10 Hot Tips To Make Your Lab Data Look Spooky For Halloween

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.

Gaussian distribution with eyes so it looks like a little ghost, saying Boo!

2. Haunted P-Values

You think a p-value of 0.08 is scarily insignificant? Turn your calculator upside down for another scare: BOO

A sketch of an upside-down calculator so 0.08 looks like it spells 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!

Two survival curves, one climbs upward.,

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!

A fluorescent microscopy image that looks like a skull
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!

as sketch of a western blot

6. Coffin Plots

Don’t ever let anyone say your box plots are boring… Get your spook on and turn them into coffins!

a box plot, but instead of boxes, there are 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!

scatter plot shaped like a bat

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!

666 in fiery font

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!

a random graph in orange and black

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! 

a picture of a old computer with the windows 95 starting screen

World’s Tiniest Violinist

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.

And while we might not think of spiders as tiny musicians, their world is made up of vibrations, so perhaps that is our key to communicating with these tiny little weavers!

But first: what is a spider web?

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.

Spiderweb with frost
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.

It is this form of communication that inspired a team of scientists to create an interactive musical instrument, using the three-dimensional structure of a spider web. This “Spider’s Canvas,” combined with virtual reality, allows people to interact and perhaps even learn to understand the vibrational language of spiders.

“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.

GIF of Mr Krabs playing the Smallest Violin
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.

Bonus number 2: Here’s a song about the World’s Smallest Violin

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That’s some old beer!

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 archeologist Travis 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!


Read the full news story here: https://www.bbc.com/future/article/20210622-how-shipwrecked-yeasts-could-change-the-taste-of-your-beer

Read the publication about the yeasts found in the shipwreck: https://onlinelibrary.wiley.com/doi/full/10.1002/jib.641

Read more about Travis Rupp: https://www.npr.org/sections/thesalt/2019/05/26/723983713/beer-archaeologists-are-reviving-ancient-ales-with-some-strange-results

Whoops! Recent Graduate Realizes That Having A PhD Does Not Make Someone Employable

Originally published on the satire science journal website DNAtured

Job interviewee taking notes during an interview and looking concentrated
Photo by Anna Shvets from Pexels

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.

Aww! Nobel Prize Winner Thanks Post-Docs For Generously Allowing Him To Take Credit For Their Discovery

Originally published on the satire science journal website DNAtured

Hand holding up a Nobel Prize (coin shaped with Alfred Nobel's profile)
Photo by Adam Baker, CC BY 2.0, via Wikimedia Commons

Editor’s note: to protect the identity and avoid embarrassment for the people involved, we have retracted the name and field of the Laureate – though if you were assuming it was a man, you’d be right. Not that it narrows the possibilities by much.

Academics around the world are applauding a recent Nobel Laureate for remembering to thank his overworked post-doctoral students after their discovery helped him win the notorious award. 

A leaked draft of the Nobel Laureate’s acceptance speech revealed some open secrets about his true feelings toward his underlings, which many have described as “out of touch.”. The full draft reads:

“I am truly thrilled and honored to receive this prestigious award all by myself, with no co-winners. I would like to thank the Nobel Prize committee for continuing the decade-long tradition of giving this prize to a man, the obviously bigger-brained of the sexes.”

“I suppose I should thank all the people who made this possible, including the many researchers before me who laid the groundwork for this science, but it’s not my fault that I simply did it better (neener neener)! “

“I’d like to thank my undergraduate minions who have worked endless hours in the lab for experience and no pay, my grad students who have given up their chance of any personal relationship to make this research a success, and finally, my post-docs who have generously allowed me to take credit for years of their work.” 

“I hope all the members of my lab are equally as thankful for the prestige of working in the lab of a Nobel Prize Winner! 

Since my graduate students will benefit tremendously from the increased status this award brings to the lab, I trust that they will understand when I cut their graduate stipends by 50%.”

The iridescent truth behind iridescence (and hummingbirds)

“It was octarine, the colour of magic. It was alive and glowing and vibrant and it was the undisputed pigment of the imagination, because wherever it appeared it was a sign that mere matter was a servant of the powers of the magical mind. It was enchantment itself.

But Rincewind always thought it looked a sort of greenish-purple.”

― Terry Pratchett, The Color of Magic

I’ve always imagined octarine to be that green-purple metallic color of bird feathers. You know, that color that seems to change depending on the incidence of light?

peacock feather macrophoto with some water drops on it
Peacock feathers always looked octarine to me. From StockSnap

Just humming outside our window

We have a plant outside our window. It has tiny yellow flowers that bloom in the winter and seem like they taste delicious. Or would taste delicious if I were a hummingbird.

photo of two bushes with tiny yellow flowers with trees in the background
The feeding ground, bird not included.

We have at least two regular hummy-visitors, that I’ve seen. Just buzzing around just outside our window, usually, when I’m on a phone call and I lose my train of thought and end up sounding (even more) incoherent on my call.

In my defense, I grew up in a place where hummingbirds aren’t that common, so they are pretty amazing for me to see.

Hummingbirds are amazing. They are the only birds that can fly not only backward, but also upside down. They are tiny, and weigh almost nothing; the average ruby-throated hummingbird weighs about 3 grams (one-tenth of an ounce), which is about the weight same as a penny! Some species can fly for up to 22 hours non-stop during their migration over the Gulf of Mexico. And a flock of hummingbirds is called either a bouquet, a glittering, a hover, a shimmer, or a tune – which is just beautiful.

But, I think the most fascinating part is how their color seems to change. From one angle, one of the two birds has a deep red colored throat. Change the angle slightly, and it looks completely different.

What bird are we seeing?

First things first, there are over 330 hummingbird species worldwide, at least 23 types in North America and – we’re narrowing things down – 6 commonly found in the region we live, the Pacific North West.

Considering we’re seeing these tiniest of birds in the winter, and there are only one species that don’t migrate south for the winter, we are probably seeing Anna’s Hummingbird (Calypte anna), named after Anna Masséna the wife of a nineteenth-century bird collector.

Male Anna’s Hummingbirds have a brightly colored neck. There are about 1.5 million of these hummingbirds in existence. They are quite common, and seemed to have adapted well to urban environments – they surely don’t seem to mind buzzing outside our window and distracting me from phonecalls!

a tiny hummingbird with a reddish neck sitting on a treebranch
Nature photography is hard.

Why do hummingbird feathers (seem to) change color?

Hummingbird feathers aren’t “the color of magic,” they show the optical phenomenon called iridescence. Iridescent surfaces seemingly change color depending on the view or illumination angle. It’s the same effect that causes that rainbow sheen on a soap bubble, that lenticular-looking effect on some minerals, the changing colors of the tapetum lucidum, and that metallic shine on butterflies and bird wings.

The colors of the material are not due to a pigment (though that can determine the base color), but due to microstructures within the material that interfere with light in different ways (structural coloration).

Structural coloration: reflection, refraction, interference

Let’s take the example of a soap bubble. A soap bubble can be considered a thin film, it basically has two interfaces: the air-soap interface, and the soap-water interface. Light will interact with those interfaces in two ways: some light will be reflected (like on a mirror), and some will transmit and refract (change of angle due to material change).

So if we consider a single incoming ray of light, it will be reflected twice, once at each interface – and two rays will interact with each other by interference. Constructive interference happens when the light is in phase, destructive when it’s out of phase.

Depending on the angle of the incoming light, the angle of where we observe the light, the thickness of the film, etc. certain wavelengths (or colors) will be visible to the observer, because the rays constructively interfere, while others colors will be cancelled out.

This phenomenon is called thin-film interference, an effect that occurs when the material thickness is of the same order as the wavelength of visible light (380-750 nm).

physics schematic of light interacting with a thin film
Light reflects off the two surfaces and interferes constructively or destructively. Then *physics* happens. Image source.

Changing angles

When we change the angle of incoming light (by changing from which angle we observe), the thickness through which the light has to travel changes, changing its interference pattern. For example, looking straight on might make the film look red, while at an angle the same material will look orange or green or blue. This is how we see a rainbow effect on a soap bubble.

illustration of how color changes as the angle changes of light interacting with a thin film
Different light incidence angles change the color observed. Created using a thin film simulator.

A lot of tiny little mirrors

The same thing happens when we have certain crystalline structures, which is why some minerals show iridescence, or materials that are basically just a bunch of tiny little mirrors (like CDs).

The same is true for bird feathers, they show a regular crystalline nanostructure: individual tiny mirrors are spaced out just right to cause constructive interference of certain colors at a certain wavelength. And that’s why the Anna’s Hummingbird that chills* out outside our window sometimes looks like he has a bright Fuschia neck, and sometimes he does not.

Structural colours in nature that have attracted significant biomimicry efforts. (A) Typical Morpho butterfly (Morpho didius) and SEM images of the scale, each covered with ridges whose lateral profile has the typical ''Christmas tree'' shape (adapted with permission from ref. 73, r 2006 Society of Photo Optical Instrumentation Engineers); the ridges are supported by a gyroid crystal structure that also produces structural colours. (B) Structural colours of the plumage in the Eastern Bluebird (Sialia sialis, left) originate from quasi-order b-keratin tubular nanostructures, while in the Plum-throated Cotinga (Cotinga maynana, centre), the structures are spheres (reproduced with permission from ref. 74, r 2009 Royal Society of Chemistry); peacock feathers (right) show 2D photonic crystals of melanin rods embedded in keratin (image of blue peacock Pavo cristatus: wikimedia commons; micrographs reproduced with permission from ref. 52, r 2003 National Academy of Sciences, USA). (C) Jewelled Beetles (Chrysina gloriosa) and the Pollia condensata fruit display circularly-polarized iridescence thanks to a structure of chitin (left micrograph) and cellulose (right micrograph) fibrils, respectively, similar to assemblies found in cholesteric liquid crystal shown in Fig. 7 (adapted with permission from ref. 41, r 2009 American Association for the Advancement of Science, and from ref. 46, r 2012 National Academy of Sciences, USA). (D) Natural opals display iridescent colours because of the crystal arrangement of silica spheres (image: wikimedia commons; electron micrograph reproduced with permission from ref. 54, r 1964 Nature Publishing Group).  
Different examples of iridescent structures as found in nature.
From Parry, Ahu & Savin, Thierry. (2016). Recent advances in the biomimicry of structural colours. Chem. Soc. Rev.. 45. 10.1039/C6CS00129G.

Anyway, to me, octarine is real, and not only on Discworld.


*Actually, I’m not sure hummingbirds now how to “chill.”

Grad Student Becomes Lab’s Go-To Graphic Designer After Making Half-Decent Image In Powerpoint

Originally published on the satire science journal website DNAtured

Cartoon of a woman giving a PowerPoint presentation showing a pie graph.
(Image: Wikimedia Commons)

Grad student Anna Esquivel’s duties, which already include carrying out her research project, managing the lab, and TAing twice a week, have now expanded to include creating all poster and presentation images for her group after she created a half-decent image of a protein for a lab meeting.

“It was so amazing to see,” said Dr. Lyndon Vang, a postdoc in the same lab as Anna who attended the lab meeting in question. “The Prof was incredibly impressed by Anna’s ability to turn the standard shapes available in Powerpoint to an adequate representation of a protein. You should have seen the Prof’s face when the animation started!”

Anna has now been tasked to create all the images that the lab will use for all future talks, posters, and publications – including a (virtual) poster presentation that Dr. Vang’s due to present tomorrow. “Good thing I have Anna to help me,” Dr. Vang says. “So far, all I have is a title and half an abstract.”

Jadine Sparks, another grad student in the same lab, is an aspiring science illustrator. “It’s kind of frustrating; I’ve spent hours creating scientifically accurate figures in Adobe illustrator, both for scientific posters I’ve presented and to expand my portfolio – I want to make a career out of this. But apparently, all my figures look “too professional” for a scientific conference.”

Anna allegedly also knows how to do conditional conditioning in Excel, implying that soon she will also be designated the lab’s biostatistician.


Bonus: here’s an actual image I made in PowerPoint for my PhD theses. It took me embarrassingly long:

Schematic of the crypt and villus structure that lines the gut, indicating the different cell types.
Schematic representation of a crypt and villus in the small intestine and its cell types. From The biomechanical properties of epithelial cells and tissue in two and three dimensionsBentivegna, V. (Author). 2019
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Ending 2020 in (penguin) style

I have not made it a big secret that I think penguins are pretty cool.
(Does that count as a pun? “Cool,” because they live on the South Pole, get it? Get it?)

So to end this crazy year in style, I want to share some of the news and novel science related to our favorite tuxedo-wearing friends. In style, because tuxedoes are fancy!
(Get it?)

Sidenote: While researching “Best Penguin Moments of 2020” I learned that the Pittsburg Penguins are a hockey team (and not a lovely group of penguins in the Pittsburg zoo) and that there are many top Penguin book lists circulating on the internet. Not quite what I was looking for!

1. Penguin picture wins Ocean Photograph Award 2020

Starting things off with some cuteness, a picture of two penguins that had apparently lost their penguin partners and were seemingly comforting each other, won the Community Choice Award at Oceanographic magazine’s Ocean Photograph Awards 2020.

That’s all you need to know. Now wallow in cuteness.

2. Penguin Birthday Party

Wellington, a Rockhopper penguin in Chicago’s Shedd Aquarium who gained viral fame earlier this year thanks to a video of him hanging out with a Beluga whale, celebrated his 33rd birthday this year, with a day of fishy deliciousness.

3. TIL, Penguins get vaccinated too!

Birds get the flu too! And more importantly, birds can get vaccinated against the bird flu!

Copenhagen, Denmark – Humboldt penguins get a vaccine against bird flu at the city zoo. Photograph: Ritzau Scanpix/Reuters

Let this be a reminder that if you are able too, it is worth getting vaccinated against the flu, and when if becomes available to you, against SARS-CoV-2 as well!

4. Penguins make the best of a bad situation

In a tiny bit of silver lining to climate change, recent research showed that Adelie penguins may actually thrive in warmer years. In years where there is less ice, Adelies spend more time swimming, saving energy, and covering more foraging ground. The researchers predict the population is likely to grow as the ice caps decline.

5. Penguins suffer in a bad situation

On the flip side of the story above, warming waters near Antarctica may be the reason for the biggest king penguin colony declining in size, having lost 900,000 birds over the past few decades. If anything, changing climate is causing species to adapt, and some will be okay, while others will not.

6. Penguins celebrate the holidays too!

Okay they don’t, but earlier this year we 3D printed some penguins, and they have now found their home!

4 penguins 3D printed in orange resin. 3 are standing upright with wings spread out, one is on its belly.
A Waddle of Penguins
Two penguins in clamps while being painted: black body, white belly, orange beak and feet
Getting Tuxed up!
Two penguins, with yellow markings on the side of their head, standing around wrapped gifts with some trees in the background.
Macaroni Penguins love presents too!

I hope you all have a wonderful New Year, full of waddling and warmth and tasty fish!

Valerie & Penguinone

The molecule penguinone as ASCII text

Grad Student Desperate For Feedback Thrilled To Receive “K.” From Supervisor After Just 3 Months

Originally published on the satire science journal website DNAtured

Fourth year graduate student Virinder Singh was excited to find a new email from his supervisor in his inbox last Friday at 11:13 PM. Responding to a three-month-old request for feedback on a first draft, his supervisor had sent the following message:

K.

Sent from my iPhone

“I was having a drink when I checked my phone and noticed a new email,” Singh says. “I immediately rushed back into the office to start getting back to work. It was then that I realized that Prof McNally had forgotten to include the attachment.”

Singh’s supervisor, Dr. Alistair McNally is known for his open door policy: students can come to him anytime with questions. The door to his office is always open. He, however, is never there.

Dr. Jena Li, a postdoc in Dr. McNally’s group, seemed disgruntled: “Good for Virinder, I hope he’s able to finish that paper. I’ve been waiting more than a year for a reply to an email asking for a meeting. I’m not even sure Dr. McNally knows I exist!”

When asked for a statement, Dr. McNally replied “K.”

Text bubble with "k". Meaning (okay), noun. used when things are really, in fact, not okay

Whoops! This Research Chemist Forgot To Add “But Not For Drugs” At The End Of Their Google Search And Now They’re On A Watch List

Originally published on the satire science journal website DNAtured

Upset Oh No GIF by Broad City
(From Giphy)

Research Chemist Dr. Jamie Dennis was shocked to discover that they were on the FBI watch list after googling the chemical structure of phenylalanine, without specifying that they did not intend to make meth.

“I’m usually so careful,” says Dr. Dennis. “One of the first lessons you learn in a chemistry undergrad course is to always, always, put “but not for drugs” in a google search. Especially if you’re looking at crystallization temperatures.”

This is not the first time a member of the chemistry department has been flagged. In 2015, a grad student was temporarily suspended bringing blue rock candy to an after-class happy hour.

Breaking Bad Pizza GIF
(From Giphy)

“For the last decade or so, we’ve had to be a lot more careful,” said FBI Agent Susan Pearson. “We’ve put tabs on all chemistry teachers, chemistry grad students, and chemistry researchers, just to be safe. With those paltry teaching salaries, everyone wants to be the new Walter White.”

Dr. Dennis says that they’ve learned their lesson, but after comparing their postdoc stipend to the money that could be made from a few illegal synthesis reactions, says they will now simply complete future searches in Incognito mode.

ninja turtles lol GIF
(From Giphy)