Earlier this year, I attended a UW Libraries Digital Storytelling workshop and spent 4 weeks writing, filming, recording, and editing a little digital story that acts as an overview of what the Akamatsu Lab, where I currently work as a research scientist and lab manager, focuses on.
You can watch “What drives collective behavior in cells?” below.
In another world, during my blogging days, I’d write some thoughts, some lessons learned, some musings. But let me just tell you to watch the movie, and enjoy the ridiculousness of stop motion, goggly eyes, and silly faces. And maybe you’ll also learn a little bit about my current favorite protein: actin. Enjoy!
I recently started a new job, and in its novelty, it feels somehow quite familiar. Once again, I find myself in a building named after my field, wierdly literally; once again, I find myself on the top floor; and once again, I have a view over a body of water.
And once again, I have a view over a bridge that humans have built across said body of water.
The inspiration: William Topaz McGonagall and the Tay Bridge
7 years ago, I wrote about the Tay Bridge, and how the poet William Topaz McGonagall–no relation to Minerva, obviously, who is fictional–seemed quite obsessed with that bridge. In August 1877, he wrote an ode to the Beautiful Railway Bridge of the Silv’ry Tay, in which he praised its arches and pillars, and prayed that no accident would ever befall the passengers crossing the bridge by train, for that would be most awful to be seen.
But alas, with the very writing of his poem about the majestic bridge, it seems he had unintentionally caused it doom. Two years later, in December 1879, the bridge collapsed during a storm causing a passenger train to fall into the river Tay and inspiring McGonagall to write what would become his most famous bad poem: The Tay Bridge Disaster.
I’m not here today to talk about McGonagall, actually, except to point out that he has inspired me to write my own poem, of a bridge that I now have the joy of seeing every day (weekdays from 9 to 5).
Depending how much time you have, and before you judge my incredible poetry skills (it is, as I said, a tribute to William Topaz McGonagall who is generally considered to be the worst poet to have ever lived), I recommend you check out some of his poems, especially those related to the Tay Bridge, in order of appearance:
In the year 1962, on the 18th day of December A bridge opened up that was sure to be remembered A largest of it’s kind in the beautiful Northwest And dare I say, by some considered the best Bridges as majestic, there are few Like the one connecting down town to district-U
It’s here the interstate of the number five Uses steel upon which cars can drive For the full 4,429 feet that it is long All cars belong 182 feet high, they often stand in queue Making their way downtown from the district of U
Spanning across Portage Bay It’s double-deck steel will never lead you astray The upper deck goes both ways Even on the most rainy of days And down below, express lanes take you Southbound in the morning, and in the afternoon to the U
It’s truly a magnificent sight to see Whether from the high buildings of the university Or from a boat floating on Union Lake The Ship Canal Bridge is sure to withstand any quake For truly, dare I say, bridges as majestic, there are few Like the one connecting down town to district-U
I know, it’s been a while. 2021 has just been, I don’t know, an extension of 2020? However, despite a lot of things going on, we have managed to brew some final batches to close out the year. So here is a quick breakdown of batches 5 and 6, with some extra surprises along the way!
Wait, you brew beer at home?
Oh, we sure do. You can find a walkthrough of our first batch (which explains all the steps of brewing) in my series of posts on “Brewing for Beginners:”
While usually not a huge fan of IPAs, mostly because of an abundance of supply (I may have written a song about that), our hazy juicy IPA turned out to be our best brew yet. Keeping a constant temperature during brewing (and a heatwave), definitely paid off! It’s almost as if more experience yields a better outcome, who knew?
It had a pretty great head on it, was easy to pour, and was beautifully refreshing on a hot summer day.
Just look at this beut.
Little did we know, that this would be the last of our bottled beers, because A. decided to invest in… a Kegerator.
What is a kegerator and why I’m stoked we have one!
Instead of spending a day bottling beer, thanks to a chilled box in which we can put a keg and directly tap from – or: “a kegerator” – we can skip that very annoying step! In addition, it has some other really fun perks!
1. Instant Carbonation
As I said, no need for bottling, or adding extra sugar at that step for carbonation purposes. No, just hook it all up to a CO₂ tank and that will take care of carbonation. Oh, you like nitro? We can do that too!
For clarity, it’s not instant and takes a week or so before all nice and bubbly. But still beats bottling!
2. Stickers!
It provided a huge white space upon which stickers could be added! Well, there’s not that much space left now…
This is only a quarter of our sticker collection…
3. Life handed us some lemons
And you know what that means, make lemonade! Basically, anything can be carbonated this way, including ginger beer, lemonade, water, or water put into a keg that previously had lemonade so it tastes slightly lemony. No LaCroix in our home!
“You say I must eat so many lemons because I’m so bitter!”
4. Tapping is just fun
Tapping is just a lot more fun than pouring out of a bottle if we’re honest.
Batch #5: Maple Brown Ale
In October, we embarked on our next brewing adventure, a Maple Brown Ale (see recipe at the end of this post), getting some beautiful darkness with Chocolate malt. While, unfortunately, the maple didn’t quite come through in the taste as much as we’d hoped, it still came out tasting excellent and light (ABV 4.99%). The spent grain we had was also quite excellent. I’ve become quite skilled at spent grain pistolets and waffles if I say so myself!
Bonus: we need some mead!
Because we somehow had a giant jar of honey available, and some fruit that was in need of use, we made some mead! We didn’t really use a recipe, just heated water with the honey, added chopped-up apples and pears (that were sort of almost fermenting on their own), and eventually yeast (Safale S-04 dry ale yeast).
Getting the mixture to cool down enough to add the yeast.
After three weeks or so in the carboy, we transferred it over to a keg.
And now we have mead! It came out relatively dry (how I like it), with a taste of honey and cider. And a reason to get all our friends introduced to mead!
Not quite sure how strong this one ended up.
Batch #6: Cherry Chocolate Milk Stout
Our final brew of the year was a Cherry Chocolate Milk Stout, based on a recipe we found on Brewer’s friend. The trick to milk stouts is adding outs (for extra creamy foam), lactose, and dark roasted malts. To add the cherry and chocolate notes, we boiled some cocoa nibs and cherries, and added that flavorful water, when cooled, to the keg.
After transferring to the keg, we first hooked it up to the CO₂ tank for a few days, and then switched to nitro.
And the result? We learned that we definitely need more cherries and chocolate next time. The stout came out tasting very stouty (hurray), and oh my, the nitro is satisfying! The bubbles, they go down!
(Please ignore the audio)
Also, the foam results in a pretty fun stache.
Foam stache alert!
Starting 2022 with the following on tap:
I don’t know about you, but that’s not too bad to start off 2022! I hope you all have a wonderful, safe, healthy, and interesting year ahead. Hopefully with some more content from yours truly!
Throughout the past two years, I’ve colored my hair several times, leaning in extra hard on my manic pixie dream girl persona – I’m just quirky like that. At the moment, my hair is green. With this new color, I thought it’d be fun to dive a little deeper into the hairy world of… well, hair.
That means that over the course of a year, your hair might grow somewhere between 10-15 cm (or 5 to 6 inches, ish). Which, if you’re trying to grow out your hair, seems slow. On the other hand, if you’re trying to maintain bangs, it’s really fast.
Fun fact: that means it took Cousin Itt about 8 years to grow their hair, assuming their hair grew at the speed average for humans – so who knows – and taking into account that the actor that plaid Cousin Itt was just under 4 ft tall.
But don’t worry, at that same time about 99,900 other hairs are happily growing along. On average we have 100,000 hair follicles on our scalp, all there at birth (which is why usually children have denser hair – our scalp expands as we grow older).
Follicles don’t all grow hair at the same time: in fact, hair just grows for a few years, before the follicle decides to take a little break. That’s when the hair in the follicle falls out. Because all your follicles take turns, you typically won’t halve all 100,000 of your scalp hairs fall out at once, so you won’t notice losing hairs.
That said, some follicles stop growing hair as you grow older, which is why some people get thinner hair when they get older (or go bald).
Unless you’re stressed…
3. Hair loss and stress are related
On that note, high stress levels may cause hair loss. There are a few conditions associated with increased hair loss, including telogen effluvium (where stress causes large number of hair follicles into resting phase, see point 2), alopecia areata (a condition in which the body’s immune system attacks hair follicles, causes may include severe stress), and trichotillomania (the urge to pull out hair, which for some people is a way to deal with negative feelings).
4. Most of your hair is dead
Hair grows from your follicle out, with new cells rapidly dividing in the root, pushing previously formed cells in the hair strand out of the follicle. The cells forming hair are the second-to-fastest dividing cells in your body (after cells in your bone marrow), which is why people undergoing chemotherapy sometimes lose their hair: chemotherapy targets rapidly dividing cells.
By the time your hair is at the skin’s surface, the cells in the hair strand aren’t alive anymore. So all the hair you see on your body is already dead! The hair shaft is made out of a protein called keratin, which is the same protein that makes up your nails, feathers, horns, claws on hooves. Well, maybe not yours.
While on the topic of death (also, it’s Halloween), it’s a common misconception that hair and fingernails continue to grow after a person dies. This is untrue, though it may seem like hair and fingernails appear longer after death: after a person dies, their skin and soft tissues dehydrate causing shrinkage.
Cells stop deviding when they die, and that counts for hair cells as well. I guess that means Vampires should be really sure about cutting their hair!
I’ve made a grave mistake!
5. The record for longest hair is 5.62m (18 ft 5 in)
Scalp hair actively grows for two to six years (oh, there goes my Cousin Itt estimate), depending on the person. That’s why some people have a hard time growing their hair long, while others have a really long active phase of growth and can get those long locks.
The record for longest hair is held by Xie Qiuping, who started growing her hair in 1973 when she was 13 years old. Math tells us her hair grows a bit faster than usual (about 18 cm/year), and her active hair growth phases are just, non-existent?
In any case, over 5 meters is really impressive. It’s more than twice the height of André the Giant impressive. Or as long as a giraffe is tall impressive. And we all know that’s pretty impressive to me.
Hair on other places of your body, such as your arms, legs, brows, has a short active phase growth of one month to one month-and-a-half, before falling out. That’s why that hair is so much shorter. Though some impressively long eyebrow hairs have been known to exist.
There, we’ve learned some facts about hairs. In a convenient listicle format. Maybe someday I should make a listicle about the effectiveness of listicles?
Originally published on the satire science journal website DNAtured
Think your regular data isn’t scary enough for Halloween? Try these tips to put the “ahhhh!” in your analysis!
1. Ghostian Curves
Casper is no longer the cutest ghost in town! Draw eyes on a Gaussian distribution curve to make yourself a spooky lil’ ghost.
2. Haunted P-Values
You think a p-value of 0.08 is scarily insignificant? Turn your calculator upside down for another scare: BOO
3. Zombie Survival Curves
Night of the living dead? Night of the living rats! Turn those survival curves upside down – or back up – by summoning your test subjects black to life with some Michael Jackson in the background!
4. Witching Hour Gel Electrophoresis
Want some Wicked-ly good pictures? Add a splash of green fluorescent protein to make your image light up like slimy goo!
Photo by @heysciencesam
5. Bloody Western Blots
Messed up your assay and now you have a smeared Western blot? No problem! It looks just like smeared blood! The horror!
6. Coffin Plots
Don’t ever let anyone say your box plots are boring… Get your spook on and turn them into coffins!
7. Scary scatter plots
Need more spooky plots? Turn your scatter plots into any scary shape: a witch’s hat, a jack o’ lantern, a spider web, or a bat! All you need to do is get rid of those terrifying outliers!
8. Beastly n-Values
666 summons the devil, so if you have three experimental conditions, make sure your sample number is n=6 for each!
9. Black & Orange Graphs
As a last resort, colour code your excel sheet with some spooky colors, we recommend methyl orange. As if using excel for data handling isn’t scary enough, you monster!
10. Dangerous Data Storage Systems
And if nothing else works, live on the edge with the scariest lab data of all: stored on an old, barely functional computer that runs on Windows 94 and hasn’t been backed up in decades!
Some have theorized that the universe is made completely out of strings. Some creatures, however, really see the world in strings. You know, spiders. With their spider webs.
Many types of spiders produce a strong, sticky, proteinaceous fiber from their butt spinneret gland. They use it to build webs, sometimes quite pretty and sometimes spooky, to catch their prey in.
Fun fact: even spiders that don’t build webs produce silk, and it is important in, you know, seducing the other sex.
Spider webs are useful for many things, reproduction (as mentioned), but also to capture and immobilize prey, build nests, move around in the world (some spiders build tiny parachutes), communicate, and leave pheromonal trails. Spider silk is known to have exceptional mechanical properties, having a tensile strength comparable to that for high-grade steel, and a toughness that equals some synthetic polymers.
(Tensile strength relates to the maximum force to which a material can be pulled before breaking, while toughness relates to how much a material can deform and absorb energy before breaking. In any case, spider silk is a natural material that material scientists would just love to emulate. Biomimetics, you know.)
Spider silk is also very sticky. You know. To catch the foods.
Source: Wikipedia commons
Feelin’ those good vibrations
For those spiders who use their web to capture prey, vibrations are a key to success in their endeavor. When an unsuspecting fly, mosquito, or human, wanders into the web, it induces a vibration that the spider can easily distinguish from oscillations created by a breeze, thanks to tiny little hairs that cover their body and legs.
“The virtual reality environment is really intriguing because your ears are going to pick up structural features that you might see but not immediately recognize,” Markus Buehler of MIT explained. “By hearing it and seeing it at the same time, you can really start to understand the environment the spider lives in.”
Here’s an example of one of their spider web sonifications:
Talking to spiders
Each web strand has a different length, which the scientists translated to a sound frequency to create a musical cacophony (if we’re honest) based on the vibrations created by a perturbation. The researchers were even able to develop an algorithm to differentiate between different types of vibrations that might occur, such as “trapped prey,” “web under construction,” or “hot spider just wandered into my web and wants to get busy.
“Now we’re trying to generate synthetic signals to basically speak the language of the spider,” Buehler said. “If we expose them to certain patterns of rhythms or vibrations, can we affect what they do, and can we begin to communicate with them? Those are really exciting ideas.”
But for now, I would just like to imagine spiders as tiny little violinists, creating music with their webs, mocking the sorrowful life of the individual how just blindly wandered into their web.
Mr. Krabs knows what’s going on.
Bonus number 1: Scientists gave some spiders some drugs. And then those spiders spun some webs. And they looked weird.
Researchers recently found a treasure of 125-year-old, unopened, beer bottles in a shipwreck off the Scottish coast. In those bottles, preserved thanks to the cold ocean water, was even more of a treasure: live yeast.
Beer Archeology
It was only recently that I learned about the field of “beer archeology,” after hearing a talk by the beer archeologistTravis Rupp. I was delighted to learn that there is a whole field dedicated to recreating ancient beers, as far back as ancient Greece and Rome, only using materials, ingredients, and methods that would have been available at the time. Or as close as still available.
Inspired by old techniques, Travis Rupp has developed a series of beers named “Ales of Antiquity.” There’s an ancient-Egypt-inspired beer and a Viking-inspired beer. Of course, there is also a Belgian-style beer as well!
If I’d been interested in beer at the same time I was interested in archeology (the latter was when I was about 8 years old), who knows where I would have (could have) ended up?
Yeast explorers
The yeast found in the Scotting shipwreck is only one of the many endeavors of brewers resurrecting old strains, which cannot only be used to brew historical beers but may have applications in cleaning up pollutions and in the perfume industry (though the article states that the smell of the beer was quite atrocious).
That doesn’t mean noone tried brewing a beer, of course they did! Scientists at Brewlab, a spin-out from University of Sunderland, isolated two types of yeast from the Wallachia shipwreck beer: Brettanomycas and Debaryomyces. With that, they brewed a 7.5% stout that, apparently, had some coffee and chocolate notes. Certain byproducts of the fermentation products create a distinct flavor that is specific to the yeasts used.
And resurrecting ancient yeasts can yield more interesting flavors, compared to the limited stains that are used by most modern brewers today. Maybe something to try in our next batch of homebrew? Time to go diving, I guess!
After some time – you’d think that a pandemic would be an excellent time to do some more brewing but that didn’t seem to happen – we have decided to make another attempt at brewing our own beer. Batch 3 has not been documented (it was a brown ale that had that slightly too much Irish moss in it, making it an excellent drink for singing sea shanties or while sitting at a beach), but I made sure to keep track of our summer 2021 brew: a “Hazy Juicy IPA.” Our recipe is mostly based on this Hazy Juicy IPA recipe on brewersfriend.com, with some minor modifications due to availability.
Because, we do live in Seattle, the capital of beer [citation needed], with an average of 12 available IPAs in any given brewery [citation needed].
You can find a more step-by-step walkthrough in our first brewing experiment, so I will not repeat all the steps, but rather document some key changes we made since the last time!
Here’s some insight into our brewing process: the first step is biking over to the homebrew supply store to acquire some ingredients, and most excitingly, watch a whole lot of grains get milled up.
Amélie would love this step too
Day 1: Making grain soup
For once, we did not make the mistake of trying to do the beer-shopping and beer-brewing on the same day. Otherwise, the steps were pretty straightforward, except that we had learned that keeping things at temperature is not that important and that we could hang out and be pretty chill about things.
This little nifty trick, A. found on the internet (such a vast resource for nifty tricks!) Who knew that draining hot liquid between two oven shelves would be easier than with your bare hands!
Extra note: we also learned that the leftover grain mush, especially the part that had a lot of oats, is quite delicious for breakfast!
Specific gravity at this point (preboil) was 1.049. The closest we’ve ever been!
Just adding in some drama
The bag in the previous picture actually wasn’t very helpful and all the hops came out anyway.
Cooling
Transfer time!
And now for the best part:
During this round, we tried to keep the carboy at a lower temperature, especially because Seattle was going through an unprecedented heatwave, not ideal conditions for brewing yeast. We had the carboy sitting in a bath of water where we occasionally threw in some ice. Other than that, things just went a lot smoother than the last 3 times, mostly because we made sure to take the time, let everything cool down enough, and were better prepared…
Day 3: Two weeks later…
We forgot to take the specific gravity measurement, but the beer sure smelt hoppy, and tasted pretty good two (considering it’s not carbonated yet), so fingers crossed we have a good batch! Check in for a first-taste-update in two weeks or so!
A recent grad student, who has asked to remain anonymous as to not influence their perspective chances at finding a job, has come to the unfortunate realization that having a PhD does not make them automatically employable.
“I was told during an interview last week that I was overqualified,” complained the student. “But in the next sentence, they said I didn’t have enough experience. How can it be both?”
Tragically, like many other prospective PhDs, the student thought that having a plethora of knowledge in a niche scientific area would be applicable outside academia.
“In today’s day and age, we are looking for candidates who can thrive in interdisciplinary teams,” Ms. Laurie Durham, Senior Recruiter at Biotech Intl., “not people who can recite the base pairs that code for the angiotensin-converting enzyme within one minute.”
“I can do that, but at this point, it’s basically just a party trick” confirmed the grad student. “When I started listing them off in my interview, the recruiter just looked at me in confusion.”
For other recent graduates concerned about running into the same problem, resume experts suggest adding “soft skills” to your resume. Being able to distinguish blobby lines and gather meaningful blot information, being able to turn hours of “data analysis” into doom scrolling, and being able to convince your supervisor that you need three more weeks to finish a powerpoint presentation are, in fact, very transferable to work life.
