Read Scientists Call for Academic Shutdown in Support of Black Lives (Gizmodo)
White supremacy is baked into science and academia, from racist language in textbooks to a culture that excludes Black scientists from innovating and advancing at the same pace as their colleagues. But rather than more milquetoast statements and diversity initiatives, researchers want action. Organizers are asking the scientific community to participate in a work stoppage on Wednesday, June 10 to bring attention to racism in the world of research.

A Short Essay on the Relationship of STEM and Racist Ideas

I’ve seen many tweets today with the hashtag #shutdownSTEM. Some of them included some people asking why such a thing would be necessary. What does STEM (science, technology, engineering, and mathematics) have to do with racism they ask? 

I find myself seeing some immediate and excellent historical examples in Dr. Ibram X. Kendi‘s book Stamped from the Beginning. In chapter nine of the book he discusses the variety and flavors of racism espoused by Thomas Jefferson in his book Notes on the State of Virginia (1785), which would become the most  consumed American nonfiction book until well into the mid-nineteenth century.

Shortly afterward Samuel Stanhope Smith countered portions of Jefferson’s racist ideas in the 1787 annual oration to the august American Philosophical Society. This annual lecture was already one of the most heralded scholarly lectures in America and was attended by the wealthy and elite leaders and thinkers in the country. The lecture would be published as the influential Essay on the Causes of Variety of Complexion and Figure in the Human Species

While Smith used the lecture to attack the abhorrent racist idea of polygenesis, he did espouse a wide array of other racist tropes including assimilationist climate theory. Dr. Kendi specifically notes that he may have picked up this idea from James Bowdoin’s opening oration of the newly established American Academy of Arts and Sciences in Boston on May 4, 1780.
To quote Dr. Kendi:

Samuel Stanhope Smith joined those preeminent intellectuals in Boston’s American Academy of Arts and Sciences and Philadelphia’s American Philosophical Society in attacking polygenesists, in reviving climate theory in America. His scholarly defense of scripture was quickly printed in Philadelphia, in London, and in Lord Kames’s back-yard, Edinburgh. By the time he sat down in Princeton’s presidential chair in 1795, he had amassed an international scholarly reputation.

So in just a few pages Kendi lays out some serious evidence of the direct spread of a wide variety of racist ideas by not only by the academic elite, but the leaders of multiple influential universities and scientific and philosophical institutions in America. The reverberating echos of these wrongs are still haunting us today. They still need to be addressed and righted. We need to use our moral alembic and distill these racist ideas out of science in America.

Lest one wonder about the influence of Samuel Stanhope Smith’s essay, I’ll note that Noah Webster cited Smith directly in Webster’s 1828 Dictionary in the definition of philosophy. The citation was from  Smith’s second edition of his Essay on the Causes of Variety of Complexion and Figure in the Human Species (1810). The quote as given: “True religion, and true philosophy must ultimately arrive at the same principle.”

We’re obviously still seeking both true religion and true philosophy.

While you’re thinking about #shutdownSTEM on June 10th and long thereafter, I recommend you spend some time sitting with the ideas that have been handed down to us and question them closely, for this is what science and philosophy are all about. If you find you can’t do that hard work–and it is hard, then perhaps read a bit of Dr. Kendi’s excellent and ardent text Stamped from the Beginning.

Watched Learn Morse Code from a Memory Champ (in 15 minutes) by Nelson Delis from YouTube
This is a video I've been wanting to do for a while (in part because I've wanted to learn Morse Code myself, for years!) and I've also had many requests for it.
The first method is also useful for letter frequencies (or playing something like Wheel of Fortune) while the second is actually useful for the sound memory needed to practice Morse code.
Bookmarked Application of information theory in systems biology by Shinsuke Uda (SpringerLink)
Over recent years, new light has been shed on aspects of information processing in cells. The quantification of information, as described by Shannon’s information theory, is a basic and powerful tool that can be applied to various fields, such as communication, statistics, and computer science, as well as to information processing within cells. It has also been used to infer the network structure of molecular species. However, the difficulty of obtaining sufficient sample sizes and the computational burden associated with the high-dimensional data often encountered in biology can result in bottlenecks in the application of information theory to systems biology. This article provides an overview of the application of information theory to systems biology, discussing the associated bottlenecks and reviewing recent work.
Bookmarked Nonadditive Entropies Yield Probability Distributions with Biases not Warranted by the Data by Ken Dill (
Different quantities that go by the name of entropy are used in variational principles to infer probability distributions from limited data. Shore and Johnson showed that maximizing the Boltzmann-Gibbs form of the entropy ensures that probability distributions inferred satisfy the multiplication rule of probability for independent events in the absence of data coupling such events. Other types of entropies that violate the Shore and Johnson axioms, including nonadditive entropies such as the Tsallis entropy, violate this basic consistency requirement. Here we use the axiomatic framework of Shore and Johnson to show how such nonadditive entropy functions generate biases in probability distributions that are not warranted by the underlying data.
Read a tweet (Twitter)
Bookmarked Genomic epidemiology of novel coronavirus (

Maintained by the Nextstrain team. Enabled by data from GISAID
Showing 838 of 838 genomes sampled between Dec 2019 and Mar 2020.

Latest Nextstrain COVID-19 situation report in English and in other languages. Follow @nextstrain for continual updates to data and analysis.

This phylogeny shows evolutionary relationships of hCoV-19 (or SARS-CoV-2) viruses from the ongoing novel coronavirus COVID-19 pandemic. This phylogeny shows an initial emergence in Wuhan, China, in Nov-Dec 2019 followed by sustained human-to-human transmission leading to sampled infections. Although the genetic relationships among sampled viruses are quite clear, there is considerable uncertainty surrounding estimates of transmission dates and in reconstruction of geographic spread. Please be aware that specific inferred transmission patterns are only a hypothesis.

Site numbering and genome structure uses Wuhan-Hu-1/2019 as reference. The phylogeny is rooted relative to early samples from Wuhan. Temporal resolution assumes a nucleotide substitution rate of 8 × 10^-4 subs per site per year. Full details on bioinformatic processing can be found here.

Phylogenetic context of nCoV in SARS-related betacoronaviruses can be seen here.

We gratefully acknowledge the authors, originating and submitting laboratories of the genetic sequence and metadata made available through GISAID on which this research is based. A full listing of all originating and submitting laboratories is available below. An attribution table is available by clicking on "Download Data" at the bottom of the page and then clicking on "Strain Metadata" in the resulting dialog box.

Bookmarked Tg-list -- transgenic-list (

The transgenic-list (tg-l) was created by Peter Sobieszczuk in 1996, to serve the global research community specializing in genetic modifications of laboratory animals. Since then, three academic institutions have hosted the tg-l: the IGBMC in Strasbourg, France; the University of Manchester, UK; and the Imperial College in London, UK. In 2011, the transgenic-list was moved to the ISTT web server. The ISTT would like to acknowledge the excellent work of Peter and his assistants in establishing the list for the benefit of everyone who has been a part of this list. The tg-l has proven to be a valuable source of knowledge and advice, helping many newcomers to the field of animal transgenesis, and facilitating the exchange of protocols and experiences.

The ISTT is most proud to host the tg-l for the benefit of the entire community of scientists, technicians, students and all others, interested in animal transgenesis.

Tg-l members are active researchers at all levels, from graduate students to full professors, and the technicians, managers, and directors who operate transgenic core facilities.

The tg-l is public (subject to email address verification), unmoderated (messages will not be altered by the list administrator) and closed (only subscribers may post messages). The tg-l currently has about 1800 subscribers from all over the world.

To see the collection of prior postings to the list, visit the Tg-list Archives. (The current archive is only available to the list members.)

Read The Wuhan Virus: How to Stay Safe by Laurie Garrett (Foreign Policy)
As China’s epidemic continues to spread, things may seem scary. Here are 10 simple precautions that can protect you from contracting the coronavirus.

Some simple and easy to carry out precautions for the coming months.

On the Media Black Swans ()

Read Zocurelia - Inspiring Learners to Read and Discuss by Axel DürkopAxel Dürkop (
With Zocurelia you can increase the fun of reading online literature together. The browser tool shows the activity of a reading community directly in the context of the texts being read and discussed. This way learners can be motivated to participate and join the discussion - hopefully hypothetically. In this article I will explain my motivation, ideas and decisions that led to the development of Zocurelia.

For those interested in online reading groups, journal clubs, OER, open education, marginal syllabus, etc., Axel Dürkop has created quite a lovely little tool that mixes Zotero with

Using his online version (though the code is open source and it looks like I could pretty quickly host my own), it only took me a few minutes to mock up a collaborative space using an Econ Extra Credit group I’d tried to encourage. This could be quite cool, particularly if they continued the series past the first recommended textbook.

I could easily see folks like Remi Kalir using this as part of their marginal syllabus project and allowing students to recommend texts/articles for class and aggregating discussions around them.

First of all, I wanted to learn more about how to inspire learners to read. And this means for me as an educator to create a technical and social environment that is welcoming and easy to participate in.

Annotated on March 03, 2020 at 08:01PM

I want to have ways to show learners that I chose the texts for them, as I’m convinced that empathy is motivating.

I quite like this idea as a means of pedagogy.
Annotated on March 03, 2020 at 08:03PM

Read Be careful what you copy: Invisibly inserting usernames into text with Zero-Width Characters by Tom Ross (Medium)
Zero-width characters are invisible, ‘non-printing’ characters that are not displayed by the majority of applications. F​or exam​ple, I’ve ins​erted 10 ze​ro-width spa​ces in​to thi​s sentence, c​an you tel​​l? (Hint: paste the sentence into Diff Checker to see the locations of the characters!). These characters can be used to ‘fingerprint’ text for certain users.

A cool little trick with text for embedded steganography, security, or other communication purposes. 

This could also be used for pseudo-private communication via Webmention even. Just hide your messages inside of public messages.

Aaron Parecki bookmark Be careful what you copy: Invisibly inserting usernames into text with Zero-Width Characters ( ()

Watched The Unitive Web from YouTube

This explains our proposal for a new generation of the Web, which we call The Unitive Web. Currently, there is a growing movement from the independence of the web, towards dominant companies. These companies offer organized information, but this comes at a price. We lose our independence more and more. The Unitive Web is a proposal to have both organized information and independence. It offers one generic approach closely compatible with the current web, which makes it possible to create a global open virtual space of information that is responsive and reliable. It offers open customization of user interaction, open bottom-up schema mapping, integration of (AI) algorithms, and facilitates in the protection of privacy. Kickstarter project will be launched if/when there is some interest first.

I only got about halfway through this watching at 1.5x. I’m purposely not embedding the video.

Some of the basic ideas about complexity theory are intriguing here, but it feels more like they’re trying to ground their ideas in solid science when they likely don’t have the proper grounding. I can’t help but thinking about Claude Shannon’s article The Bandwagon and seeing the same things that happened with information theory now taking place with complexity theory.

They’re also proposing a huge amount of infrastructure that is tenuous at best. I’m more than happy to await a minimal example before considering this further.

It almost kills me that they can’t be bothered to create a Kickstarter without “further interest.”