I found this great post on drug shortages that appeared in BMJ today. Among all of the other great gems in it, was this incredibly interesting article on the creation of a mechanical bloodletting device. Jean-Baptiste Sarlandière, a French anatomist and inventor, created the “mechanical leech”, a device intended to extract a controlled amount of blood from the body. Sarlandiere intended the device to replace leeches, which were subject to increasing demand, were becoming expensive, were difficult to cultivate, and were subject to shortages in the Netherlands, who was a large producer of leeches at the time.
A paper was written on the device back in 2009, and within there is a dataset of leech imports and exports to France, which includes data on the monetary value of leeches and public consumption. Of course, I couldn’t resist pulling this data out and doing something with it (despite having better things to do.)
Here is the data, pulled from yet another paper (Alexandre E Baudrimont, Adolphe J Blanqui, et al., Dictionnaire de l’industrie manufacturie`re, commerciale et agricole, Paris, J-B Baillière, 1833–1841, pp. 25–30.):
|Year||Number of leeches imported||Value in Francs||National consumption||Exports||Import export ratio||Value per leech|
Of course, I am fascinated with this. The number of leeches exported from France rose during this period as did the market price of each leech. Though the entire industry would eventually collapse because other medical advances of the nineteenth century would supercede it, it is clear that increased demand and expense led to innovation to create devices to replace it. I don’t know whether the “mechanical leech” led to the development of other medical devices, but would like to think that even batshit ideas like how swamp worms draw out blood to cure any and all medical conditions would lead to the creation of methods which do improve health.
I started this blog way back in 2007, when I was a Masters student at the University of Michigan. At the time, it felt like a good way to get writing out there, and communicate ideas in a public forum. When I was at my peak on this blog (and my life, it seems) I was writing daily, sometimes posting the data analyses equivalent to many (low quality) published scientific papers, writing travel logs, doing interviews, broadcasting psychological traumas, posting photos… it was a good time.
At some point, I lost focus, got busy with other things, got on the wrong track, the right track, it really isn’t clear to me what happened, but I posted less and wrote less. The result was that my writing suffered, because the daily posts provided a great opportunity to keep my writing in shape, and explore interesting scientific topics in depth without worrying about the bureaucratic demands of peer review or research collaborators. While peer review and research collaborations are important, every science needs a forum with which to explore ideas.
Now, though, as I move back into my academic career, I am wondering…. is blogging worth it anymore? I just read Rachel Strohm’s final post . Rachel started blogging about the same time I did, and has since moved on to a fruitful career in development and academia and now lives in Kenya. She has recently stopped blogging, noting that “The development blogging ecosystem is basically dead. ” (I do wonder if her move to Kenya might have killed her motivation for blogging, the same way it killed mine.) I have also noticed that the authors of several blogs I used to read have also moved on.
Strohm offers that direct newsletter updates and Twitter might be a better platform for dissemination blog-like information for people. I think Twitter is a pretty terrible platform for anything at all outside of haranguing right wingers or sending cat videos, so I am not sure that it would do what blogging would have done for me. While I do not have a large Twitter presence, it seems to be a major time suck, with little reward and multiple costs (like blood pressure.)
Newsletters are interesting. Even as a musician, I find that directly engaging people who might be interested in my music is far better than any of the social media platforms, which do their best to make sure that no one ever sees what you do, unless you have a thousand dollar PR budget.
I liked the blogging format. I still do. I think it could still work, but wonder…. do people even read long form writing anymore? Does it have any impact? Is blogging going the way journalism is? What is a good platform anymore? Does writing mean anything at all anymore?
Currently, I am a part of a project looking at climate change impacts on the distribution of tree and grass pollens in the US and associations with allergy and asthma related emergency room visits
As part of that, we are collecting baseline data on symptomatic profiles of patients who are sensitive to tree and grass pollens and are currently undergoing immunotherapy in local clinics.
Our survey is two fold, the first a baseline survey of types of demographics, types of allergies, seasonal sensitivities, general symptoms and lifestyle impacts, the second a three week survey of sleep quality and allergy and asthma related events.
We hope to gather data to see how the ragweed season might impact general health and well being using a coarse raster of predicted pollen distribution.
The survey is being conducted at the University of Michigan Allergy Specialty Clinic and Food Allergy Clinic at Domino’s Farms and will include approximately 50 people.
At least that’s what we hope happens. Yesterday, I had the opportunity to join the Detroit Communities Reducing Energy and Water (use) project, focusing on Parkside, a subsidized housing community in Detroit, MI.
The project aims to help residents make changes to the electrical and plumbing infrastructure of their homes to reduce the energy costs. Residents in poor communities often live in housing that has old, inefficient and sometimes faulty electrical wiring, kitchen appliances and aging or damaged pipes, showers and toilets.
The University of Michigan School of Public Health has a community based participatory research project with the residents of Parkside, the Friends of Parkside, a local advocacy group.
We administered a survey on energy, housing conditions and health to about twenty residents who came to the event. Following the consumption of copious amounts of pizza, the goals of the study were explained to everyone in a group meeting and consent was obtained.
They then moved to another room and took the survey. Many of the residents were elderly, mostly women. All had interesting stories to tell about broken air conditioners, unresponsive maintenance crews, family, friends, kids…. everything you find in these kinds of surveys.
After they were done, they all got some ca$h and were provided with a temperature monitor so that we can better understand what they are experiencing in their homes during these hot summer months. We will then conduct a follow up survey to assess the impact of a home based educational program on energy use and health.
It had been a long time since I was involved in community and I was grateful to be a part of. Some people don’t like this kind of work, I really don’t understand what’s not to like about hanging out with survey respondents who feel invested in the project and their communities.
New chapter from myself in a Springer volume: “Access to Health Care in Sub-Saharan Africa: Challenges in a Changing Health Landscape in a Context of Development”
I wrote a chapter for “Health in Ecological Perspectives in the Anthropocene” edited by Watanabe Toru and Watanabe Chiho. I have no idea if they are related. Either way, my chapter “Access to Health Care in Sub-Saharan Africa: Challenges in a Changing Health Landscape in a Context of Development” occupies pages 95-106 in the volume.
Check it out, you can buy the book through Amazon for a cool $109, or just my chapter through the Springer site for $29 or you can simply write me and I’ll give you a synopsis.
Here’s the abstract for the book:
This book focuses on the emerging health issues due to climate change, particularly emphasizing the situation in developing countries. Thanks to recent development in the areas of remote sensing, GIS technology, and downscale modeling of climate, it has now become possible to depict and predict the relationship between environmental factors and health-related event data with a meaningful spatial and temporal scale. The chapters address new aspects of environment-health relationship relevant to this smaller scale analyses, including how considering people’s mobility changes the exposure profile to certain environmental factors, how considering behavioral characteristics is important in predicting diarrhea risks after urban flood, and how small-scale land use patterns will affect the risk of infection by certain parasites, and subtle topography of the land profile. Through the combination of reviews and case studies, the reader would be able to learn how the issues of health and climate/social changes can be addressed using available technology and datasets.
The post-2015 UN agenda has just put forward, and tremendous efforts have been started to develop and establish appropriate indicators to achieve the SDG goals. This book will also serve as a useful guide for creating such an indicator associated with health and planning, in line with the Ecohealth concept, the major tone of this book. With the increasing and pressing needs for adaptation to climate change, as well as societal change, this would be a very timely publication in this trans-disciplinary field.
2018 was a fantastic year for music in just about every genre imaginable. I have tried to boil down my favorites, but I will most assuredly miss either some I might have forgotten or some great records I have yet to hear.
In any case, here we go. The list is in no particular order.
- Seun Kuti and Egypt 80 – “Black Times” – What a monster this record is. While the record promo makes a huge deal out of Carlos Santana’s cameo on the title track, he could just as easily be any other guy with a guitar playing on the most aggressively dance-able record in years. I am normally not a fan of afrobeat, but while this record is afrobeat-esque due in no small part to the presence of Fela Kuti royalty (Fela Kutis band), Seun imbues a driving power that this music always deserved. Standouts: Bad Man Lighter, Kuku Kee Me.https://www.youtube.com/watch?v=AGtxf07vE2U
- Yob – “Our Raw Heart” – And raw this is indeed. I barely got out of the crushing first track, which I listened to on repeat for a couple of days. The rest of the record is as good, punishing soundscapes of heavy sludge, with not an ounce of cheese. Yob has long been a favorite of mine since 2005’s “the Unreal Never Lived” and the band continues to be a mind altering exploration of sound.
- Ammar 808 – “Maghreb United” – Someone, somewhere made the claim that Tunisian born and European based Sofyann Ben Youssef was a space alien come to earth in the search of the lowest bass imaginable. I can’t really disagree. Youssef takes traditional Tunisian tunes and merges them with modern(ish) electronics seamlessly. The songs aren’t simply academic explorations but as fresh, powerful and as exciting as one would expect the originals to be had not the cruel poison of cultural preservation put them in a stale corner. Really a fantastic record. I loved his other band Bargou 08. Can’t wait to hear more from him.
- Ekuka – s/t – Holy jesus is this a good record. I can’t get enough of it really. Ekuka Morris Sirikiti is a presumably well known mbira player from Uganda, apparently so well known that people would record his performances off the radio and listen to them on repeat. It is unknown whether Ekuka actually put out his own record, but this compilation of second hand recordings is probably more than sufficient. The bent sounds of the mbira, with all it’s spider web undertones and warped resonance, along with his bizarre foot contraption for the beat, make this sound like some kind of brilliant darkwave as filtered through the shores of Lake Victoria. I have yet to convert anyone to the cult of Ekuka, but if you are willing, I am here to convert you. Fantastic.
- Mehr Ali and Sher Ali – “Qawwali, the essence of desire” – Do you need a reason to live? Then listen to side A of this record on repeat and hear the sounds of the entire human experience, from joy, to sadness, to longing to savoring what it is to be alive.
- Deafheaven – “Ordinary Corrupt Human Love” – I like sound. I like sound a lot. I like a lot of sound. And Deafheaven do not disappoint me. While some may disregard Deafheaven as testosterone fueled dudes in tight black pants, I think they miss the point. Deafheaven are black metalish, yet subdued and atmospheric, much like another favorite of mine Ulver.
- Sarah Davachi – “Gave in Rest” – I really liked the ambient weirdness of “All My Circles Run” so I was incredibly excited to see that Davachi had a new record out, just about the time I heard that one. Collages of acoustic and orchestral sounds reaching out to touch the sliver of light coming over the horizon on a morning in January in Michigan, just past the solstice…. that’s what I think this sounds like and I love it.
- Prince – “Piano and a Microphone 1983” – Yeah, so this isn’t from 2018 and had been rolling around on the bootleg circuit for quite sometime, but I am a Prince latecomer. While I always thought he was interesting, I never really got his genius until the man died, unfortunately. The first track on this, with the mighty, mighty Prince on the piano and a mic might actually bring tears to the eyes. It is just that good.
- V/A – Music of Northern Laos – This is part of a two part series, one featuring music from Northern Laos, and the other music from the South. Without at all being dismissive of the Southern record, the Southern record wins. Haunting female chants and slow dance swing horns, this is a great collection of sounds to to send you into a haunting ethereal space that you haven’t been to before.
- John Coltrane – “Both Directions at Once” – Not much needs to be said here.
I have nothing to say, I just want to see if this works
I found this post and wanted to see if it actually works (sometimes the code included in blog posts does not…actually, this code in this one did not. I had to make some modifications to get this to work.).
Apprently, I can include images, so I’ll include the most popular image on my site:
I can include R code
Which is great, because I do a lot of R work
So here’s some R code. You can see that it is formatted properly:
summary(mtcars) plot(mtcars$mpg, mtcars$cyl, main="myplot", xlab="mpg", ylab="cyl")
2. I can even include videos (I think), like this horrifying clip from Slithis Survival Kit:
Well, two packages, at least. Having not posted in well… forever… this is a decent move back into the world of blogging (which is far harder in 2018 than it was in, say, 2009.)
I have been working on Shiny based mapping apps recently and found the Zip Radius Package potentially convenient. I even made a map of zip codes and population within 100 miles of 48104.
The fieldRS package provides a convenient way of classifying and mapping remote sensing data, which will be extremly handy when doing the snake project, for example. An open question was how to access localized risk based on topography and landuse. I had no convenient way of assessing this at the time.
While other blog posts will do a much better job of explaining the Data Explorer package in R, it still seemed useful to mention it here.
A huge hurdle to data analysis is data cleaning, and to effectively develop a strategy to efficiently prepare data for analysis, a basic snapshot of the data is helpful.
Enter the Data Explorer package, a set of tools that can provide minimal descriptive information for not much effort at all. With a single command, you can take a raw dataset, and produce a useful report that you can use to start working on your plan of data cleaning attack.
I downloaded a portion of the Social Indicators Survey from Columbia University, and picked a small subset of variables.
Using this small set of code, I produced the report below.
sis_sm <- as.data.frame(with(sis, cbind(sex, race, educ_r, r_age, hispanic, pearn,
Data Profiling Report
The data is 34.8 Kb in size. There are 453 rows and 12 columns (features). Of all 12 columns, 9 are discrete, 3 are continuous, and 0 are all missing. There are 1,245 missing values out of 5,436 data points.
Data Structure (Text)
## 'data.frame': 453 obs. of 12 variables: ## $ sex : Factor w/ 2 levels "1","2": 2 1 2 1 2 2 1 2 2 1 ... ## $ race : Factor w/ 4 levels "1","2","3","4": 3 1 1 2 3 3 3 4 1 4 ... ## $ educ_r : Factor w/ 4 levels "1","2","3","4": 4 4 2 2 2 1 1 4 4 2 ... ## $ r_age : num 40 28 22 24 31 42 36 63 69 24 ... ## $ hispanic: Factor w/ 2 levels "0","1": 2 1 1 1 2 2 2 1 1 1 ... ## $ pearn : num 14400 14400 12000 15000 8000 9600 2400 9600 NA NA ... ## $ assets : num 5000 50000 4000 NA NA 6000 NA 1250 100000 NA ... ## $ poor : Factor w/ 2 levels "0","1": 1 1 1 2 2 2 2 2 2 2 ... ## $ read : Factor w/ 4 levels "1","2","3","4": NA NA NA NA NA NA NA NA NA NA ... ## $ homework: Factor w/ 4 levels "1","2","3","4": NA NA NA NA 4 1 1 NA NA NA ... ## $ black : Factor w/ 2 levels "0","1": 1 1 1 2 1 1 1 1 1 1 ... ## $ police : Factor w/ 2 levels "0","1": 2 2 1 1 2 2 1 NA 2 2 ...
Data Structure (Network Graph)
The following graph shows the distribution of missing values.
Continuous Features (Histogram)
Discrete Features (Bar Chart)