Thursday, July 29, 2021

Friday Thinking 30 July, 2021

Friday Thinking is a humble curation of my foraging in the digital environment. Choices are based on my own curiosity and 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 is what skills the cat -
for life of skillful means .
Jobs are dying - Work is just beginning.
Work that engages our whole self becomes play that works.

The emerging world-of-connected-everything - digital environment - 
computational ecology - 
may still require humans as the consciousness of its own existence. 

To see red - is to know other colors - without the ground of others - there is no figure - differences that make a defference.  

‘There are times, ‘when I catch myself believing there is something which is separate from something else.’

“I'm not failing - I'm Learning"
Quellcrist Falconer - Altered Carbon




Wittgenstein said, “Philosophy is a battle against the bewitchment of our intelligence by means of our language.” We have the same problem when we attempt to express our understanding of biology and ultimately brains. We don’t understand general intelligence because of the limits of our language. “The limits of my language mean the limits of my world.” according to Wittgenstein.

Wittgenstein introduced the ‘language-turn’ to philosophy. The language-turn was introduced into biology via biosemiotics. Recently, the language-turn has had an immense contribution to the field of Deep Learning in the impressive capabilities of language models like GPT-3. 

Metaphors that are intuitive to grasp by humans are the kinds that we can assimilate via our daily experiences. The fortunate thing about language is that we are immersed in it and thus we have an intuitive understanding of its nuances.

Metaphors are like models. All metaphors are wrong, but some are more useful than others. I propose then that the metaphor of language be the primary metaphor used to understand general intelligence.

The Language-Turn Metaphor and AGI




I’ve long assumed that historical fiction is fundamentally speculative. We revise factual history as we learn more about the past, and we alter our sense of how the past was in accordance. Our sense of what the Victorians were about bears little resemblance to our parents’ sense of that. If the Victorians were able to see what we think of them now, they’d consider us mad. Given that, the creation of an imagined past is like the creation of an imagined future, but even more demanding. The most demanding form of science fiction, it seems to me, is alternate history, of which I’d offer Kingsley Amis’s The Alteration as a singularly successful example.

I have a nagging suspicion that evolution (a wholly random process, though too few of us understand that) has left most of us unable to grasp the idea of an actual apocalypse being possibly of several centuries’ duration. 

I’m yet to discover any record of a culture whose imagined apocalypse was a matter of centuries. I doubt anyone has ever stood out on a street corner wearing a sandwich board reading, “THE WORLD IS COMING TO AN END IN A FEW HUNDRED YEARS.” Even before we became as aware as some of us now are of climate change, and of the fact that our species has inadvertently caused it, we seemed to be losing our sense of a capital-F Future. Few phrases were as common throughout the 20th century as “the 21st century,” yet how often do we see “the 22nd century”? Effectively, never.

Tracking Reality’s “Fuckedness Quotient”: An Interview with William Gibson






This is another fascinating signal in our understanding - not only of DNA but of an evolutionary agent.
Their vast size, ranging between more than 600,000 and about 1 million DNA base pairs in length, is one feature that distinguishes Borgs from many other ECEs. In fact, Borgs are so huge that they are up to one-third of the length of the main chromosome in their host microbes,

Massive DNA ‘Borg’ structures perplex scientists

Researchers say they have discovered unique and exciting DNA strands in the mud — others aren’t sure of their novelty.
The Borg have landed — or, at least, researchers have discovered their counterparts here on Earth. Scientists analysing samples from muddy sites in the western United States have found novel DNA structures that seem to scavenge and ‘assimilate’ genes from microorganisms in their environment, much like the fictional Star Trek ‘Borg’ aliens who assimilate the knowledge and technology of other species.

These extra-long DNA strands, which the scientists named in honour of the aliens, join a diverse collection of genetic structures — circular plasmids, for example — known as extrachromosomal elements (ECEs). Most microbes have one or two chromosomes that encode their primary genetic blueprint. But they can host, and often share between them, many distinct ECEs. These carry non-essential but useful genes, such as those for antibiotic resistance.

Borgs are a previously unknown, unique and “absolutely fascinating” type of ECE, says Jill Banfield, a geomicrobiologist at the University of California, Berkeley. She and her colleagues describe their discovery of the structures in a preprint posted to the server bioRxiv1. The work is yet to be peer-reviewed.


Another signal of new science capabilities emerging with combinatorial innovations. 

Single-cell analysis enters the multiomics age

A rapidly growing collection of software tools is helping researchers to analyse multiple huge ‘-omics’ data sets.
It takes about 20 days for a mouse to grow from fertilized egg to newborn pup. Ricard Argelaguet and his colleagues were interested in what exactly happens inside the cells of a mouse embryo between days 4.5 and 7.5, when the stem cells shift into three layers: the ectoderm, which develops into the nervous system; the mesoderm, which develops into muscle and bone; and the endoderm, which develops into the gut and internal organs.

Researchers can easily distinguish between these three layers by looking at which genes are expressed in individual cells. But the team wanted a more nuanced picture. So, in 2019, the researchers combined the gene-expression data with two other sources of information1. The first was methylation, a chemical modification that alters how genes are expressed. The second was chromatin accessibility: how modifications to chromatin, the knotty complex of proteins and DNA in eukaryotic nuclei, affect which parts of the DNA are accessible for transcription into RNA. Both are factors in epigenetics, the non-genetic elements that influence how genes are expressed.

Combining the three data sources revealed something unexpected: in the absence of external stimuli, embryonic stem cells will become ectoderm. “This was the most essential contribution of the paper,” Argelaguet says. It showed “that there is kind of a hierarchy of cell fate specification at the epigenetic level”. Argelaguet, a computational biologist at the Babraham Institute in Cambridge, UK, was one of four first authors on the study, which was supervised by Babraham investigator Wolf Reik, as well as John Marioni at the EMBL-European Bioinformatics Institute in nearby Hinxton, and Oliver Stegle at the German Cancer Research Center in Heidelberg.

Their result explains the decades-old observation that embryonic stem cells in culture will preferentially differentiate into neurons. And it’s a finding, says Argelaguet, that would have been impossible to make using just a single type of data.


A small signal of our domestication of DNA is offering much needed possibilities of increasing our agricultural productivity - which will be vital in handling the transformation of how we and the planet can flourish together. 
"The change really is dramatic," said University of Chicago Prof. Chuan He, who together with Prof. Guifang Jia at Peking University, led the research. "What's more, it worked with almost every type of plant we tried it with so far, and it's a very simple modification to make."

RNA breakthrough creates crops that can grow 50% more potatoes, rice

Manipulating RNA can allow plants to yield dramatically more crops, as well as increasing drought tolerance, announced a group of scientists from the University of Chicago, Peking University and Guizhou University.

In initial tests, adding a gene encoding for a protein called FTO to both rice and potato plants increased their yield by 50% in field tests. The plants grew significantly larger, produced longer root systems and were better able to tolerate drought stress. Analysis also showed that the plants had increased their rate of photosynthesis.


And in the same channel of signals - this one suggests more acceleration in science progress.

Single chip tests thousands of enzyme mutations at once

The technique vastly speeds up understanding of how the proteins function and how to target drugs.
Figuring out how a protein or enzyme works, and understanding how genetic mutations affect these molecules that are fundamental to life, can often take years. Researchers must alter hundreds of the molecule’s amino acid building blocks one by one, produce each mutated enzyme in the lab and test how each mutation affects the enzyme’s ability to carry out its job.

Now, a glass chip etched with tiny channels could reduce that time to mere hours by allowing researchers to test more than 1,000 mutations at a time. A 22 July paper1 in Science describes how the new system, called High-Throughput Microfluidic Enzyme Kinetics (HT-MEK), could provide a faster way for scientists to study disease-causing proteins, develop enzymes that break down environmental toxins and understand the evolutionary relationships between different species.

To develop HT-MEK, bioengineer Polly Fordyce and biochemist Daniel Herschlag at Stanford University in California and their colleagues worked for six years, ending up with a US$10 chip about 7 cm2 in size. The chip contains 1,568 tiny wells that can each contain a mutated version of the enzyme, and a microfluidic system that delivers reagents to all the mutants at the same time.


Another signal of our progress in developing new materials with biotechnologies. While efforts to manufacture commercial quantities of spider silk are decades old - so much more is known.
"After our previous work, I wondered if we could create something better than spider silk using our synthetic biology platform," Zhang said.

Microbially produced fibers: Stronger than steel, tougher than Kevlar

Spider silk is said to be one of the strongest, toughest materials on the Earth. Now engineers at Washington University in St. Louis have designed amyloid silk hybrid proteins and produced them in engineered bacteria. The resulting fibers are stronger and tougher than some natural spider silks.

Their research was published in the journal ACS Nano.

To be precise, the artificial silk—dubbed "polymeric amyloid" fiber—was not technically produced by researchers, but by bacteria that were genetically engineered in the lab of Fuzhong Zhang, a professor in the Department of Energy, Environmental & Chemical Engineering in the McKelvey School of Engineering.


This is a very interesting signal - related to robotics, AI and data.
OpenAI first widely demonstrated its robotics work in October 2019, when it published research detailing a five-fingered robotic hand guided by an AI model with 13,000 years of cumulative experience. The best-performing system could successfully unscramble Rubik’s Cubes about 20% to 60% of the time, which might not seem especially impressive. But the model notably discovered techniques to recover from challenges, like when the robot’s fingers were tied together and when the hand was wearing a leather glove.

“The sad thing is, if we were a robotics company, the mission of the company would be different, and I think we would continue. I believe quite strongly in the approach that [the] robotics [team] took and the direction,” Zaremba added. “But from the perspective of what we want to achieve, which is to build [artificial general intelligence], there were some components missing.”

OpenAI disbands its robotics research team

OpenAI has disbanded its robotics team after years of research into machines that can learn to perform tasks like solving a Rubik’s Cube. Company cofounder Wojciech Zaremba quietly revealed on a podcast hosted by startup Weights & Biases that OpenAI has shifted its focus to other domains, where data is more readily available.

“So it turns out that we can make a gigantic progress whenever we have access to data. And I kept all of our machinery unsupervised, [using] reinforcement learning — [it] work[s] extremely well. There [are] actually plenty of domains that are very, very rich with data. And ultimately that was holding us back in terms of robotics,” Zaremba said. “The decision [to disband the robotics team] was quite hard for me. But I got the realization some time ago that actually, that’s for the best from the perspective of the company.”

In a statement, an OpenAI spokesperson told VentureBeat: “After advancing the state of the art in reinforcement learning through our Rubik’s Cube project and other initiatives, last October we decided not to pursue further robotics research and instead refocus the team on other projects. Because of the rapid progress in AI and its capabilities, we’ve found that other approaches, such as reinforcement learning with human feedback, lead to faster progress in our reinforcement learning research.”

It’s an open secret that robotics is a capital-intensive field. Industrial robotics company Rethink Robotics closed its doors months after attempting unsuccessfully to find an acquirer. Boston Dynamics, considered among the most advanced robotics firms, was acquired by Google and then sold to SoftBank before Hyundai agreed to buy a controlling stake for $1.1 billion. And Honda retired its Asimo robotics project after over a decade in development.


And on the other hand - if anyone saw the opening of the Tokyo Olympics one wonders how soon the drone cloud demonstrated there will be weaponized by someone.

Swarms of tiny dumb robots found to carry out sophisticated actions

A team of researchers affiliated with several institutions in Europe has found that swarms of tiny dumb vibrating robots are capable of carrying out sophisticated actions such as transporting objects or squeezing through tunnels. In their paper published in the journal Science Robotics, the group describes experiments they conducted with tiny dumb robots they called "bugs."

The team became interested in the movements of small objects in a closed setting through vibration. The Electric Football Game is one example. Players move about a small metal table painted to look like a football field when vibrations are applied from below. In their work, the researchers used small, plastic, buglike objects outfitted with a device that made them vibrate instead of using a vibrating base (they are currently for sale as a children's toy). They then created a variety of courses for the bugs to traverse by changing the positioning of the walls. Then they added the bugs and sat back to watch what would happen.


There are a number of overlaps between the technologies of gaming and the applications of technology for science. This one may provide a pathway to abundant energy.
"You need this level of speed and precision with plasmas because they have such complex dynamics that evolve at very high speeds. If you cannot keep up with them, or if you mispredict how plasmas will react, they have a nasty habit of going in the totally wrong direction very quickly," 

Gaming graphics card allows faster, more precise control of fusion energy experiments

Nuclear fusion offers the potential for a safe, clean and abundant energy source.
This process, which also occurs in the sun, involves plasmas, fluids composed of charged particles, being heated to extremely high temperatures so that the atoms fuse together, releasing abundant energy.

One challenge to performing this reaction on Earth is the dynamic nature of plasmas, which must be controlled to reach the required temperatures that allow fusion to happen. Now researchers at the University of Washington have developed a method that harnesses advances in the computer gaming industry: It uses a gaming graphics card, or GPU, to run the control system for their prototype fusion reactor.
The team published these results May 11 in Review of Scientific Instruments.


This is a small signal of the possible trajectory of our understanding of reality - and also our capacity to eventually manipulate reality on fundamentally deeper levels - worms holes, warp drives? Who knows.

Electromagnetism is a property of spacetime itself, study finds

The link between general relativity and electromagnetism becomes clear by assuming that the so-called four-potential of electromagnetism directly determines the metrical properties of the spacetime. In particular, our research shows how electromagnetism is an inherent property of spacetime itself. In a way, spacetime itself is therefore the aether. Electric and magnetic fields represent certain local tensions or twists in the spacetime fabric. Our research shows that the Lagrangian of electrodynamics is just the Einstein-Hilbert action of general relativity; it reveals how Maxwell's equations of electromagnetism are an optimality condition for the metric of spacetime to be sufficiently flat. As Einstein's theory of general relativity provides that the metric is optimal in a sense, electromagnetism is hidden in the nonlinear differential equations of general relativity. On the other hand, this means that general relativity is a generalized theory of nonlinear electromagnetism.

John Wheeler, the famous physicist, put forward the idea that all of the material world is constructed from the geometry of the spacetime. Our research strongly supports this kind of natural philosophy. It means that the material world always corresponds to some geometric structures of spacetime. Tensions in spacetime manifest themselves as electric and magnetic fields. Moreover, electric charge relates to some compressibility properties of spacetime. Electric current seems to be a re-balancing object, which transports charge in order to keep the spacetime manifold Ricci-flat. This is aesthetically pleasing, as nature seems to strive for harmony, efficiency and simplicity.



#micropoem



pondering - 
child-parent - 
dynamics - 
from the wonder of her -
as a baby-mine - 
infant-toddler-mine - 
to adolescent - 
young-adult - middle-age-professional - 
authority - 
mhm - 
so many new - 
I - eyes - 
to keep entangled - 

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