Author: Yaman

AIDS, COVID-19, Angels

By Yaman · · , · 1 Comment

Yesterday, December 1st, was World AIDS Day, an international day designated to further awareness about the AIDS pandemic and evaluate the world’s progress in ending it. Each year international agencies such as WHO (World Health Organization), UNAIDS (Joint United Nations Programme on HIV/AIDS) and other grassroots organizations dedicated to tackle HIV/AIDS also choose themes for the day, and UNAIDS theme for this year was “Global solidarity, Shared responsibility”. Needless to say, this theme is inspired by the experiences of the the current COVID-19 pandemic and this short video statement from the UNAIDS Executive Director Winnie Byanyima explains it quite well:

Winnie Byanyima’s World AIDS Day Statement

Pandemics and Epidemics thrive on and exacerbate the already existing inequalities as we have been seeing during COVID-19 and through our readings. While the nature of the diseases might differ, there is a huge overlap between which groups are most affected, mostly the ones that are are already marginalized. This year, COVID-19 made the HIV/AIDS pandemic even worse by disrupting care and medical supply networks and it affected the populations that were suffering from or highly vulnerable to HIV even more severely. However, the fight against these pandemics cannot be fought by some groups alone and hence a “shared responsibility” is needed.

The differences between the abilities of different countries based on the development of their public health infrastructure also requires “global solidarity” to eradicate the pandemic from the face of the world. Organizations such as UNAIDS recognize COVID-19 as the most immediate threat to furthering the progress against AIDS pandemic and are urging governments and companies from countries that have been able to develop vaccine candidates to waive their IP rights. Only this sort of a global collaboration will make sure that vaccines reach vulnerable populations in countries that do not have the capacity to develop them. Otherwise, the pandemic will create even more inequality across the globe. (A great opinion piece regarding this was published in the gazelle this week as well!)

On a different note, amfAR (American Foundation for AIDS Research) is another organization that has been funding research to end AIDS but is now focusing on COVID-19 as well. Recently, they organized a fundraising film on YouTube for these initiatives: “The Great Work Begins: Scenes from Angels in America”, where as the title suggests, 5 key scenes from the play were re-created. All the filming was done by the actors in isolation, and then put together using computer wizardry. The whole 50 minutes of the film are just amazing and I especially liked the effects and background score that complemented the acting. Even if you have not finished the play, as the title card suggests, you can “let the scenes was over you”. So I am not going to bore you further now and will leave you with the link for the film:

amfAR’s The Great Work Begins: Scenes from Angels in America

The plague for amphibians

By Yaman · · · 2 Comments

We have been tackling COVID-19 in our daily lives and pondering over other forms of contagions such as the plague, sins, memes, information, beliefs, syphilis, family values, memories, influenza, AIDS, and even fictional diseases like the Shen fever every Monday and Wednesday morning. However, our discussions have been concerned about how humans are affected by and react to these contagions. Through this short post, I want to introduce you to a different perspective on contagion through the example of chytridiomycosis, an infectious disease discovered around 20 years ago that is known to have caused the decline of hundreds of amphibian species, including 90 presumed extinctions (Scheele et al. 2019).

Kermit the Frog might be in danger (Via Giphy)

Chytridiomycosis is a fungal infection caused by the spread of Bd/Bsal (Batrachochytrium dendrobatidis/Batrachochytrium salamandrivorans) fungi through contact with spore-infected water or other infected hosts. The fungus replicates rapidly on the skin of the host and kills it off by blocking their breathing metabolism (most amphibians breathe through their skin). The contagious nature of the disease thus leads to mass die-offs in certain regions, and has been wreaking havoc on amphibians throughout the past half-century. Similar to COVID-19, Chytridiomycosis is also hard to detect without testing and thus in the absence of proper testing, the global trade network has also led to its spread across the continents. So while humans initially might not have been directly responsible for this plague on amphibians, the trade of animals without realizing its consequences has certainly exacerbated the problem.


Taxonomic distribution of chytridiomycosis-associated amphibian declines: Each bar represents one species, and color denotes the severity of its decline. Concentric circles indicate, from inner to outer, order (Caudata or Anura), family, and genus.  (Scheele et al. 2019)

Most prevention and detection efforts for Chytridiomycosis are currently being led by researchers (funding for which is also quite scarce, since the issue is quite low priority among governments) who test the amphibians for Bd/Bsal in suspected habitats. The results take 2-3 days to be processed in a lab and till then the tested individuals are kept isolated from their natural habitat in containers (quite similar to the practice of quarantine until COVID-19 test results come), which is quite undesirable (I think we all agree about that from our quarantine experiences). Finally, based on the results, the amphibians are released or treated for the disease using medicated baths and further measures are taken to prevent the spread of the disease from the area tested.

To aid the efforts to fight against this disease, the NYUAD iGEM team (which I am also a part of hehe!) has also been developing a diagnostic device that can be used in the field itself to give rapid and accurate results about the presence of Bd/Bsal. This will not only eliminate the need for isolating the animals for days, it will also encourage more testing, especially at trading ports, so that the disease can be prevented from spreading. Our progress this year has been slow due to restricted lab access, but the pandemic has also provided us with the opportunity to learn from some great (and still ongoing) rapid diagnostics research that was prompted by COVID-19. We are hopeful that we will be finishing the device soon and achieve our goals! I will leave you now with our 2-min project description video that illustrates most of what I have talked about quite well:

NYUAD iGEM Project Description Video

What’s in a name?

By Yaman · · , · 2 Comments

In Katherine Ann Porter’s short novel Pale Horse, Pale Rider, the protagonist Miranda Gay has a near-death experience with the 1918 influenza pandemic . However, “influenza” was not the only name which was used for this globally spread disease and the pattern of naming it across the world is actually quite interesting. The British science journalist Laura Spinney writes in her 2017 book Pale Rider: The Spanish Flu of 1918 and How It Changed the World:

….people followed the time-honoured rules of epidemic nomenclature and blamed the obvious other. In Senegal it was the Brazilian flu and in Brazil the German flu, while the Danes thought it ‘came from the south’. The Poles called it the Bolshevik disease, the Persians blamed the British, and the Japanese blamed their wrestlers: after it first broke out at a sumo tournament, they dubbed it ‘sumo flu’.


Spinney, Laura. (2017). Pale rider: the Spanish flu of 1918 and how it changed the world. Vintage. p. 36. 

As wartime censorship suppressed the reporting of the flu in allied countries, the news of its spread in Spain (which was neutral in WW1) went across and countries like America, France, and Britain were quick to assign the name and the blame- “Spanish flu”. Thus, as the disease arrived across nations, the practice of blaming an already existing common “national enemy” or a particular group was followed.

This also relates to what we read earlier in the Justin Stearns’ 2009 essay “New Directions in the Study of Religious Responses to the Black Death”. Stearns writes:

One irony deserves to be mentioned in this context, namely that where Jewish authors at times refer to the plagues God sent upon Pharaoh and the Egyptians as a sign of God’s ability to punish sinners, Muslim scholars at times cite a Prophetic tradition explaining that the origin of plague lies in a punishment that God sent down upon the Jews long ago, and Pope Clement VI noted in a mass the example of David’s sin resulting in the punishment of the people of Israel by plague (Second Samuel 24:15–19).


Stearns, Justin. (2009). New Directions in the Study of Religious Responses to the Black Death 1. History Compass, vol. 7(5), p. 1363-1375.

Religious groups also promptly assigned the blame of the plague on other groups, finding a common enemy and cause for their own group (reminds me of this meme). For example, with the current pandemic in India, this was done by blaming Muslims, an already persecuted minority, by pointing to a Muslim religious gathering as the root cause of the infection’s rampage in the country.

This practice of blaming gives a persona to the hitherto unfamiliar and strange disease and provides an unjustified but easy channel for venting out the anger and hate against the disease by putting it on the blamed group. To prevent such unjustified names (and to some extent the blames) from sticking around or even making it to official proceedings, the World Health Organization (WHO) has instated naming conventions that prevent the use of specific identifiers such as places, people or animals. The naming COVID-19, shorthand for COronaVIrus Disease – 2019, does follow these protocols. However, we are all also familiar with the American president calling COVID-19 the “Chinese Virus”. Hence, it is up to us and especially leaders in power, to be careful of the implication of the names we do use in our vocabulary.

P.S. On the lighter side of things, sometimes this name and blame game does not have to come down to a particular group as was the case when the 1918 influenza pandemic came to Spain:

So who were Spaniards to blame? A popular song provided the answer. The hit show in Madrid at the time the flu arrived was The Song of Forgetting, an operetta based on the legend of Don Juan. It contained a catchy tune called ‘The Soldier of Naples’, so when a catchy disease appeared in their midst, Madrileños quickly dubbed it the ‘Naples Soldier’.


Spinney, Laura. (2017). Pale rider: the Spanish flu of 1918 and how it changed the world. Vintage. p. 36. 

Is it only a numbers game?

By Yaman · · , · 1 Comment

Johnson’s talk at Google regarding his book The Ghost Map celebrates the mid-19th century physician John Snow and a local amateur Henry Whitehead’s effort in finding the reason for cholera outbreaks in the city of London. At the centerpiece of their efforts is the construction of a map — a map of all cholera-related deaths near a neighborhood water pump, bounded by the walking path around the neighborhood. Johnson tells us how this map spectacularly illustrated Snow’s theory that cholera was caused due to drinking contaminated water, going against the commonly accepted miasma theory of diseases being caused by bad smells, or the airborne particles that caused them, and not carriers such as water.

Snow and Whitehead’s Map of cholera deaths around Broad street water pump- each black bar marks a cholera death in the house and the area is bounded by walking path. Image via

However, in his paper titled “Incorporating Quantitative Reasoning in Common Core Courses: Mathematics for The Ghost Map,” describing quantitative reasoning approaches that could be included while reading or teaching The Ghost Map, the Beloit College Professor John R. Jungck urges Johnson’s readers to ask whether these quantitative tools such as the cholera map actually just spit out the truth as Johnson seems to suggest?

He reminds us of Florence Nightingale, who herself had pioneered in the practice of data analysis and visualization, and is credited to have invented the famous coxcombs to illustrate the mortality causes for British soldiers in the Crimean war and successfully advocated in the parliament for better nursing practices and sanitation. But as a contemporary of Snow, even after seeing the map, Nightingale did not believe in Snow’s theory of cholera being waterborne.

Florence Nightingale’s famous coxcomb charts. Image via

While Johnson blames Nightingale’s disbelief on factors such as ideology, social prejudice, and limited imagination, in essence pointing that she did not understand Snow’s data, Jungck urges us to ask whether this data and its visualizations might actually support multiple clashing interpretations? He argues that the process of finding the truth is not just as straightforward as its revelation using the data but that it involves argumentation, controversy, and reconciliation with multiple alternate interpretations of the same data, a lengthy but robust process.

Jungck’s argument reminds me of my own changing interpretations of the COVID-19 case numbers over time. While the numbers remain the same, I see 1000 daily cases very differently now than I did a month ago. This interpretation can change from person to person, while Nightingale might have found 1000 COVID-19 cases normal (the new normal I mean), maybe Snow might have thought them to be extremely high. And even beyond that, behind these numbers is the story of how they are even generated: How many tests were done that day? What kind of tests were they? Where in the country were they done? Can we actually trust these numbers?, questions that require even further query than just the daily case numbers. Thus, varying interpretations and seemingly endless questions that ask for even more data are sufficient to remind us that a data set and visualizations alone cannot completely represent the truth.

Finally, tying back to the mortality bills we read about in Defoe’s Journal of the Plague Year, at the start of the plague when the deaths are quite low, the narrator H.F. interprets those deaths as being caused by the spread of the infection rather than dismissing them as just normal variation. I want to leave you to think about how much of his interpretation was caused due to his anticipation of the coming of plague?