Content
Quotes:
A touch of absurdity can help to wrap your mind around reality
Articles:
How a Canadian Newsroom Launched a Co-Op to Save Itself from Bankruptcy
African scientists leverage open hardware
Society Is Becoming Germaphobic. Let’s Not Stay That Way.
The information theory of individuality
The Genome Aggregation Database (gnomAD)
Humans and Neanderthals: Less different than polar and brown bears
City foxes are becoming more similar to domesticated dogs as they adapt to their environment
New molecule stops drug cravings in mice, with fewer side effects
New technology enables fast protein synthesis
Researchers develop 'poisoned arrow' to defeat antibiotic-resistant bacteria
Spreading the Word on a Possible Alzheimer’s Treatment
What happens when we experience the ‘Ground’ as the ‘Figure’?
According to research on the ‘meaning maintenance model’ of human reasoning, surreal and absurd art can be so unsettling that the brain reacts as if it is feeling physical pain, yet it ultimately leads us to reaffirm who we are, and sharpens the mind as we look for new ways to make sense of the world. The findings also suggest new ways to improve education, and even help to explain our responses to some of the more absurd political events of recent years.
The meaning maintenance model was first proposed by three psychologists – Steven Heine, Travis Proulx and Kathleen Vohs – in 2006. They were inspired by the French-Algerian philosopher Albert Camus, who argued that the human mind continuously attempts to construct a view of reality as a single, coherent whole – an urge he described in The Myth of Sisyphus (1942) as ‘nostalgia for unity’.
Heine and his team proposed that our mental representation of the world is like a delicate web of interconnected beliefs, documenting the relations between ourselves and the people, places and objects around us. When we are confronted with an apparently inexplicable event that appears to break that framework, we feel profound uncertainty – the ‘feeling of the absurd’.
A touch of absurdity can help to wrap your mind around reality
Kauffman (2019, 12 - 13) states that Weinberg is categorically wrong and points out, “One thing missing in the world according to physics is the crucial idea of agency… Given agency, meaning exists in the universe.” He then asks "How did the universe get from matter to mattering? In the meaningless, numb universe of Weinberg, where does mattering come from?” Mattering, in Kauffman’s play on words, is simply meaning or information and information is about the informing of a living agent that is able to
propagate its organization. Physics has no explanation of agency or an agent capable of propagating its organization.
A living agent to create and propagate its organization must be able to take energy from its environment and convert it into work which requires constraints. The constraint of the cylinder in an automobile engine that directs the energy of the gasoline air mixture explosion to push against the piston and hence do work is an example of the necessity of constraints to do work. In a paper entitled Propagating Organization: An Enquiry (Kauffman, Logan, et al. 2007) we argued that the constraints are information and hence possess meaning or meaningfulness. According to Kauffman, this ability for a system to self-organize in such a way as to propagate its organization is the extra ingredient that cannot be explained by physics.
Review of Stuart Kauffman’s A World Beyond Physics and Its Parallel with McLuhan’s Reversal of Cause and Effect
https://jps.library.utoronto.ca/index.php/nexj/article/view/34237/26220
When datasets are created and archives accessed digitally, users aren’t viewing a simple facsimile of the original materials. They are looking at computer files that will have undergone a series of transformations that mask the assumptions built into the digital architecture, as well as the conditions under which the data was produced. Besides, for the majority of historians, ‘historical facts’ are not discrete items that exist independently, awaiting scholars who will hunt them down, gather them up and catalogue them safely. They need to be created and interpreted. Textual archives might seem relatively easy to reproduce, for example, but, just as with archaeological digs, the physical context in which documents are found is essential to their interpretation: what groups, or items, or experiences did past generations value and record, and which of these must be salvaged from the margins of the archives? What do the marginalia tell us about how the meanings of words have changed?
Mathematical, data-driven, quantitative models of human experience that aim at detachment, objectivity and the capacity to develop and test hypotheses need to be balanced by explicitly fictional, qualitative and imaginary efforts to create and project a lived future that enable their audiences to empathically ground themselves in the hopes and fears of what might be to come. Both, after all, are unequivocally doing the same thing: using history and historical experience to anticipate the global future so that we might – should we so wish – avoid civilisation’s collapse. That said, the question of who ‘we’ are does, always, remain open.
Are there laws of history?
Foucault argued that if you look at the way in which prisons operate, that is, at their mechanics, it becomes evident that they are designed not so much to lock away criminals as to submit them to training rendering them docile. Prisons are first and foremost not houses of confinement but departments of correction. The crucial part of this institution is not the cage of the prison cell, but the routine of the timetables that govern the daily lives of prisoners. What disciplines prisoners is the supervised morning inspections, the monitored mealtimes, the work shifts, even the ‘free time’ overseen by a panoply of attendants including armed guards and clipboard-wielding psychologists.
Importantly, all of the elements of prison surveillance are continuously made visible. That is why his book’s French title Surveiller et punir, more literally ‘Surveil and Punish’, is important. Prisoners must be made to know that they are subject to continual oversight. The purpose of constant surveillance is not to scare prisoners who are thinking of escaping, but rather to compel them to regard themselves as subject to correction. From the moment of morning rise to night’s lights out, the prisoners are subject to ceaseless behavioural inspection.
The crucial move of imprisonment is that of coaxing prisoners to learn how to inspect, manage and correct themselves. If effectively designed, supervision renders prisoners no longer in need of their supervisors. For they will have become their own attendant. This is docility.
The power thinker
This is a good even if weak signal of a possible future trajectory for news media enterprises.
“If last fall we didn’t feel the community was ready to donate, contribute and participate, we probably would have had to stop everything,” said Gilles Carignan, Le Soleil’s director general. “Now, the focus on the community is clearer than ever.”
Readers’ eagerness to support the newsroom financially provided an unexpected jolt. “The biggest surprise for us at the time was a lot of readers wrote to us to say they wanted to help, saying, ‘Hey, I want to maintain local information in Quebec. But I don’t want paper, and you give everything free on the web,’” recalled Carignan.
How a Canadian Newsroom Launched a Co-Op to Save Itself from Bankruptcy
https://gijn.org/2020/05/29/how-a-canadian-newsroom-launched-a-co-op-to-save-itself-from-bankruptcy/
As COVID-19 has brought newsrooms worldwide to their knees, one French Canadian outlet is flourishing — less than a year after going bankrupt.
Quebec City’s Le Soleil doubled its number of readers this spring as the pandemic swept the globe. The French-language daily newspaper converted this into 3,500 new subscribers by the end of April, including 1,000 over a single 10-day period, according to Simon Audet, Le Soleil’s head of digital development.
Driving this success is a revamped, reader-first editorial strategy. But first, Le Soleil had to stave off bankruptcy. They did so by forming Canada’s largest newsroom cooperative. Along the way, they found their readers were eager to help save their local news source.
The co-op business model was just a first step. Any sustainable path forward for Le Soleil required an overhauled editorial approach, too, explained Carignan.
As Le Soleil restructured last fall, newsroom staff reached out to readers. They invested in conversations with them, and welcomed feedback. Readers wanted more than just surface-level reporting, Le Soleil found. “[Our readers] gave us all the answers we needed to adjust our content,” said Carignan. “People want content. They will be ready to invest in us, to subscribe if we give them local news but with substance.”
Another important signal of the future of citizen and open-source science and more.
“Open-science hardware is not only important in Africa but all over the world,” Chagas says. “If you have the blueprint for a piece of equipment, you can understand how it works. You can repair your equipment if it breaks down, and, even more importantly, adapt it to your local needs.”
African scientists leverage open hardware
A growing emphasis on do-it-yourself science is helping researchers to equip labs in resource-limited areas.
Founded in 2011 by Lucia Prieto-Godino, now at the Francis Crick Institute in London, Sadiq Yusuf at the Uganda Technology and Management University in Kampala and Tom Baden at the University of Sussex in Brighton, UK, TReND in Africa encourages do-it-yourself research with a focus on low-cost, open-source science. Courses cover such topics as fly genetics, neuroscience and hardware development.
In one example, TReND in Africa instructor and University of Sussex bioengineer André Maia Chagas joined a team including Prieto-Godino and Baden in 2017 to design a microscope. It was built using off-the-shelf and 3D-printed components, and dubbed the €100 lab.
At US$122.91, the device is a fraction of the cost of commercial systems, which can amount to $6,000 or more. The resulting paper in HardwareX helped Kumbol to secure funding from the Mozilla Foundation to organize a follow-up workshop last July at the University of Health and Allied Sciences in Ho, Ghana. He has demonstrated Actifield at the Kwame Nkrumah University of Science and Technology, and has built actimeters for the science department there.
What a fascinating signal that sort of blows up the notion of people on social media being in a bubble or echo-chamber. It also signals the challenge of educating and socializing the digital natives that are coming of age now and will come of age in the future.
Teens on TikTok are exposing a generational rift between parents and kids over how they treat Black Lives Matter protests
https://theintercept.com/2020/03/31/zoom-meeting-encryption/
TikTok has been flooded with #blacklivesmatter content following the killing of George Floyd in police custody, and the subsequent protests that have rippled across the globe.
Many Gen Z kids have found themselves clashing with parents over racial justice issues.
Now, some are taking to TikTok to express their frustration over the difficult conversations they're having with the parents and relatives to bring them up to speed on the Black Lives Matter movement.
Social media is awash with earnest shows of support for the Black Lives Matter movement. The best of these posts have been materially useful to the cause. Others, less so. But on TikTok, Gen Z is modeling the most important tenet of allyship: taking it upon yourself to research, point out, and confront racism, especially when it feels risky or uncomfortable to do so.
This is an important signal for the future of our health.
Society Is Becoming Germaphobic. Let’s Not Stay That Way.
LET’S FACE IT. We’re all germaphobes now.
what if this anxiety crystallizes into a long-term, habitual fear of germs? I believe that such a cultural shift wouldn’t just be unhelpful, it would potentially be a danger to public health — and to the broader social sphere.
To understand why, it’s helpful to remind ourselves that viruses can have beneficial effects. Some viruses, including many bacteriophages, possess life-saving medical powers. Others, including herpesviruses, can lead to serious infections, but in their dormant state may also train the human immune system to fight Listeria food poisoning and bubonic plague. And studies have shown that moderate levels of exposure to pathogenic viruses during early childhood can offer a protective effect later on in life. A study published in the journal Pediatrics in 2016, for instance, found that children who attended daycare before their first birthday experienced fewer bouts of stomach flu later in childhood than peers who didn’t attend daycare. (That study tracked participants only up to age six, though the authors suggest that the protective effect may extend much longer.) In an attempt to completely rid our lives of viruses, we could rob ourselves of some of the protections they afford.
Moreover, the sanitizers and soaps we’re using to immobilize the new coronavirus can also wipe out bacteria that are essential to human health. The human microbiome, the diverse collection of microbes living in and on the human body, has now been established as hugely important to digestive health, metabolic function, and immune responses. Jonathan Eisen, a microbiologist at the University of California, Davis, noted in an interview with Popular Science that hand sanitizer can disturb the microbiome of our skin. (This may allow more dangerous pathogens to take root.) Used excessively, Eisen added, hand sanitizers might also promote antibiotic resistance, another public health threat.
This is a very interesting signal of the future of our understanding of identity and the individual.
From the perspective of physics and chemistry, biological life is surprising. There is no physical or chemical theory from which we can predict biology, and yet if we break down any biological system into its elementary constituents, there is no chemistry or physics remaining unaccounted for
recent work suggests that viruses like microbes form collective units that facilitate infection .... These observations suggest that viruses in aggregate are individuals but not in the conventional sense. Rather they are what Krakauer … has called “chimerical individuals.”
without a rigorous definition of both the environment and the agent it is difficult to speak consistently of individuals. This is analogous to figure-ground separation in gestalt psychology or computer vision. The background of an image carries as much if not more information than the object, and the challenge is to separate the two rather than assume that they are already distinct and independent.
The information theory of individuality
https://link.springer.com/content/pdf/10.1007/s12064-020-00313-7.pdf
Abstract
Despite the near universal assumption of individuality in biology, there is little agreement about what individuals are and few rigorous quantitative methods for their identification. Here, we propose that individuals are aggregates that preserve a measure of temporal integrity, i.e., “propagate” information from their past into their futures. We formalize this idea using information theory and graphical models. This mathematical formulation yields three principled and distinct forms of individuality—an organismal, a colonial, and a driven form—each of which varies in the degree of environmental dependence and inherited information. This approach can be thought of as a Gestalt approach to evolution where selection makes figure-ground (agent–environment) distinctions using suitable information-theoretic lenses. A benefit of the approach is that it expands the scope of allowable individuals to include adaptive aggregations in systems that are multi-scale, highly distributed, and do not necessarily have physical boundaries such as cell walls or clonal somatic tissue. Such individuals might be visible to selection but hard to detect by observers without suitable measurement principles. The information theory of individuality allows for the identification of individuals at all levels of organization from molecular to cultural and provides a basis for testing assumptions about the natural scales of a system and argues for the importance of uncertainty reduction through coarse-graining in adaptive systems.
The question we seek to address is more limited. How do we identify individuals without relying on features like cell membranes that may be solutions to challenges faced by particular systems for maintaining integrity rather than foundational properties? We want to allow for the possibility that microbes and loosely bound ecological assemblages such as microbial mats and cultural and technological systems, when viewed with a mathematical lens, qualify as individuals even though their boundaries are more fluid than the organisms we typically allow. It may also be the case that entities currently considered individuals are indeed individuals but not in the way we think—organisms are more complicated than typical individuality definitions acknowledge.
Individuality can be nested. Given that life is hierarchically organized into trophic and functional levels, we allow the possibility of multiple, parallel levels of individuality. We take this position to be related to the recent suggestion of (Rieppel 2013) where he argues for individuals based on hierarchical complexes of homeostatic properties and (Flack 2017a) who has proposed biological systems are information hierarchies resulting from the collective effects of components estimating, in evolutionary or ecological time, regularities in their environments by coarse-graining or compressing time series data and using these perceived regularities to tune strategies. As coarse-grained (slow) variables become for components better predictors than microscopic behavior (which fluctuates), and component estimates of these variables converge, new levels of organization consolidate.
It may seem like a much longer time since the first full human genome was sequenced - but it is still very early days as not just the genome but proteonic and other molecules are being increasingly understood.
The Genome Aggregation Database (gnomAD)
A collection of research articles and related content from the gnomAD Consortium that describe and analyse human genetic variation.
The human genome comprises both our protein-coding genes and the regulatory information that controls when, and to what extent, those genes are expressed. While humans mostly share the same repertoire of genes and regulatory elements, the underlying sequences are as diverse as the people on Earth; each individual’s genome is unique. To reflect this diversity and to capture the extent of variation among a large group of individuals on an unprecedented scale, the Genome Aggregation Database (gnomAD) has aggregated 15,708 whole genomes and 125,748 exomes (the protein-coding part of the genome). Analyses of this rich resource have created a catalogue of the different types of variation present, and revealed their potential functional impact and how this information could help to identify disease-causing mutations and to prioritize potential drug targets.
This is a good signal that despite apparent diversity - there is more in common with all humans.
"Our desire to categorize the world into discrete boxes has led us to think of species as completely separate units. Biology does not care about these rigid definitions, and lots of species, even those that are far apart evolutionarily, swap genes all the time. Our predictive metric allows for a quick and easy determination of how likely it is for any two species to produce fertile hybrid offspring. This comparative measure suggests that humans and Neanderthals and Denisovans were able to produce live fertile young with ease."
Humans and Neanderthals: Less different than polar and brown bears
Ancient humans, Neanderthals and Denisovans were genetically closer than polar bears and brown bears, and so, like the bears, were able to easily produce healthy, fertile hybrids according to a study, led by the University of Oxford's School of Archaeology.
The study, published 3 June in the journal Proceedings of the Royal Society B, shows that the genetic distance values between humans and our ancient relatives were smaller than the distance between pairs of species which are known to easily hybridize and have fertile young.
When the distance values between humans, Neanderthals and Denisovans were calculated, they were even smaller than the values between several pairs of species which are known readily and easily to hybridize—including polar bears and brown bears, and coyotes and wolves. This suggests we could have predicted the existence of Neanderthals and Denisovans in our genomes as soon as the first genetic sequences were generated.
An interesting signal of the evolution of evolution even in built environments.
while urban foxes are certainly not domesticated, they are changing in ways that move them closer to what is seen in many domesticated animals.
City foxes are becoming more similar to domesticated dogs as they adapt to their environment
Urban red foxes are becoming more similar to domesticated dogs as they adapt to their city environment, according to a new analysis.
A team led by Dr. Kevin Parsons, of the University of Glasgow's Institute of Biodiversity, Animal Health and Comparative Medicine, has carried out an analysis into the differences between urban and rural red foxes in the UK.
Their findings go some way to explaining how dogs could have evolved into our current pets.
With our current lockdown measures due to the COVID-19 pandemic we are seeing a number of animals more frequently in our cities. It has been known for some time that cities create new habitats for wild populations. While many can't cope, it is recognized that some types of animals are especially good at living within cities. Red foxes are prevalent within several cities within the UK and elsewhere where they have become well-established.
This is an interesting signal for the future of some forms of drug addiction.
New molecule stops drug cravings in mice, with fewer side effects
Duke University researchers have developed a synthetic molecule that selectively dampen the physiological rewards of cocaine in mice. It also may represent a new class of drugs that could be more specific with fewer side effects than current medications.
In mice that were treated with the stimulant cocaine or methamphetamine, the new molecule was found to calm their drug-induced hyperactivity and interfere with the dopamine system's ability to change metabolism in the brain's rewards center.
In mice that were allowed to self-administer cocaine, the treatment slowed down their drug use in 20 minutes to an hour, and reduced the amount of drug they used by more than 80 percent, compared to a control group of mice.
This is a signal of the emerging progress in developing more types of proteins to explore their efficacy for various purposes.
"You could design new variants that have superior biological function, enabled by using non-natural amino acids or specialized modifications that aren't possible when you use nature's apparatus to make proteins," says Brad Pentelute, an associate professor of chemistry at MIT and the senior author of the study.
New technology enables fast protein synthesis
Many proteins are useful as drugs for disorders such as diabetes, cancer, and arthritis. Synthesizing artificial versions of these proteins is a time-consuming process that requires genetically engineering microbes or other cells to produce the desired protein.
MIT chemists have devised a protocol to dramatically reduce the amount of time required to generate synthetic proteins. Their tabletop automated flow synthesis machine can string together hundreds of amino acids, the building blocks of proteins, within hours. The researchers believe their new technology could speed up the manufacturing of on-demand therapies and the development of new drugs, and allow scientists to design artificial proteins by incorporating amino acids that don't exist in cells.
In a paper appearing today in Science, the researchers showed that they could chemically produce several protein chains up to 164 amino acids in length, including enzymes and growth factors. For a handful of these synthetic proteins, they performed a detailed analysis showing their function is comparable to that of their naturally occurring counterparts.
A signal of important ongoing work that promises very good news about antibiotic resistance.
"This is the first antibiotic that can target Gram-positives and Gram-negatives without resistance," said Zemer Gitai, Princeton's Edwin Grant Conklin Professor of Biology and the senior author on the paper. "From a 'Why it's useful' perspective, that's the crux. But what we're most excited about as scientists is something we've discovered about how this antibiotic works—attacking via two different mechanisms within one molecule—that we are hoping is generalizable, leading to better antibiotics—and new types of antibiotics—in the future."
Researchers develop 'poisoned arrow' to defeat antibiotic-resistant bacteria
Poison is lethal all on its own—as are arrows—but their combination is greater than the sum of their parts. A weapon that simultaneously attacks from within and without can take down even the strongest opponents, from E. coli to MRSA (methicillin resistant Staphylococcus aureus).
A team of Princeton researchers reported today in the journal Cell that they have found a compound, SCH-79797, that can simultaneously puncture bacterial walls and destroy folate within their cells—while being immune to antibiotic resistance.
Bacterial infections come in two flavors—Gram-positive and Gram-negative—named for the scientist who discovered how to distinguish them. The key difference is that Gram-negative bacteria are armored with an outer layer that shrugs off most antibiotics. In fact, no new classes of Gram-negative-killing drugs have come to market in nearly 30 years.
This is an interesting weak signal of the potential of new forms of treatment modalities - as we learn more about how entangled we are with all manner of phenomena.
“We had noticed in our own data, and in that of other groups, that 40-hertz rhythm power and synchrony are reduced in mouse models of Alzheimer’s disease,” she said, as well as in patients with the disease. Apparently, if you have Alzheimer’s, your brain doesn’t produce strong brain waves in that particular frequency. In 2016, her graduate student Hannah Iaccarino reasoned that perhaps boosting the power of these weakened gamma waves would be helpful in treating this severe and irreversible dementia.
…. the strobe lights had an additional effect on mice: They also cleared out amyloid plaques. But it wasn’t clear exactly how the optogenetic stimulation or the flashing-light therapy could do that.
Spreading the Word on a Possible Alzheimer’s Treatment
Discoveries that transcend boundaries are among the greatest delights of scientific research, but such leaps are often overlooked because they outstrip conventional thinking. Take, for example, a new discovery for treating dementia that defies received wisdom by combining two formerly unrelated areas of research: brain waves and the brain’s immune cells, called microglia. It’s an important finding, but it still requires the buy-in and understanding of researchers to achieve its true potential. The history of brain waves shows why.
Scientists must specialize to succeed. Biologists studying microglia don’t tend to read papers about brain waves, and brain wave researchers are generally unaware of glial research. A study that bridges these two traditionally separate disciplines may fail to gain traction. But this study needed attention: Incredible as it may sound, the researchers improved the brains of animals with Alzheimer’s simply by using LED lights that flashed 40 times a second. Even sound played at this charmed frequency, 40 hertz, had a similar effect.
In an expanded study in Cell, they reported that just as seeing flashes at 40 hertz resulted in fewer plaques in the visual cortex, sound stimulation at 40 hertz reduced amyloid protein in the auditory cortex. Other regions were similarly affected, including the hippocampus — crucial for learning and memory — and the treated mice performed better on memory tests. Exposing the mice to both stimuli, a light show synchronized with pulsating sound, had an even more powerful effect, reducing amyloid plaques in regions throughout the cerebral cortex, including the prefrontal region, which carries out higher-level executive functions that are impaired in Alzheimer’s.
One signal exploring the possible evolution of a social self.
What happens when we experience the ‘Ground’ as the ‘Figure’?
http://www.johnverdon.com/2020/05/what-happens-when-we-experience-ground.html
Human experience emerges through its entanglements with environments. Entanglements become evident in their own mutual-enactments. To exist is to simultaneously act – in-act/enact. To act is to make a change. A Change is a difference-that-makes-a-difference – which is simultaneously ‘taking a measure’ of a (or the) situation. Taking a measure of the situation – simultaneously enacts accounting -taking account-of the situation.
The question is which differences are ones that make a difference – because to make a difference-that-makes-a-difference – is an accounting of something of ‘value’ – of something worthy of ‘standing out’ – a way of valuing values.
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