A Cat-astrophic Ordering Mishap at Two U-Penn Labs

Image credit: @GaryBeck

April 17, 2021

In mid-March, formalin-preserved cat cadavers were unexpectedly delivered to two independent scientific laboratories at the University of have Pennsylvania. Both labs had anticipated orders of 50 mL conical tubes.

It was a late Friday afternoon when Jane Evergreen* signed for a package in her lab. She and her laboratory at University of Pennsylvania had been expecting a delivery of 50 mL conical tubes from Fisher Scientific for months. The 50 mL conicals are standard research lab supplies used to mix solutions, and just one of many products backordered amid the COVID-19 pandemic. Evergreen cut open the cardboard box, expecting to see the typical blue, quarter-sized caps of the conicals arranged in their standard grid pattern. Instead, there were cat cadavers.

While Fisher also sells the cat cadavers, Carolina TM Formalin Cats, as, “ideal dissection specimens” for research and educational purposes, it is unclear how such a mistake occurred.

Soon after the box was opened, Evergreen tweeted, “Fischer, if you’re out of 50 ml conicals, you coulda just told us…” The tweet initiated a flurry of retweets, questions, and even commiseration.

Dr. Daniel Phillip*, another scientist at University of Pennsylvania and head of a lab, replied, “I’m a little jealous. We only got one cat.”

Phillip’s lab had placed the order for 50 mL conical tubes from Fisher in November. Commiserate with Evergreen’s experience, Phillip “instead received a dead cat (albeit, very well preserved)”

After 24 hours, there were over 600 retweets, 2.7k likes, and a few jokes:

“Have you checked inside the cats for the tubes?” – @MercerLab)

“Worst packing peanuts ever” – @JoeFlowImmuno)

“Well, the cat’s out of the bag and in the bag” – @Weinbergerrrrr)

“Does ‘vcat’ on the label mean, ‘very cat’?”  

“Schrodinger’s cat?” -@Urso_bruto)

“Are you kitten me?” -@PhDistance

“Stop ordering from Schrodinger’s lab supply…” -@kkeilts

“Looks like there is a reason it is called a ‘cat’alog” -@tweet2Rbhadani

Other researchers shared their newfound suspicions of some unusually long boxes they received at the end of the workday on Friday, labeled “50 mL conical.” Most have stated their intentions to leave the boxes unopened throughout the weekend. Indeed, a box of dead cats is a Monday Problem if there ever was one.

Evergreen thanked the Twitterverse for “going on that journey” with her lab. The journey and associated humor were probably a welcome distraction from the fact that her lab still lacks the supplies it needs to conduct research experiments.

It is likely that the mishap is an absurd side-effect of the current national plastic shortage due to the U.S. Defense Production Act. This action was initiated by the U.S. government last April to allocate “health resources” (e.g., lab grade plastic used for the conical flasks) for COVID testing supplies.

In addition to the 50 mL conicals, other essential lab products have been backordered for months including plastic pipette tips. These tips are used to transfer small aliquots of liquid between various tubes and solutions during experiment. Both the conicals and pipette tips are as essential to an experiment as measuring cups and spoons are for a tricky recipe.

Hopefully the plastic shortage will end, research can resume its steady pace toward progress, and this cat-atrophic mixup will be a terribly strange memory of the Pandemic Years.

NPR Morning Edition recently discussed the plastic shortage. Click here to listen.

*Names have been changed

I have a thesis defense date!

March 30, 2021

It’s official: I have a defense date scheduled for August 10 at 11 am. MARK YOUR CALENDARS, FRIENDS! Also hit me up for that Zoom link. The buildup to this has been pretty stressful, so I am ecstatic that is worked out and I get to leave.

Before August 10, I have to write a thesis — specifically, I turn it in July 6! The average PhD thesis is around 75,000 words. The task is pretty daunting, but I have a strategy to tackle it. Basically, I will write about 15,000 words of introduction, about the same for a discussion, and my two papers will go in between. Older graduate students in my program have called the strategy, “the sandwich method.”

After I write and defend, my next step is a move to Research Triangle Park, North Carolina. My partner has accepted a job at the Environmental Protection Agency, which is AWESOME and I am so freakin’ proud. On my end, I aspire (dream) to become a science journalist that covers environmental health news and toxicology. I have accepted that I might not be able to get there right out of the gate, so I have been casting a wide net with my job applications and career search. I have applied for science communication multimedia fellowships and toxicology consulting and risk assessment positions. Additionally, this week I am meeting with some mentors to *gulp* inquire about post-docs. Ideally the post docs would be at the National Toxicology Program or NIEHS, and have an obvious public-health focus and maybe even value science communication and outreach. Does such a specific post-doc exist?! I have no idea. Hopefully time (and the right contacts) will tell.

At work, my main responsibilities have shifted from laboratory work, writing, and extracurricular activities to mainly writing all day, every day. Honestly, thank GOODNESS because 1) I love to write/edit and 2) I have gotten to the point in my PhD where I want to bang my head against the black Masonite benchtop every other day. Apparently, that level of frustration is a good indication that a student is ready to leave.

Another indication is a publication record.

I published my first first-author manuscript in Toxicology last fall, which is the unwritten base-requirement (in addition to completing coursework and maintaining good academic standing) to graduate from my program. However, my advisor wanted a second first-author publication from me before he would let me go.

At first, I was basically like “heck no this is dumb and I am tired” but in slightly more articulate and professional language, of course. Eventually (and begrudgingly), I acquiesced. While I’m proud of myself for doing it, I must credit a supportive committee member who gave me the tough love I needed to “just write the damn paper and get out.” In a three week span, I pivoted from an obstinate stance against writing the paper at all, to having the first draft completed and sent to my advisor.

That draft has been sitting in his inbox for over a week now, but it’s not productive to dwell…

Anyway, I’m really proud of myself for setting my mind to something and just doing it, even though I very much did not want to. I’m leaving out a lot of details, such as panic attacks and angsty walks to work. In any case, please trust me when I say that my experience with the second paper is pretty emblematic of the grind of a PhD: it can be mentally grueling.

Now would be an opportune time to say something along the lines of, “if it was any other way, everyone would do it.” Approximately 2% of the U.S. population has a PhD, according to Inside Higher Ed. Sure, a small fraction of people in general complete the PhD. Here’s a thought: what if we made it less mentally grueling?! Surely more people would have a PhD. Why is that such a bad thing? I digress. This is definitely a topic for a future post.

Nevertheless, I’m looking forward to joining a tiny nerd-guild of Toxicologists in the very near future.

Methylmercury pollution is a problem – can Hollywood help?

January 29, 2021

The story of the world’s worst methylmercury poisoning disaster comes to the screen in February. The film, Minamata stars Johnny Depp as American photojournalist, W. Eugene Smith, whose work publicized the disaster in Minamata, Japan. Hopefully the film will renew public interest in mercury pollution, which remains a major threat to global public health.

(Warning – spoiler alert) The movie is set in Minamata in 1971, where Smith and his wife, Aileen, visited the small coastal fishing village for a journalistic expedition. The pair learn how Minamata and surrounding towns were ravaged by methylmercury water pollution from the chemical factory owned by Chisso Corporation. Smith captures the tragedy on his camera, which leads to an infamous eight-page spread in Life Magazine in 1972. Based on the trailer, centerpiece of the film is likely to be Smith creating this photospread.

The photos captured emotional scenes of the distorted, frail bodies of poisoning victims. To implicate Chisso, Smith sequentially arranged the photos: shots of factory wastewater followed by people fishing to explain the exposure, and lastly images of physically crippled victims in their daily life.

Left: Industrial waste from the Chisso Chemical company. Middle: Fishermen in Minamata Bay. Right: Tomoko Uemura is bathed by her mother. Photo credit: W. Eugene Smith.

Methylmercury is a potent neurotoxicant, a poisonous substance that causes brain damage. In the case of methylmercury, the damage is permanent. With high levels of exposure, such as those at Minamata, the brain damage results symptoms akin to cerebral palsy: erratic, uncoordinated movements and cognitive impairment.

A peculiar attribute of methylmercury is that it accumulates in fish tissue. Even small amounts in the environment can lead to extraordinarily high levels in fish. Thus, people who ate fish from the bay in Minamata were poisoned. Chisso stopped dumping wastewater in 1968, but hundreds of Japanese had already been crippled or killed by the poison. To date, approximately 3,000 victims been officially recognized, according to a recent report in the Japan Times.

Dr. John O’Donoghue, toxicologic neuropathologist based in Rochester, New York, first learned of Minamata after seeing Smith’s photo spread in Life Magazine many years ago. “One particular black and white photo has stayed in my mind ever since,” he said. “It was a picture of a woman who was bathing her crippled daughter with such care and tenderness – the child was precious to her.” In Smith’s photobook, Let Truth Be the Prejudice, the photo is called “Tomoko Uemura is bathed by her mother,” and is also pictured above.

Dr. Celia Chen, director of the Dartmouth Toxic Metals Superfund Research Program, was similarly struck by the same photo. “Seeing the degree of physical impact of a toxin through the environment was really sobering,” she said. “It was painful and inspiring as well – there are so many emotions with the photograph.”

The story of Minamata is powerful, but Dr. Chen stressed that the poisoning event was distinct from most mercury exposures. “Minamata was like a punch to the gut,” she said. Chen explained that the more subtle low-level exposures experienced most often today can still be dangerous. The most sensitive populations to methylmercury are unborn babies, who are exposed through contaminated seafood eaten by the mother. While all fish contain some level of mercury, the most concerning are large predatory species like swordfish, tuna, and shark; these are the ones clinicians advise pregnant mothers to avoid. Another way to protect the next generation is by reducing the amount of mercury in fish to begin with. For this reason, international limits on mercury emissions are crucial.

Indeed, the international Minamata Convention of Mercury was formed limit mercury emissions into the environment. According to Chen the Minamata Convention “is like the Treaty of Paris for carbon emissions.” Italy joined the Convention on January 5, 2021, bringing the total number of participating nations to 127.

Chen said that coal fire-power plants have the highest mercury emissions in the U.S. In order to regulate power plant mercury emissions, the U.S. Environmental Protection Agency (EPA) finalized the Mercury and Air Toxics Standards (MATS) in 2012. Chen explained that the MATS rule helps the U.S. meet commitments under the Minamata Convention.

The MATS rule has helped substantially reduce mercury emissions. According to EPA data, mercury emissions from the U.S. coal-fire power plants have declined by 85% from 92,000 pounds in 2006 to 14,000 pounds in 2016. Additionally, the estimated number of children born in the U.S. each year with pre-natal exposure to methylmercury levels exceeding the EPA reference dose has decreased by half.

Despite such progress, the EPA recently stepped back from its commitment to reduce mercury emissions.  On April 16, 2020, the Agency deemed that it is not, “appropriate and necessary” to regulate mercury and other hazardous pollutants from coal-fired power plants under section 112 of the Clean Air Act. According to legal scholars, this decision undermines the foundation of the MATS rule and invites challenges to mercury emissions standards.

While the Biden administration is likely to consider more stringent environmental regulations, it’s noteworthy that our new President neglected to include coal-fired power plants in his January 27th executive order limiting emissions (coal leasing) on federal lands.

Nevertheless, movies like Minamata can help people take notice of important environmental issues surrounding mercury. Public awareness and understanding of such issues can help protect the next generation from the health threats of methylmercury.

Researchers who study mercury today such as Chen, O’Donoghue, and myself are hopeful that the public reception of the film will be similar to that of prior historical dramas with an environmental interest. In the 1984 film, Silkwood, Meryl Streep brought a story of corporate negligence and plutonium radiation toxicity into the public eye. Mark Ruffalo did so more recently for perfluoroalkyl and polyfluoroalkyl substances (PFAS) in Dark Waters.

As Chen succinctly put it, These kinds of movies, whether on mercury or PFAS, are so important because the public will go see a movie and gain interest. Movies can be an on-ramp for people to care about important environmental issues.”

A new era

January 20, 2021

“The best social program is a job,” reads a sticker on a garbage bin at the curb of my parent’s driveway. The sticker pays homage to Roland Reagan, 40th president of the United States. I’ve never known their intention for putting the sticker there.

In 2016, and again leading up to 2020, I learned the extent of my folks’ conservatism. As dyed in the wool Republicans, they will throw their support behind any candidate the Party puts forth. Ironically, they claim to have voted for Donald Trump because he, “was not a party politician.”

I don’t think people throw their support behind a candidate based solely their beliefs. Reagan also once said, “I believe in the idea of amnesty for those who have put down roots and who have lived here even though sometime back they may have entered illegally.” Yes, really.

Like many other people my age, the political polarization in America has elevated the tension in my family. I don’t understand it at all. I’m reading Why We’re Polarized by Ezra Klein, American political journalist. Klein has studied politics for over 20 years, so hopefully his expertise can help me come up with some more ideas.

In the meantime, I don’t think my familial rift will dissipate any time soon. The current climate is tense, but I remain optimistic that personal relationships will heal. I hope that the whole nation will come together again. I’m feeling especially hopeful today, on inauguration day.

As I write this, Joe Biden is being inaugurated as 46th president of the United States with his wife Dr. Jill Biden as the new First Lady. Kamala Harris, a black woman of Indian heritage will make history as the first female VP. This is a huge moment in history; the glass ceiling is breaking!! Unfortunately half of America is petrified that the shards will fall on them. Half of Americans have intentionally distanced themselves from their progressive neighbors, and maybe that means they face more discomfort in the coming years.

VP Kamala Harris being sworn in via FB page of Biden Inaugural Committee

If slight discomfort for a privileged few means that more Americans than ever before have a shot at a better life, I think it’s worth it.

I’m looking forward to America rejoining the Paris Agreement. I’m looking forward to consistent and unequivocal public messaging on the Coronavirus. I’m looking forward to leadership that trusts science rather than scoffs at it. I’m looking forward to a (slow) return public trust in journalists. I’m looking forward to a foreign policy that makes me feel safer and does not rely on scapegoat tactics. There’s just so much to look forward to for the first time in a while.

I’m hopeful and optimistic. Plus, I just got a Twitter notification that there is a new @WhiteHouse account #finally. Whatever the medium or platform, I trust the new president to follow through and be the leader we desperately need right now.

Also check this out: “Biden is now president. Here’s what he wants to do in office” https://www.vox.com/22237275/joe-biden-inauguration-policy-build-back-better

“To live together and work together. That’s how I see America. That’s how I see the presidency, and that’s how I see the future.” – Joe Biden in October 2020, inspired by FDR

Female fruit flies expect great love songs

December, 2020
Have you ever wished your partner would treat you to a sweet serenade? If you’re a fruit fly, you don’t just wish for it, you expect it. A team of researchers at Howard Hughes Medical Institute’s Janelia Research Campus recently mapped out the neural networks that underlie female response to a potential mate’s song.

How to woo a female fruit fly

If a male fruit fly successfully woos a receptive female, the pair will mate. To entice his partner, the male fly “sings” by extending a wing and vibrating it to produce an acoustic signal. The fly song consists of two repeating verses: brief trains of shrill tones followed by continuous soft hums. Previously, the researchers had uncovered the neural networks behind the male’s courtship song, but how the female perceives the melody was largely unknown.

In the new paper, the team investigated how the female fruit fly brain integrates the song to respond to a potential suitor. If she accepts the advance, her vaginal plates will open to allow mating. The team found that female receptivity depends not only on a good male performance, but also on the intrinsic mating status of the female.

Brain circuitry

Inside the female fruit fly brain, the right song is transduced into sensory information, which feeds to a special class of neurons and integrates with information from a second set of neurons. The second set of neurons conveys information about the mating status of the female. In response to a male song or mating status, both sets of neurons will produce a series of “stop” or “go” signals that eventually connect to the muscles of the vaginal plate. If the female has not yet mated, and if she “hears” a good enough song, the neuronal circuitry in her brain will produce a net “go” signal to the vaginal plate muscles. The vaginal plate will then open to allow mating. Alternatively, if she’s not satisfied, she will reject the male.

The researchers used a series of elegant genetic and physical manipulations of transgenic female flies to establish the relationships between different neuron types and vaginal plate opening. Using genetic tricks (GAL4/UAS and optogenetics) analogous to operating a molecular switchboard, the researchers determined in what context neurons will fire in response to a male song or mating status, as well as where these signals integrate.

Removing the aristae

The team physically removed the “hearing” organs of the female flies, the aristae, or the wings of the male flies. In each case, they observed that neurons which respond to male song did not fire in a pattern that normally leads to the vaginal plate opening response.

Additionally, the song of a different species of fly could not woo the female.

These experiments showed how crucial it is for the female to perceive the right male’s song. The researchers also established that the receptivity of the female was governed by whether or not she had previously mated.

In other words, if a female fly “hears” the right song from the right male, and has not previously mated, she’s DTF.

Maps to set the mood

In certain conditions, the male sang and sang, but to no avail. The female would not open her vaginal plates. The team synthesized information of these particular experimental conditions to assemble a map of the neural pathway that governs female fly receptivity to sex. The paper is important because it establishes how three components of a fundamentally important mating behavior are wired together as a unit.

While the paper is fun to read (who doesn’t like learning about fruit fly sex?!), it’s important to understand the big picture of this research.

Understanding neural circuity behind female sexual receptivity in the fruit fly may help us better understand signal processing that influences behavioral decisions across a range of species, including humans.

The female fruit fly maintains high standards for a love song; she turns down potential suitors that can’t hit the right tune. From an evolutionary standpoint, it’s probably good to set the bar the high to get the best partners.

Keep your standards high, ladies and gents.

“If I cannot fly, let me sing” – Stephen Sondheim (American Composer)

Link to the original paper, published in the November issue of Nature: https://www.nature.com/articles/s41586-020-2972-7#Sec2

Quitting the PhD: when you could and why you shouldn’t

November 12, 2020

The challenges that face PhD students in science programs are frequent and often seem insurmountable. When faced with obstacles, is it better to just quit? Spoiler alert — NO! Its not!

Approximately a quarter of graduate students in science or engineering PhD programs in the U.S. will quit within 3 years of matriculation, according to data gathered by the Council of Graduate Schools. Moreover, of the estimated 24,165 graduate students in U.S. natural science doctoral programs, 6,041 will not defend their thesis to earn a PhD.

There are numerous reasons why quitting may be appropriate or inappropriate. Ultimately, the decision to throw in the towel (or not) is extremely personal.

Anecdotally, I have heard that the main reasons for quitting a PhD in the natural sciences include losing interest in the research, wishing to pursue a different passion, and feeling disheartened by academia. These are all totally understandable reasons, and I have felt them too.

There are other struggles, too. Personally, I sometimes think my experimental design is such a mess that my research is not going to help the world in a meaningful way. Every now and then, I consider the possibility that I am only in a PhD program by some fortuitous combination of personal fraud and admissions committee error. Additionally, I often worry that my future career will not require my high level of education. These feelings have certainly been exacerbated by the mental toll of the ongoing COVID19 pandemic, but they had existed before March 2020.

Nevertheless, I won’t quit, and I argue against quitting a PhD in general.

The pandemic will be over, eventually. In the meantime, there is no shame in struggling during these uniquely stressful times, or ever, actually. Change is really hard, and it’s OK to struggle. Pandemic aside, the process of a PhD involves constant changes: moving to a new city, rotating in different laboratories, joining a lab and moving to a new office, forming relationships with your committee members, working through summers, and a revolving door of lab members, to name a few.

While we (usually) can’t control the changes, we can control how we respond to the changes. My thoughts of quitting partially stem from my responses to change: being supportive versus resistant of the changes experienced in academia influence my mood/outlook, which in turn influence how often the thought of quitting occurs.

PPT - Positive Response to Change PowerPoint Presentation, free download -  ID:476522
Personal responses (supportive to resistant) to change (in general) in academia over time

I’m usually in a pretty good mood and want to keep on keeping on, but I have periods of doubt that basically correspond to whenever there is a change. Indeed, I’ve felt the urge to call my advisor and hang up my lab-coat many times over the past few months, but I will not. The doubt will pass. I will defend my thesis sometime in the next two years.

Overcoming this whole mess, and emerging with a PhD is essential for me, and other candidates. Although the degree represents the contribution of new knowledge to the world about a (very specific) problem, the educational process is the most meaningful part. A PhD is an endurance event — basically a marathon. The finish is great, but the race itself is where you learn and grow against a backdrop of constant change.

Sticking it out and holding steady through the “race” is tough. However, like endorphins for a runner, the benefits of a PhD journey increase as you go on. During my PhD so far, I have become educated in much more than Toxicology. I’ve learned how to be kind yet constructive, that PI’s are just people, and that my to-do list is never too long for a run (and other means of self-care!). I want to continue to learn more while I can, so I will stick around. But not too long!

The decision to leave or stay is personal, and I realize I have certain privileges (I don’t have children, I have more free time, etc…) that enable me to make this decision more easily. Nevertheless, should “the benefits of the process” not be a sufficient reason for you to stay, I offer some others:

  1. You worked too hard to get here to quit now.
  2. The effort you have previously put in will amount to a degree that opens doors to subsequent opportunities
  3. You may inspire others to pursue a PhD
  4. By struggling, you have gained experience that you may share with mentees you can guide and help
  5. You CAN do it — anything worth doing is difficult — If it were easy, everyone would have a PhD!
    • Indeed, 2% of the United States population has a PhD., according to US Census Bureau data from 2019.

Although I urge you to stay rather than quit, spending time in a PhD program means you learned something about yourself, and made an informed decision.

“At the center of your being, you have the answer; you know who you are, and you know what you want.” – Lao-Tzu (604 – 531 BC)

Have you thought about quitting? What are your thoughts on the process of getting a PhD? What made it worthwhile for you?

Bike to work in the winter (!/?)

October 21, 2020

Bicycles flew off the shelves in the early phases of the pandemic to provide exercise and anxiety relief to many. The weeks went on, and employees slowly returned to work – many by bike! Now that winter is fast approaching, the feasibility of the bike-to-work commute is called into question.

One serendipitous outcome of the COVID19 pandemic is that many people have discovered they can easily commute to work by bike, and reap the benefits. Riding a bicycle for just 20 minutes a day — a very reasonable length of time for a commute — has tremendous benefits for long-term personal health. The reduced carbon-footprint from not driving a car is also a plus.

For those who commute to the University of Rochester Medical Center (e.g. me, and hundreds of others), which is the largest employer of Rochester, biking to work also means not having to deal with parking and vehicle traffic. The Erie Canal, Greenway Trail, and Genesee River Trail provide a way for people living in various areas to get directly to the Medical Center. Bike commuters can smugly zip past the horrendous parking situation in Lot 1 on a regular workday, and head straight for the bike rack located right outside the University doors.

The aforementioned benefits of commuting by bike don’t necessarily go away with the warm weather. When the snow comes, certain trails are plowed and salted, just as the roadways. Although, many year-round bike commuters think that there is better traction on the non-plowed surfaces.

Timothy Anderson, a graduate student at the University of Rochester succinctly explained that, ”it’s not a big deal, as long as you’re not a little bitch.”*

*note- he is joking, obviously. But really, it’s not as terrible as one might think!

In preparation for his first Rochester winter, Anderson opted to purchase a fat-tire bike, which has more contact with the ground, thus can provide more traction. Additionally, many local bike stores in Rochester can help “winterize” your current bike. This entails switching out standard slick tires for studded tires. The stores can also provide you with flashers and lights, as rush hours in the winter are especially dark.

In my opinion, fenders are the most important equipment for your winterized bike. In addition to snow, winter douses the roads with a wet mixture of slush, salt, and dirt. Fenders prevent the rear wheel spinoff from lining your back and butt with dirt lines.

Fenders are also a must for the rainy season that precedes winter (i.e. right now). I have been riding in the rain this week and it has not been super great. Installing my fenders this weekend will be a welcome update!

Alternatively, you can forgo fenders and bring a change of clothes each day to work. This is what I have been doing. My PI, who also bikes to work, employs this strategy as well.

Indeed, biking to work throughout the harsh Rochester winter isn’t impossible. Should commuting in the winter seem feasible for you, perhaps your current motor vehicle is due for a more unconventional trade-in.

Misuse Of Acronyms is Not Stellar (MOANS)

August 23, 2020

I feel like I’m generally able to roll with the obscurities and absurdities that plague academia. Average of 21 years from PhD to full-professor status in Toxicology? Fine, I won’t think about it. Lack of eye-care in my student health-insurance package? No problem; my outdated prescription doesn’t mean I’m blind (yet)! Non-employee student status that prevents me from saving for retirement (or unionizing)? Probably unfair, but it’s not productive to dwell.

However, one thing I cannot brush off is the confusion that surrounds acronyms in academia. We use acronyms, abbreviations, and initialisms to communicate faster; unfortunately, this does not necessarily mean that their use helps us communicate better. My main qualm is that I think that having so many acronyms in science makes it confusing to convey meaning across disciplines because acronyms can be mis-used to impede communication.

My favorite example of this is “MHC.” If you’re talking among biologists or schmoozing the histology core staff, MHC is understood as, “myosin heavy chain.” However, if you’re an immunologist or medical professional – your first thought might be “major histocompatibility complex.” And if you’re checking your student health insurance coverage, you may want to make sure your “mental health counselor” is still free due to COVID.

I’m pretty stuck on student health insurance issues lately… can you tell?

A recent eLife meta-analysis of the growth of acronyms in science found that acronym use is going up and acronym re-use is going down. It also suggested that journals which have policies that prohibit acronym use in the title do not enforce that rule.

The authors of the meta-analysis analyzed 24,873,372 titles and 18,249,091 abstracts published between 1950 and 2019, from which they observed over 1.1 million unique acronyms.

Introducing new acronyms so often while not using existing ones creates an alphabet-soup of terms in literature repositories (e.g. PubMed) that scientists and interested readers have to sift through. Furthermore, it is unlikely that one can completely evade this by limiting a search to titles. I want to clarify that I’m not against the use of acronyms; I oppose their misuse/abuse. The aforementioned level of acronym mis-use bugs the crap out of me.

Devil’s advocate: Given a fluent reader of the same language and discipline, acronyms certainly help scientists and writers rapidly convert print to meaning by reducing wordiness. The abstract in my most recent publication had a total of 25 acronyms or abbreviations; I would be WAY over the allotted word-count without their assistance.

Acronyms also help us wrangle long, unruly, and sometimes overly-quirky gene names. As someone who studies Drosophila, I’m familiar with (and partial to) an ensemble of whimsical gene names. They are more often referred to by their more digestible abbreviations: Multiple edematous wings (mew), kon-tiki (kon), son of sevenless (sos), held out wings (how), to name a few. Interestingly, some researchers have recently changed the names of genes in order to avoid issues when reading data sets in Microsoft Excel. The most obvious conclusion is that they should have been using Drosophila for their research…

I’m also partial to charismatic acronyms that I come across outside of the Drosophila community, which I want to share:

  • McSELFIE: McGill Self-Efficacy of Learners for Inquiry Engagement
  • GANDALF: Genetic variation and Altered Leucocyte Function
  • BEAVER: Biodeasel Exhaust, Acute Vascular and Endothelial Responses
  • PENIS: Proton Enhanced Nuclear Induction Spectroscopy

*courtesy of Academia Obscura.*

Although acronym misuse bugs me, I acknowledge it’s a moot point; researchers usually need to convey their point in print in as few characters as possible.

Nevertheless, scientists around the world need to be able to effectively communicate across disciplines to solve some of the greatest problems we face such as climate change, pollution, food insecurity, and infectious disease (#covid19). If we’re really in favor of increased efficiency, we should focus on improving interdisciplinary collaborations by communicating better, not faster.

Here are some propositions for how to communicate better:

1) Maintain consistent acronym use in a given field. Example: if an acronym exists in your field, resist the urge to create a new one. I suspect this is often done for the sake of personal branding.

2) Define the acronym once in each part of a manuscript: abstract, intro, result, discussion AND figure legends. It will require dedicated space in that precious word count, sure.

3) During oral presentations, speak the full phrase at least twice before using the acronym.

4) During oral presentations, refrain from using acronyms that have the same number of syllables as the phrase (e.g. “SC” for “stem cell” both have two, and it bothers me when I hear this acronym. However, “HUCAPS” for “Harvard Ultra-fine Concentrated Ambient Particle System” makes much sense).

5) Hire someone to communicate science. In academia, we wear SO many hats (teacher, researcher, mentor, writer, speaker, graphic designer, etc). Be comfortable seeking professional help with the one that makes your science accessible to the rest of humanity.

“You can’t take over the world without a good acronym.”

-C.S. Woolley, UK author

First-time blood donation

July 24, 2020

Two weeks ago, I donated blood to the Red Cross for the first time. The decision was pretty abrupt TBH; I downloaded the app and made an appointment using my iPhone on a random Friday evening. Tim glanced up from his card game with our friend Matt to ask what I was doing, to which I replied, “signing up to give blood.”

I’d been feeling intrinsic pressure to donate because I was under the impression that I had precious O-negative “universal-donor” blood. I’m not sure where this personal health note originated, but it had been implanted in my mind and regarded as truth until I checked the Red Cross donor app after my donation:

Turns out it’s LITERALLY in my blood to be obnoxiously optimistic. Dang.

Giving blood, even amidst a pandemic, was straightforward. The whole process took an hour, and that’s primarily because I was chit-chatting a lot with the phlebotomist Elisa, and the nurse. They were great. One underrated reason to love these health care professionals (HCP) is that they compliment you in ways many don’t.

HCP: You have BEAUTIFUL veins!

Me: Awe, shucks!

Or, my personal favorite:

HCP: Your heart rate is very low- you must exercise pretty regularly!

Thanks, running.

Which reminds me – running has unfortunately taken a hit following the donation.

Losing one pint of blood for the donation, plus additional vials for the complementary COVID19 antibody test, has meant I have significantly less RBC’s circulating. I may have registered to give blood with serum hemoglobin levels of 14.5 g/dL (as a vegetarian😉!), but I have felt a bit “off” in the days following the donation. I’ve slept-in almost every day since, and my runs have been noticeably more challenging. It’s really fascinating though – I’m astonished by the impact that losing only 10% of my blood volume has had on my constitution and peppiness.

Perhaps I should have taken the admonitions to refrain from exercise a bit more seriously?  nah.

As a child of the 21st century – I obviously Googled my experience immediately. I learned that the sluggishness I feel on runs will pass; I expect to feel up to workouts again this week or next! I also expect to give blood in September, since RBC’s need 120 days to regenerate!

I’m looking forward to running some workouts again. I’m not training for anything per-se, but I think workouts are fun (…type II fun), and I like how strong and confident I can feel during them. I want to build up some strength and confidence as I enter my 4th year of graduate school in August & start the new academic year.

One last thing: The Red Cross website has a really awesome site with interactive graphics and fun facts about different blood types and info about donations. I pulled some of tid-bits for those of you who don’t want to venture off platform:

  • Blood types are determined by different sugar and protein molecules on your red blood cells (RBCs)
  • The “+” and “-” refer to the presence or absence of protein called the Rh factor.
  • The rarest blood type is type AB-
  • The most common blood type is O+
  • About 9% of the population has B+ blood (like me!), but the site can break it down further to compare how it relates to the whole U.S. population:
Photo credit: Red Cross
  • The universal RBC donor has type O – blood
  • The universal plasma donor has type AB blood
  • Red cells can be stored for up to 42 days.
  • For a short time, the Red Cross is testing all blood donations for the presence of COVID19 antibodies — this is “the antibody test.” Learn more.
    1. I am negative.
  • You can track what happens to your donated blood after the donation using the app or this website!
  • The implication that blood type A+ is prognostic for COVID19 has recently been dispelled by researchers at HMS in Boston. If you are curious about this you can venture off platform by clicking the hyperlinks:
    1. You can read the original article on pubmed.
    2. You can read the press-release on the study, too.

“Starve the mosquitoes; give blood.” – Anonymous

What matters most during COVID19

March 31, 2020

In the second grade, my classmates and I were once tasked with making lion or lamb masks during arts-and-crafts. The purpose of this was to demonstrate that March in New York state tended to “come in like a lion and go out like a lamb…or vice versa. We were supposed to predict the outcome. I wonder if part of the activity was for us to demonstrate precocious skill in meteorology or something. Where I’m from, seeing snow midway through April is not out of the question.

The lion-and-lamb simile was so profound, that it transcended to my endeavors in higher-education. In college, if I had a bad race or did poorly on a test in the beginning of March, surely, I had to do well at the end of March!

My logic is sound!

I still think about this. For 2020, I predicted that March would come in like a lion and go out like a lamb. I was banking on this because I scheduled a lot of important things at the end of March: An international conference (SOT) in California, my annual seminar to the department, and a committee meeting. I wanted them to all go well. March had to cooperate! But, it didn’t. Darn. March ended up being extremely hectic for me, and the rest of the world. It somehow entered and left like a lion. That’s not supposed to happen! Perhaps the predictive powers are limited to the weather, after all.

In March, we saw increasingly aggressive measures to limit the spread of the novel coronavirus infectious disease 2019, “COVID-19.”

The actual virus is called SARS-Cov2. SARS is an acronym for Severe Acute Respiratory Syndrome. Although some initial cases were linked to a fish market in Wuhan, China, its origin, intermediate hosts and more of transmission to humans are still largely unknown. Here is my favorite COVID19 info-video: https://ourworldindata.org/kurzgesagt-coronavirus-video

On March 6th, the University advised against travel to conferences. On March 9th: SOT was officially cancelled and by March 13th: all classes, committee meetings, and PhD thesis defenses were told to move to Zoom. On March 15th, Rochester had its first COVID-related death, which hastened the city’s efforts to limit the spread. On March 18th, research labs at the U of R were expected to already be “ramping-down” in preparation for a research lab shutdown. And on March 20th Tim and I began a 14-day quarantine in our apartment, that was advised for people in NY. The virus’ spread was exponential, and the response needed to match.

The response really peaked when I began receiving emails from places like SurveyMonkey or Gap about their response to COVID19 (*eye roll*).

I was decidedly not attending SOT prior to the official statement. Nonetheless, I was relieved that the flagship academic society of my discipline (SOT) was adhering to the precautionary principle. As toxicologists, the precautionary principle is canon. To not practice what we preach would be to undermine what really matters – protecting public health.

While going to conferences, performing experiments, and running marathons all matter for my personal aspirations including my career, protecting public health is #1. While trying to explain an extreme measure (the possibility of shelter-in-place) to a city in Illinois, the governor said, “It’s hard to have a livelihood if you don’t have a life.”

I agree with the governor in that I think what really matters is public health. That includes the health of all the people I care about as well as my own. It also includes hundreds of other humans who step on the line beside me before a marathon, or travel from far and wide to present their research at conferences. Whether we know each other personally doesn’t really matter, but the mutual respect we have for each other does. To care about public health is to respect the lives of other people that share the world with you.

I respect my fellow humans enough to run solo, to stay home, and to avoid expanding my network of contacts that could potentially spread the virus. This is difficult for me because it feels so limiting. When physical interaction is suddenly limited, the change is uncomfortable. The changes we’re experiencing now (the quarantine, isolations, and other precautions) demonstrate how interconnected we normally are. We rely on human interaction on massive scales for our work and play.

On the bright side, I think the changes also demonstrate how adaptive we can be. I’ve been impressed with solutions and creativity that my immediate networks have come up with during all of this.

At the University:

-Gatherings of 5 or more people no longer an option,so we transitioned to Zoom-based meetings

-University students can’t return to campus, so all classes moved online, classes have weekly check-ins for students too.

(shout out to all the responsible University leaders who decided to put health above wealth here… and shame on those who didn’t… *cough* Liberty *cough* *cough*)

-Committee Meetings and PhD thesis defenses became Zoom based

After my Zoom-seminar to my department, Presentation Pants and all💫

– Proctor exams via Zoom

-Took some of my transgenic fly stocks home to manage. I need to care for my lil fly babies ❤

Running community:

-My running buddies and I decided to run 6 feet apart or solo.

-Races that were cancelled morphed into to “virtual races”

-Races (like the Boston Marathon and some fun local races) postponed to the fall

*For those of you who had the Boston Marathon postponed – time to get HELLA fit for Fall!!

Community:

-Bars and restaurants close to dine-in, and pick up, but offer drive-through-based takeout

Still showing our love&support for Swiftwater!

– Group viewing of movies. GSS is hosting “virtual” movie nights once a week, as well as other activities.

@U of R students who read this – we have a free account on Kanopy (the video streaming service) through Miner Library.

Our apartment:

– Finally bought an Wi-fi router

– Set up our work-from-home stations

(i.e. a fuzzy blanket nest with books and coffee mugs within arms’ reach at all times)

-Baked 4 batches of granola, 2 loaves of bread

– Zoom/FaceTime hangouts with our friends

Yes, even Jakob, who lives across the street! #socialdistancing

-We created a third housemate, Cheryl, to blame dirty dishes and small messes on.

-Learned that “What do you Meme” can’t really ever be a two-person game.

– Played blockus a dozen times or so (Tim won every single time…)

I feel that I’ve learned how to be adaptable as both a graduate student researcher and a runner. The impossibility of planning for every potential outcome kind of demands that. Whether I’m managing an injury, planning when to run during a work-day, salvaging an experiment, or getting through this pandemic, learning to roll with the punches is essential.

I know many of you reading this have had your goal-races cancelled at a time when you’re feeling especially fit, and that sucks. It’s not fair, but it is what it is. The best we can all do is keep on keeping on. Reset, set new goals, and take comfort in the fact that if we do the right thing now, we can be back to running sooner. Onward & upward!

@Followers, thanks for reading this, and I hope you’re all staying safe and feeling healthy ❤