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.”

Listened to Cancel This! from On the Media | WNYC Studios

The impeachment; coronavirus rumors go viral; the controversy around Joe Rogan's Bernie Sanders endorsement; and the perils of "cancel culture."

As the coronavirus continues to spread, the World Health Organization has declared a state of emergency. This week, On the Media looks at how panic and misinformation are going viral, too. Plus, a controversial endorsement for Bernie Sanders puts the spotlight on Joe Rogan, and has renewed the debate over "cancel culture." And, the impeachment proceedings continue to move toward a conclusion. 

1. Brooke [@OTMBrooke] reflects on the impeachment proceedings as they come to an anti-climactic ending. Listen.

2. Alexis Madrigal [@alexismadrigal] of The Atlantic explains how panic online is spreading faster than the coronavirus itself. Listen.

3. Devin Gordon [@DevinGordonX] talks about why Joe Rogan is so popular, and reflects on the controversy surrounding his tentative endorsement of Bernie Sanders. Listen.

4. Natalie Wynn, creator of the Youtube channel ContraPoints, lays out her criticism of "cancel culture" and takes an honest look at her own "cancellations." Listen.

The last two segments were particularly interesting reporting. Areas I was tangentially aware of, but missing portions of the deeper dive and perspective that they gave.
Darwin Day & Attachment
unopened condition

In honor of Darwin Day: An interior page on natural selection in an unopened original of the Proceedings of the Linnean Society. Note that the octavos in the edition haven’t been cut accounting for the top of the page being curved in the picture (because of the attachment of the adjoining pages). Science changed dramatically that day.

Annotated Blogroll by Dan MacKinlay (
ITBio – Chris Aldrich (feed)
Hey, wait! He’s not only following me, but a very distinct subset of my posts! 🙂

This is the first time I’ve ever seen someone indicate that they’ve done this in the wild.

I’ll also admit that this is a really great looking blogroll too! I’m going to have to mine it for the bunch of feeds that I’m not already following. 

Listened to Fake news is # Solvable from The Rockefeller Foundation

Anne Applebaum talks to Renée DiResta about building a more trustworthy Internet.

Renée DiResta is the Director of Research at New Knowledge and a Mozilla Fellow in Media, Misinformation, and Trust. She investigates the spread of malign narratives across social networks, and assists policymakers in understanding and responding to the problem. She has advised the United States Congress, the State Department, and other academic, civic, and business organizations, and has studied disinformation and computational propaganda in the context of pseudoscience conspiracies, terrorism, and state-sponsored information warfare.

Many talk about the right to freedom of speech online, but rarely do discussions delve a layer deeper into the idea of the “right to reach”. I’ve lately taken to analogizing the artificial reach of bots and partisan disinformation and labeled the idea social media machine guns to emphasize this reach problem. It’s also related to Cathy O’Neill’s concept of Weapons of Math Destruction. We definitely need some new verbiage to begin describing these sorts of social ills so that we have a better grasp of what they are and how they can effect us.

I appreciate Renee’s ideas and suspect they’re related to those in Ezra Klein’s new books, which I hope to start reading shortly.