👓 On digital archaeology | Andrew Eckford

On digital archaeology by Andrew Eckford (A Random Process)
The year is 4018. German is widely studied by scholars of classical antiquity, but all knowledge of the mysterious English language has died out. Scene: A classics department faculty lounge; a few professors are relaxing.

I worry about things like this all the time. Apparently it’s a terrible affliction that strikes those with a background in information theory at higher rates than the general public.

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🔖 Reproducibility Workshop: Best practices and easy steps to save time for yourself and other researchers

Reproducibility Workshop: Best practices and easy steps to save time for yourself and other researchers (codeocean.com)
Gain insight into a range of tools that can help you share and extend your research. Join us on January 25th at Caltech.

Sadly I missed this having only heard about it after it was already over.

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👓 Which problems make good research problems? | Back Reaction

Which problems make good research problems? by Sabine HossenfelderSabine Hossenfelder (Back Reaction)
Scientists solve problems; that’s their job. But which problems are promising topics of research? This is the question I set out to answer in Lost in Math at least concerning the foundations of physics. A first, rough, classification of research problems can be made using Thomas Kuhn’s cycle of scientific theories. Kuhn’s cycle consists of a phase of “normal science” followed by “crisis” leading to a paradigm change, after which a new phase of “normal science” begins. This grossly oversimplifies reality, but it will be good enough for what follows.

A nice little article on a question many of us should be asking ourselves more often. This one has some additional nice overview of bits of physics in addition, but circling back around to the original question is always very valuable.

I’m going to have to track down a copy of Sabine Hossenfelder’s book Lost in Math: How Beauty Leads Physics Astray.

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🔖 NetSci 2018 11-15 June 2018 in Paris, France

NetSci 2018 (NetSci 2018)
NetSci 2018, the flagship conference of the Network Science Society, aims to bring together leading researchers and practitioners working in the emerging area of network science. The conference fosters interdisciplinary communication and collaboration in network science research across computer and information sciences, physics, mathematics, statistics, the life sciences, neuroscience, environmental sciences, social sciences, finance and business, arts and design. NetSci 2018 in Paris, France will be a combination of: * An International School for students and non-experts (June 11-12, 2018) * Satellite Symposia (June 11-12, 2018) * A 3-day Conference (June 13-15, 2018) featuring research in a wide range of topics and in different formats, including keynote and invited talks, oral presentations, posters, and lightning talks.

Registration Deadlines:
February 8: Registration opens.
March 20: Registration for presenters of accepted contributions ends.
April 10: Early registration ends.
May 28: Online registration ends.

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🔖 9th International Conference on Complex Systems | NECSI

9th International Conference on Complex Systems | NECSI (necsi.edu)
The International Conference on Complex Systems is a unique interdisciplinary forum that unifies and bridges the traditional domains of science and a multitude of real world systems. Participants will contribute and be exposed to mind expanding concepts and methods from across the diverse field of complex systems science. The conference will be held July 22-27, 2018, in Cambridge, MA, USA. Special Topic - Artificial Intelligence: This year’s conference will include a day on AI, including its development and potential future. This session will be chaired by Iyad Rahwan of MIT's Media Lab.

A great looking conference coming up with a strong line up of people who’s work I appreciate. It could certainly use some more balance however as it’s almost all white men.

In particular I’d want to see:
Albert-László Barabási (Northeastern University, USA)
Nassim Nicholas Taleb (Real World Risk Institute, USA)
Stuart Kauffman (Institute for Systems Biology, USA)
Simon DeDeo (Carnegie Mellon University, USA)
Stephen Wolfram (Wolfram Research)
César Hidalgo (MIT Media Lab, USA)

Others include:
Marta González (University of California Berkeley, USA)
Peter Turchin (University of Connecticut, USA)
Mercedes Pascual (University of Chicago, USA) Pending confirmation
Iyad Rahwan (MIT Media Lab, USA)
Sandy Pentland (MIT Media Lab, USA)
Theresa Whelan (U.S. Department of Defense) Pending DOD approval
H. Eugene Stanley (Boston University, USA)
Ricardo Hausmann (Harvard University, USA)
Stephen Grossberg (Boston University, USA)
Daniela Rus (MIT Computer Science & Artificial Intelligence Lab, USA) Pending confirmation
Olaf Sporns (Indiana University Network Science Institute, USA)
Michelle Girvan (University of Maryland, USA) Pending confirmation
Cameron Kerry (MIT Media Lab, USA)
Irving Epstein (Brandeis University, USA)

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👓 ‘Fits neatly inside a lizard’s cloaca’: Scientists are leaving Amazon reviews, and it’s amazing | Washington Post

'Fits neatly inside a lizard's cloaca': Scientists are leaving Amazon reviews, and it's amazing by Avi Selk (Washington Post)
There are worse things you can put through a tea strainer than ants.

Scientist reviews on Amazon are just spectacular! I think there are a few things I could add to the pile…

I love the Post’s disclaimer about Bezos’ ownership of the Post:

Disclaimer: The Washington Post is owned by Jeffrey P. Bezos, who also runs Amazon, though we really don’t think we’re doing the site any favors with this article.

Also noted: They’ve quietly hidden the key word “poop” into the meta data for the article!

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🔖 Decoding Anagrammed Texts Written in an Unknown Language and Script

Decoding Anagrammed Texts Written in an Unknown Language and Script by Bradley Hauer, Grzegorz Kondrak (Transactions of the Association for Computational Linguistics)
Algorithmic decipherment is a prime example of a truly unsupervised problem. The first step in the decipherment process is the identification of the encrypted language. We propose three methods for determining the source language of a document enciphered with a monoalphabetic substitution cipher. The best method achieves 97% accuracy on 380 languages. We then present an approach to decoding anagrammed substitution ciphers, in which the letters within words have been arbitrarily transposed. It obtains the average decryption word accuracy of 93% on a set of 50 ciphertexts in 5 languages. Finally, we report the results on the Voynich manuscript, an unsolved fifteenth century cipher, which suggest Hebrew as the language of the document.

Aside: It’s been ages since I’ve seen someone with Refbacks listed on their site!

👓 Sexual harassment allegations roil Princeton University | WHYY

Sexual harassment allegations roil Princeton University by Avi Wolfman-Arent (WHYY)
Another high-profile instance of sexual harassment has rocked a major institution — this time Princeton University in New Jersey. And students say administrators didn’t act transparently or strongly enough when disciplining the alleged perpetrator, a decorated professor.

Once you start reaching Sergio Verdu’s age, and particularly with his achievements, your value to the University becomes more geared toward service. How much service can a professor do with an albatross like this hanging around their neck?

It would be nice if Universities were required to register offenders like this so that applicants to programs would be aware of them prior to applying–a sort of Megan’s Law for the professoriate. Naturally they don’t do this because it goes against their interests, but by the same token this is how a lot of issues run out of control within their sports programs as well. If someone did create such a website, I imagine the chilling effects on colleges and universities would be such that they might change their tunes about how these cases are handled. Immediately recent cases like Michigan State’s athletics problem, USC’s Medical School Dean issues, Christian Ott at Caltech come to mind, but I’m sure there must be hundreds if not thousands of others.

Maybe we need a mashup site that’s a cross between RateMyProfessors.com and California’s Megan’s Law site, but which specifically targeted Universities?

Fortunately even given Sergio’s accomplishments and profile, it will probably take forever for web searches for his name to not surface the story within the top couple of links, but this is sad consolation, particularly in a field like Information Theory which is heavily underrepresented already.

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👓 Read Professor Verdu’s emails to student where he invites her over to watch explicit film before sexually harassing her | The Tab

Read Professor Verdu’s emails to student where he invites her over to watch explicit film before sexually harassing her (Princeton University)
‘P.S. Please call me Sergio ☺️’

I was just wondering why Sergio Verdu was so quiet on Twitter. Then I wondered why his Twitter account had disappeared.

Now I know the sad and painfully disappointing answer.

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👓 Mysterious 15th century manuscript finally decoded 600 years later | The Independent

Code in the 'world's most mysterious book' deciphered by AI (The Independent)
Artificial intelligence has allowed scientists to make significant progress in cracking a mysterious ancient text, the meaning of which has eluded scholars for centuries.

Interesting news if it’s really true! Though I do feel a bit sad as there are some methods I had wanted to try on this longstanding puzzle, but never had the time to play with.

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🔖 [1801.06022] Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors | arXiv

Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors by Yonatan Yehezkeally and Moshe Schwartz (arxiv.org)
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction problem, which is applicable whenever multiple reads of noisy data are available. This strategy is uniquely suited to the medium, which inherently replicates stored data in multiple distinct ways, caused by mutations. We consider noise introduced solely by uniform tandem-duplication, and utilize the relation to constant-weight integer codes in the Manhattan metric. By bounding the intersection of the cross-polytope with hyperplanes, we prove the existence of reconstruction codes with greater capacity than known error-correcting codes, which we can determine analytically for any set of parameters.
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“My ten hour white noise video now has five copyright claims! :)” by Sebastian Tomczak (Twitter)

Information Theory and signal processing FTW!

(Aside: This is a great example of how people really don’t understand our copyright system or science in general.)

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🔖 Nonlinear Dynamics 1 & 2: Geometry of Chaos by Predrag Cvitanovic

Nonlinear Dynamics 1 & 2: Geometry of Chaos by Predrag CvitanovicPredrag Cvitanovic (Georgia Institute of Technology)
The theory developed here (that you will not find in any other course :) has much in common with (and complements) statistical mechanics and field theory courses; partition functions and transfer operators are applied to computation of observables and spectra of chaotic systems. Nonlinear dynamics 1: Geometry of chaos (see syllabus) Topology of flows - how to enumerate orbits, Smale horseshoes Dynamics, quantitative - periodic orbits, local stability Role of symmetries in dynamics Nonlinear dynamics 2: Chaos rules (see syllabus) Transfer operators - statistical distributions in dynamics Spectroscopy of chaotic systems Dynamical zeta functions Dynamical theory of turbulence The course, which covers the same material and the same exercises as the Georgia Tech course PHYS 7224, is in part an advanced seminar in nonlinear dynamics, aimed at PhD students, postdoctoral fellows and advanced undergraduates in physics, mathematics, chemistry and engineering.

An interesting looking online course that appears to be on a white-labeled Coursera platform.

I’ve come across Predrag Cvitanovic’s work on Group Theory and Lie Groups before, so this portends some interesting work. I’ll have to see if I can carve out some time to sample some of it.

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📖 Read pages 19-52 of The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📖 Read Chapter 1: What is Life? pages 19-52 in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane (W.W. Norton,
, ISBN: 978-0393088816)

Lane lays out a “brief” history of the 4 billion years of life on Earth. Discusses isotopic fractionation and other evidence that essentially shows a bottleneck between bacteria and archaea (procaryotes) on the one hand and eucaryotes on the other, the latter of which all must have had a single common ancestor based on the genetic profiles we currently see. He suggest that while we should see even more diversity of complex life, we do not, and he hints at the end of the chapter that the reason is energy.

In general, it’s much easier to follow than I anticipated it might be. His writing style is lucid and fluid and he has some lovely prose not often seen in books of this sort. It’s quite a pleasure to read. Additionally he’s doing a very solid job of building an argument in small steps.

I’m watching closely how he’s repeatedly using the word information in his descriptions, and it seems to be a much more universal and colloquial version than the more technical version, but something interesting may come out of it from my philosophical leanings. I can’t wait to get further into the book to see how things develop.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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📗 Started reading The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

📗 Started reading pages 1-18 Introduction: Why is Life the Way it is in The Vital Question: Energy, Evolution, and the Origins of Complex Life by Nick Lane

A quick, but interesting peek into where he intends to go. He lays out some quick background here in the opening. He’s generally a very lucid writer so far. Can’t wait to get in further.

Some may feel like some of the terminology is a hurdle in the opening, so I hope he circles around to define some of his terms a bit better for the audience I suspect he’s trying to reach.

book cover of Nick Lane's The Vital Question
The Vital Question: Energy, Evolution and the Origins of Complex Life by Nick Lane
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