Archive for the ‘random thoughts’ Category

What can two-way communication between scientists and citizens enable?

September 24th, 2023

The Washington Post quoted NIH researcher Paul Hwang: “Amazing findings in medicine are sometimes based on one patient”.

The findings here are a breakthrough discovery in a disease called ME/CFS – commonly known as chronic fatigue syndrome or myalgic encephalomyelitis – which led to a recent PNAS paper. This is an amazing moment: Without biomarkers, it’s been a contested disease “you have to fight to get”.

What really strikes me, though, is the individual interactions that created a space for knowledge production: an email from one citizen (Amanda Twinam) to one scientist (Paul Hwang); “serendipitous correspondence” from another scientist (Brian Walitt) with access to “an entire population” (9 of the 14 tested for the PNAS paper were similar to Amanda). Reading the literature, writing well-timed correspondence, and “hearing about” synergistic work going on in another lab all seem to have contributed.

Mady Hornig, a researcher not involved in the project, told the reporter: “It’s not very common that we do all of these … steps, having doctors who are really persistent about what is happening with one individual and applying a scientific lens.”

But what if we did?


Dumit, Joseph (2006). Illnesses you have to fight to get: Facts as forces in uncertain, emergent illnesses. Social Science & Medicine, 62(3), 577–590. https://doi.org/10.1016/j.socscimed.2005.06.018

Wang, Ping-yuan, Ma, Jin, Kim, Young-Chae, Son, Annie Y., Syed, Abu Mohammad, Liu, Chengyu, Mori, Mateus P., Huffstutler, Rebecca D., Stolinski, JoEllyn L., Talagala, S. Lalith, Kang, Ju-Gyeong, Walitt, Brian T., Nath, Avindra, & Hwang, Paul M. (2023). WASF3 disrupts mitochondrial respiration and may mediate exercise intolerance in myalgic encephalomyelitis/chronic fatigue syndrome. Proceedings of the National Academy of Sciences, 120(34), e2302738120. https://doi.org/10.1073/pnas.2302738120

Vastag, Brian (2023, September 19). She wrote to a scientist about her fatigue. It inspired a breakthrough. Washington Post. https://www.washingtonpost.com/health/2023/09/17/fatigue-cfs-longcovid-mitochondria/ Temporarily open to read via this gift link.

Tags: , , , ,
Posted in information ecosystem, random thoughts, scholarly communication | Comments (0)

Avoiding long-haul air travel during the COVID-19 pandemic

October 28th, 2020

I would not recommend long-haul air travel at this time.

An epidemiological study of a 7.5 hour flight from the Middle East to Ireland concluded that 4 groups (13 people), traveling from 3 continents in four groups, who used separate airport lounges, were likely infected in flight. The flight had 17% occupancy (49 passengers/283 seats; 12 crew) and took place in summer 2020.
(Note: I am not an epidemiologist.)

The study (published open access):
Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

Irish news sites including RTE and the Irish Times also covered the paper.

Figure 2 from
Figure 2 from “A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020” https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

Caption in original “Passenger seating diagram on flight, Ireland, summer 2020 (n=49 passengers)”
“Numbers on the seats indicate the Flight Groups 1–4.”


The age of the 13 flight cases ranged from 1 to 65 years with a median age of 23 years. Twelve of 13 flight cases and almost three quarters (34/46) of the non-flight cases were symptomatic. After the flight, the earliest onset of symptoms occurred 2 days after arrival, and the latest case in the entire outbreak occurred 17 days after the flight. Of 12 symptomatic flight cases, symptoms reported included cough (n = 7), coryza (n = 7), fever (n = 6) and sore throat (n = 5), and six reported loss of taste or smell. No symptoms were reported for one flight case. A mask was worn during the flight by nine flight cases, not worn by one (a child), and unknown for three.

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624 (Notes to Figure 1 Caption)

“It is interesting that four of the flight cases were not seated next to any other positive case, had no contact in the transit lounge, wore face masks in-flight and would not be deemed close contacts under current guidance from the European Centre for Disease Prevention and Control (ECDC) [1].”

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

“The source case is not known. The first two cases in Group 1 became symptomatic within 48 h of the flight, and COVID-19 was confirmed in three, including an asymptomatic case from this Group in Region A within 5 days of the flight. Thirteen secondary cases and one tertiary case were later linked to these cases. Two cases from Flight Group 2 were notified separately in Region A with one subsequent secondary family case, followed by three further flight cases notified from Region B in two separate family units (Flight Groups 1 and 2). These eight cases had commenced their journey from the same continent and had some social contact before the flight. The close family member of a Group 2 case seated next to the case had tested positive abroad 3 weeks before, and negative after the flight. Flight Group 3 was a household group of which three cases were notified in Region C and one case in Region D. These cases had no social or airport lounge link with Groups 1 or 2 pre-flight and were not seated within two rows of them. Their journey origin was from a different continent. A further case (Flight Group 4) had started the journey from a third continent, had no social or lounge association with other cases and was eated in the same row as passengers from Group 1. Three household contacts and a visitor of Flight Group 4 became confirmed cases. One affected contact travelled to Region E, staying in shared accommodation with 34 others; 25 of these 34 became cases (attack rate 73%) notified in regions A, B, C, D, E and F, with two cases of quaternary spread.”

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

“In-flight transmission is a plausible exposure for cases in Group 1 and Group 2 given seating arrangements and onset dates. One case could hypothetically have acquired the virus as a close household contact of a previous positive case, with confirmed case onset date less than two incubation periods before the flight, and symptom onset in the flight case was 48 h after the flight. In-flight transmission was the only common exposure for four other cases (Flight Groups 3 and 4) with date of onset within four days of the flight in all but the possible tertiary case. This case from Group 3 developed symptoms nine days after the flight and so may have acquired the infection in-flight or possibly after the flight through transmission within the household.”

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

“Genomic sequencing for cases travelling from three different continents strongly supports the epidemiological transmission hypothesis of a point source for this outbreak. The ability of genomics to resolve transmission events may increase as the virus evolves and accumulates greater diversity [23].”

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

Authors note that a large percentage of the flight passengers were infected:

“We calculated high attack rates, ranging plausibly from 9.8 % to 17.8% despite low flight occupancy and lack of passenger proximity on-board.”

Murphy Nicola, Boland Máirín, Bambury Niamh, Fitzgerald Margaret, Comerford Liz, Dever Niamh, O’Sullivan Margaret B, Petty-Saphon Naomi, Kiernan Regina, Jensen Mette, O’Connor Lois. A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020. Euro Surveill. 2020;25(42):pii=2001624. https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624

Among the reasons for the uncertainty of this range is that “11 flight passengers could not be contacted and were consequently not tested.” (A twelfth passenger “declined testing”.) There is also some inherent uncertainty due to incubation period and possibility of “transmission within the household”, especially after the flight; authors note that “Exposure possibilities for flight cases include in-flight, during overnight transfer/pre-flight or unknown acquisition before the flight.”

Beyond the 13 people on the flight, cases spread to several social groups, across “six of the eight different health regions (Regions A–H) throughout the Republic of Ireland”. Flight groups 1 and 2 started their travel from one continent; Flight group 3 from another; Flight group 4 from a third continent.

Figure 3 from
Figure 3 from “A large national outbreak of COVID-19 linked to air travel, Ireland, summer 2020” https://doi.org/10.2807/1560-7917.ES.2020.25.42.2001624
caption in original: “Diagram of chains of transmission, flight-related COVID-19 cases, Ireland, summer 2020 (n=59)”

Tags: , , , , , , , , ,
Posted in random thoughts | Comments (0)

#ShutDownSTEM #strike4blacklives #ShutDownAcademia

June 10th, 2020

I greatly appreciated receiving messages from senior people about their participation in the June 10th #ShutDownSTEM #strike4blacklives #ShutDownAcademia.

In that spirit, I am sharing my email bounce message for tomorrow, and the message I sent to my research lab.


Email bounce:

I am not available by email today: 
This June 10th is a day of action about understanding and addressing racism, and its impact on the academy, and on STEM. 
-Jodi


Email to my research lab

Wednesday is a day of action about understanding and addressing racism, and its impact on the academy, and on STEM.

I strongly encourage you to use tomorrow for this purpose.

Specifically, I invite you to think about what undoing racism – moving towards antiracism – means, and what you can do. One single day, by itself, will not cure racism; but identifying what we can do on an ongoing basis, and taking those actions day after day – that can and will have an impact.

And, if racism is vivid in your daily life, make #ShutDownSTEM a day of rest.

If tomorrow doesn’t suit, I encourage you to reserve a day over the course of the next week, to replace your everyday duties.

What does taking this time actually mean? It means scheduling a dedicated block of time to learn more; rescheduling meetings; shutting down your email; reading books and articles and watching videos; and taking time to reflect on recent events and the stress that they cause every single person in our community.

What am I doing personally? I’ve cancelled meetings tomorrow, and set an email bounce. I will spend part of the day to think more seriously about what real antiracist action looks like from my position, as a white female academic.

This week I will also be using time to re-read White Fragility, to finish Dreamland Burning (a YA novel about the 1921 Tulsa race riot), and to investigate how to bring bystander training to the iSchool. I will also be thinking about the relationship of racism to other forms of oppression – classism, sexism, homophobia, transphobia, xenophobia.

If you are looking for readings of your own, I can point to a list curated by an Anti-Racism Task Force:
https://idea.illinois.edu/education

For basic information, #ShutDownSTEM #strike4blacklives #ShutDownAcademia website:
https://www.shutdownstem.com
Physicists’ Particles for Justice:
https://www.particlesforjustice.org

-Jodi

Tags: , , ,
Posted in random thoughts | Comments (0)

QOTD: Doing more requires thinking less

December 1st, 2018

by the aid of symbolism, we can make transitions in reasoning almost mechanically by the eye which would otherwise call into play the higher faculties of the brain.

…Civilization advances by extending the number of important operations that we can perform without thinking about them. Operations of thought are like cavalry charges in a battle — they are strictly limited in number, they require fresh horses, and must only be made at decisive moments.

One very important property for symbolism to possess is that it should be concise, so as to be visible at one glance of the eye and be rapidly written.

– Whitehead, A.N. (1911). An introduction to mathematics, Chapter 5, “The Symbolism of Mathematics” (page 61 in this version)
HT to Santiago Nuñez-Corrales (Illinois page for Santiago Nuñez-Corrales, LinkedIn for Santiago Núñez-Corrales) who used part of this quote in a Conceptual Foundations Group talk, Nov 29.

From my point of view, this is why memorizing multiplication tables is not now irrelevant; why new words for concepts are important; and underlies a lot of scientific advancement.

Tags: , , ,
Posted in information ecosystem, random thoughts | Comments (0)

Evidence Informatics

January 20th, 2015

I sent off my revised abstract to ECA Lisbon 2015, the European Conference on Argumentation. Evidence informatics, in 75 words:

Reasoning and decision-making are common throughout human activity. Increasingly, human reasoning is mediated by information technology, either to support collective action at a distance, or to support individual decision-making and sense-making.

We will describe the nascent field of “evidence informatics”, which considers how to structure reasoning and evidence. Comparing and contrasting evidence support tools in different disciplines will help determine reusable underlying principles, shared between fields such as legal informatics, evidence-based policy, and cognitive ergonomics.

Tags: , , , , , ,
Posted in argumentative discussions, information ecosystem, random thoughts, scholarly communication | Comments (0)

QOTD – physical computing

October 13th, 2013

Personal computers have evolved in an office environment in which you sit on your butt, moving only your fingers, entering and receiving information censored by your conscious mind. That is not your whole life, and probably not even the best part. We need to think about computers that sense more of your body, serve you in more places, and convey the physical expression in addition to information.

Dan O’Sullivan and Tom Igoe, Physical Computing: Sensing and Controlling the Physical World with Computers

via Jon Froehlich at DSST 2013 in his talk about the UMd HCIL hackerspace.

Slides for Jon’s talk, “If You Build It, They Will Come: Reflecting on the Successes (and Failures) of Building a Collaborative Workspace to Support Creativity, Experimentation, and Making”, are available via his talks page, as a huge PPTX here). Highly recommended if you’re interested in makerspaces/hackerspaces in academic institutions.

Tags: , , , ,
Posted in random thoughts | Comments (0)

Temperature conversions for Americans living in mild climates

August 12th, 2012

Converting temperatures in your head is a good trick for Americans living abroad.

So here’s the trick. You memorise the following correspondences:

0 °C = 32 °F
10 °C = 50 °F
20 °C = 68 °F
30 °C = 86 °F
Then, to convert any temperature that is near these, approximate 1 °C = 2 °F. This will allow you to convert almost any naturally occurring outdoor temperature in the UK in either direction to within 1° accuracy.

Let’s try it. As I write the current temperature in Edinburgh is 14 °C. This is 10 °C plus 4° extra. From memory convert the 10 °C to 50 °F. Then convert 4 °C extra to 8 °F extra and add it back on. This gives you 14°C = 58°F. This is not exact, but close enough that you know to wear a jumper. The exact formula is

14 * 9 / 5 + 32 = 57 F
Good luck doing that in your head.

from Charles Sutton’s Converting Fahrenheit into Celsius.

A jumper, for Americans, is “A pullover sweater.”

Tags: , , , ,
Posted in random thoughts | Comments (1)

“Excuse my typo” signature lines, a collection

July 16th, 2012
For about a year I’ve been collecting email signature lines. After receiving an email purporting to be “Sent from my rotary phone” I thought it was time to share.
  • Touched, not typed
  • Sent from my $DEVICENAME
  • Consider any misspellings my gift to you
  • Typed with thumbs
  • Sent with mobile solution
  • Sent from a mobile operating system. Which one isn’t of any importance to you, the receiver. However, if you feel that knowing this detail would affect positively your reading of this email you can, of course, ask me.
  • Sent from my smartphone platform of choice….hint not a fruit
  • I prefer robots to fruit.
  • Fruits are for fruitcakes, Robots are for emailing.
  • bots best for smart phones
  • Smart fruit is an oxymoron
  • Sent via a really tiny keyboard
  • Sent from a mobile device. Erroneous words are a feature, not a typo.
  • Sent from mobile; pls excuse typos
  • $DEVICENAME = specific mobile operating system of choice
  • Sent from my stationary operating system of choice.
  • Erroneous words are a feature, not a typo.
  • (Short, curt and ill-formed message sent from my portable telephone machine.)
  • > Sent wirelessly from my BlackBerry device on the Bell network.
    > Envoyé sans fil par mon terminal mobile BlackBerry sur le réseau de Bell.
  • *Sent from a mobile phone – please excuse the brevity of the message
  • via small communication device/pardon random autocorrects and fat finger typos.
  • Warning: I either dictated this to my device, or I typed it clumsily. Expect typos and weirdness.
  • Sent from a mobile device. Excuse brevity and typos.
  • Typed by thumbs and sent by my Verizon Wireless gadget
  • Sent from a mobile device. Please excuse brevity and tpyos.
  • Sent from my Verizon Wireless 4G LTE smartphone
  • Sent from tiny touchscreen gizmo, excuse any auto correct nonsense that slips in…
  • Sent from my rotary phone
  • Sent with my thumbs (Thanks to Andy Powell.)
  • sent from my shoe (Thanks to Larry Hynes.)
  • Sent while walking into stuff(Thanks to Ryan Sarver (via Laura Dragan and Tim O’Reilly; used by David Cohen)


Previously discussed on Twitter (thanks to David Crowley and Becky Yoose for spreading my question). Apparently desktop users want forgiveness too.

Tags: , , ,
Posted in random thoughts | Comments (8)

Google Docs ‘research’ tab

May 19th, 2012

Increasingly, I’m using Google Docs with collaborators. Yesterday, one of them pointed out the new “Research” search tab within Google Docs. (Tools->Research). I’m a bit surprised that your searches don’t show up on your collaborators’ screen. I’m particularly surprised that sharing searches doesn’t seem possible.

Google Docs' new 'Research' tab promotes search within Google Docs.

Apparently, it is pretty new. More at the Google Docs blog.

Tags: ,
Posted in information ecosystem, random thoughts, scholarly communication | Comments (0)

Attached?

May 7th, 2012

I noticed that GMail is warning about missing attachments and heard that Thunderbird does this, too, from Arber Borix, who also responded to a request for a screenshot (below). Thanks, Arber!

Thunderbird: Found an attachment keyword: attached. Add Attachment... Remind Me Later

Tags: , , ,
Posted in random thoughts | Comments (2)