I’m back!

Hello, blog. It’s been a while. So many things have happened. I am now a doctor!

Let me tell you about how this happened. For starters, I gave an exit talk.


Then I gathered the signatures of all four committee members and I submitted my dissertation.

Screenshot from 2015-08-11 11:26:02

Finally, I got a lollipop. I could hardly believe it. I did it. I fooled them all.


[Not pictured: I got a “dissertation muffin top,” which is what I think we should call all those studies you started with your advisor during more optimistic times, that don’t fit neatly into the muffin cup of your thesis, but instead spill over into the rest of your life indefinitely. Currently responding to reviewers on a paper, for which I collected data in my FIRST YEAR of graduate school. Let that sink in.]

My first order of business as a doctor was, of course, to go to Burning Man.


It was a dusty one.


I came back, dusted myself off, and started a new job!


Which brings me to the reason for my return to the blogosphere. It’s been a nice summer-long hiatus during which all of my writing efforts were poured into “real science.” I figured I’d start writing for the internet again sometime, and that time is now. I have new goals, a new environment, a new perspective.

I’m a Thinking Matters fellow at Stanford (for real! It’s a kind of demi-professor post, so no, Mom, I’m not a real professor), which means I’ve been placed on three teams (one each for the fall, winter, and spring quarters of the school year) to teach a special set of classes designed for freshmen. They show up, having survived whatever insane gauntlet of courses and extracurriculars got them here in the first place, and they are required to take at least one of these courses to help them transition, pick up collegiate study skills, and level up on their critical thinking and rhetorical prowess. Given that these students will have a range of preparation from their high school years, I am excited to be a part of this great equalizer.

More selfishly, the curriculum and team dynamic of my first course, The Science of Mythbusters, are nothing short of perfect for me. I get to indulge all of the vendettas I’ve been fermenting for the last six years, by dropping truth bombs about how we do science onto the next generation of world leaders. That’s right, someone gave this angry woman a platform. Oh sure, I spend 4 hours a day commuting, sometimes crossing the bog of eternal stench that is the south bay on a very slow bus. And sure, I’m still getting used to some things (like how here, if a projector doesn’t work, it’s expected that something can be done about it–I guess that’s how money works). But the important thing is: I don’t hate my job.

In fact I really really really like my job.

I like my job so much that my ideas are starting to come back. I’ve been mining old notebooks for writing topics, reveling in my continued university-affiliated PubMed access, and scribbling down anecdotes that tumble from the mouths of some of the most ridiculously enthusiastic and engaged academics I’ve yet met. I’m still pretty sure that my still being in a university means I can’t access press releases on embargoed studies (holler at me if you think different, EurekAlert!), but then, how many times have I heard from my science writing idols that it’s lame to only cover things because they’re new? Challenge accepted.

Look for a new post soon–I wouldn’t be writing if I didn’t already have a special paper in mind. I’ve got three years in this here writing incubator. The work is fun, the people are nice, and the air here is rich with inspiration.

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Dissertation meals

I’ve had some recent success in keeping it together nutritionally while also writing a dissertation. Some success–not 100%, but some (I definitely packed cereal & almond milk for a lunch meeting today, and I’m not proud of it, but shit was getting kind of real today). It occurs to me that perhaps I owe this success to completely forgetting that recipes and recipe sites (I’m looking at you, Deb and Heidi) and cookbooks exist and just leaning into spring. Saying no to big weekend plans means you, my friend, can find time for a little farmer’s market jaunt. And then, when you’ve overbought at the farmers’ market, it’s usually not because you had a recipe in mind, but instead because it’s finally asparagus season or that fennel was huge or that sign said it’s the last week for those little tomatoes you like!

Anyway, here are some super easy things I throw together when my brain isn’t working and takeout, cereal for dinner, and cooking a dang recipe are all out of the question. All of the below ideas are uncomplicated ways of dealing with spring farmers’ market overzeal. They also have very few ingredients and therefore can be shopped for on the way home, in a stupor, lacking a plan (I realize that if you’ve read this, it’s become a plan, and to that I say shh).

Cherry asparagus tacos with queso fresco and cilantro. FRIENDS, ‘TIS THE SEASON! Toss asparagus in olive oil, salt & pepper, and roast at 400 for 10 minutes. Pit some cherries while you wait. This is extra fun if you have a cherry pitter. Add pitted cherries, toss, roast for 20 more minutes. Work while you wait. Serve in a tortilla with queso fresco & cilantro. Stolen from here, and don’t bother making the asparagus salsa. You won’t care, and ain’t nobody got time for that.

Fennel roasted in olive oil & balsamic with raisins, walnuts, goat cheese, and fennel fronds. Cut up the fennel. Toss with olive oil & balsamic. Roast at 400 for like 20. Go do some work. Toss in raisins and chopped walnuts. Roast for like 20 more. Go do some more work. Throw on goat cheese and chopped fronds. Looks fancy, right?

Mushrooms with rosemary, Italian parsley, shallots, lemon & parmesan, on pasta. Say, is your fungiphobe partner out of town? Well party! Buy pre-cut baby bellas or cut them up. While cooking pasta, sautee shallots in olive oil first, then add mushrooms. Work while you wait, stirring as needed. When they look pretty good, add a bunch of chopped fresh rosemary & parsley. Turn heat off. Squeeze lemon juice on it, sprinkle parmesan, and serve over pasta. Eat while working.

Kale sauteed with garlic, red chili flakes, olive oil, & salt. Egg on top. Probably rip up, de-stem, a bunch of kale. Chop up some garlic. Sautee the garlic in olive oil for a bit, then add kale, salt, and red chili flakes. When that looks good, put it in a face trough, make an over-easy egg, and throw it on there. Eat while working.

Avocado grapefruit salad. Ina, gurl. I don’t know who came up with this first, you or Alice, but your version is easier than that bitch Alice’s. So cut up your avocado, get as much of the grapefruit flesh out of the segment casings as you care to bother with, and douse the whole thing in a mix of olive oil, dijon, salt, & pepper, and lemon juice (or just the grapefruit juice if there is a lot and you’re lazy). Eat while writing blog post about dissertation meals.

Happy dissertating.

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Lately: Fresh writings!

It’s been a good month for writing! Dissertation AND extracurricular, I’m happy to say. I’m almost a doctor!

But first, we’ve got some important science to talk about. After hatching the idea (ha) at Zoo Bar, a grubby box across the street from the National Zoo in Washington, DC, my favorite story of all time has finally become an actual piece of writing on the internet. I emailed the zoo’s information line and soon found myself Skyping with Chris Crowe, whose last name by the way is Crowe. This bird man had the sweetest, weirdest story I’d ever heard, and it was incredibly fun to spin the gold he was giving me in the interview. Walnut the Crane who fell in love with her zookeeper trended for like a whole Saturday on the Verge until some Game of Thrones episodes leaked and wrecked her lead. It was a good day.

Still high off crane love, I went up to the Lawrence Hall of Science to cover their STEM Career Showcase for Students with Disabilities for the Berkeley Science Review blog. There, I got to meet Dr. Josh Miele, whose work I really admire. I first learned about him while researching the Sonic Eye for last fall’s issue of the BSR. He works on engineering smarter assistive devices for blind people, a field he got into out of plain necessity as he worked on his research in physics. Finding workarounds, and finding a community of people who knows workarounds too, is key to carving out a career when you have a disability. At the event, I talked with student attendees, panelists, and staffers at the Hall. The panelists shared so much of their passion and creativity with attendees who had faced similar challenges. I left the event excited about the work Miele and others are doing to make STEM careers more universally accessible.

Finally, the Spring 2015 issue of the Berkeley Science Review Magazine is out! It’s always nice to see in print: the design team does some truly stunning work, and I want to frame every page. For my last semester here as a grad student, I wrote a brief on how some people’s brains resist the buildup of plaques thought to be a marker of Alzheimer’s Disease. The piece is called Staying Sharp, and again I got to interview really nice people working on interesting stuff: Bill Jagust and Jeremy Elman. They were part of a team in Jagust’s lab whose results provide fresh evidence that the brain is plastic across the lifespah. Alzheimer’s Disease affects so many people, and as humans live longer, soon there won’t be so many young people to take care of the old people. Some days it terrifies me so much I think we should just dump the whole NIH budget into it. Anyway, enjoy the read!

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Brains and blinky lights: an update

An art installation at the Exploratorium’s Cognitive Technologies exhibit

Wow, post-SfN fatigue really took its toll on my posting frequency, eh? But I would like to draw your attention to a few pieces I’ve been working on that came out elsewhere recently, and share a few photos I took at the Exploratorium last week.

Here’s my labmate Alit trying out the brain-machine interface at the Exploratorium.

Just today, my coverage of the Exploratorium’s new exhibit went live. My dear pal Natalia invited me to cover it and I’m so glad she did. I highly recommend going to check it out. Invite me if you go, because there were a few things I didn’t get to try out because of all the people milling around. The exhibit contains the flashiest of flashies, and yet, I think its greatest contribution lies in its willingness to allow people to experience the limitations of what brain decoding and other technologies can do. Go put on an EEG headset, and when it tells you you’re relaxed, or excited, or whatever, ask yourself if you think that’s true. Then go tell your anti-vaccine relatives what you learned about the difference between being a single datapoint and really synthesizing a literature. Go ahead, I’ll wait.

Dry electrodes stud a repurposed scuba cap to drive a brain-machine interface. DIY at its finest!

Dry electrodes stud a repurposed scuba cap to drive a brain-machine interface. DIY at its finest!

A bit ago, I wrote about my favorite poster at SfN, by former Berkeley grad student Taraz Lee. Check it out here. Taraz studies choking under pressure, and he uses both non-invasive brain imaging techniques and mad scientist brain-zapping techniques to get a handle on what’s going on. Truth be told, I’m more excited about the preliminary brain-zapping results he told me about, although I covered his imaging work here. Can’t wait to see where he goes with it!

Oh no, it's....THE CLAWWW!!!

Oh no, it’s….THE CLAWWW!!!

Finally, the Helen Wills Neuroscience Institute, my home, my science family, got a freshly revamped website! They’ve focused on compiling their very own news section, pulling coverage from around the interwebs, but also recruited me and other grad students to do some ($$$PAID$$$) in-house public relations. It’s been a long time coming, but the first of three pieces I wrote for them, singing the praises of our legitimately awesome Brain Imaging Center, is here. In writing these pieces, I’ve had so much fun interviewing lots of Berkeley people, some I knew, most I did not. This one, the BIC writeup, is close to my heart because I’ve always known that the BIC was special for the level of independence and education it gives its users, and this gave me a chance to hear the real backstory.

A schematic from the Cog Tech exhibit

A schematic from the Cog Tech exhibit

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Four impossible things before breakfast: Amy Bastian’s empathic logic

I had wanted to write up Amy Bastian‘s excellent 8:30 am talk from SfN, and finally it is happening. That’s right, my hangover and I were front and center so you didn’t have to be. I’m looking at you, #sfnbanter. You’re welcome. A couple of weeks late.

This talk was excellent not least of all because Bastian understood that at 8:30 am, no one was functioning quite properly yet. There was going to have to be a lot of hand-holding, and a lot of balloon walkers. Bastian’s talks are always clear and engaging, and this one was particularly merciful to boot. Bastian walked us gently through four of her papers (instead of a thousand like some other speakers who shall remain nameless), and that is why I retained enough to write you all this (let’s be honest) listicle.

I will start with a point she finished with, which is that many injuries like stroke, trauma, or even surgeries that remove up to half of the brain to stop epilepsy, cannot be treated with drugs, operations, or even fancy stuff like lasers or tampering with DNA. All of which is to say that, and I’m paraphrasing Bastian here, we must engage in some rational way with the patients’ motor processes. We must play their game to figure out how they work, get them to give up their secrets. If you think you’ve heard me gush about this before, it’s because you have. I am a sucker for a paper that reads like a Roadrunner vs. Coyote storyline. That, and I once had a total meltdown upon breaking a piece of equipment that was worth more than I made in a year, so no, I don’t like using fancy equipment.

But physical therapists like Bastian, in particular, wow me with this incredible empathy. Bastian says, it’s easy for friends and family to shout at their injured loved one, “you can do it!” or “just take a bigger step!” Indeed, this is how we encourage babies. But people aren’t babies–their brains are not the doughy, plastic things that babies’ are. They are a loaf of bread with a jagged slice taken out of it, and you need to make a learn-to-walk-again sandwich.

So in this case–and this is what I love about this research–the rational, logical thing to do is to accept what is and work with it. You can’t make someone heal by telling them what to do, and there are no guarantees they’ll heal fully or only partly. This letting go of control is probably the hardest thing asked of scientists, Type A monsters that they are. To promote healing, often it is the brain’s implicit, rather than explicit, learning mechanisms that must take the wheel. You don’t learn to do a cartwheel by poring over an instruction manual, and you don’t learn to walk again by having your mom shout “Walk, baby, walk!” at you as you struggle to rise, unfortunately. You have to play by the rules of whatever brain part is still working, and these might be radically different from what you are used to, as a person who used to have a much wider repertoire of movement capabilities.

Bastian’s work is focused on figuring out what those rules are and playing by them. During her talk, I saw a little girl with half a brain walk around like any other kid, like it was no big deal. She should be paralyzed on one side of her body and who knows what else. But if you’re wily and you listen, you might think up the right question to ask the motor system, and it might say, ok, you got me. Here are my secrets. She can walk if you do x, y, and z, and then bam: walking girl.

Here are some crazy secrets of the motor system I learned very early one morning a couple of weeks ago.

1. Think of your brain as your 16-year-old self, learning to drive a car, except instead of a car it’s your body. At 16, you figured out how to drive a car, and as a baby, your brain figured out how to drive your body. The cerebellum creates a match between your brain and your body, even when your body changes. Depending what parts of the cerebellum are damaged, you might think parts of your body have more or less inertia, and therefore think they’re heavier or lighter than they really are. Bastian’s team modeled each patient’s “too light/too heavy” body/brain mismatch and corrected for it using robots that hold the arm as it moves. With their arms guided by the robots, the patients’ biases were corrected and their movements became more normal. These models could also be run in reverse: they could program them into the robot arms, strap in a healthy person, and get the healthy person’s arm to move as though they had a bias like that of the cerebellar damage patients. This is promising–in the future, perhaps prosthetic devices could capitalize on these models to provide corrective force to patients’ movements.

[Bhanpuri, Okamura, & Bastian 2014]

2. We rely on predictive control–that is, the ability to predict the consequences of our actions. When we make a mistake, we use that information to update our predictions. But patients with cerebellar damage can’t. This could be for two reasons: It’s possible that the cerebellum generates quick-fix adjustments to movements as we make them. If this is so, patients’ poor ability to adjust is because they can’t come up with these motor adjustments. It’s also possible that it deals with the senses more than movement, generating predictions about what sensory information to expect. If this is so, patients lack the proper predictive power to select the right motor plan for the sensory feedback they’re trying to get (say, shooting a ball into a hoop or bringing the coffee mug to their mouth). Well, it turns out we update our sensory predictions. They figured this out by having patients and controls make “shooting” and “pointing” movements. In shooting movements, they had to point straight to a target while their feedback was manipulated, eliminating the possibility of correcting for the manipulation on the way to the target. In pointing, they were allowed to correct on the way. Patients were impaired at both, meaning that it can’t be the motor adjustments driving learning–it made no difference when they were allowed to make them. Instead, if our sensory system learns that no, our arm will go over there,  not over there, when we engage certain muscles, then the next time we have that goal we’ll be able to pull up the right motor trajectories for that goal. So learning to predict the future, the future within our arm’s reach anyway, is to learn to control it.

[Tseng, Diedrichsen, Krakauer, Shadmehr, & Bastian 2007]

3. On to some of Bastian’s split-belt treadmill stuff. She asked, why do we learn? Why don’t we just keep limping after an injury–what’s wrong with that? Well, limbs are expensive, metabolically speaking. If you walk symmetrically, you exert much less effort. Bastian’s team measured people’s carbon dioxide output as they walked on a treadmill that was split down the middle, causing their two legs to walk at different speeds. Remarkably, people can deal with this and even get so good at it that their walk goes from a limp to a swagger. You hardly notice their legs have different step sizes, the walk becomes so smooth. Crazily, people can also walk forward with one leg and backward with the other. They found that when you learn a new speed, it is learned in a leg-specific and a direction-specific way. What you learn walking forward, your motor system doesn’t automatically assume will apply to walking backward. Ditto for the right and left legs–they each seem to have independent systems for learning. With this specificity of learning, the brain does upkeep for its expensive locomotion habit by straightening things out whereever needed, should we become injured, wear a pair of high-heeled shoes, or gain or lose weight. This knowledge can be leveraged to help customize people’s rehabilitation regimens, targeting the limbs and movements that need it most.

[Choi & Bastian 2007]

4. Now, this last one is my favorite, so, congratulations to you for reading this far. Imagine your friend is injured. What do you do when you go see them in the hospital? Do you offer to help them out of bed, or do you poke at them as they try to get up and laugh? I hope you said you help them, you monster. Well you’re wrong! I mean, no, you’re right, but not as right as you’d think. To rehabilitate someone, you’d think it would be a big help to hold their hand and walk them through whatever it is they’re relearning. That’s how you learned to ride a bike, right? Someone running along behind you, holding the seat? While this is nice, unless you intend to follow your friend around forever, you better knock it off. Patients learn better if you exacerbate their errors. That’s right. If someone’s limping a bit one way, push them a bit farther that way (Clarification: don’t you push them, and don’t tell anyone I told you to–this is what their PT should be doing, you dingus). This will help them learn to push back. If they’re making do with a limp, push them off-kilter enough that they have to catch themselves. Importantly, though, be gentle–the error you cause has to be within a somewhat normal range for them. If you push someone so far they’ve never experienced pushing back that much, they won’t be able to do it. You’ve got to push them to adjust more frequently for errors that are above-average in size. Eventually, they’ll be able to correct for their limp.

[Torres-Oviedo & Bastian 2012]

And so, dear readers, this is of course the part in my rhapsodizing where I tell you What It All Means, because this pushing a limping person thing, it is a metaphor for life. When life knocks you down, all you want to do is hole up in your comfort zone with some Ben & Jerry’s and Toddlers & Tiaras National Geographic documentaries. But no, you need to get out there, slugger, and push yourself, but only within your limits. Try new and difficult things, but be realistic about what you can do. It is the only way you will heal.



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SfN Day 3 (?) Highlight: A BMI in V1

That I stopped blogging my SfN highlights the same day I took care of Ned the Neuron is no coincidence. That guy loves making new connections.

While plugging into an outlet to power up, Ned and I looked up to see our friend Ryan Neely at his poster! Hi, Ryan! And so, while keeping careful watch of our possessions, Ned and I learned about what Ryan is up to these days. Ryan works with Jose Carmena on brain-machine interfaces (BMIs). A BMI usually consists of a sensor implanted in the brain, some kind of actuator like a cursor or a robot arm, an encoding algorithm to act as a lookup table between brain activation patterns and body movements, and a decoding algorithm to translate brain activity into action. An early goal of BMI research was to help patients who had lost a limb or function of a limb by reinstating control over their environment.

Work by Aaron Koralek, a recent Carmena lab alum, showed that rodents could learn to control the auditory tone they heard, from high to low, by ramping the activity of one group of neurons up and ramping the activity of a different group of neurons down. If they hit just the right tone and sustained it, they got a reward. And to show that these animals had truly learned a new skill and not picked up a new habit, they showed that if they offered a reward that the animal was at the moment sick of, either sugar or chow, they stopped working for it. These new skills seemed to rely on the strengthening of the circuits between the primary motor cortex and the striatum, an area deep within the brain implicated in both learning and storing habits and skills.

These animals had sensors implanted in their motor cortex, and without moving, they were able to drive activity in targeted groups of neurons up or down. How these groups form their allegiances, we aren’t sure. We do know that BMIs work better when both the encoding algorithm and decoding algorithm are allowed to be flexible, learning each other as both the brain and the algorithms update.

But so far, having only decoded from motor cortex, we figure the brain activity that drives all our encoding model’s power comes from motor imagery. When we imagine a movement, the brain is activated in a strikingly similar way, compared to when we actually execute movements. Motor imagery is so reliable, in fact, that it was used to detect signatures of consciousness in people in vegetative states. Simply asking them to imagine playing tennis or walking around their home, and then analyzing the patterns of brain activation, yielded reliable “yes” and “no” answers. Crazy.

So, ok, now imagine you’re a BMI researcher and you want to know, does this work for motor imagery only? Are we limited to making BMIs that do what arms and legs do? Which is awesome, but we’re not even really sure why decoding motor imagery into motor behavior works. Those “two groups of neurons” that are ramped up or down to raise or lower the tone of a cursor? Dunno. Statistics and magic. We call each group an “ensemble,” because they act together, but it’s unclear what, subjectively, the animal (or human) would be doing to change these ensembles’ activity. For all we know, the animals could be envisioning playing tennis to make the tone go higher or walking around his home to make it go lower.

Enter Ryan. Ryan is doing something kind of crazy, which is measuring activity in V1, or the primary visual cortex. At first blush, this seems like it will never work. We can consciously control our motor cortex’s activity by using motor imagery, but the visual cortex is a sensory area. Sen-so-ry. Got that? It’s in the business of input, not output.

Wait, what’s that you say? It worked. Hell yeah it worked. You see, the visual cortex is not as passive as its moniker would have you believe. It receives inputs from areas sandwiched between motor and visual cortex, and these areas are involved in attention. Injury to these regions in one side of the brain results in an inability to pay attention to things on the opposite side of space (visual input switches sides, left-to-right, on its way from the eye to the brain). Attention is thought to rain down on primary visual cortex to sharpen, enhance, and otherwise hasten your response to, whatever it is that you’re paying attention to.

So were the animals just changing how much they paid attention to things? Maybe. Don’t care. Turns out you can use a sensory cortex to drive a brain-machine interface. That is nuts. Does this mean you could someday use visual imagery to control robots? Does it mean robots could control you by showing you pictures? Does it mean having a “vision” for something really does, in a weird scientific/metaphorical fusion, sell us on the “If you can dream it you can do it” thing? Who knows! Science is fun and weird.

That was all of the science Ned and I took in that day, but we did have an awesome time at #sfnbanter, meeting Twitter folks. Whether we were up the next day for our 8:30 am talk, well, we’ll find that out in the next installment. Ciao for now, you beautiful, powerful mental imagery machines. Ciao.

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The Fall 2014 issue of the Berkeley Science Review is out!

Photo courtesy of the Berkeley Science Review. Original by me, image processing magic by Natalia Bilenko.

Photo courtesy of the Berkeley Science Review. Original by me, image processing magic by Natalia Bilenko.

You can peruse the issue online here. Or I can save you a click and you can skip right to MY piece here. I had a lot of help from my muses, the people I was writing about, in helping this feature get done on time, because as it turns out, features are hard! I thought it would be like that Mark Twain line, “I would have written a shorter letter, but I didn’t have time.” I thought longer would somehow be easier. Well, not if you want it to be good. So, thanks to them for keeping me close to the truth when time pressures almost ruined everything, round after round of edits. They are amazing people and friends and I’m proud to have publicized their admirable hustle.

Ned gets distracted from the poster sessions at SfN 2014.

Ned gets distracted from the poster sessions at SfN 2014.

In other news, obviously my post-a-day habit for SfN petered out after only a few days. To be fair, what really killed it was taking Ned the Neuron around to make new “connections” all day, including at the delightful Twitter party #sfnbanter. I’ll tell you, if you want a date to a Twitter party, you can’t beat Ned. He is so universally beloved, I actually lost track of him at the bar once or twice (don’t tell his mom!). But, we managed to leave together, both of us in one piece, AND still make it to an 8:30 am talk as well as my afternoon poster the next day. Which, by the way, thanks to everyone who stopped by!

Done with my poster! Woo hoo!

Done with my poster! Woo hoo!

I will post on the remainder of the amazing things from SfN soon. But as long as I’m yammering about SfN-related things that aren’t actual scientific content, I will close with three pieces of advice I received while at SfN, in descending order of utility:

1. “If you’re leaving academia to be a science writer, your dissertation is the least important thing you will write for the rest of your career, because only a few people will read it.” — A future science writing role model I was lucky to chat with

2. “I think I finally figured out why we have death. We need turnover of ideas. Can you imagine if all these old people never died and we were stuck with their shitty ideas forever?” — Not so much advice as perspective from a past advisor/role model

3. “Just keep saying to yourself, ‘It’s only a movie. It’s only a movie.'” — My present advisor, upon hearing that Berkeley’s fMRI scanner will be down for the month in which I’d scheduled 18 fMRI subjects, my dissertation’s Chapter 3. Sometimes there just isn’t any good advice, I guess.

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