Thursday, March 5, 2020

Friday Thinking 6 Mar 2020

Friday Thinking is a humble curation of my foraging in the digital environment. My purpose is to pick interesting pieces, based on my own curiosity (and the curiosity of the many interesting people I follow), about developments in some key domains (work, organization, social-economy, intelligence, domestication of DNA, energy, etc.)  that suggest we are in the midst of a change in the conditions of change - a phase-transition. That tomorrow will be radically unlike yesterday.

Many thanks to those who enjoy this.

In the 21st Century curiosity will SKILL the cat.

Jobs are dying - Work is just beginning.
Work that engages our whole self becomes play that works.
Techne = Knowledge-as-Know-How :: Technology = Embodied Know-How  
In the 21st century - the planet is the little school house in the galaxy.
Citizenship is the battlefield of the 21st  Century

“Be careful what you ‘insta-google-tweet-face’”
Woody Harrelson - Triple 9


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Quotes:

Articles:



Decisions, decisions. All of us are constantly faced with conscious and unconscious choices. Not just about what to wear, what to eat or how to spend a weekend, but about which hand to use when picking up a pencil, or whether to shift our weight in a chair. To make even trivial decisions, our brains sift through a pile of “what ifs” and weigh the hypotheticals. Even for choices that seem automatic — jumping out of the way of a speeding car, for instance — the brain can very quickly extrapolate from past experiences to make predictions and guide behavior.

Place cells have been shown to fire very rapidly in particular sequences as an animal moves through its environment. The activity corresponds to a sweep in position from just behind the animal to just ahead of it. (Studies have demonstrated that these forward sweeps also contain information about the locations of goals or rewards.) These patterns of neural activity, called theta cycles, repeat roughly eight times per second in rats and represent a constantly updated virtual trajectory for the animals.

...when an animal is about to act, the neural activity associated with the theta cycles pings back and forth between different possible future paths — not just to make predictions about what’s to come, but as a kind of high-speed, back-and-forth taste test from a buffet of upcoming courses of action.

In Brain Waves, Scientists See Neurons Juggle Possible




"We hear a lot about how our own human genes influence our health and behaviors, so it may come as a shock to think that we could have molecules in the body that look and act the way they do not because of our genes, but because of another living organism," 

they analyzed 768 samples from 96 sites of 29 different organs from four germ-free mice and four mice with normal microbes. The result was a map of all of the molecules found throughout the body of a normal mouse with microbes, and a map of molecules throughout a mouse without microbes.

A comparison of the maps revealed that as much as 70 percent of a mouse's gut chemistry is determined by its gut microbiome. Even in distant organs, such as the uterus or the brain, approximately 20 percent of molecules were different in the mice with gut microbes.

How resident microbes restructure body chemistry




The movie Blade Runner was released in 1982; and was set in a future Los Angeles. Anyone here know when in the future Blade Runner is set? I mean, exactly?

The year was 2019. More precisely, next month: November.

In Blade Runner’s 2019, Los Angeles is a dark and rainy hellscape with buildings the size of mountains, flying cars, and human replicants working on off-world colonies. It also has pay phones and low-def computer screens that are vacuum tubes.

Missing is a communication system that can put everyone in the world at zero distance from everyone else, in disembodied form, at almost no cost—a system that lives on little slabs in people’s pockets and purses, and on laptop computers far more powerful than any computer, of any size, from 1982.

In other words, this communication system—the Internet—was less thinkable in 1982 than flying cars, replicants and off-world colonies. Rewind the world to 1982, and the future Internet would appear a miracle dwarfing the likes of loaves and fish.

In economic terms, the Internet is a common pool resource; but non-rivalrous and non-excludable to such an extreme that to call it a pool or a resource is to insult what makes it common: that it is the simplest possible way for anyone and anything in the world to be present with anyone and anything else in the world, at costs that can round to zero

the Internet is designed to support every possible use, every possible institution, and—alas—every possible restriction, which is why enclosure is possible. People, institutions and possibilities of all kinds can be trapped inside enclosures on the Internet. I’ll describe nine of them

So my thesis here is this: if we can deeply and fully understand what the Internet is, why it is fully important, and why it is in danger of enclosure, we can also understand why, ten years after Lin Ostrom won a Nobel prize for her work on the commons, that work may be exactly what we need to save the Internet as a boundless commons that can support countless others.

Saving the Internet—and all the commons it makes possible




In his 1988 essay collection Infinite in All Directions, Dyson speculated on why there is so much violence and hardship in the world. The answer, he suggested, might have something to do with what he called "the principle of maximum diversity." This principle, he continued,

operates at both the physical and the mental level. It says that the laws of nature and the initial conditions are such as to make the universe as interesting as possible. As a result, life is possible but not too easy. Always when things are dull, something turns up to challenge us and to stop us from settling into a rut. Examples of things which made life difficult are all around us: comet impacts, ice ages, weapons, plagues, nuclear fission, computers, sex, sin and death. Not all challenges can be overcome, and so we have tragedy. Maximum diversity often leads to maximum stress. In the end we survive, but only by the skin of our teeth.

Dyson, it seemed to me, was suggesting that we cannot solve all our problems, we cannot create heaven, we cannot find The Answer to the riddle of existence. Life is--and must be--an eternal struggle. Was I reading too much into Dyson's remarks? I hoped to find out when I interviewed him in 1993 at the Institute for Advanced Study, his home since the early 1940's.

Scientific Rebel Freeman Dyson Dies




According to Simone de Beauvoir in The Ethics of Ambiguity (1948), one of the forms that nihilism can take is nostalgia – the desire to return to how free we felt as children before we discovered as adults that freedom entails responsibility. Corporations can therefore also benefit from promoting nihilism in the form of selling us nostalgia and other ways to distract ourselves from reality. This is why we must not only recognise the nihilism in ourselves, but also recognise that it exists in the world around us, and identify the sources of that nihilism. Rather than letting ourselves feel powerless in a world that seems to have stopped caring, we should ask where nihilistic views of the world are coming from, and who benefits from our seeing the world that way.

Nihilism





This is a strong signal of ongoing progress in the domestication of DNA, proteomics and more.
“Twenty years ago, people struggled just to put a few genes together,” says Patrick Cai, a synthetic biologist at the University of Manchester, UK, who is the international coordinator of Sc2.0. “Today, people are looking at chromosomes with thousands of components.”

How to build a genome

A powerful set of molecular tools helps synthetic biologists to assemble DNA of different sizes, from the gene to the chromosome scale.
 the Boeke lab (now at New York University’s Langone Medical Center in New York City) and its collaborators in Europe, Asia and Australia are close to producing recoded versions of all 16 Saccharomyces cerevisiae chromosomes, as well as a 17th, artificial, ‘neochromosome’.

Only a handful of genomes have been synthesized so far, mostly for bacteria. Synthetic biologist Jason Chin and his colleagues at the MRC Laboratory of Molecular Biology in Cambridge, UK, have rewritten the genome of Escherichia coli, and researchers at the J. Craig Venter Institute (JCVI) in La Jolla, California, have constructed a ‘minimal’ genome for Mycoplasma mycoides, which has all non-essential genes deleted2. Sc2.0 will synthesize the first genome of a eukaryote (a cell that has a nucleus enclosed within a membrane), and marks a huge advance in the engineering and assembly of DNA sequences.

The tools and techniques used to synthesize genomes are proving powerful at smaller scales, too. They are, for example, allowing researchers to string together custom-built metabolic pathways so that cells can manufacture drugs such as opioids and antibiotics. But cells are not as easy to rewire as circuit boards, and the field is still unable to achieve its ultimate goal: designing complex biological systems that give predictable results. “The complexity of genome design remains much higher than our current tools can support,” says Cai.


This is a great signal of the emerging world of domesticated DNA - we can expect huge leaps in the next decade. I’m still convinced that at least one nation will undertake a genome census of its population by 2025 and by 2030 may be a must do for advanced nations. The reason is simple - the gene pool is our common wealth.
“I think there is some natural skepticism about whether it’s really for real,” says Stacey Gabriel, director of the genomics platform at the Broad Institute, in Cambridge, Massachusetts. “But if it’s $100, that would be several-fold cheaper. There is a little bit of buzz because there has not been a big sequencing announcement for a couple of years.”
Since the first human genome was decoded in 2003, costs have dropped precipitously. A decade ago, decoding one person's genome cost around $50,000. Today, the cost (mostly for chemicals) is around $600 for the largest sequencing centers.
To hit an even lower mark, BGI’s new system will employ a robotic arm and a roomful of chemical baths and imaging machines.
For the last five years, the cost of genome sequencing has been kept at $1,000. I don’t think that is because of technology stagnation, but because Illumina has a monopoly

China’s BGI says it can sequence a genome for just $100

Super-cheap DNA sequencing could boost cancer screening, prenatal tests, and research into population genetics.
Using technology originally acquired in the US, the Chinese gene giant BGI Group says it will make genome sequencing cheaper than ever, breaking the $100 barrier for the first time.

The Shenzhen company says the low cost will be possible with an "extreme" DNA sequencing system it plans to offer that is capable of decoding the genomes of 100,000 people a year. 

The claim, made today at a DNA technology conference in Marco Island, Florida, could intensify competition between BGI and Illumina, the California firm whose speedy instruments have dominated the gene-sequencing scene for more than a decade.

… as some large initiative takes shape. For instance, a project funded by the National Institutes of Health, All of Us, intends to create a health database containing the sequence of one million Americans volunteers. The UK is already sequencing 500,000 people as part of its own national program.


This remains a weak-ish signal - it is a growing one. In the next decade we may well have ways to remain younger while we age.

Anti-aging drugs

Drugs that try to treat ailments by targeting a natural aging process in the body have shown promise.
The first wave of a new class of anti-aging drugs have begun human testing. These drugs won’t let you live longer (yet) but aim to treat specific ailments by slowing or reversing a fundamental process of aging.

The drugs are called senolytics—they work by removing certain cells that accumulate as we age. Known as “senescent” cells, they can create low-level inflammation that suppresses normal mechanisms of cellular repair and creates a toxic environment for neighboring cells.

In June, San Francisco–based Unity Biotechnology reported initial results in patients with mild to severe osteoarthritis of the knee. Results from a larger clinical trial are expected in the second half of 2020. The company is also developing similar drugs to treat age-related diseases of the eyes and lungs, among other conditions.

Senolytics are now in human tests, along with a number of other promising approaches  targeting the biological processes that lie at the root of aging and various diseases.


One signal toward the domestication of DNA for the treatment of disease.

Diabetes in mice cured rapidly using human stem cell strategy

Researchers have converted human stem cells into insulin-producing cells and demonstrated in mice infused with such cells that blood sugar levels can be controlled and diabetes functionally cured for nine months.

The findings, from researchers at Washington University School of Medicine in St. Louis, are published online Feb. 24 in the journal Nature Biotechnology.

"These mice had very severe diabetes with blood sugar readings of more than 500 milligrams per deciliter of blood—levels that could be fatal for a person—and when we gave the mice the insulin-secreting cells, within two weeks their blood glucose levels had returned to normal and stayed that way for many months," said principal investigator Jeffrey R. Millman, Ph.D., an assistant professor of medicine and of biomedical engineering at Washington University.


Here is a great weak signal on the future of a biocomputing paradigm.
"We built a kind of biological computer in the living cells. In this computer, as in regular computers, circuits carry out complicated calculations," said Barger. "Only here, these circuits are genetic, not electronic, and information are carried by proteins and not electrons."
Our research takes synthetic biology one step further and makes biology an accurate and planned science,

Researchers turn bacterial cell into biological computer

Researchers at the Technion have created a biological computer, constructed within a bacterial cell and capable of monitoring different substances in the environment. Currently, the computer identifies and reports on toxic and other materials. Next up: the ability to warn about hemorrhaging in the human body.

The research by Ph.D. student Natalia Barger and Assistant Professor Ramez Daniel, head of the Synthetic Biology and Bioelectronics Lab at the Technion's Faculty of Biomedical Engineering, was published in September 2019 in the journal Nucleic Acids Research (NAR).

In recent decades, the barriers between engineering and life sciences have been falling, and from the encounter between the two different disciplines, a new science—synthetic biology—was born. Synthetic biology introduces engineering into biology, makes it possible to design and build biological systems that don't exist in nature, and supplies an innovative toolbox for reprogramming the genetic code in living creatures, including humans.

In their NAR article, the researchers present a reorganization of the complex genetic structure of bacterial luciferase—proteins involved in the creation of light by bacterial cell.


This may be a very scary signal for many - but it is a signal of domesticating DNA.
“What is unique about this technology is that it is species-specific, so the released diamondback male moths only mate with female diamondback moths and do not affect other beneficial organisms in the field, such as pollinators or beneficial biological control insects,”
“This technology will not eliminate the pest species because the gene disappears from the environment after a few generations,” Shelton added. “Diamondback moths will continue to survive in other fields and on wild hosts.” 

Scientists Release Genetically Engineered Moths for First Time

Of course, the release of any genetically engineered organism into the wild brings with it a slew of concerns.
The diamondback moth is a huge pest. It eats a variety of crops, but is largely resistant to insecticides, resulting in upwards of $5 billion in losses every year.

That could soon change, though, as an international team of researchers has created a strain of genetically engineered diamondback moths that could suppress the pest population in a sustainable way — and they just released them into the wild for the first time.

For the study, published in the journal Frontiers in Bioengineering and Biotechnology, the researchers engineered the moths so that when the males of the strain mated with wild females, the female offspring would die during the caterpillar life stage.


This is another important signal in the progress in imaging the small - and therefore accelerating the domestication of DNA.
This power and versatility will enable a new wave of molecular precision to be brought to diverse problems in vacinnology, virology, neurodegenerative plaques and disease biology in general.
"Whether directly characterizing different strains of viruses or profiling different vaccine formulations, our new technology now can be deployed directly on these protein-containing samples to pursue the most urgent challenges of the day," 

Technology provides a new way to probe single molecules

Biology can be murky, and medicine involves dealing with very complex mixtures of molecules. A new technology developed at Northwestern University now offers some clarity to scientists with precision measurements of proteins down to their atoms.

The powerful new approach, called individual ion mass spectrometry, or I2MS, can determine the exact mass of a huge range of intact proteins. It weighs each and every molecule on an individual basis. This ability promises to aid the understanding of disease and infection and accelerate the design of vaccines for deadly viruses, such as the coronavirus.

Details on this fundamentally new way to weigh single molecules of proteins or their assemblies, such as whole viruses, is published March 2 by the journal Nature Methods.


This is a fascinating signal pointing to progress in our understanding of the quantum realm.
The "film" displays the evolution during the measurement process. The individual pictures show tomography data where the height of the bars reveal the degree of superposition that is still preserved. During the measurement some of the superpositions are lost—and this loss happens gradually—while others are preserved as they should be for an ideal quantum measurement.

Scientists 'film' a quantum measurement

Measuring a quantum system causes it to change—one of the strange but fundamental aspects of quantum mechanics. Researchers at Stockholm University have now been able to demonstrate how this change happens. The results are published in the scientific journal Physical Review Letters.

Despite the importance of the measurement process within the theory, it still holds unanswered questions: Does a quantum state collapse instantly during a measurement? If not, how much time does the measurement process take and what is the quantum state of the system at any intermediate step?

A collaboration of researchers from Sweden, Germany and Spain has answered these questions using a single atom—a strontium ion trapped in an electric field. The measurement on the ion lasts only a millionth of a second. By producing a "film" consisting of pictures taken at different times of the measurement they showed that the change of the state happens gradually under the measurement influence.


This is an important signal - not only of the progress in energy efficiency but also of how to think about future trends that are influenced by other trends -including active human effort.
"While the historical efficiency progress made by data centers is remarkable, our findings do not mean that the IT industry and policymakers can rest on their laurels," said Eric Masanet, who led the study. "We think there is enough remaining efficiency potential to last several more years. But ever-growing demand for data means that everyone—including policy makers, data center operators, equipment manufacturers and data consumers—must intensify efforts to avoid a possible sharp rise in energy use later this decade."

Data centers use less energy than you think

If the world is using more and more data, then it must be using more and more energy, right? Not so, says a comprehensive new analysis.
Researchers at Northwestern University, Lawrence Berkeley National Laboratory and Koomey Analytics have developed the most detailed model to date of global data center energy use. With this model, the researchers found that, although demand for data has increased rapidly, massive efficiency gains by data centers have kept energy use roughly flat over the past decade.

This detailed, comprehensive model provides a more nuanced view of data center energy use and its drivers, enabling the researchers to make strategic policy recommendations for better managing this energy use in the future.


This is another good signal of the transformation of energy geopolitics.

Australia could soon export sunshine to Asia via a 3800-km cable

Australia is the world's third largest fossil fuels exporter – a fact that generates intense debate as climate change intensifies. While the economy is heavily reliant on coal and gas export revenues, these fuels create substantial greenhouse gas emissions when burned overseas.

Sun Cable was announced last year by a group of Australian developers. The project's proponents say it would provide one-fifth of Singapore's power supply by 2030, and replace a large share of fossil fuel-generated electricity used in Darwin.

To export renewable energy overseas, a high-voltage (HV) direct current (DC) cable would link the Northern Territory to Singapore. Around the world, some HVDC cables already carry power across long distances. One ultra-high-voltage direct current cable connects central China to eastern seaboard cities such as Shanghai. Shorter HVDC grid interconnectors operate in Europe.


The world of fake news is ancient and long standing in the 20th century (see Chomsky’s “Manufacturing Consent” and any form of advertising. Also product placement (or not) in film and other forms of visual media aims to shape narratives. Despite being the overwhelmingly popular operating system for phones - when is the last time you saw Android phones or Chrome or Windows computers in film?

Apple won’t allow villains to use its products on screen

Apple is trying really, really hard to always come off as the good guys. According to Rian Johnson, director of Knives Out, Apple won’t let villains use iPhones on-screen.
THIS IS SILLY — Smartphones have become as ubiquitous in movies as they are in real life, but apparently there are still limits to how closely we can mirror reality. Apple is so obsessed with how the public conceptualizes its products that the company has taken steps to ensure none of the bad guys ever use its phones in movies. 
Meanwhile, anyone can go out and buy an iPhone — there’s no doubt in my mind that plenty of bad people use Apple products.
Apple has legions of loyal fans who are very unlikely to be swayed by a movie villain using an iPhone.




This is a wonderful signal of new approaches to live theatre with audience participation and integrated technology. I encourage everyone who will be in Ottawa during the performance to join the action.  The time is getting close so please register to attend.
As an extra bonus -the Friday night performances will be followed by a short panel discussions after the Friday night shows discussing the issues raised in the play, panellists including Tracey Lauriault (Professor of Critical Media Studies, Carleton U.), Murad Hemmadi (journalist for The Logic), and Anthony Scavarelli (Algonquin Professor and VR researcher).

Strata Inc.

Dates: March 6, 7, 13, and 14, at 8pm
Location: Rebel.com, 377 Dalhousie Street
Tickets available here:
Written by Megan Piercey Monafu
Sound design by Johnny Wideman 

As a teen, Victoria was an infamous hacker. Now a young adult, she has created a powerful virtual reality platform and agreed to work for a giant corporation to bring that platform to a huge audience. As users plunge into, trip over, and run away from the new Internet reality of VR experiences, exploring online privacy, connection, security, and access, Victoria must choose: run the multinational responsible, or escape from her own invention.

Strata Inc. is based on real developments in VR as it intersects with marketing, the world of work, and new outlets for the imagination. Strata Inc. uses individual audience headphones, sound design, and mic’d actors to echo the transportational abilities of VR while creating an in-person communal audio experience.

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