Category: Science

Energy and Matter at the Origins of Life by Nick Lane | Santa Fe Institute

Bookmarked Energy and Matter at the Origin of Life by Nick Lane (Santa Fe Institute Community Event (YouTube))
All living things are made of cells, and all cells are powered by electrochemical charges across thin lipid membranes — the ‘proton motive force.’ We know how these electrical charges are generated by protein machines at virtually atomic resolution, but we know very little about how membrane bioenergetics first arose. By tracking back cellular evolution to the last universal common ancestor and beyond, scientist Nick Lane argues that geologically sustained electrochemical charges across semiconducting barriers were central to both energy flow and the formation of new organic matter — growth — at the very origin of life. Dr. Lane is a professor of evolutionary biochemistry in the Department of Genetics, Evolution and Environment at University College London. His research focuses on how energy flow constrains evolution from the origin of life to the traits of complex multicellular organisms. He is a co-director of the new Centre for Life’s Origins and Evolution (CLOE) at UCL, and author of four celebrated books on life’s origins and evolution. His work has been recognized by the Biochemical Society Award in 2015 and the Royal Society Michael Faraday Prize in 2016.
https://www.youtube.com/watch?v=HmLLo0WC5xg

h/t Santa Fe Institute

The Chemical Basis of Morphogenesis by Alan Turing

Reposted a tweet by Michael Nielsen (Twitter)

Looks like Alan Turing, like Claude Shannon, was interested in microbiology too! I’ll have to dig into this. [pdf]

👓 Half the universe’s missing matter has just been finally found | New Scientist

Read Half the universe’s missing matter has just been finally found by Leah Crane (New Scientist)
About half the normal matter in our universe had never been observed – until now. Two teams have finally seen it by combining millions of faint images into one

👓 A 2017 Nobel laureate says he left science because he ran out of money and was fed up with academia | QZ

Read A 2017 Nobel laureate left science because he ran out of money (Quartz)
Jeffrey Hall, a retired professor at Brandeis University, shared the 2017 Nobel Prize in medicine for discoveries elucidating how our internal body clock works. He was honored along with Michael Young and his close collaborator Michael Roshbash. Hall said in an interview from his home in rural Maine that he collaborated with Roshbash because they shared...
This is an all-too-often heard story. The difference is that now a Nobel Prize winner is telling it about himself!

👓 Las Vegas Is Only the Deadliest Shooting in US History Because They Don’t Count Black Lives | The Root

Read Las Vegas Is Only the Deadliest Shooting in US History Because They Don’t Count Black Lives by Michael Harriot (The Root)
News reporters and anchors have repeatedly referred to the recent tragedy in Las Vegas as the “worst mass shooting in U.S. history.” Like all things that are constantly repeated, the proclamation has become fact.
There’s some great history here. It reminds me about the podcast Seeing White which I’ve been listening to recently.

📺 These 3D animations could help you finally understand molecular science | PBS NewsHour

Watched These 3D animations could help you finally understand molecular science from PBS NewsHour
Art and science have in some ways always overlapped, with early scientists using illustrations to depict what they saw under the microscope. Janet Iwasa of the University of Utah is trying to re-establish this link to make thorny scientific data and models approachable to the common eye. Iwasa offers her brief but spectacular take on how 3D animation can make molecular science more accessible.
https://www.youtube.com/watch?v=s9NDXk7Gs8Y

Visualizations can be tremendously valuable. This story reminds me of an Intersession course that Mary Spiro did at Johns Hopkins to help researchers communicate what their research is about as well as some of the work she did with the Johns Hopkins Institute for NanoBioTechnology.

👓 Ergodic | John D. Cook

Read Ergodic by John D. Cook (John D. Cook Consulting)
Roughly speaking, an ergodic system is one that mixes well. You get the same result whether you average its values over time or over space. This morning I ran across the etymology of the word ergodic.
I’d read this before, but had a nice reminder about it this morning.

🔖 Upcoming Special Issue “Information Theory in Neuroscience” | Entropy (MDPI)

Bookmarked Special Issue "Information Theory in Neuroscience" (Entropy | MDPI)
As the ultimate information processing device, the brain naturally lends itself to be studied with information theory. Application of information theory to neuroscience has spurred the development of principled theories of brain function, has led to advances in the study of consciousness, and to the development of analytical techniques to crack the neural code, that is to unveil the language used by neurons to encode and process information. In particular, advances in experimental techniques enabling precise recording and manipulation of neural activity on a large scale now enable for the first time the precise formulation and the quantitative test of hypotheses about how the brain encodes and transmits across areas the information used for specific functions. This Special Issue emphasizes contributions on novel approaches in neuroscience using information theory, and on the development of new information theoretic results inspired by problems in neuroscience. Research work at the interface of neuroscience, Information Theory and other disciplines is also welcome. A special issue of Entropy (ISSN 1099-4300). This special issue belongs to the section "Information Theory". Deadline for manuscript submissions: 1 December 2017

👓 The First Species to Have Every Individual’s Genome Sequenced | The Atlantic

Read The First Species to Have Every Individual’s Genome Sequenced by Ed Yong (The Atlantic)
It’s an endearing, giant, flightless, New Zealand parrot, and it’s a poster child for the quantified-self movement.
Kakapo

👓 How the NSA identified Satoshi Nakamoto | Alexander Muse

Read How the NSA identified Satoshi Nakamoto by Alexander Muse (Alexander Muse | Medium)
The ‘creator’ of Bitcoin, Satoshi Nakamoto, is the world’s most elusive billionaire. Very few people outside of the Department of Homeland Security know Satoshi’s real name. In fact, DHS will not publicly confirm that even THEY know the billionaire’s identity. Satoshi has taken great care to keep his identity secret employing the latest encryption and obfuscation methods in his communications. Despite these efforts (according to my source at the DHS) Satoshi Nakamoto gave investigators the only tool they needed to find him — his own words. Using stylometry one is able to compare texts to determine authorship of a particular work. Throughout the years Satoshi wrote thousands of posts and emails and most of which are publicly available. According to my source, the NSA was able to the use the ‘writer invariant’ method of stylometry to compare Satoshi’s ‘known’ writings with trillions of writing samples from people across the globe. By taking Satoshi’s texts and finding the 50 most common words, the NSA was able to break down his text into 5,000 word chunks and analyse each to find the frequency of those 50 words. This would result in a unique 50-number identifier for each chunk. The NSA then placed each of these numbers into a 50-dimensional space and flatten them into a plane using principal components analysis. The result is a ‘fingerprint’ for anything written by Satoshi that could easily be compared to any other writing.
The article itself is dubious and unsourced and borders a bit on conspiracy theory, but the underlying concept about stylometry and its implications to privacy will be interesting to many. Naturally, it’s not much new.

👓 Show authors more ❤️ with 👏’s | Medium

Read Introducing Claps, a new way to react on Medium by Katie Zhu (Medium)
Rolling out to Medium users over the coming week will be a new, more satisfying way for readers to give feedback to writers. We call it “Claps.” It’s no longer simply whether you like, or don’t like, something. Now you can give variable levels of applause to a story. Maybe clap once, or maybe 10 or 20 times. You’re in control and can clap to your heart’s desire.
Yet another way to “like” a post….

This reminds me a lot of Path’s pivot to stickers. We all know how relevant it has made them since.

And all this just after Netflix, the company that has probably done more research on ranking than any other, has gone from a multi-star intent to a thumbs up/thumbs down in the past month.

Most of the measurements social media and other companies are really trying to make are signal to noise ratios as well as creating some semblance of dynamic range. A simple thumbs up creates almost no dynamic range compared to thumbs up/nothing/thumbs-down. Major platforms drive enough traffic that the SNR all comes out in the wash. Without the negative intent (dis-like, thumbs down, etc.) we’re missing out on some important data. It’s almost reminiscent to the science community only publishing their positive results and not the negative results. As a result scientific research is losing a tremendous amount of value.

We need to be more careful what we’re doing and why…

SFI and ASU to offer online M.S. in Complexity | Complexity Explorer

Bookmarked SFI and ASU to offer online M.S. in Complexity (Complexity Explorer)
SFI and Arizona State University soon will offer the world’s first comprehensive online master’s degree in complexity science. It will be the Institute’s first graduate degree program, a vision that dates to SFI’s founding. “With technology, a growing recognition of the value of online education, widespread acceptance of complexity science, and in partnership with ASU, we are now able to offer the world a degree in the field we helped invent,” says SFI President David Krakauer, “and it will be taught by the very people who built it into a legitimate domain of scholarship.”

👓 Link: The futility of science communication conferences by John Hawks

Read Link: The futility of science communication conferences by John Hawks (johnhawks.net)
Rich Borschelt is the communication director for science at the Department of Energy, and recently attended a science communication workshop. He describes at some length his frustration at the failed model of science communication, in which every meeting hashes over the same futile set of assumptions: “Communication, Literacy, Policy: Thoughts on SciComm in a Democracy. After several other issues, he turns to the conferences’ attitude about scientists...
John’s note reminds me that I’ve been watching a growing and nasty trend against science, much less science communication, in the past several years. We’re going to be needing a lot more help than we’re getting lately to turn the tide for the better. Perhaps more scientists having their own websites and expanding on the practice of samizdat would help things out a bit?

I recently came across Science Sites, a non-profit web company, courtesy of mathematician Steven Strogatz who has a site built by them. In some sense, I see some of what they’re doing to be enabling scientists to become part of the IndieWeb. It would be great to see them support standards like Webmention or functionality like Micropub as well. (It looks like they’re doing a lot of building on SquareSpace, so by proxy it would be great if they were supporting these open standards.) I love that it seems to have been created by a group of science journalists to help out the cause.

As I watch some of the Domain of One’s Own community in higher education, it feels to me that it’s primarily full of humanities related professors and researchers and doesn’t seem to be doing enough outreach to their science, engineering, math, or other colleagues who desperately need these tools as well as help with basic communication.

🔖 Self-Organized Resonance during Search of a Diverse Chemical Space

Bookmarked Self-Organized Resonance during Search of a Diverse Chemical Space (Physical Review Letters)
ABSTRACT Recent studies of active matter have stimulated interest in the driven self-assembly of complex structures. Phenomenological modeling of particular examples has yielded insight, but general thermodynamic principles unifying the rich diversity of behaviors observed have been elusive. Here, we study the stochastic search of a toy chemical space by a collection of reacting Brownian particles subject to periodic forcing. We observe the emergence of an adaptive resonance in the system matched to the drive frequency, and show that the increased work absorption by these resonant structures is key to their stabilization. Our findings are consistent with a recently proposed thermodynamic mechanism for far-from-equilibrium self-organization.
Suggested by First Support for a Physics Theory of Life in Quanta Magazine.