Bookmarked Leaving Neverland (HBO Documentaries)
Filmmaker Dan Reed’s two-part documentary film Leaving Neverland explores the separate but parallel experiences of two young boys, James “Jimmy” Safechuck, at age 10, and Wade Robson, at age 7, who were both befriended by the star. They and their families were invited into his singular and wondrous world, entranced by the singer’s fairy-tale existence as his career reached its peak.

🔖 Virtually Connecting March 18-20 at Digital Pedagogy Lab Toronto!

Bookmarked Virtually Connecting March 18-20 at Digital Pedagogy Lab Toronto! by greeneterry (Virtually Connecting)
The Digital Pedagogy Lab – Toronto event is on March 18-20, 2019. We are virtually connecting to you from the Gladstone Hotel in Queen West Village with two (maybe three!) opportunities to connect to this wonderful event from afar. Join us at a distance for a hangout with keynotes, track...

🔖 Hemingway Editor

Bookmarked Hemingway Editor (hemingwayapp.com)

Hemingway App makes your writing bold and clear.

The app highlights lengthy, complex sentences and common errors; if you see a yellow sentence, shorten or split it. If you see a red highlight, your sentence is so dense and complicated that your readers will get lost trying to follow its meandering, splitting logic — try editing this sentence to remove the red.

You can utilize a shorter word in place of a purple one. Mouse over them for hints.

I could see some serious value in this if I could use it as a web app with Micropub support, which would allow it to almost any CMS or platform. It’s a bit reminiscent of Quill, though that doesn’t have the grammar and writing help.

There’s a $20 desktop version that can publish to WordPress and Medium.

Possibly missing for a full editor experience: the ability to add images.

As a sample, I tried putting in some prior writing. Apparently I overuse adverbs. It said I was writing at grade 13 and I should aim for grade 9! (It was something I had already attempted to “dumb down”.)

🔖 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

🔖 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!)

Acquired The Witches, Salem, 1692 by Stacy Schiff

Acquired The Witches, Salem, 1692 by Stacy Schiff (Little, Brown and Company)

The Pulitzer Prize-winning author of Cleopatra, the national bestseller, unpacks the mystery of the Salem Witch Trials.

It began in 1692, over an exceptionally raw Massachusetts winter, when a minister's daughter began to scream and convulse. It ended less than a year later, but not before 19 men and women had been hanged and an elderly man crushed to death. 

The panic spread quickly, involving the most educated men and prominent politicians in the colony. Neighbors accused neighbors, parents and children each other. Aside from suffrage, the Salem Witch Trials represent the only moment when women played the central role in American history. In curious ways, the trials would shape the future republic.

As psychologically thrilling as it is historically seminal, THE WITCHES is Stacy Schiff's account of this fantastical story-the first great American mystery unveiled fully for the first time by one of our most acclaimed historians.

Purchased at UCLA Store for $8.99+tax

🔖 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.

Acquired The Emergence of Biological Organization by Henry Quastler

Acquired The Emergence of Biological Organization by Henry Quastler (Yale Univ Press; First Edition edition (1964))

In 1964 Quastler's book The Emergence of Biological Organization was published posthumously. In 2002, Harold J. Morowitz described it as a "remarkably prescient book" which is "surprisingly contemporary in outlook". In it Quastler pioneers a theory of emergence, developing model of "a series of emergences from probionts to prokaryotes".

The work is based on lectures given by Quastler during the spring term of 1963, when he was Visiting Professor of Theoretical Biology at Yale University. In these lectures Quastler argued that the formation of single-stranded polynucleotides was well within the limits of probability of what could have occurred during the pre-biologic period of the Earth. However, he noted that polymerization of a single-stranded polymer from mononucleotides is slow, and its hydrolysis is fast; therefore in a closed system consisting only of mononucleotides and their single-stranded polymers, only a small fraction of the available molecules will be polymerized. However, a single-stranded polymer may form a double-stranded one by complementary polymerization, using a single-stranded polynucleotide as a template. Such a process is relatively fast and the resulting double-stranded polynucleotide is much more stable than the single single-stranded one since each monomer is bound not only along the sugar phosphate backbone, but also through inter-strand bonding between the bases.

The capability for self-replication, a fundamental feature of life, emerged when double-stranded polynucleotides disassociated into single-stranded ones and each of these served as a template for synthesis of a complementary strand, producing two double-stranded copies. Such a system is mutable since random changes of individual bases may occur and be propagated. Individual replicators with different nucleotide sequences may also compete with each other for nucleotide precursors. Mutations that influence the folding state of polynucleotides may affect the ratio of association of strands to dissociation and thus the ability to replicate. The folding state would also affect the stability of the molecule. These ideas were then developed to speculate on the emergence of genetic information, protein synthesis and other general features of life.

Lily E. Kay says that Quastler's works "are an illuminating example of a well reasoned epistemic quest and a curious disciplinary failure". Quastler's aspiration to create an information based biology was innovative, but his work was "plagued by problems: outdated data, unwarranted assumptions, some dubious numerology, and, most importantly, an inability to generate an experimental agenda." However Quastler's "discursive framework" survived.

Forty-five years after Quastler's 1964 proposal, Lincoln and Joyce described a cross-catalytic system that involves two RNA enzymes (ribosymes) that catalyze each other's synthesis from a total of four component substrates. This synthesis occurred in the absence of protein and could provide the basis for an artificial genetic system.

The Emergence of Biological Organization

There was a single used copy in the UK for $12.49 and all the rest are $149.00+ so I snapped it up. Should be an interesting read in and of itself, but I suspect it’s got an interesting niche of the history of science covered with respect to bit history, complexity, and biological organization.

Should arrive some time between March 13 – March 25.

📑 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…