My 10th Anniversary on Facebook

Apparently, according to Facebook, today is my 10th Anniversary using their service. Mostly I remember that it was pretty lonely for that first year as very few people I knew even had an idea what it was. Fortunately more than 1,300 people I know have joined since and made it a much more enriching experience.

Yesterday I got a thank you from Foursquare for 7 years, and it’s easily been over 8 years on Twitter. Sadly, I miss a lot of the services that started around that time that are no longer with us. Toward that end, I’ll post some thoughts tomorrow about a more pivotal anniversary about which I’m much more excited, and which portends better things for the internet…

Some light poolside reading

Some light poolside reading.
At Home in the Universe: The Search for the Laws of Self-Organization and Complexity by Stuart Kauffman

Instagram filter used: Clarendon

Photo taken at:Gerrish Swim & Tennis Club

Physicists Hunt For The Big Bang’s Triangles | Quanta Magazine

Bookmarked Physicists Hunt for the Big Bang'€™s Triangles (Quanta Magazine )

“The notion that counting more shapes in the sky will reveal more details of the Big Bang is implied in a central principle of quantum physics known as “unitarity.” Unitarity dictates that the probabilities of all possible quantum states of the universe must add up to one, now and forever; thus, information, which is stored in quantum states, can never be lost — only scrambled. This means that all information about the birth of the cosmos remains encoded in its present state, and the more precisely cosmologists know the latter, the more they can learn about the former.”

How can we be sure old books were ever read? – University of Glasgow Library

Bookmarked How can we be sure old books were ever read? by Robert MacLean (University of Glasgow Library)
Owning a book isn’t the same as reading it; we need only look at our own bloated bookshelves for confirmation.
This is a great little overview for people reading the books of others. There are also lots of great links to other resources.

Saddened to hear of the passing of Sir David J.C. MacKay, FRS

Earlier this morning, I was saddened to hear that one of my information theory heroes passed away today.

David MacKay blackboard

I’ve been following a Google Alert for “information theory,” and so on an almost a daily basis for over 15 years I’ve seen thousands of notices and references to his excellent textbook Information Theory, Inference, and Learning Algorithms, which he kindly chose to freely share with the world. It’s really a great little textbook, and I recommend that everyone download it or purchase it and give it a read. In addition he has a fabulous series of video lectures to go with it as well. (Someone had actually asked me for information theory lectures on Quora last week, and his are some of the best.)

An instant classic, covering everything from Shannon’s fundamental theorems to the postmodern theory of LDPC codes. You’ll want two copies of this astonishing book, one for the office and one for the fireside at home.

Bob McEliece, information theorist and professor, California Institute of Technology

 
Information Theory, Inference and Learning Algorithms

Sir David J.C. MacKay was the Regius Professor of Engineering at Cambridge University and a former professor of natural philosophy in the Department of Physics at at Cavendish Laboratory, University of Cambridge. He was also a leading figure in energy and climate change having written the accessible and highly praised book Sustainable Energy: Without all the Hot Air, which is also available for free on his site. In 2009 he was appointed to a five year term as Chief Scientific Advisor of the Department of Energy and Climate Change, United Kingdom.

His TED talk will give you an idea of some of his work in this area:

MacKay was elected a Fellow of the Royal Society in 2009. His nomination reads:

David MacKay introduced more efficient types of error-correcting code that are now used in satellite communications, digital broadcasting and magnetic recording. He advanced the field of Machine Learning by providing a sound Bayesian foundation for artificial neural networks. Using this foundation, he significantly improved their performance, allowing them to be used for designing new types of steel that are now used in power stations. He used his expertise in information theory to design a widely used interface called “dasher” that allows disabled people to write efficiently using a single finger or head-mounted pointer.

Sir David MacKay was knighted in the 2016 New Year Honours for services to scientific advice in government and to science outreach.

For those interested, he a great little blog. Here’s his last blogpost.

Below, from a variety of information theorists, mathematicians, and scientists is just the beginning of the outpouring of loss the world is experiencing today:



RIP David MacKay, former DECC Chief Scientific Adviser. He was passionate, original, brave. A truly good man. Deep condolences to his family

— Ed Miliband (@Ed_Miliband) April 14, 2016

Thoughts on “Some academics remain skeptical of Academia.edu” | University Affairs

Replied to Some academics remain skeptical of Academia.edu (University Affairs)
They warn scholars to €œthink twice€ before sharing their work on the popular social network.
This morning I ran across a tweet from colleague Andrew Eckford:

His response was probably innocuous enough, but I thought the article should be put to task a bit more.

“35 million academics, independent scholars and graduate students as users, who collectively have uploaded some eight million texts”

35 million users is an okay number, but their engagement must be spectacularly bad if only 8 million texts are available. How many researchers do you know who’ve published only a quarter of an article anywhere, much less gotten tenure?

“the platform essentially bans access for academics who, for whatever reason, don’t have an Academia.edu account. It also shuts out non-academics.”

They must have changed this, as pretty much anyone with an email address (including non-academics) can create a free account and use the system. I’m fairly certain that the platform was always open to the public from the start, but the article doesn’t seem to question the statement at all. If we want to argue about shutting out non-academics or even academics in poorer countries, let’s instead take a look at “big publishing” and their $30+/paper paywalls and publishing models, shall we?

“I don’t trust academia.edu”

Given his following discussion, I can only imagine what he thinks of big publishers in academia and that debate.

“McGill’s Dr. Sterne calls it “the gamification of research,”

Most research is too expensive to really gamify in such a simple manner. Many researchers are publishing to either get or keep their jobs and don’t have much time, information, or knowledge to try to game their reach in these ways. And if anything, the institutionalization of “publish or perish” has already accomplished far more “gamification”, Academia.edu is just helping to increase the reach of the publication. Given that research shows that most published research isn’t even read, much less cited, how bad can Academia.edu really be? [Cross reference: Reframing What Academic Freedom Means in the Digital Age]

If we look at Twitter and the blogging world as an analogy with Academia.edu and researchers, Twitter had a huge ramp up starting in 2008 and helped bloggers obtain eyeballs/readers, but where is it now? Twitter, even with a reasonable business plan is stagnant with growing grumblings that it may be failing. I suspect that without significant changes that Academia.edu (which is a much smaller niche audience than Twitter) will also eventually fall by the wayside.

The article rails against not knowing what the business model is or what’s happening with the data. I suspect that the platform itself doesn’t have a very solid business plan and they don’t know what to do with the data themselves except tout the numbers. I’d suspect they’re trying to build “critical mass” so that they can cash out by selling to one of the big publishers like Elsevier, who might actually be able to use such data. But this presupposes that they’re generating enough data; my guess is that they’re not. And on that subject, from a journalistic viewpoint, where’s the comparison to the rest of the competition including ResearchGate.net or Mendeley.com, which in fact was purchased by Elsevier? As it stands, this simply looks like a “hit piece” on Academia.edu, and sadly not a very well researched or reasoned one.

In sum, the article sounds to me like a bunch of Luddites running around yelling “fire”, particularly when I’d imagine that most referred to in the piece feed into the more corporate side of publishing in major journals rather than publishing it themselves on their own websites. I’d further suspect they’re probably not even practicing academic samizdat. It feels to me like the author and some of those quoted aren’t actively participating in the social media space to be able to comment on it intelligently. If the paper wants to pick at the academy in this manner, why don’t they write an exposé on the fact that most academics still have websites that look like they’re from 1995 (if, in fact, they have anything beyond their University’s mandated business card placeholder) when there are a wealth of free and simple tools they could use? Let’s at least build a cart before we start whipping the horse.

For academics who really want to spend some time and thought on a potential solution to all of this, I’ll suggest that they start out by owning their own domain and own their own data and work. The movement certainly has an interesting philosophy that’s a great start in fixing the problem; it can be found at http://www.indiewebcamp.com.

A new view of the tree of life

Bookmarked A new view of the tree of life (Nature Microbiology)
An update to the €˜tree of life has revealed a dominance of bacterial diversity in many ecosystems and extensive evolution in some branches of the tree. It also highlights how few organisms we have been able to cultivate for further investigation.

Abstract

The tree of life is one of the most important organizing principles in biology. Gene surveys suggest the existence of an enormous number of branches, but even an approximation of the full scale of the tree has remained elusive. Recent depictions of the tree of life have focused either on the nature of deep evolutionary relationships or on the known, well-classified diversity of life with an emphasis on eukaryotes. These approaches overlook the dramatic change in our understanding of life’s diversity resulting from genomic sampling of previously unexamined environments. New methods to generate genome sequences illuminate the identity of organisms and their metabolic capacities, placing them in community and ecosystem contexts. Here, we use new genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included. The depiction is both a global overview and a snapshot of the diversity within each major lineage. The results reveal the dominance of bacterial diversification and underline the importance of organisms lacking isolated representatives, with substantial evolution concentrated in a major radiation of such organisms. This tree highlights major lineages currently underrepresented in biogeochemical models and identifies radiations that are probably important for future evolutionary analyses.

Laura A. Hug, Brett J. Baker, Karthik Anantharaman, Christopher T. Brown, Alexander J. Probst, Cindy J. Castelle, Cristina N. Butterfield, Alex W. Hernsdorf, Yuki Amano, Kotaro Ise, Yohey Suzuki, Natasha Dudek, David A. Relman, Kari M. Finstad, Ronald Amundson, Brian C. Thomas & Jillian F. Banfield in Nature Microbiology, Article number: 16048 (2016) doi:10.1038/nmicrobiol.2016.48

 

A reformatted view of the tree in Fig. 1in which each major lineage represents the same amount of evolutionary distance.
A reformatted view of the tree in Fig. 1in which each major lineage represents the same amount of evolutionary distance.

Carl Zimmer also has a nice little write up of the paper in today’s New York Times:

Carl Zimmer
in Scientists Unveil New ‘Tree of Life’ from The New York Times 4/11/16

 

Gay Men’s Chorus of Los Angeles presents Bette, Babs & Beyoncé

What a great show last night!
It was a great buttoned down opening with a free-for-all closing. Standout performances on “Rhythm Nation” and the penultimate song “Maybe This Time” were particularly powerful. The sign language interpreter completely stole the show for me in terms of performance.

Gay Men's Chorus of Los Angeles presents Bette, Babs & Beyoncé - What a great show last night!

Instagram filter used: Nashville

Photo taken at: Alex Theatre

Online Lectures in Information Theory

Replied to Where can I find good online lectures in information theory? (quora.com)
There aren’t a lot of available online lectures on the subject of information theory, but here are the ones I’m currently aware of:

Introductory

Advanced

Fortunately, most are pretty reasonable, though vary in their coverage of topics. The introductory lectures don’t require as much mathematics and can probably be understood by those at the high school level with just a small amount of basic probability theory and an understanding of the logarithm.

The top three in the advanced section (they generally presume a prior undergraduate level class in probability theory and some amount of mathematical sophistication) are from professors who’ve written some of the most commonly used college textbooks on the subject. If I recall a first edition of the Yeung text was available via download through his course interface. MacKay’s text is available for free download from his site as well.

Feel free to post other video lectures or resources you may be aware of in the comments below.

Editor’s Update: With sadness, I’ll note that David MacKay died just days after this was originally posted.