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

Ending 2020 in (penguin) style

Winter landscape painting in the background with three block figures in front of it: a baby penguin, a chirstmas tree, and an adult penguin.

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:


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)

Alfabetober – Part 4

[Part 1]

[Part 2]

[Part 3]

Alfabetober – Part 3

[Part 1]

[Part 2]

Alfabetober – Part 2

Did you know that in Dutch, usually “ph” spelling is an “f”? For example, the Dutch word for “alphabet” is “alfabet.”

[You can find Part 1 here]

Alfabetober – Part 1

Every October, artists all over the world take on a challenge: make a piece of art (usually within a certain theme, using a specific media, and using a prompt list) every day for one month.

While I would not call myself an artist (though, art and science do have things in common), I took up a hobby I’d started a few months back: brushlettering or handlettering. One letter a day. And of course, I picked a science theme.

So here you go, part 1 of #Alfabetober, inspired by Carla Kamphuis (I realize that there are only 26 letters, while there are 31 days, there are some rest days).

Is there such a thing as a wunderkind?

A black and white drawing of Einstein
Einstein was widely regarded as a genius, but he did not have an unusually large brain, which I know because I researched it for a book once.

I recently watched the documentary The Inventor: Out For Blood In Silicon Valley. And boy, do I have some thoughts.

Theranos: Therapy meets Diagnostics

The documentary depicts on the rise and fall of Elizabeth Holmes, founder, and CEO of the biotech company Theranos. Briefly, here is what happened:

At the age of 19, she dropped out of university and founded a company on the idea of creating a diagnostic blood test that could test for over 200 different markers using only a few drops of blood, that could be taken with a prick of a fingertip. You know, the kind they use to measure your hemoglobin when you donate blood.

The aspiration was to give the power of therapeutics and diagnostics (Theranos = THERApy + diagNOSis) to the individual, making tests significantly cheaper, less scary (no needles!), and easier for the consumer to interpret. And earlier disease detection means earlier treatment and better survival!

She founded the company in 2003 and raised over $700 million from venture capitalists and private investors in the next decade. By 2013, the company was valued at $10 billion. In 2015, the validity of technology was questioned and Holmes, and Theranos with her, fell. Three years later, in 2018, Holmes and Ramesh “Sunny” Balwani, former Theranos Chief Operating Officer and President, were both charged with fraud and conspiracy. The Theranos saga had ended.

You can read more about Theranos and Holmes’ rise and fall on the interwebs, or watch one of the several documentaries made about the story. Rather than give you the details of Theranos, I’d like to talk more about my thoughts after watching this documentary – as a bioengineer who in 2013 was studying nanotechnology, working on a project involving “theranostics” (THERApeutics + diagNOSTICS, sound familiar?) and has more recently worked in a startup environment.

Nanotechnology and Microfluidics

From 2011 and 2013, right when Theranos was about to hit its peak, I was studying nanotechnology. The technology Theranos’ system was based on (or so they claimed) was exactly the same type of stuff I was learning about. To be able to do diagnostics on small samples, the liquid handling and detection techniques need to be scaled down, using principles of microfluidics (I was also learning about that).

I distinctly remember giving a presentation about microfluidic chips that could process blood in a way to split out the different components, i.e. centrifugation at a teeny tiny scale.

From what I remember, at that time most of this technology was still in the research phase: individual university research groups and some research institutions coming up with new approaches to handle small blood samples for diagnostic testing. Were they able to do 200s of tests on the samples? Not that I know. Was any of the technology commercially viable at the time? Not that I know. But then again, I was only studying this stuff and in no way an expert.

More importantly, I don’t remember hearing about Theranos. It clearly had not made enough of a buzz, scientifically, to reach across the pond.

When I was watching the documentary, it talked a little bit about the technology and my reaction was: “That won’t work. You can try to scale down one or two of these tests to work with small samples OR you can try to do a lot more tests with the same amount of sample. But not both at the same time, that’s just sounds idealistic!”

Clearly, it didn’t. (Obviously, otherwise, there would not have been as many articles written about this, or documentaries made.)

Blood samples are typically collected in tubes that look like this, a few mL at a time

Why we still love a genius

Part of the reason people bought into the Theranos story, is because it was enticing. This young women, who wore turtlenecks (Steve Jobs much?) and felt like she had to lower her voice to be taken more seriously, Silicon Valley just loved her. Part of being part of startup culture is being good at selling a story – whether it’s factual or not, realistic or not, is beside the point.

Another reason Theranos was successful at first and able to raise so much money was that Holmes was extremely well connected. She was charismatic. She was able to surround herself with big names, from the world of investment, military, law and even politics.

Here’s the thing, I get it. Seeing images of this young woman, who clearly is motivated by making the world a better place, who clearly made an effort to hire an inclusive and diverse workforce, who was able to found a company at such a young age, after dropping out of college no less, I would have admired her too! Making it “big” as a woman in the male-dominated tech world is not an easy feat and she seemed to have made it happen (at the time).

But here’s another thought: why do we so want to love the story of a “genius”? We love hearing about wunderkinder and how they become the youngest to do this or the first to do that. Is it because somehow we think that we too can be a genius. That we can have our own great amazing story. But most of us won’t (and that’s okay).

Maybe we should stop glorifying individuals in science, research, and tech, because especially nowadays, science doesn’t happen in isolation. Progress happens in small steps with massive groups of people collaborating to make it happen.

(Yet, we still have Nobel Prizes and love celebrating greatness.)

Why we love to see someone fall

We love to admire an individual making it happen against all odds, working so hard so they can make it, despite the system working against them. But similarly, we love seeing someone on the top fall. Perhaps we like seeing them fail so we can feel better about ourselves not “succeeding” as they did. And then didn’t

What I disliked about “The Inventor,” is that it made it seem like it was all Holmes’ fault. They spoke to some of the men that invested in her company, that believed in her, and they all tried to shift the blame to her, like she had “seduced” them into supporting her too idealistic cause.

Holmes’ surrounded herself with Yes-men. Surround yourself with people who keep telling you that you’re great, and you will start thinking you’re great. Just like being told over and over again that your not good enough for something will get to your head.

The documentary, with overly dramatic animations of blood getting into a microcentrifuge system and a dice rolling, makes Holmes look evil. And the person around her, who enabled her, as victims of her charm. And the same type of men then went ahead to explain how she failed.

Of course, Holmes’ did play a big part in this story, but she’s not the only one to blame. It’s the system that gives people the privilege of better networks and connections to succeed without really having to try. It’s the culture of Silicon Valley that celebrates taking risks when they are completely ridiculous to take. It’s the startup mentality of “Fake it till you make it,” forgetting that quite often they won’t actually make it. It’s all of us, that love hearing about wunderkinder and geniuses and celebrate the individual instead of the collective for their achievements.

The end

How to I end this word vomit about how perhaps glorification of geniuses is perhaps not the healthiest thing?

Well, people do have good ideas. And sometimes the high-risk, high-reward world of tech and startups is the way to make these good ideas happen. And sometimes those ideas fail and we should just admit to ourselves why we enjoy watching that happen.

To quote the YouTuber MedLife Crisis (paraphrased): We shouldn’t hype medicine. Thank you vfor coming to my MedTalk.