BorisVSchmid

For the scientific domain there is https://elicit.org/

You could sign up at https://www.clojuriststogether.org/ They do a pretty good job sponsoring both new-ish and critical projects within the clojure ecosystem

I can imagine that a dominant hypothesis could play a role in the predictions of future trajectories of climate on earth, but not so much for things like measuring past temperature / sea level rise.

To twist the analogy back to Alzheimer - all these scientists still agreed on the patient-level diagnosis of Alzheimer.

Depending on the complexity of the model it would take me at least a month for a single paper. What makes it fully unbelievable to me is the claim of detecting p-value hacking in many of these 130 papers while doing 3 papers every 2 days.

To make that claim for a single paper I would 1. have to be able to reproduce their p-value, and 2. spend enough time with the model to understand how/what assumptions were unfairly tweaked to get to that p-value.

Just running your own implementation of a model on your own dataset and getting an insignificant or different p-value is not enough. You might just have implemented the model wrongly.

Still using Light Table as my favorite light-weight IDE.

I hope things like https://clojuriststogether.org/ or possibly patreon will make clojure open source projects more sustainable for developers.

Depends on how you mean the question. ancient DNA analysis has settled that the first two plague pandemics were Yersinia pestis, so if your question was on what kind of bacterium caused the Black Death - that is Yersinia pestis.

If it is about the manifestation of the disease (the clinical symptoms), those we only know from historical descriptions and that is not something a model can change :-). So yeah, many infected people would still have had buboes. Buboes are also the expected result from plague acquired from fleas (whether they were human fleas or rat fleas).

What might be less known is that there is a pretty high chance (10-20%) that a person suffering from bubonic plague progresses to pneumonic plague. That basically is a death warrant for that person, but it also means that he/she might spread the disease further through air-droplets. If the conditions are right, you might get a pneumonic plague epidemic intermingled with a bubonic plague epidemic. Model-wise, that is one scenario we haven't looked into, but we have seen something like that play out in Madagascar last year.

Paper is online now :-).

I also put a popular science summary of the paper online here: https://medium.com/@boris.schmid/human-ectoparasites-and-the...

Potentially, but I am a bit sceptical. Plague reached a lot of new territory during the third pandemic (for example, australia and the americas), while still having a low mortality. One could check whether native populations to those continents were especially hard hit compared to people from European descent. I haven't heard anything like that.

Thanks! You might be able to postpone the panicking. Although I haven't looked into head lice (we specifically looked at body lice), this redditor had some links in that head lice apparently are less likely to carry diseases.

https://www.reddit.com/r/news/comments/7qopqf/black_death_sp...

There were indeed hundreds of outbreaks during those centuries. The outbreaks we selected were the ones for which we could find daily or weekly mortality records, as that gives you an epidemic curve that you can fit mathematical model to.

We didn't use all of the cities for which we had outbreaks, but selected nine that covered a large part of the time period, and a large geographic region. Here is the list:

Givry, France, 1348. Florence, Italy, 1400. Barcelona, Spain, 1490. London, England, 1563-1564. Eyam, England, 1666. Gdansk, Poland, 1709. Stockholm, Sweden, 1710-1711. Moscow, Russia, 1771. Malta, Malta, 1813.

Not a bad first impulse :-). It often pays in science to wait a few years/follow-up studies before fully accepting something. What is thought to be true in plague is especially fluid now with ancient DNA studies on human remains coming out regularly, each with its own narrative on how to explain the phylogenetic tree.

That said, there are some long-standing questions in plague research, one of which is why the first and second plague pandemic were that much more lethal than the third plague pandemic. Prior to the aDNA work, people speculated that medieval plague was a different pathogen altogether, but that hypothesis has been put to rest now. An alternative theory has been that plague could spread through human ectoparasites, and we found a novel way to test that theory. That resulted in this paper.

You are right that there have been people speculating about it for a long time, going back more than a hundred years. Some of the earliest reports are from the time of the Indian Plague Commission, and there have been some snippets of evidence since then.

One of the groups that is doing most of the research on body lice as vectors of plague is the group of Didier Raoult. Michelle Ziegler made a nice summary of that work here:

https://contagions.wordpress.com/2016/11/17/the-case-for-lou...

That indeed could be. We didn't test mixed models of transmission, but we took the first step here by testing all three models independently.

Xavier Didelot did some work on testing mixed models for two cities, 17th century Eyam and 19th century Cairo. He did have to further simplify the models though - there are some restrictions on how many floating parameters you can have while the models are trying to converge to the parameter set that results in the best match with the observations.

Epidemiological analysis of the Eyam plague outbreak of 1665–1666: http://rspb.royalsocietypublishing.org/content/283/1830/2016...

Model-based analysis of an outbreak of bubonic plague in Cairo in 1801: http://rsif.royalsocietypublishing.org/content/14/131/201701...

The 2017 madagascar one might actually have been a combination of rats and pneumonic plague. But yeah, it is good to pay attention to all possible routes of transmission and see where you can intervene.

There are some studies that looked at the ectoparasites found during plague outbreaks, but just finding an ectoparasite with plague-infected blood in it doesn't tell you much yet on the importance of the transmission route.

Piarroux R, et al. (2013) Plague epidemics and lice, Democratic Republic of the Congo. Emerg Infect Dis 19:505–506.

Laudisoit A, et al. (2007) Plague and the human flea, Tanzania. Emerg Infect Dis 13: 687–693.

Ratovonjato J, Rajerison M, Rahelinirina S, Boyer S (2014) Yersinia pestis in Pulex irritans fleas during plague outbreak, Madagascar. Emerg Infect Dis 20:1414–1415.

Last author here. The paper itself comes out this week on PNAS, but the press embargo is lifted already. When it comes out, you can find it here: http://www.pnas.org/cgi/doi/10.1073/pnas.1715640115

What we have done is compare the rise and fall of daily or weekly mortality levels during plague outbreaks against three models of plague transmission - two that are generally accepted (rat-borne plague and pneumonic plague), and one that has been speculated about for a long time (human ectoparasites like body lice and fleas). We allowed the models to achieve the best fit they could within biological parameter constraints, and see how well each of these models could mimic the observed mortality curve.

There is a bit more detail in this interview: https://news.nationalgeographic.com/2018/01/rats-plague-blac...

The code/models we used are available online for one of the outbreaks (Barcelona 1490) https://zenodo.org/record/1043924

A pre-review version of the paper is available as a poster here: http://www.mn.uio.no/cees/english/people/phd/katharrd/kd_yer... Note that we changed the lice model a bit since then, on recommendation of one of the reviewers.

I think right now for clojure, Anglican is the one furthest along. It took me some effort to get into it, with the documentation being a little bit all over the place, but I got it working for me.

Do remember that Anglican is a partial language in clojure, so you can't use all clojure functions (and I think none of the macros) within anglican's defqueries.

Looks nice!

I would suggest to enable import from ORCID. Seems to be the best initiative around to give a unique identifier to scientists.

http://orcid.org/0000-0003-0452-623X

Must be for a strange value of "free", when you see http://www.cdc.gov/measles/cases-outbreaks.html

  From January 2 to September 10, 2016, 54 people from 16 states (Alabama, 
  Arizona,California, Colorado, Connecticut, Florida, Georgia, Hawaii, Illinois, 
  Massachusetts, Minnesota, New York, North Carolina, Tennessee, Texas, and Utah) were 
  reported to have measles.

It looks like that with "free" they mean that there is no self-sustainable epidemic possible anymore in the Americas, given the degree of vaccine coverage. Nice.

Most infectious diseases in humans are known to have originated from wildlife, so eradicating all current diseases will still leave us with new diseases entering the human population. Current rate at which new diseases establish themselves in the human population is about ~1 per year, moreso under unstable climate [Greger, Woolhouse].

http://czbiohub.org/projects/infectious-disease/

Looks like Chan and Zuckerberg's initiative on infectious diseases is focused on a rapid response once a disease establishes itself in humans. There is certainly a lot to win there, but it is still acting after the fact, rather than prevention. Would have liked part of the effort to be focused on monitoring wildlife to understand which diseases are at risk of jumping over.

Greger, M.Crit. Rev. Microbiol. 33, 243–299 (2007). https://www.ncbi.nlm.nih.gov/pubmed/18033595

Woolhouse, M .E.J. Trends Microbiol. 10, s3–s7 (2002). https://www.ncbi.nlm.nih.gov/pubmed/12377561

The average length of intact Y. pestis DNA that researchers are capable of extracting from medieval teeth is something in the order of 55 basepairs.

To put that into perspective - Y. pestis' main chromosome is a little over 4 million basepairs. So it is only broken pieces of code that they can recover, not the whole, intact bacterium. No risk here.

http://www.nature.com/nature/journal/v478/n7370/full/nature1...

Samuel Pepys was another diary writer at that time. Pretty interesting read, and you can get a quick overview of how much he was occupied by the plague from the following site:

https://goldin.shinyapps.io/Search_Pepys/

(enter plague as keyword, click on the tab marked histogram, or browse the entries)

I am happy with every new ancient DNA sequence of plague that becomes available. Combined, they can be used to figure out the way the disease spread across Eurasia and persisted in Europe.

That said, I would like these news articles to actually link to the scientific paper, or if the paper is not published yet/still under review, at least mention that.

For those interested, below is the lecture of Krause on that topic, discussing the results in more detail.

http://eccmidlive.org/#resources/ancient-pathogen-genomics-w...

A big challenge is how to translate the genetic relatedness of plague strains spreading across Europe during successive pandemics to the actual location of its historic reservoirs. Location of the infected humans does not necessarily tell you much about the origin of that outbreak, especially with so much plague being moved by about ship.

There is a lively discussion about these papers on twitter, between a few of us spanning history, microbiology and computational biology, if you want to hear about these things earlier.

https://twitter.com/BorisVSchmid/status/726792491257724928

Authors can be wrong in interpreting the available (or lack of available) information. According to Ole Benedictow, there is little or no surviving records of plague in Sweden, but I would be curious to know why Larsson and Marklunds interpret that as that there was little plague there?

Ole Benedictow's chapter on Sweden (mainly discussing the lack of evidence, except for church donations) https://books.google.no/books?id=ZtjwPOB7aMkC&pg=PA170&dq=%2...

Stockholm in 1710-1711 had no problem in being rather brutally infected, with at its peak 1500 burials per week.

The Last plague in the Baltic Region from Frandsen: https://books.google.no/books?id=F3bNWrVRMb8C&pg=PA65&dq=%22...

It basically comes down to data availability, and some historian digging through the available archives.

For example, Givry is a tiny place somewhere in France, but for which by happenstance the parish registers at the time of the Black Death survived. They record the daily number of deaths, which end abruptly when presumably the priest died after recording ~620 deaths since the beginning of the epidemic in that town. The town's population is estimated at around 1170 people, based on the death rate in the earlier months, leading to a lower end estimate of 53% mortality (if the death of the priest was also the end of the epidemic).

    (from page 306 of http://www.persee.fr/doc/bec_0373-6237_1939_num_100_1_449196)

    [0 0 0 0 2 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 2 0 0 0 0 0 3 2 0 0] ;; jul. . approximate start of epidemic somewhere during jul.
    [0 4 4 1 0 2 1 7 5 3 1 1 4 5 3 3 4 1 5 2 2 4 3 6 2 2 2 6 3 8 4 6 10] ;; aug.
    [6 9 8 8 4 6 15 3 11 24 7 10 15 10 14 11 17 8 6 3 17 6 11 16 7 16 12 5 10 7] ;; sept
    [7 6 7 7 8 7 6 6 9 4 7 9 3 14 5 5 4 8 6 7 3 2 5 4 4 2 3 1 3 0 6] ;; oct
    [3 4 3 4 0 2 1 0 4 3 2 1 0 0 5 0 0 0 3] ;; nov, records end with the dead of the priest, worst of the epidemic is over.

The Black Death was followed by about 400 years of plague outbreaks in Europe. It also struck the Middle East, Africa, the Caucausus and Russia. It is bloody hard to make a total tally of how many people died by plague.

But the Black Death itself was special in that it was such a condensed and intense disaster. If you have the chance to read the eyewitness accounts, as collected by Rosemary Horrox it is quite impressive.

http://www.amazon.com/Black-Death-Manchester-Medieval-Source...

Glanced at the abstract, and the amazon reviews. The medieval medical guilds were well aware of the clinical symptoms of the Black Death, so I wonder how Mike Baillie connects the characteristic buboes of the plague with meteor strikes?

I enjoyed reading this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632865/

The paper highlights several aspects of plague that were different between the second and third plague pandemic, and which caused a scientific movement that searched for alternative explanations for the Black Death - that is, until the Yersinia pestis bacterium got sequenced from multiple Black Death mass graves.

That is a valid Frankfurt :-) see https://en.wikipedia.org/wiki/Frankfurt_(Oder)

Ran into a lot of examples like that when merging two existing georeferenced datasets of plague outbreaks in Europe. Had to do quite some manual checking, and made good use of the damerau-levenshtein distance between two strings to recognize alternative spellings.

end-result here: https://figshare.com/articles/plague_outbreaks_in_medieval_E...

"Published in History TodayVolume 55 Issue 3 March 2005"

The article is a bit old, and misses out on the large amount of genetic evidence since then sequenced and analyzed. Cui et al found that the closest living relatives to the Black Death stem from north-west China. That is about the only evidence we have on where the Black Death came from, and it does point to an origin in or near China.

http://www.pnas.org/content/110/2/577.figures-only