Deep Thought, to DeepMind…

Topics: Artificial Intelligence, Biology, Research, Science Fiction

“Deep Thought” was the name of the computer in “Hitchhiker’s Guide to the Galaxy,” where it took millions of years to find the answer to “life, the universe, and everything” is 42.

An artificial intelligence (AI) network developed by Google AI offshoot DeepMind has made a gargantuan leap in solving one of biology’s grandest challenges — determining a protein’s 3D shape from its amino-acid sequence.

DeepMind’s program, called AlphaFold, outperformed around 100 other teams in a biennial protein-structure prediction challenge called CASP, short for Critical Assessment of Structure Prediction. The results were announced on 30 November, at the start of the conference — held virtually this year — that takes stock of the exercise.

“This is a big deal,” says John Moult, a computational biologist at the University of Maryland in College Park, who co-founded CASP in 1994 to improve computational methods for accurately predicting protein structures. “In some sense the problem is solved.”

‘It will change everything’: DeepMind’s AI makes gigantic leap in solving protein structures, Ewen Callaway, Nature

Quasiparticles, and Graphene…

Telltale traces In this doping vs magnetic field conductance map, the magnetic field is varied along the vertical axis. Horizontal yellow streaks show Brown-Zak fermions propagating along straight trajectories with high mobility (low resistance), whereas slanted indigo lines show the cyclotron motion around Brown-Zak fermions. The slope of these lines enabled the researchers to obtain the degeneracy (and find an additional quantum number) of these new quasiparticles. (Courtesy: J Barrier)

Topics: Fermions, Graphene, Nanotechnology, Quantum Mechanics

Researchers at the University of Manchester in the UK have identified a new family of quasiparticles in superlattices made from graphene sandwiched between two slabs of boron nitride. The work is important for fundamental studies of condensed-matter physics and could also lead to the development of improved transistors capable of operating at higher frequencies.

In recent years, physicists and materials scientists have been studying ways to use the weak (van der Waals) coupling between atomically thin layers of different crystals to create new materials in which electronic properties can be manipulated without chemical doping. The most famous example is graphene (a sheet of carbon just one atom thick) encapsulated between another 2D material, hexagonal boron nitride (hBN), which has a similar lattice constant. Since both materials also have similar hexagonal structures, regular moiré patterns (or “superlattices”) form when the two lattices are overlaid.

If the stacked layers of graphene-hBN are then twisted, and the angle between the two materials’ lattices decreases, the size of the superlattice increases. This causes electronic band gaps to develop through the formation of additional Bloch bands in the superlattice’s Brillouin zone (a mathematical construct that describes the fundamental ideas of electronic energy bands). In these Bloch bands, electrons move in a periodic electric potential that matches the lattice and do not interact with one another.

New family of quasiparticles appears in graphene, Isabelle Dumé, Physics World

Truthiness, to Truth Decay…

Image Source: Wikipedia link below

Topics: Civics, Civil Rights, Existentialism, Fascism, Human Rights, Politics

Truthiness is the belief or assertion that a particular statement is true based on the intuition or perceptions of some individual or individuals, without regard to evidencelogicintellectual examination, or facts. Truthiness can range from ignorant assertions of falsehoods to deliberate duplicity or propaganda intended to sway opinions.

The concept of truthiness has emerged as a major subject of discussion surrounding U.S. politics during the 1990s and 2000s because of the perception among some observers of a rise in propaganda and a growing hostility toward factual reporting and fact-based discussion.

American television comedian Stephen Colbert coined the term truthiness in this meaning as the subject of a segment called “The Wørd” during the pilot episode of his political satire program The Colbert Report on October 17, 2005. By using this as part of his routine, Colbert satirized the misuse of appeal to emotion and “gut feeling” as a rhetorical device in contemporaneous socio-political discourse.


Roger Ailes was very explicit as to why he wanted, and created Fox News: he wanted a news outlet friendly to conservative interests in the wake of Watergate, and the resignation of President Richard Nixon. I don’t think we realize how astonishing that was, and that we’ve mythologized those times as “halcyon days” of yore.

Richard Nixon ran on “law and order,” and the fear of violence in the wake of the deaths of Martin Luther King and Robert Kennedy. He subtly stoked white grievance, the so-called “Southern Strategy,” infamously described by political operative Lee Atwater. It worked. He rode to power in 1968, and a landslide forty-nine out of fifty state win in 1972, where he became the first Republican to sweep the south.

Nixon didn’t need the plumbers to break into the DNC headquarters Watergate building, but there’s evidence he used government resources instructing them to do so. His Vice President, Spiro Agnew, was accepting “bags of money” at the White House – as he did as governor of Maryland – to do political “favors” on Capitol Hill. For all intents and purposes, that is bribery. Nowadays, they attach lawyers to it, and call it lobbying.

The Justice Department was in a conundrum: if they indict the sitting president for an illegal breakin, they have to indict the sitting Vice President for usury. Plus, that pesky thing called The Constitution said if removed from office, the next in line was the Speaker of the House of Representatives, then, as now, a Democrat. The “memo” came out, without legal standing, or precedence, that you “cannot indict a sitting president.”

We did not have cable television, cell phones, or social media apps. Every single American, presumably many who voted for Nixon’s landslide victory, got the same information from three television outlets: ABC, CBS and NBC news. Telegrams, letters, phone calls, letters to the editor in local newspapers and polls showed the country’s mood had turned against Nixon, plus his promise to get us out of the Vietnam War turned out to be a boondoggle: many families were welcoming their loved ones home in body bags in a war it clearly looked like we weren’t going to win. Altruism and fealty to The Constitution had nothing to do with Republicans then, or now. The party talked Agnew into leaving on a lesser charge to get Gerald Ford – a congressman from Ohio, with no association to Nixon, or Agnew – in as Vice President. Then, the republicans could keep power at the Executive Branch if an Impeachment in the House led to conviction in the Senate, and forced removal.

The speed of a sprinter, a thrown fastball, the luminescence of a distant star, or the Hawking’s Radiation of a Black Hole is demonstrable, measurable facts. They are not subject to opinions, “alternative facts,” quackery, or spin. On the one hand, first, second, and third place is determinable, the speed of a Rookie fastball pitched from a mound can be logged; the astrophysical properties of distant objects can be studied because, in sports and physics, there is an agreement on what IS true, and what is false.

“Science is far from a perfect instrument of knowledge. It’s just the best we have. In this respect, as in many others, it’s like democracy. Science by itself cannot advocate courses of human action, but it can certainly illuminate the possible consequences of alternative courses of action.”

“The scientific way of thinking is at once imaginative and disciplined. This is central to its success. Science invites us to let the facts in, even when they don’t conform to our preconceptions. It counsels us to carry alternative hypotheses in our heads and see which best fit the facts. It urges on us a delicate balance between no-holds-barred openness to new ideas, however heretical, and the most rigorous skeptical scrutiny of everything — new ideas and established wisdom. This kind of thinking is also an essential tool for a democracy in an age of change.”

“The whole idea of a democratic application of skepticism is that everyone should have the essential tools to effectively and constructively evaluate claims to knowledge.”

― Carl Sagan, The Demon-Haunted World: Science as a Candle in the Dark, also Brain Pickings: Science, and Democracy

The premiere of Stephen Colbert’s witty and insightful show probably had a lot to do with the “truthiness” on Weapons of Mass Destruction in Iraq. That was demonstrably a lie. Yet, time and comparison to our current tweet-addicted sociopath make memories fail, as even George W. Bush now can pay respects to John Lewis: he was one of three living presidents to do so. The current occupant is too racist, devoted to his base, and fantasy to do so.

Ted Cruz is a Harvard-trained lawyer, and like President Obama, an editor of the Harvard Law Review. He’s taken to Twitter to spread baseless conspiracy theories, and promote a right-wing social media app, Parler, financed by Rebecca Mercer, who like her billionaire hedge fund father, funds right-wing causes around the globe. It also shows his disdain for the people in Texas that are his constituents: he thinks they’re fools, and probably wants to run for president again on the gravy train of lunacy Orange Satan built. The Republican Party genuinely fear their own base. They’ve stoked them every time a Democrat ascends to the presidency that the great purge of “coming to take your guns” is around the corner, any minute now. There were more guns sold during the Obama administration than the current imbecilic nightmare. I assume gun industry sales will improve apace.

The irony is, Parler is a completely enclosed silo. Part of the perverse joy of social media by sociopaths is “owning the libs,” a badge of honor after frustrating arguments back and forth on a platform that you get blocked. Similar I’m sure, to throwing pollutants in the air from smokestacks on trucks, thinking oneself immune from the effects on Earth-Two. There are few “libs” on Parler to own. It also shows the tech company’s regard for the intelligence of conservatives is limited, but they can see an opportunity, like most snake oil salesmen and conmen, to make a fast buck off gullible marks.

You cannot measure a sporting achievement without a knowledge of the rules, and adherence to them to make a judgment on performance.

You cannot have a STEM field without knowing the foundations of its knowledge, what is, and is not possible, and adherence to The Scientific Method to make an evaluation of the outcome of an experiment, and the world.

You cannot have a Democratic Republic with truth decay. To list them together is an oxymoron. Unless your ultimate goal is a fascist state.

Integrated Nanodiamonds…

Nanophotonic integration for simultaneously controlling a large number of quantum mechanical spins in nanodiamonds. (Image: P. Schrinner/AG Schuck)

Topics: Nanotechnology, Quantum Computer, Quantum Mechanics, Semiconductor Technology

(Nanowerk News) Physicists at Münster University have succeeded in fully integrating nanodiamonds into nanophotonic circuits and at the same time addressing several of these nanodiamonds optically. The study creates the basis for future applications in the field of quantum sensing schemes or quantum information processors.

The results have been published in the journal Nano Letters (“Integration of Diamond-Based Quantum Emitters with Nanophotonic Circuits“).

Using modern nanotechnology, it is possible nowadays to produce structures which have a feature sizes of just a few nanometers.

This world of the most minute particles – also known as quantum systems – makes possible a wide range of technological applications, in fields which include magnetic field sensing, information processing, secure communication or ultra-precise time keeping. The production of these microscopically small structures has progressed so far that they reach dimensions below the wavelength of light.

In this way, it is possible to break down hitherto existent boundaries in optics and utilize the quantum properties of light. In other words, nanophotonics represent a novel approach to quantum technologies.

Controlling fully integrated nanodiamonds, Westfälische Wilhelms-Universität Münster

Planes, Trains, and Automobiles…

Topics: Biology, COVID-19, Research

With COVID-19 reaching the most dangerous levels the U.S. has seen since the pandemic began, the country faces a problematic holiday season. Despite the risk, many people are likely to travel using various forms of transportation that will inevitably put them in relatively close contact with others. Many transit companies have established frequent cleaning routines, but evidence suggests that airborne transmission of the novel coronavirus poses a greater danger than surfaces. The virus is thought to be spread primarily by small droplets, called aerosols, that hang in the air and larger droplets that fall to the ground within six feet or so. Although no mode of public transportation is completely safe, there are some concrete ways to reduce risk, whether on an airplane, train or bus—or even in a shared car.

At a casual glance, air travel might seem like the perfect recipe for COVID transmission: it packs dozens of people into a confined space, often for hours at a time. But many planes have excellent high-efficiency particulate air (HEPA) filters that capture more than 99 percent of particles in the air, including microbes as SARS-CoV-2, the coronavirus that causes COVID. When their recirculation systems are operating, most commercial passenger jets bring in outside air in a top-to-bottom direction about 20 to 30 times per hours. This results in a 50–50 mix of outside and recirculated air and reduces the potential for airborne spread of a respiratory virus. Many airlines now require passengers to wear a mask during flights except for mealtimes, and some are blocking off middle seats to allow more distancing between people. Companies have also implemented rigorous cleaning procedures between flights. So how does this translate into overall risk?

“An airplane cabin is probably one of the most secure conditions you can be in,” says Sebastian Hoehl of the Institute for Medical Virology at Goethe University Frankfurt in Germany, who has co-authored two papers on COVID-19 transmission on specific flights, which were published in JAMA Network Open and the New England Journal of Medicine, respectfully. Still, a handful of case studies have found that limited transmission can take place onboard. One such investigation of a 10-hour journey from London to Hanoi starting on March 1 found that 15 people were likely infected with COVID-19 in-flight—and that 12 of them had sat within a couple of rows of a single symptomatic passenger in business class. (The results were published this month in the U.S. Centers for Disease Control and Prevention’s journal Emerging Infectious Diseases.) Most of these flights occurred early on in the pandemic, however, and in the case of the March 1 flight, masks were likely not worn, the researchers wrote. Meanwhile a recent Department of Defense study modeled the risk of in-flight infection using mannequins exhaling simulated virus particles and found that a person would have to be exposed to an infectious passenger for at least 54 hours to get an infectious dose. This finding assumes the infected passenger is wearing a surgical mask, however, and it does not account for the dangers involved in removing the mask for meals or talking or in moving about on the plane.

Evaluating COVID Risk on Planes, Trains and Automobiles, Sophie Bushwick, Tanya Lewis, Amanda Montañez, Scientific American

Science Literacy, and Democracy…

Derived from Carl Sagan in “The Demon-Haunted World: Science as a Candle in the Dark,” on Baloney Detection Kit Sandwich (infographic)

Topics: Civics, Civil Rights, Education, Existentialism, Human Rights, Politics

“The human understanding is no dry light, but receives infusion from the will and affections; whence proceed sciences which may be called ‘sciences as one would.’ For what a man had rather were true he more readily believes. Therefore he rejects difficult things from impatience of research; sober things, because they narrow hope; the deeper things of nature, from superstition; the light of experience, from arrogance and pride; things not commonly believed, out of the deference to the opinion of the vulgar. Numberless in short are the ways, and sometimes imperceptible, in which the affections color and infect the understanding.” Sir Francis Bacon, NOVUM ORGANON (1620)

“A clairvoyance gap with adversary nations is announced, and the Central Intelligence Agency, under Congressional prodding, spends tax money to find out whether submarines in the ocean depths can be located by *thinking hard* at them.”

Both quotes from “The Demon-Haunted World: Science As A Candle in the Dark,” chapter 12 – “The Fine Art of Baloney Detection,” Sir Francis Bacon’s quote is in the chapter intro.

The steps of the scientific method go something like this:
1. Make an observation or observations. 2. Ask questions about the observations and gather information. 3. Form a hypothesis — a tentative description of what’s been observed, and make predictions based on that hypothesis. 4. Test the hypothesis and predictions in an experiment that can be reproduced. 5. Analyze the data and draw conclusions; accept or reject the hypothesis or modify the hypothesis if necessary. 6. Reproduce the experiment until there are no discrepancies between observations and theory. Source: Live Science – Science & the Scientific Method

Writing a physics and nano blog, one wants the audience (be they somewhat limited), to catch on to the central theme of the weblog: science, and the promotion of science literacy, for citizens of this country, and since this is the web, Earth.

SCIENCE IS FOR ALL STUDENTS. This principle is one of equity and excellence. Science in our schools must be for all students: All students, regardless of age, sex, cultural or ethnic background, disabilities, aspirations, or interest and motivation in science, should have the opportunity to attain high levels of scientific literacy.

Scientific literacy implies that a person can identify scientific issues underlying national and local decisions and express positions that are scientifically and technologically informed.

National Science Education Standards (1996), Chapter 2: Principles and Definitions, National Academies Press

This blog is a continuing, meaningful discussion about scientific and technological literacy (STL), and its importance in fostering a society of informed citizens – indeed, a prerequisite for participatory democracy – conversant in emerging fields as consumers and eventual future participant contributors. In the language of scripture, I would like to “begat” citizens versed in technology that want to research, discover, and publish in it. For a world so impacted by it, it is imperative we’re all versed in it, scientists, engineers, artists, and lay citizens alike.

We have gone through a dizzying four-year experiment with technology and authoritarianism. No less than Foreign Affairs (Does Technology Favor Tyranny?) has studied the impact. It was fostered by a birther lie, and technology (Twitter). Though I doubt the current flailing will change election results, we have a number of citizens, in the words of Tom Nichols, who voted for the sociopath. Some of our fellow citizens “created their own realities” (Karl Rove), or delved in “alternative facts” (Kellyanne Conway). His political party could stop him, but they’re too cowardly, afraid of him and his base. Sadly, these are NOT their constituents: most members of Congress are multimillionaires, worth well over the salaries we pay them. They serve, for want of a better term, American Oligarchs (Andrea Bernstein), and the businesses they give endless tax breaks to.

E Pluribus Unum is probably the first Latin phrase you’ve ever heard, or read: “out of many, one.” It’s the nation’s motto, and poetic, but in the era of news feeds, echo chambers, and social media groups, E Pluribus Multis is more illustrative and quite apropos.

We must depart, somehow, in the next succession of days, from the false empowerment of divisive Multis, into a future fully embracing science literacy, and Unum for the survival of the species. Our baloney detection kits must be tuned to high gear.

“I have a foreboding of an America in my children’s or grandchildren’s time — when the United States is a service and information economy; when nearly all the manufacturing industries have slipped away to other countries; when awesome technological powers are in the hands of a very few, and no one representing the public interest can even grasp the issues; when the people have lost the ability to set their own agendas or knowledgeably question those in authority; when, clutching our crystals and nervously consulting our horoscopes, our critical faculties in decline, unable to distinguish between what feels good and what’s true, we slide, almost without noticing, back into superstition and darkness…

The dumbing down of American is most evident in the slow decay of substantive content in the enormously influential media, the 30 second sound bites (now down to 10 seconds or less), lowest common denominator programming, credulous presentations on pseudoscience and superstition, but especially a kind of celebration of ignorance”

“We’ve arranged a global civilization in which most crucial elements profoundly depend on science and technology. We have also arranged things so that almost no one understands science and technology. This is a prescription for disaster. We might get away with it for a while, but sooner or later this combustible mixture of ignorance and power is going to blow up in our faces.”

― Carl Sagan, The Demon-Haunted World: Science as a Candle in the Dark

We owe it to Carl’s grandkids, and our children’s futures, to get this right.

Clocking Dark Matter…

Clocking dark matter: optical clocks join the hunt for dark matter. (Courtesy: N Hanacek/NIST)

Topics: Dark Matter, Modern Physics, Quantum Mechanics

An optical clock has been used to set new constraints on a proposed theory of dark matter. Researchers including Jun Ye at JILA at the University of Colorado, Boulder, and Andrei Derevianko at the University of Nevada, Reno, explored how the coupling between regular matter and “ultralight” dark matter particles could be detected using the clock in conjunction with an ultra-stable optical cavity. With future upgrades to the performance of optical clocks, their approach could become an important tool in the search for dark matter.

Although it appears to account for about 85% of the matter in the universe, physicists know very little about dark matter. Most theoretical and experimental work so far has been focussed on hypothetical dark-matter particles, including WIMPS and axions, which have relatively large masses.  Alternatively, some physicists have proposed the existence of “ultralight” dark matter particles with extremely small masses that span many orders of magnitude (10−16–10−21 eV/c2).

According to the laws of quantum mechanics, the very smallest of these particles would have huge wavelengths, comparable to the sizes of entire dwarf galaxies – meaning they would behave like classical fields on scales we can easily measure.

Optical clock sets new constraints on dark matter, Sam Jarman, Physics World

Diamond Nanoneedles…

Credit: Z. Shi et al., Proc. Natl. Acad. Sci. USA 117, 24634 (2020)

Topics: Materials Science, Modern Physics, Nanotechnology, Semiconductor Technology

If you ever manage to deform a diamond, you’re likely to break it. That’s because the hardest natural material on Earth is also inelastic and brittle. Two years ago, Ming Dao (MIT), Subra Suresh (Nanyang Technological University in Singapore), and their collaborators demonstrated that when bulk diamonds are etched into fine, 300-nm-wide needles, they become nearly defect-free. The transformation allows diamonds to elastically bend under the pressure of an indenter tip, as shown in the figure, and withstand extremely large tensile stresses without breaking.

The achievement prompted the researchers to investigate whether the simple process of bending could controllably and reversibly alter the electronic structure of nanocrystal diamond. Teaming up with Ju Li and graduate student Zhe Shi (both at MIT), Dao and Suresh have now followed their earlier study with numerical simulations of the reversible deformation. The team used advanced deep-learning algorithms that reveal the bandgap distributions in nanosized diamond across a range of loading conditions and crystal geometries. The new work confirms that the elastic strain can alter the material’s carbon-bonding configuration enough to close its bandgap from a normally 5.6 eV width as an electrical insulator to 0 eV as a conducting metal. That metallization occurred on the compression side of a bent diamond nanoneedle.

Diamond nanoneedles turn metallic, R. Mark Wilson, Physics Today

Right-Handed Photons…

Topics: Modern Physics, Particle Physics, Quantum Mechanics, Quarks

Note: A primer on quarks at Hyperphysics

On 17 January 1957, a few months after Chien-Shiung Wu’s discovery of parity violation, Wolfgang Pauli wrote to Victor Weisskopf: “Ich glaube aber nicht, daß der Herrgott ein schwacher Linkshänder ist” (I cannot believe that God is a weak left-hander). But maximal parity violation is now well established within the Standard Model (SM). The weak interaction only couples to left-handed particles, as dramatically seen in the continuing absence of experimental evidence for right-handed neutrinos. In the same way, the polarisation of photons originating from transitions that involve the weak interaction is expected to be completely left-handed.

The LHCb collaboration recently tested the handedness of photons emitted in rare flavour-changing transitions from a b-quark to an s-quark. These are mediated by the bosons of the weak interaction according to the SM – but what if new virtual particles contribute too? Their presence could be clearly signalled by a right-handed contribution to the photon polarization.

In pursuit of right-handed photons, A report from the LHCb experiment, CERN Courier

Argonne, and STEM…

Students and instructors wave bye to each other after the close of a virtual session of All About Energy. (Image by Argonne National Laboratory.)

Topics: Education, Energy, Research, STEM

Argonne Educational Programs and Outreach transitioned to virtual summer programming, ensuring that Argonne continues to build the next generation of STEM leaders.

At the U.S. Department of Energy’s (DOE) Argonne National Laboratory, scientists and educators have found new ways to balance their work with safety needs as the laboratory’s Educational Programs and Outreach Department successfully transitioned all of its summer programming to a virtual learning environment.

By connecting scientific and research divisions across the laboratory, Argonne was able to create multiple virtual programs, helping young people stay connected and engage with the laboratory’s science, technology, engineering and math (STEM) education opportunities.

“Providing STEM opportunities and a constant presence with our next generation of STEM professions during a time that is unsettling and turbulent for everyone, but especially our school age and university student populations, was our top priority.” — Meridith Bruozas, Educational Programs and Outreach manager

“Argonne continues to adapt and lead impactful science during the ongoing pandemic, a strategy that includes strengthening the STEM pipeline with unique education programs for future scientists and engineers,” said Argonne Director Paul Kearns. ​“For years, hundreds of students have pursued summer learning opportunities at Argonne that are not available anywhere else. I’m pleased that in 2020 our lab community came together to maintain these high-quality STEM experiences through a successful virtual program for next-generation researchers.”

Argonne provides STEM opportunities for more than 800 students during pandemic, Nathan Schmidt, Argonne National Laboratory