for the journal cover dress. Ross and I have had a lot of practice working together musically. Over the years, we’ve done Lady Gaga duets during our lab karoke outings and on-stage during our departmental retreat. We have no shame.

3.) Describe your lab?

RW: The Doudna lab has a long history of research into the mechanisms of RNA biology. Although our work on Cas9 has received plenty of attention lately due to the implications for genome engineering, Mary Anne and I study Dicer and its role in microRNA biogenesis. We joke about a unification of these two sides of the lab in the “group meeting” segment of the video, where a Cas9-Dicer fusion enzyme is facetiously suggested to allow time travel.

MAK: Work hard, play hard. Jennifer Doudna has created great lab environment and like the rest of the lab, she is really encouraging of all our crazy ideas (scientific and otherwise). Watch out for her cameo at the end of the video!

Professor Doudna and her lab: working hard and playing harder

Professor Doudna and her lab: working hard and playing hard

4.) What is your research focus?

RW: My research centers on the interplay of the endonuclease Dicer and its protein partners in ensuring quality control of the microRNAs responsible for gene regulation in mammals.

MAK: I study how small RNAs are created but the RNase Dicer and its accessory proteins for RNA interference. I’ve primarily used biochemistry and single-molecule experiments to analyze how these small RNAs are made and understand their role in gene silencing.

5.) Fess up, who is the Lady Gaga fan?

RW: Mary Anne and I are both massive fans of Lady Gaga and had a great time attending a concert of hers together earlier this year.

 MAK: Incidentally, the idea for the PLOS video came when we were watching Lady Gaga as a lab. We booked a conference room for a late night viewing of her recent show and her music inspired us.

6.) How long did the video take to produce?

RossRW: After incorporating all the desired themes into the lyrics, Mary Anne and I recorded the audio during a weekend afternoon. For the video portion, we spent a few hours recording in the wake of our lab holiday party, followed by a long night of editing in order to make the deadline for the annual UC Berkeley “MCB Follies” screening scheduled for the following evening.

MAK: We had the idea percolating around for a few months which helped streamline the recording process. We had more ideas than we could squeeze into the video and actually ended up cutting the recording a little. While I don’t want to subject people to more of my singing, Ross and I wish they could hear the line: “Why waste your time with magazines, when there’s PLOS, there’s PLOS, there’s PLOS.”

8.) What is the most interesting feedback/comment that you have received?

RW: I think it’s really interesting how much each viewer brings to the interpretation of the video. If someone is particularly obsessed with impact factor, they tend to think we’re poking fun at the idea of open access. In contrast, if someone is keen on open access they are likely to pick up on the ways we were critical of the status quo. Ultimately, I think this is a complex issue worthy of consideration and I hope that were able to maintain some of the nuance inherent to the debate in what should be an enjoyable video first and foremost.

MAK: After our first screening of the video, a Berkeley professor asked “What about eLife?”

Doudna_lab1

Thanks for the awesome video DLab Follies!

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JOURNYS: a leading high school science journal. A note from the Editor in Chief

Hello World!

My namjournyspic2e is Sarah Bhattacharjee, and I am the Editor-in-Chief of JOURNYS. the Journal of Youths in Science. Two times each school year, JOURNYS, or Journal of Youths in Science publishes a science journal that is put together by high school students in its entirety. JOURNYS, based at Torrey Pines High School in San Diego, is now one of the leading high school journals across the nation as it outreaches to schools throughout the world.

I have participated in JOURNYS from my freshman year and have seen it grow into the renowned publication that it is today. JOURNYS involves high school students from multiple areas; we search for editors, designers, artists, and writers and unite

Issue of Spring 2013

Issue of Spring 2013

them through an appreciation of the sciences. As we have expanded into numerous chapters, we have been able to foster interest in STEM education wherever JOURNYS is published. This journal gives students a chance to discuss their findings in an experiment or an interesting aspect of science outside their usual curricula that they would like to share.  JOURNYS provides these students, among with many others, a platform from which they can impact the education of other students miles away.

Through JOURNYS, students can expand their knowledge and are granted the chance of getting published in a science journal accessible by their peers. If you would like to participate in JOURNYS, whether as an author, editor, or subscriber, please send an email to eic@journys.org, or check out our website at  www.journys.org.

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Science of Stress – Berkeley Scientific Journal’s Fall 2013 Issue

This post is cross-posted with Berkeley Scientific Journal

Twice each year, Berkeley Scientific publishes undergraduate research, interviews with distinguished Cal faculty, and feature articles spanning diverse scientific disciplines.

If you are a student and are in the midst of studying for final exams, stress is not an uncommon feeling. In this semester’s issue, we chose to explore stress in different realms of scientific thought. How does one clearly define stress? In the human body, stress takes on the form of various chemicals and stress-inducing hormones, thereby altering the body’s physiology. In the current issue, Preethi Kandhalu explores the biological mechanisms of stress and Jenna Koopman provides a cautionary description on the dangers stress can have on fertility. Integrative Biology Professors Michael Shapira and George Bentley talk about their research and how it pertains to biological mechanisms of stress.

However, stress is not limited to the biological systems. Engineers depend heavily on creating safe structures in which extreme levels of physical stress are applied.

Structural failures result in perilous consequences, as witnessed by the devastating building collapse in Savar, Bangladesh earlier this year. Aditya Limaye sheds light on the current technology surrounding carbon nanotubes and its properties that make it a suitable candidate for 21st century infrastructure. Tensile strength is not limited to large physical objects, however— read Alex Power’s entertaining article on how spider silk is perhaps strong enough to withstand an oncoming train.

With new scientific information filling new textbooks annually, how do we decide what particular ideas to stress? On a more philosophical level, Jahlela Hasle writes about the “language of science” and its inevitable evolution over the years. We invite you to join us in exploring the many ways in which stress factors in our lives, from the social to the biological, to the mechanical, to the linguistic.

 

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Prashant is a senior undergraduate student studying biochemistry and molecular biology at the University of California, Berkeley. He currently is Editor-in-Chief of Berkeley Scientific Journal, where he became interested in science journalism and its propensity to motivate general audiences.  Read the current issue here. Follow BSJ on Twitter.

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Bridging the Gap Between Science and Design: Biologically Inspired Design

Being from a very different background than my fellow bloggers, it can be a challenge to find a topic to write about. I mean, I’m an Industrial Design major and that’s pretty far from science and labs and stuff, right? WRONG!

A couple weeks ago, my studio mates and I were assigned a new project: To make a biologically inspired lamp with an alternate power source. Before I tell you more, let me distinguish between biologically inspired design and design based on biomimicry. The latter is a more straightforward approach. For example, I like the shape of a honeycomb and would like to make a light that mimics it. Biologically inspired design, on the other hand, digs deeper and looks to solve a problem. For example, a light that draws biological inspiration from honeycomb might use the honeycomb as a charging station for lights for, say, students studying in the library. They would come get a task light for their desk from the honeycomb and return it to recharge when done.

The research for our project began with help of an expert from the Center for Biologically Inspired Design. He discussed numerous types of inspiration that exist in nature and it wasn’t until then that I realized how much design does and can borrow from science. For example, an Aerospace Engineer would never think to put ridges on a windmill blade, but after assessing the fins of whales, designers, scientists and engineers found that a blade with ridges would produce more lift and work better at steeper angles without stalling.

With biologically inspired design, the use of science is being explored in numerous capacities in the field of Industrial Design. This interdisciplinary study is an especially successful approach because it has an advantage of being based on an existing solution. Furthermore, the fact that it bridges disciplines gives not only a larger database of information to borrow from, but also the flexibility to gain the best of both worlds. Oftentimes, our areas of study can get cornered off, but by bridging two disciplines like science and design, a world of possibilities is open.

As we progress in the areas of engineering, science, and design, we are getting more and more interdisciplinary. For example, engineers, designers, and scientists merged to better understand flight of the herring gull. The result was Smart Bird, which “can start, fly and land autonomously – with no additional drive mechanism.” This technology fuels ideas to enhance hybrid drive technology while optimizing energy consumption. Future generations, especially, will be faced with the challenge of having to borrow heavily from natural resources. It is in our benefit, then, that we explore fields outside our area of expertise and integrate them with ours to solve these complex problems that do and will arise. After all, it is only for so long that we can rely on the techniques of traditional disciplines to solve current issues.

 

Tanaya Joshi is back for round  2 at Georgia Institute of Technology to pursue a Masters in Industrial Design. Her previous degree was a Bachelors of Science in Aerospace Engineering. She is is looking to bridge the gap between engineering and art through Industrial Design and hopes to focus on using design as a tool to enhance feasibility in products.

 

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Making the Silent Heard and the Obscure Tangible: Black Hole Coalescence

In this vast Universe we cannot begin to comprehend the amount of entities within it or the amount of which we do not understand. One of the most extraordinary objects that physicists have only a shallow grasp of is the black hole. To put this into perspective, imagine an entity that is so dense, it bends the curvature of space and time so that light cannot escape its pull. Even Einstein himself could not believe this elegant Universe could contain something so strange, though his own Theory of Relativity suggested it. Yet, not only have their existences been implied, they have also been observed.

Since Einstein’s time, we have accepted black holes and physicists are now attempting to make sense of these oddities. As of now, we understand that there is a point within the hole called the singularity, where all the mass of the black hole is located.  What could this singularity be made of? How large is this point? If an object, including light, finds itself too close to the hole and passes the event horizon it is all over. The mission cannot be aborted. Though I will not cover all the BH theories within this post, that would certainly take a while, I would recommend the eager student to read “Black Holes & Time Warps: Einstein’s Outrageous Legacy” by Kip Thorne, a book suggested to me by an astrophysicist during my time at NASA Goddard Space Flight Center.

Let’s take a step back and analyze this entity from the surface. It is possible for black holes to coalesce and form a new, larger, hole. This can also happen when galaxies merge. As a student, I am amazed to read the many papers already published on these events. Every single branch of physics is needed to understand the mechanics of black hole coalescence and galaxy mergers. When we think of such violent and messy events, it can be difficult to believe that no sound can be detected within the vacuum of space. However, I recently found out that the gravitational waves that are produced by the black hole could be detected and if one had a detector close enough, could be heard.

When the two black holes merge, the system loses angular momentum to gravitational radiation and the coalescing process begins. First, an adiabatic inspiral, which includes a prolonged gravitational radiation timescale compared to the orbital period of the system. This radiation reaction force is cause by electromagnetic radiation on accelerating charged particles. Eventually, the orbit becomes relativistically dynamically unstable and the waves are emitted. During the second phase, the orbit transitions from being radiation reaction driven to violent free falling. This is called the merger phase, releasing gravitational waves that may reveal the unknowns of the dynamics of relativistic gravity in high dynamic environments (Flanagan & Hughes, 1997).  This final inspiral is the most luminous gravitational waves in the Universe.

Image Credit: NASA GSFC

Image Credit: NASA GSFC

Sound travels as waves through a medium, like air and water. When it reaches the ear, the drum vibrates. Powerful gravitational waves and produce the same effect, in that these waves rippled through space-time, stretching and compressing the curvature.  TED talks are probably one of the best sources new and inspirational ideas and I recently watched one by Professor Janna Levin from Barnard College. Her lab was able to produce a model of the “Soundtrack of the Universe”. I highly recommend watching it. It is wonderfully informative. Indeed, we can learn a lot about the Theory of Relativity and the formation of black holes by analyzing the waves emitted by coalescing holes.

Soundtrack of the Universe

the Sound the Universe Makes by Janna Levin

All the current work on black holes have made a science fiction like object become more tangible and less obscure. As an astrophysics major, that is an inspiring thing. 

Reference:

Flanagan, É. É. and Hughes, S. A., 1997, Measuring gravitational waves from binary black hole coalescences: I. The waves’ information and its extraction, with and without templates.

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