🔖 Humm | Simple self-publishing: a distributed platform for free creative expression

Bookmarked Humm | Simple self-publishing: a distributed platform for free creative expression (Humm)
Simple self-publishing: a distributed platform for free creative expression on Humm…

Looks like an interesting author platform meant that could be used for journalism as well. Has a very IndieWeb flavor.

Bookmarked From bit to it: How a complex metabolic network transforms information into living matter by Andreas Wagner (BMC Systems Biology)

Background

Organisms live and die by the amount of information they acquire about their environment. The systems analysis of complex metabolic networks allows us to ask how such information translates into fitness. A metabolic network transforms nutrients into biomass. The better it uses information on available nutrient availability, the faster it will allow a cell to divide.

Results

I here use metabolic flux balance analysis to show that the accuracy I (in bits) with which a yeast cell can sense a limiting nutrient's availability relates logarithmically to fitness as indicated by biomass yield and cell division rate. For microbes like yeast, natural selection can resolve fitness differences of genetic variants smaller than 10-6, meaning that cells would need to estimate nutrient concentrations to very high accuracy (greater than 22 bits) to ensure optimal growth. I argue that such accuracies are not achievable in practice. Natural selection may thus face fundamental limitations in maximizing the information processing capacity of cells.

Conclusion

The analysis of metabolic networks opens a door to understanding cellular biology from a quantitative, information-theoretic perspective.

https://doi.org/10.1186/1752-0509-1-33

Received: 01 March 2007 Accepted: 30 July 2007 Published: 30 July 2007

Hat tip to Paul Davies in The Demon in the Machine

Bookmarked Statistical Physics of Self-Replication by Jeremy L. England (J. Chem. Phys. 139, 121923 (2013); )
Self-replication is a capacity common to every species of living thing, and simple physical intuition dictates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self-replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self-replicating nucleic acids.
https://doi.org/10.1063/1.4818538

Syndicated copy also available on arXiv: https://arxiv.org/abs/1209.1179

Hat tip to Paul Davies in The Demon in the Machine

👓 ad-hoc sessions | IndieWeb

Bookmarked ad-hoc sessions - IndieWeb (indieweb.org)
ad-hoc sessions is the idea (which needs a better name) that we host single topic sessions every month or two online that the community can gather around and discuss.

I do like the idea of doing something like this.

It also may be worthwhile to do some regular WordPress set up sessions on a monthly basis the way we often do at camps.

🔖 Status as a Service (StaaS) | Remains of the Day

Bookmarked Status as a Service (StaaS) by Eugene Wei (Remains of the Day)

Status-Seeking Monkeys

"It is a truth universally acknowledged, that a person in possession of little fortune, must be in want of more social capital."

So wrote Jane Austen, or she would have, I think, if she were chronicling our current age (instead we have Taylor Lorenz, and thank goodness for that).

Let's begin with two principles:

  • People are status-seeking monkeys*

  • People seek out the most efficient path to maximizing social capital

* Status-Seeking Monkeys will also be the name of my indie band, if I ever learn to play the guitar and start a band

I begin with these two observations of human nature because few would dispute them, yet I seldom see social networks, some of the largest and fastest-growing companies in the history of the world, analyzed on the dimension of status or social capital.

Hat tip: Ryan Barrett

stunning analysis of social networks as products: https://www.eugenewei.com/blog/2019/2/19/status-as-a-service . many insights i’d never heard before. (beware though, almost 20k words!)

🔖 The notion of information in biology, an appraisal | Jérôme Segal | Journal BIO Web of Conferences

Bookmarked The notion of information in biology, an appraisal by Jérôme SegalJérôme Segal (Journal BIO Web of Conferences Volume 4, Page 00017, 2015; ORIGINS – Studies in Biological and Cultural Evolution)

Developed during the first half of the 20th century, in three different fields, theoretical physics, statistics applied to agronomy and telecommunication engineering, the notion of information has become a scientific concept in the context of the Second War World. It is in this highly interdisciplinary environment that “information theory” emerged, combining the mathematical theory of communication and cybernetics. This theory has grown exponentially in many disciplines, including biology. The discovery of the genetic “code” has benefited from the development of a common language based on information theory and has fostered a almost imperialist development of molecular genetics, which culminated in the Human Genome Project. This project however could not fill all the raised expectations and epigenetics have shown the limits of this approach. Still, the theory of information continues to be applied in the current research, whether the application of the self-correcting coding theory to explain the conservation of genomes on a geological scale or aspects the theory of evolution.

[pdf]

https://doi.org/10.1051/bioconf/20150400017

🔖 The Negentropy Principle of Information by Leon Brillouin | Journal of Applied Physics: Vol 24, No 9

Bookmarked The Negentropy Principle of Information by Leon Brillouin (Journal of Applied Physics 24, 1152 (1953))

The statistical definition of information is compared with Boltzmann's formula for entropy. The immediate result is that information I corresponds to a negative term in the total entropy S of a system.
S=S0−I
. A generalized second principle states that S must always increase. If an experiment yields an increase ΔI of the information concerning a physical system, it must be paid for by a larger increase ΔS0 in the entropy of the system and its surrounding laboratory. The efficiency ε of the experiment is defined as ε = ΔI/ΔS0≤1. Moreover, there is a lower limit k ln2 (k, Boltzmann's constant) for the ΔS0 required in an observation. Some specific examples are discussed: length or distance measurements, time measurements, observations under a microscope. In all cases it is found that higher accuracy always means lower efficiency. The information ΔI increases as the logarithm of the accuracy, while ΔS0 goes up faster than the accuracy itself. Exceptional circumstances arise when extremely small distances (of the order of nuclear dimensions) have to be measured, in which case the efficiency drops to exceedingly low values. This stupendous increase in the cost of observation is a new factor that should probably be included in the quantum theory.

https://doi.org/10.1063/1.1721463

First appearance of the word “negentropy” that I’ve seen in the literature.

📑 Walter Pitts by Neil Smalheiser | Journal Perspectives in Biology and Medicine

Bookmarked Walter Pitts by Neil SmalheiserNeil Smalheiser (Journal Perspectives in Biology and Medicine. Volume 43. Issue 2. Page 217 - 226.)
Walter Pitts was pivotal in establishing the revolutionary notion of the brain as a computer, which was seminal in the development of computer design, cybernetics, artificial intelligence, and theoretical neuroscience. He was also a participant in a large number of key advances in 20th-century science.  

This looks like an interesting bio to read.

📑 A logical calculus of the ideas immanent in nervous activity by Warren S. McCulloch, Walter Pitts

Bookmarked A logical calculus of the ideas immanent in nervous activity by Warren S. McCulloch, Walter Pitts (The bulletin of mathematical biophysics December 1943, Volume 5, Issue 4, pp 115–133)
Because of the “all-or-none” character of nervous activity, neural events and the relations among them can be treated by means of propositional logic. It is found that the behavior of every net can be described in these terms, with the addition of more complicated logical means for nets containing circles; and that for any logical expression satisfying certain conditions, one can find a net behaving in the fashion it describes. It is shown that many particular choices among possible neurophysiological assumptions are equivalent, in the sense that for every net behaving under one assumption, there exists another net which behaves under the other and gives the same results, although perhaps not in the same time. Various applications of the calculus are discussed.

Found reference to this journal article in a review of Henry Quastler’s book Information Theory in Biology. It said:

A more serious thing, in the reviewer’s opinion, is the complete absence of contributions dealing with information theory and the central nervous system, which may be the field par excellence for the use of such a theory. Although no explicit reference to information theory is made in the well-known paper of W. McCulloch and W. Pitts (1943), the connection is quite obvious. This is made explicit in the systematic elaboration of the McCulloch-Pitts’ approach by J. von Neumann (1952). In his interesting book J. T. Culbertson (1950) discussed possible neural mechanisms for recognition of visual patterns, and particularly investigated the problems of how greatly a pattern may be deformed without ceasing to be recognizable. The connection between this problem and the problem of distortion in the theory of information is obvious. The work of Anatol Rapoport and his associates on random nets, and especially on their applications to rumor spread (see the series of papers which appeared in this Journal during the past four years), is also closely connected with problems of information theory.

Electronic copy available at: http://www.cse.chalmers.se/~coquand/AUTOMATA/mcp.pdf

🔖 Information Theory in Biology by Henry Quastler (editor) | University of Illinois Press (1953)

Bookmarked Information Theory in Biology (University of Illinois Press (1953))

I’d love to have a copy of this book that I don’t think I’d heard of before. I’ve got his later Symposium of Information Theory In Biology (1958) already. That volume gives credit to this prior book as inspiration for the symposium.

I suspect based on the Wikipedia article for Quastler that this may also be the same book as the slightly differently titled Essays on the Use of Information Theory in Biology. (Urbana: University of Illinois Press, 1953). There’s also a 1955 review of the text with this name available as well.

Google uses the first title with 273 pages and the Symposium text specifically cites Information Theory in Biology as the correct title several times.

The tough part seems to be that there are very few copies available online and the ones that are are certainly used, in poor condition, and priced at $100+. Ugh…

Call for Speakers | WordCamp Santa Clarita

Bookmarked Call for Speakers by Joe Simpson, Jr. (WordCamp Santa Clarita)

The New Frontier Awaits! Speak at WordCamp Santa Clarita!

Everyone has a unique story to share, and we really want to hear yours. We want a rustic blend of talks that will be engaging for all skill levels within the WordPress Community. We’re seeking passionate speakers with a flair for the dramatic onstage, technical brilliance, community leaders or business acumen, and everything in-between. We’re open to any and all your ideas for presentation topics, whether you’re a first-timer or well known throughout the WordCamp space.

Rushing to finish my talk proposal for the innaugural WordCamp Santa Clarita Valley. #wcscv

🔖 Quip

Bookmarked Quip (quip.com)
Quip is a new way of collaborating that fuels a culture of action. Empower your employees to get things done faster with less email, and fewer meetings.

I’d looked at this as they launched, but might be worth revisiting to see it’s current status. It’s a silo service that I’ve noticed Ryan Dawidjan sort of using as a personal commonplace book/journal.

🔖 The Age of Surveillance Capitalism: The Fight for a Human Future at the New Frontier of Power by Shoshana Zuboff

Bookmarked The Age of Surveillance Capitalism: The Fight for a Human Future at the New Frontier of Power by Shoshana Zuboff (PublicAffairs; 1 edition)

Shoshana Zuboff's interdisciplinary breadth and depth enable her to come to grips with the social, political, business, and technological meaning of the changes taking place in our time. We are at a critical juncture in the confrontation between the vast power of giant high-tech companies and government, the hidden economic logic of surveillance capitalism, and the propaganda of machine supremacy that threaten to shape and control human life. Will the brazen new methods of social engineering and behavior modification threaten individual autonomy and democratic rights and introduce extreme new forms of social inequality? Or will the promise of the digital age be one of individual empowerment and democratization?

The Age of Surveillance Capitalism is neither a hand-wringing narrative of danger and decline nor a digital fairy tale. Rather, it offers a deeply reasoned and evocative examination of the contests over the next chapter of capitalism that will decide the meaning of information civilization in the twenty-first century. The stark issue at hand is whether we will be the masters of information and machines or its slaves.

book cover of The Age of Surveillance Capitalism by Shoshana Zuboff

Can’t wait to get this…

On first blush, I’ll note that the cover looks a lot like that of Pikkety’s Captialism in the 21st Century. Certainly an interesting framing by the publisher.

🔖 Listen Notes: The best podcast search engine

Bookmarked Listen Notes: The best podcast search engine by Wenbin FangWenbin Fang (Listen Notes)
The most comprehensive podcast database online. Discover best podcasts. Search podcast show notes and audio transcripts by people, places, or topics.

An interesting looking service to be sure. Reminds me a bit of some of the functionality of Jeremy Keith’s Huffduffer, but it’s also a social silo of sorts for listening related content. It allows you to bookmark podcast episodes to listen later and includes an RSS feed for those so you can subscribe directly to your feed in a podcast player. It also does listen clips and comments. Sadly it doesn’t look like its got listen posts to allow you to keep track of what you’ve actually listened to. It does have an API for those who want to play around with it though.

I’m curious what folks like Kim Hansen, Ben Werdmüller, or Erin Jo Richey think of it. Are there better small tools out there?

hat tip: This Week in Google

🔖 Ethical alternatives to popular sites and apps | switching.social

Bookmarked Ethical alternatives to popular sites and apps (switching.social)

This looks interesting… Sadly a lot of their options seem to be very ActivityPub-centric, despite the fact that the site itself is run on WordPress (and they neglect to list it as an option as far as I can tell). Admittedly they do seem to be directed toward the non-technical user, but there are lots of options they’re also not listing here too. They’re also not mentioning the potential for abuse that some of these software present, particularly when they’re run by other people, or collectives of other people. While switching from Twitter to Mastodon may be a short term solution, your choice of particular instance could end you right back where you came from if you’re not careful or not running your own personal instance.

Missing from many of these lists are things like micro.blog and a plethora of IndieWeb-related projects.

With that said, it’s at least a start on overcoming some of the hurdles that exist for finding alternatives.

hat tip: Ryan Barrett