Category: Science

Read No, someone hasn’t cracked the code of the mysterious Voynich manuscript [Updated] by Jennifer OulletteJennifer Oullette (Ars Technica)

Medieval scholar: "Sorry, folks, 'proto-Romance language' is not a thing."

The Voynich manuscript is a famous medieval text written in a mysterious language that so far has proven to be undecipherable. Now, Gerard Cheshire, a University of Bristol academic, has announced his own solution to the conundrum in a new paper in the journal Romance Studies. Cheshire identifies the mysterious writing as a "calligraphic proto-Romance" language, and he thinks the manuscript was put together by a Dominican nun as a reference source on behalf of Maria of Castile, Queen of Aragon. Apparently it took him all of two weeks to accomplish a feat that has eluded our most brilliant scholars for at least a century.

📑 Solomon Golomb (1932–2016) | Stephen Wolfram Blog

Annotated Solomon Golomb (1932–2016) by Stephen Wolfram (blog.stephenwolfram.com)

As it happens, he’d already done some work on coding theory—in the area of biology. The digital nature of DNA had been discovered by Jim Watson and Francis Crick in 1953, but it wasn’t yet clear just how sequences of the four possible base pairs encoded the 20 amino acids. In 1956, Max Delbrück—Jim Watson’s former postdoc advisor at Caltech—asked around at JPL if anyone could figure it out. Sol and two colleagues analyzed an idea of Francis Crick’s and came up with “comma-free codes” in which overlapping triples of base pairs could encode amino acids. The analysis showed that exactly 20 amino acids could be encoded this way. It seemed like an amazing explanation of what was seen—but unfortunately it isn’t how biology actually works (biology uses a more straightforward encoding, where some of the 64 possible triples just don’t represent anything).  ❧

I recall talking to Sol about this very thing when I sat in on a course he taught at USC on combinatorics. He gave me his paper on it and a few related issues as I was very interested at the time about the applications of information theory and biology.

I’m glad I managed to sit in on the class and still have the audio recordings and notes. While I can’t say that Newton taught me calculus, I can say I learned combinatorics from Golomb.

👓 Solomon Golomb (1932–2016) | Stephen Wolfram

Read Solomon Golomb (1932–2016) by Stephen WolframStephen Wolfram (blog.stephenwolfram.com)

The Most-Used Mathematical Algorithm Idea in History

An octillion. A billion billion billion. That’s a fairly conservative estimate of the number of times a cellphone or other device somewhere in the world has generated a bit using a maximum-length linear-feedback shift register sequence. It’s probably the single most-used mathematical algorithm idea in history. And the main originator of this idea was Solomon Golomb, who died on May 1—and whom I knew for 35 years.

Solomon Golomb’s classic book Shift Register Sequences, published in 1967—based on his work in the 1950s—went out of print long ago. But its content lives on in pretty much every modern communications system. Read the specifications for 3G, LTE, Wi-Fi, Bluetooth, or for that matter GPS, and you’ll find mentions of polynomials that determine the shift register sequences these systems use to encode the data they send. Solomon Golomb is the person who figured out how to construct all these polynomials.

A fantastic and pretty comprehensive obit for Sol. He did miss out on more of Sol’s youth as well as his cross-town chess rivalry with Basil Gordon when they both lived in Baltimore, but before they lived across town from each other again in Los Angeles.

Many of the fantastical seeming stories here, as well as Sol’s personality read very true to me with respect to the man I knew for almost two decades.

📑 Solomon Golomb (1932–2016) | Stephen Wolfram Blog

Annotated Solomon Golomb (1932–2016) by Stephen Wolfram (blog.stephenwolfram.com)
in June 1955 he wrote his final report, “Sequences with Randomness Properties”—which would basically become the foundational document of the theory of shift register sequences.  ❧

🔖 An Introduction to Complex Systems: Making Sense of a Changing World​ | Joseph V. Tranquillo | Springer

Bookmarked An Introduction to Complex Systems: Making Sense of a Changing World​ by Joseph V. Tranquillo (Springer)
This book explores the interdisciplinary field of complex systems theory. By the end of the book, readers will be able to understand terminology that is used in complex systems and how they are related to one another; see the patterns of complex systems in practical examples; map current topics, in a variety of fields, to complexity theory; and be able to read more advanced literature in the field. The book begins with basic systems concepts and moves on to how these simple rules can lead to complex behavior. The author then introduces non-linear systems, followed by pattern formation, and networks and information flow in systems. Later chapters cover the thermodynamics of complex systems, dynamical patterns that arise in networks, and how game theory can serve as a framework for decision making. The text is interspersed with both philosophical and quantitative arguments, and each chapter ends with questions and prompts that help readers make more connections.

👓 Data sharing and how it can benefit your scientific career l Nature

Read Data sharing and how it can benefit your scientific career (Nature)
Open science can lead to greater collaboration, increased confidence in findings and goodwill between researchers.

📑 Data sharing and how it can benefit your scientific career l Nature

Annotated Data sharing and how it can benefit your scientific career (Nature)
Crowther offered everyone who shared at least a certain volume of data with his forest initiative the chance to be a co-author of a study that he and a colleague led. Published in Science in 2016, the paper used more than 770,000 data points from 44 countries to determine that forests with more tree species are more productive.
I suspect a similar hypothesis holds for shared specs, code, and the broader idea of plurality within the IndieWeb. More interoperable systems makes the IndieWeb more productive.

📑 Data sharing and how it can benefit your scientific career l Nature

Annotated Data sharing and how it can benefit your scientific career (Nature)
High-level bodies such as the US National Academies of Sciences, Engineering, and Medicine and the European Commission have called for science to become more open and endorsed a set of data-management standards known as the FAIR (findable, accessible, interoperable and reusable) principles.
Something like this could be applied to IndieWeb ideas and principles as well.

❤️ lpachter tweeted I once asked Robert McEliece whether he would mentor me.

Liked a tweet by Lior PachterLior Pachter (Twitter)

👓 Robert J. McEliece, 1942–2019 | Caltech

Read Robert J. McEliece, 1942–2019 (caltech.edu)
Alumnus and engineering faculty member Robert J. McEliece has passed away.
May is apparently the month that many of the greats in information theory pass away. I was reminded of Sol Golomb’s passing in May 2016 the other day.

I didn’t know him well, but met Dr. McEliece a handful of times and at least a few of the books in my personal information theory library are hand-me-down copies from his personal library. He’ll definitely be missed.

Three open books piled on top of each other with McEliece's signature and dates in the top right hand of the first page and CalTech bookstore price stamps in them as well.

📺 The Bit Player (Trailer) | IEEE Information Theory Society

Watched The Bit Player (Trailer) from IEEE Information Theory Society

The Bit Player Trailer from IEEE Information Theory Society on Vimeo.

In a blockbuster paper in 1948, Claude Shannon introduced the notion of a "bit" and laid the foundation for the information age. His ideas ripple through nearly every aspect of modern life, influencing such diverse fields as communication, computing, cryptography, neuroscience, artificial intelligence, cosmology, linguistics, and genetics. But when interviewed in the 1980s, Shannon was more interested in showing off the gadgets he’d constructed — juggling robots, a Rubik’s Cube solving machine, a wearable computer to win at roulette, a unicycle without pedals, a flame-throwing trumpet — than rehashing the past. Mixing contemporary interviews, archival film, animation and dialogue drawn from interviews conducted with Shannon himself, The Bit Player tells the story of an overlooked genius who revolutionized the world, but never lost his childlike curiosity.

👓 Bob Gallager on Shannon’s tips for research | An Ergodic Walk

Annotated Bob Gallager on Shannon’s tips for research (An Ergodic Walk)

Gallager gave a nice concise summary of what he learned from Shannon about how to do good theory work:

  1. Simplify the problem
  2. Relate it to other problems
  3. Restate the problem in as many ways as possible
  4. Break the problem into pieces
  5. Avoid getting locked into thinking ruts
  6. Generalize

As he said, “it’s a process of doing research… each one [step] gives you a little insight.” It’s tempting, as a theorist, to claim that at the end of this process you’ve solved the “fundamental” problem, but Gallager admonished us to remember that the first step is to simplify, often dramatically. As Alfred North Whitehead said, we should “seek simplicity and distrust it.”

I know I’ve read this before, but it deserves a re-read/review every now and then.

🎧 The Myth That Fuels the Anti-Vaxx Agenda | On the Media | WNYC Studios

Listened to The Myth That Fuels the Anti-Vaxx Agenda from On the Media | WNYC Studios

Our 2012 conversation with Seth Mnookin, author of The Panic Virus: A True Story of Medicine, Science and Fear.

This Tuesday, lawmakers in Washington heard from an 18-year-old who, against all odds, got his shots. Ethan Lindenberger, who fought with his own mother to get vaccinated, told senators, "for my mother, her love, affection, and care as a parent was used to push an agenda to create a false distress."

That "anti-vaxx" agenda, the dangerous legacy of a thoroughly debunked 1998 study in the British medical journal Lancet, was dealt yet another devastating — though not mortal — blow this week, courtesy of epidemiologists from Denmark’s Staten Serum Institute. Their new study, which included more than 650,000 children, found that the MMR vaccine did not raise the risk of developing autism. 

And yet, even in the face of study after study, and even as websites like Pinterest have moved to stamp out the spread of anti-vaxx materials on their websites, the debunked vaccine-autism link and its impact on public health live on. In this 2012 interview, Brooke spoke with Seth Mnookin, author of The Panic Virus: A True Story of Medicine, Science and Fear, about why these myths persist.

No responsible journalist should be reporting on studies with N being so small. If they do, then they should be banned from any future science journalism.