Category Archives: science

TRIUMF (Canada’s national particle accelerator centre) welcomes Nigel Smith as its new Chief Executive Officer (CEO) on May 17, 2021and some Hollywood news

I have two bits of news as noted in the headline. There’s news about TRIUMF located on the University of British Columbia (UBC) endowment lands and news about Dr. Suzanne Simard (UBC Forestry) and her memoir, Finding the Mother Tree: Discovering the Wisdom of the Fores.

Nigel Smith and TRIUMF (Canada’s national particle accelerator centre)

As soon as I saw his first name, Nigel, I bet myself he’d be from the UK (more about that later in this posting). This is TRIUMF’s third CEO since I started science blogging in May 2008. When I first started it was called TRIUMF (Canada’s National Laboratory for Particle and Nuclear Physics) but these days it’s TRIUMF (Canada’s national particle accelerator centre).

As for the organization’s latest CEO, here’s more from a TRIUMF February 12, 2021 announcement page ( the text is identical to TRIUMF’s February 12, 2021 press release),

Dr. Nigel Smith, Executive Director of SNOLAB, has been selected to serve as the next Director of TRIUMF.  

Succeeding Dr. Jonathan Bagger, who departed TRIUMF in January 2021 to become CEO of the American Physical Society, Dr. Smith’s appointment comes as the result of a highly competitive, six-month international search. Dr. Smith will begin his 5-year term as TRIUMF Director on May 17, 2021. 

“I am truly honoured to have been selected as the next Director of TRIUMF”, said Dr. Smith. “I have long been engaged with TRIUMF’s vibrant community and have been really impressed with the excellence of its science, capabilities and people. TRIUMF plays a unique and vital role in Canada’s research ecosystem and I look forward to help continue the legacy of excellence upheld by Dr. Jonathan Bagger and the previous TRIUMF Directors”.  

Describing what interested him in the position, Smith spoke to the breadth and impact of TRIUMF’s diverse science programs, stating “TRIUMF has an amazing portfolio of research covering fundamental and applied science that also delivers tangible societal impact through its range of medical and commercialisation initiatives. I am extremely excited to have the opportunity to lead a laboratory with such a broad and world-leading science program.” 

“Nigel brings all the necessary skills and background to the role of Director,” said Dr. Digvir Jayas, Interim Director of TRIUMF, Chair of the TRIUMF Board of Management, and Vice-President, Research and International at the University of Manitoba. “As Executive Director of SNOLAB, Dr. Smith is both a renowned researcher and experienced laboratory leader who offers a tremendous track record of success spanning the local, national, and international spheres. The Board of Management is thrilled to bring Nigel’s expertise to TRIUMF so he may help guide the laboratory through many of the exciting developments on the horizon.  

Dr. Smith joins TRIUMF at an important period in the laboratory’s history, moving into the second year of our current Five-Year Plan (2020-2025) and preparing to usher in a new era of science and innovation that will include the completion of the Advance Rare Isotope Laboratory (ARIEL) and the Institute for Advanced Medical Isotopes (IAMI) [not to be confused with Amii {Alberta Machine Intelligence Institute}]. This new infrastructure, alongside TRIUMF’s existing facilities and world-class research programs, will solidify Canada’s position as a global leader in both fundamental and applied research. 

Dr. Smith expressed his optimism for TRIUMF, saying “I am delighted to have this opportunity, and it will be a pleasure to lead the laboratory through this next exciting phase of our growth and evolution.” 

Smith is leaving what is probably one of the more unusual laboratories, at a depth of 2km, SNOLAB is the deepest, cleanest laboratory in the world. (more information either at SNOLAB or its Wikipedia entry.)

Is Smith from the UK? Some clues

I found my subsequent clues on SNOLAB’s ‘bio’ page for Dr. Nigel Smith,

Nigel Smith joined SNOLAB as Director during July 2009. He currently holds a full Professorship at Laurentian University, adjunct Professor status at Queen’s University, and a visiting Professorial chair at Imperial College, London. He received his Bachelor of Science in physics from Leeds University in the U.K. in 1985 and his Ph. D. in astrophysics from Leeds in 1991. He has served as a lecturer at Leeds University, a research associate at Imperial College London, group leader (dark matter) and deputy division head at the STFC Rutherford Appleton Laboratory, before relocating to Canada to oversee the SNOLAB deep underground facility.

The answer would seem to be yes, Nigel James Telfer Smith is originally from the UK.

I don’t know if this is going to be a trend but this is the second ‘Nigel” to lead TRIUMF. (The Nigels are now tied with the Johns and the Alans. Of course, the letter ‘j’ seems the most popular with four names, John, John, Jack, and Jonathan.) Here’s a list of TRIUMF’s previous CEOs (from the TRIUMF Wikipedia entry),

Since its inception, TRIUMF has had eight directors [now nine] overseeing its operations.

The first Nigel (Lockyer) is described as an American in his Wikipedia entry. He was born in Scotland and raised in Canada. However, he has spent the majority of his adult life in the US, other than the five or six years at TRIUMF. So, previous Nigel also started life in the UK.

Good luck to the new Nigel.

UBC forestry professor, Suzanne Simard’s memoir going to the movies?

Given that Simard’s memoir, Finding the Mother Tree: Discovering the Wisdom of the Forest, was published last week on May 4, 2021, this is very heady news,. From a May 12, 2021 article by Cassandra Gill for the Daily Hive (Note: Links have been removed),

Jake Gyllenhaal is bringing the story of a UBC professor to the big screen.

The Oscar nominee’s production company, Nine Stories, is producing a film based on Suzanne Simard’s memoir, Finding the Mother Tree.

Amy Adams is set to play Simard, who is a forest ecology expert renowned for her research on plants and fungi.

Adams is also co-producing the film with Gyllenhaal through her own company, Bond Group Entertainment.

The BC native [Simard] developed an interest in trees and the outdoors through her close relationship with her grandfather, who was a horse logger.

Her 30 year career and early life is documented in the memoir, which was released last week on May 4 [2021]. Simard explores how trees have evolved, have memories, and are the foundation of our planet’s ecosystem — along with her own personal experiences with grief.

The scientists’ [sic] influence has had influence in popular culture, notably in James Cameron’s 2009 film Avatar. The giant willow-like “Tree of Souls” was specifically inspired by Simard’s work.

No mention of a script and no mention of financing, so, it could be a while before we see the movie on Netflix, Apple+, HBO, or maybe a movie house (if they’re open by then).

I think the script may prove to the more challenging aspect of this project. Here’s the description of Simard’s memoir (from the Finding the Mother Tree webpage on suzannesimard.com)

From the world’s leading forest ecologist who forever changed how people view trees and their connections to one another and to other living things in the forest–a moving, deeply personal journey of discovery.

About the Book

In her first book, Simard brings us into her world, the intimate world of the trees, in which she brilliantly illuminates the fascinating and vital truths – that trees are not simply the source of timber or pulp, but are a complex, interdependent circle of life; that forests are social, cooperative creatures connected through underground networks by which trees communicate their vitality and vulnerabilities with communal lives not that different from our own.

Simard writes – in inspiring, illuminating, and accessible ways – how trees, living side by side for hundreds of years, have evolved, how they perceive one another, learn and adapt their behaviors, recognize neighbors, and remember the past; how they have agency about the future; elicit warnings and mount defenses, compete and cooperate with one another with sophistication, characteristics ascribed to human intelligence, traits that are the essence of civil societies – and at the center of it all, the Mother Trees: the mysterious, powerful forces that connect and sustain the others that surround them.

How does Simard’s process of understanding trees and conceptualizing a ‘mother tree’ get put into a script for a movie that’s not a documentary or an animation?

Movies are moving pictures, yes? How do you introduce movement and action in a script heavily focused on trees, which operate on a timescale that’s vastly different.

It’s an interesting problem and I look forward to seeing how it’s resolved. I wish them good luck.

Exotic magnetism: a quantum simulation from D-Wave Sytems

Vancouver (Canada) area company, D-Wave Systems is trumpeting itself (with good reason) again. This 2021 ‘milestone’ achievement builds on work from 2018 (see my August 23, 2018 posting for the earlier work). For me, the big excitement was finding the best explanation for quantum annealing and D-Wave’s quantum computers that I’ve seen yet (that explanation and a link to more is at the end of this posting).

A February 18, 2021 news item on phys.org announces the latest achievement,

D-Wave Systems Inc. today [February 18, 2021] published a milestone study in collaboration with scientists at Google, demonstrating a computational performance advantage, increasing with both simulation size and problem hardness, to over 3 million times that of corresponding classical methods. Notably, this work was achieved on a practical application with real-world implications, simulating the topological phenomena behind the 2016 Nobel Prize in Physics. This performance advantage, exhibited in a complex quantum simulation of materials, is a meaningful step in the journey toward applications advantage in quantum computing.

A February 18, 2021 D-Wave Systems press release (also on EurekAlert), which originated the news item, describes the work in more detail,

The work by scientists at D-Wave and Google also demonstrates that quantum effects can be harnessed to provide a computational advantage in D-Wave processors, at problem scale that requires thousands of qubits. Recent experiments performed on multiple D-Wave processors represent by far the largest quantum simulations carried out by existing quantum computers to date.

The paper, entitled “Scaling advantage over path-integral Monte Carlo in quantum simulation of geometrically frustrated magnets”, was published in the journal Nature Communications (DOI 10.1038/s41467-021-20901-5, February 18, 2021). D-Wave researchers programmed the D-Wave 2000Q™ system to model a two-dimensional frustrated quantum magnet using artificial spins. The behavior of the magnet was described by the Nobel-prize winning work of theoretical physicists Vadim Berezinskii, J. Michael Kosterlitz and David Thouless. They predicted a new state of matter in the 1970s characterized by nontrivial topological properties. This new research is a continuation of previous breakthrough work published by D-Wave’s team in a 2018 Nature paper entitled “Observation of topological phenomena in a programmable lattice of 1,800 qubits” (Vol. 560, Issue 7719, August 22, 2018). In this latest paper, researchers from D-Wave, alongside contributors from Google, utilize D-Wave’s lower noise processor to achieve superior performance and glean insights into the dynamics of the processor never observed before.

“This work is the clearest evidence yet that quantum effects provide a computational advantage in D-Wave processors,” said Dr. Andrew King, principal investigator for this work at D-Wave. “Tying the magnet up into a topological knot and watching it escape has given us the first detailed look at dynamics that are normally too fast to observe. What we see is a huge benefit in absolute terms, with the scaling advantage in temperature and size that we would hope for. This simulation is a real problem that scientists have already attacked using the algorithms we compared against, marking a significant milestone and an important foundation for future development. This wouldn’t have been possible today without D-Wave’s lower noise processor.”

“The search for quantum advantage in computations is becoming increasingly lively because there are special problems where genuine progress is being made. These problems may appear somewhat contrived even to physicists, but in this paper from a collaboration between D-Wave Systems, Google, and Simon Fraser University [SFU], it appears that there is an advantage for quantum annealing using a special purpose processor over classical simulations for the more ‘practical’ problem of finding the equilibrium state of a particular quantum magnet,” said Prof. Dr. Gabriel Aeppli, professor of physics at ETH Zürich and EPF Lausanne, and head of the Photon Science Division of the Paul Scherrer Institute. “This comes as a surprise given the belief of many that quantum annealing has no intrinsic advantage over path integral Monte Carlo programs implemented on classical processors.”

“Nascent quantum technologies mature into practical tools only when they leave classical counterparts in the dust in solving real-world problems,” said Hidetoshi Nishimori, Professor, Institute of Innovative Research, Tokyo Institute of Technology. “A key step in this direction has been achieved in this paper by providing clear evidence of a scaling advantage of the quantum annealer over an impregnable classical computing competitor in simulating dynamical properties of a complex material. I send sincere applause to the team.”

“Successfully demonstrating such complex phenomena is, on its own, further proof of the programmability and flexibility of D-Wave’s quantum computer,” said D-Wave CEO Alan Baratz. “But perhaps even more important is the fact that this was not demonstrated on a synthetic or ‘trick’ problem. This was achieved on a real problem in physics against an industry-standard tool for simulation–a demonstration of the practical value of the D-Wave processor. We must always be doing two things: furthering the science and increasing the performance of our systems and technologies to help customers develop applications with real-world business value. This kind of scientific breakthrough from our team is in line with that mission and speaks to the emerging value that it’s possible to derive from quantum computing today.”

The scientific achievements presented in Nature Communications further underpin D-Wave’s ongoing work with world-class customers to develop over 250 early quantum computing applications, with a number piloting in production applications, in diverse industries such as manufacturing, logistics, pharmaceutical, life sciences, retail and financial services. In September 2020, D-Wave brought its next-generation Advantage™ quantum system to market via the Leap™ quantum cloud service. The system includes more than 5,000 qubits and 15-way qubit connectivity, as well as an expanded hybrid solver service capable of running business problems with up to one million variables. The combination of Advantage’s computing power and scale with the hybrid solver service gives businesses the ability to run performant, real-world quantum applications for the first time.

That last paragraph seems more sales pitch than research oriented. It’s not unexpected in a company’s press release but I was surprised that the editors at EurekAlert didn’t remove it.

Here’s a link to and a citation for the latest paper,

Scaling advantage over path-integral Monte Carlo in quantum simulation of geometrically frustrated magnets by Andrew D. King, Jack Raymond, Trevor Lanting, Sergei V. Isakov, Masoud Mohseni, Gabriel Poulin-Lamarre, Sara Ejtemaee, William Bernoudy, Isil Ozfidan, Anatoly Yu. Smirnov, Mauricio Reis, Fabio Altomare, Michael Babcock, Catia Baron, Andrew J. Berkley, Kelly Boothby, Paul I. Bunyk, Holly Christiani, Colin Enderud, Bram Evert, Richard Harris, Emile Hoskinson, Shuiyuan Huang, Kais Jooya, Ali Khodabandelou, Nicolas Ladizinsky, Ryan Li, P. Aaron Lott, Allison J. R. MacDonald, Danica Marsden, Gaelen Marsden, Teresa Medina, Reza Molavi, Richard Neufeld, Mana Norouzpour, Travis Oh, Igor Pavlov, Ilya Perminov, Thomas Prescott, Chris Rich, Yuki Sato, Benjamin Sheldan, George Sterling, Loren J. Swenson, Nicholas Tsai, Mark H. Volkmann, Jed D. Whittaker, Warren Wilkinson, Jason Yao, Hartmut Neven, Jeremy P. Hilton, Eric Ladizinsky, Mark W. Johnson, Mohammad H. Amin. Nature Communications volume 12, Article number: 1113 (2021) DOI: https://doi.org/10.1038/s41467-021-20901-5 Published: 18 February 2021

This paper is open access.

Quantum annealing and more

Dr. Andrew King, one of the D-Wave researchers, has written a February 18, 2021 article on Medium explaining some of the work. I’ve excerpted one of King’s points,

Insight #1: We observed what actually goes on under the hood in the processor for the first time

Quantum annealing — the approach adopted by D-Wave from the beginning — involves setting up a simple but purely quantum initial state, and gradually reducing the “quantumness” until the system is purely classical. This takes on the order of a microsecond. If you do it right, the classical system represents a hard (NP-complete) computational problem, and the state has evolved to an optimal, or at least near-optimal, solution to that problem.

What happens at the beginning and end of the computation are about as simple as quantum computing gets. But the action in the middle is hard to get a handle on, both theoretically and experimentally. That’s one reason these experiments are so important: they provide high-fidelity measurements of the physical processes at the core of quantum annealing. Our 2018 Nature article introduced the same simulation, but without measuring computation time. To benchmark the experiment this time around, we needed lower-noise hardware (in this case, we used the D-Wave 2000Q lower noise quantum computer), and we needed, strangely, to slow the simulation down. Since the quantum simulation happens so fast, we actually had to make things harder. And we had to find a way to slow down both quantum and classical simulation in an equitable way. The solution? Topological obstruction.

If you have time and the inclination, I encourage you to read King’s piece.

New podcast—Mission: Interplanetary and Event Rap: a one-stop custom rap shop Kickstarter

I received two email notices recently, one from Dr. Andrew Maynard (Arizona State University; ASU) and one from Baba Brinkman (Canadian rapper of science and other topics now based in New York).

Mission: Interplanetary

I found a “Mission: Interplanetary— a podcast on the future of humans as a spacefaring species!” webpage (Link: https://collegeofglobalfutures.asu.edu/blog/2021/03/23/mission-interplanetary-redefining-how-we-talk-about-humans-in-space/) on the Arizona State University College of Global Futures website,

Back in January 2019 I got an email from my good friend and colleague Lance Gharavi with the title “Podcast brainstorming.” Two years on, we’ve just launched the Mission: Interplanetary podcast–and it’s amazing!

It’s been a long journey — especially with a global pandemic thrown in along the way — but on March 23 [2021], the Mission: Interplanetary podcast with Slate and ASU finally launched.

After two years of planning, many discussions, a bunch dry runs, and lots (and by that I mean lots) of Zoom meetings, we are live!

As the team behind the podcast talked about and developed the ideas underpinning the Mission: Interplanetary,we were interested in exploring new ways of thinking and talking about the future of humanity as a space-faring species as part of Arizona State University’s Interplanetary Initiative. We also wanted to go big with these conversations — really big!

And that is exactly what we’ve done in this partnership with Slate.

The guests we’re hosting, the conversations we have lined up, the issues we grapple with, are all literally out of this world. But don’t just take my word for it — listen to the first episode above with the incredible Lindy Elkins-Tanton talking about NASA’s mission to the asteroid 16 Psyche.

And this is just a taste of what’s to come over the next few weeks as we talk to an amazing lineup of guests.

So if you’re looking for a space podcast with a difference, and one that grapples with big questions around our space-based future, please do subscribe on your favorite podcast platform. And join me and the fabulous former NASA astronaut Cady Coleman as we explore the future of humanity in space.

See you there!

Slate’s webpage (Mission: Interplanetary; Link: https://slate.com/podcasts/mission-interplanetary) offers more details about the co-hosts and the programmes along with embedded podcasts,

Cady Coleman is a former NASA astronaut and Air Force colonel. She flew aboard the International Space Station on a six-month expedition as the lead science and robotics officer. A frequent speaker on space and STEM topics, Coleman is also a musician who’s played from space with the Chieftains and Ian Anderson of Jethro Tull.

Andrew Maynard is a scientist, author, and expert in risk innovation. His books include Films From the Future: The Technology and Morality of Sci-Fi Movies and Future Rising

Latest Episodes

April 27, 2021

Murder in Space

What laws govern us when we leave Earth?

Happy listening. And, I apologize for the awkward links.

Event Rap Kickstarter

Baba Brinkman’s April 27, 2021 email notice has this to say about his latest venture,

Join the Movement, Get Rewards

My new Kickstarter campaign for Event Rap is live as of right now! Anyone who backs the project is helping to launch an exciting new company, actually a new kind of company, the first creator marketplace for rappers. Please take a few minutes to read the campaign description, I put a lot of love into it.

The campaign goal is to raise $26K in 30 days, an average of $2K per artist participating. If we succeed, this platform becomes a new income stream for independent artists during the pandemic and beyond. That’s the vision, and I’m asking for your help to share it and support it.

But instead of why it matters, let’s talk about what you get if you support the campaign!

$10-$50 gets you an advance copy of my new science rap album, Bright Future. I’m extremely proud of this record, which you can preview here, and Bright Future is also a prototype for Event Rap, since all ten of the songs were commissioned by people like you.

$250 – $500 gets you a Custom Rap Video written and produced by one of our artists, and you have twelve artists and infinite topics to choose from. This is an insanely low starting price for an original rap video from a seasoned professional, and it applies only during the Kickstarter. What can the video be about? Anything at all. You choose!

In case it’s helpful, here’s a guide I wrote entitled “How to Brief a Rapper

$750 – $1,500 gets you a live rap performance at your virtual event. This is also an amazingly low price, especially since you can choose to have the artist freestyle interactively with your audience, write and perform a custom rap live, or best of all compose a “Rap Up” summary of the event, written during the event, that the artist will perform as the grand finale.

That’s about as fresh and fun as rap gets.

$3,000 – $5,000 the highest tiers bring the highest quality, a brand new custom-written, recorded, mixed and mastered studio track, or studio track plus full rap music video, with an exclusive beat and lyrics that amplify your message in the impactful, entertaining way that rap does best.

I know this higher price range isn’t for everyone, but check out some of the music videos our artists have made, and maybe you can think of a friend to send this to who has a budget and a worthy cause.

Okay, that’s it!

Those prices are in US dollars.

I gather at least one person has backed given enough money to request a custom rap on cycling culture in the Netherlands.

The campaign runs for another 26 days. It has amassed over $8,400 CAD towards a goal of $32,008 CAD. (The site doesn’t show me the goal in USD although the pledges/reward are listed in that currency.)

A 3D spider web, a VR (virtual reality) setup, and sonification (music)

Markus Buehler and his musical spider webs are making news again.

Caption: Cross-sectional images (shown in different colors) of a spider web were combined into this 3D image and translated into music. Credit: Isabelle Su and Markus Buehler

The image (so pretty) you see in the above comes from a Markus Buehler presentation that was made at the American Chemical Society (ACS) meeting. ACS Spring 2021 being held online April 5-30, 2021. The image was also shown during a press conference which the ACS has made available for public viewing. More about that later in this posting.

The ACS issued an April 12, 2021 news release (also on EurekAlert), which provides details about Buehler’s latest work on spider webs and music,

Spiders are master builders, expertly weaving strands of silk into intricate 3D webs that serve as the spider’s home and hunting ground. If humans could enter the spider’s world, they could learn about web construction, arachnid behavior and more. Today, scientists report that they have translated the structure of a web into music, which could have applications ranging from better 3D printers to cross-species communication and otherworldly musical compositions.

The researchers will present their results today at the spring meeting of the American Chemical Society (ACS). ACS Spring 2021 is being held online April 5-30 [2021]. Live sessions will be hosted April 5-16, and on-demand and networking content will continue through April 30 [2021]. The meeting features nearly 9,000 presentations on a wide range of science topics.

“The spider lives in an environment of vibrating strings,” says Markus Buehler, Ph.D., the project’s principal investigator, who is presenting the work. “They don’t see very well, so they sense their world through vibrations, which have different frequencies.” Such vibrations occur, for example, when the spider stretches a silk strand during construction, or when the wind or a trapped fly moves the web.

Buehler, who has long been interested in music, wondered if he could extract rhythms and melodies of non-human origin from natural materials, such as spider webs. “Webs could be a new source for musical inspiration that is very different from the usual human experience,” he says. In addition, by experiencing a web through hearing as well as vision, Buehler and colleagues at the Massachusetts Institute of Technology (MIT), together with collaborator Tomás Saraceno at Studio Tomás Saraceno, hoped to gain new insights into the 3D architecture and construction of webs.

With these goals in mind, the researchers scanned a natural spider web with a laser to capture 2D cross-sections and then used computer algorithms to reconstruct the web’s 3D network. The team assigned different frequencies of sound to strands of the web, creating “notes” that they combined in patterns based on the web’s 3D structure to generate melodies. The researchers then created a harp-like instrument and played the spider web music in several live performances around the world.

The team also made a virtual reality setup that allowed people to visually and audibly “enter” the web. “The virtual reality environment is really intriguing because your ears are going to pick up structural features that you might see but not immediately recognize,” Buehler says. “By hearing it and seeing it at the same time, you can really start to understand the environment the spider lives in.”

To gain insights into how spiders build webs, the researchers scanned a web during the construction process, transforming each stage into music with different sounds. “The sounds our harp-like instrument makes change during the process, reflecting the way the spider builds the web,” Buehler says. “So, we can explore the temporal sequence of how the web is being constructed in audible form.” This step-by-step knowledge of how a spider builds a web could help in devising “spider-mimicking” 3D printers that build complex microelectronics. “The spider’s way of ‘printing’ the web is remarkable because no support material is used, as is often needed in current 3D printing methods,” he says.

In other experiments, the researchers explored how the sound of a web changes as it’s exposed to different mechanical forces, such as stretching. “In the virtual reality environment, we can begin to pull the web apart, and when we do that, the tension of the strings and the sound they produce change. At some point, the strands break, and they make a snapping sound,” Buehler says.

The team is also interested in learning how to communicate with spiders in their own language. They recorded web vibrations produced when spiders performed different activities, such as building a web, communicating with other spiders or sending courtship signals. Although the frequencies sounded similar to the human ear, a machine learning algorithm correctly classified the sounds into the different activities. “Now we’re trying to generate synthetic signals to basically speak the language of the spider,” Buehler says. “If we expose them to certain patterns of rhythms or vibrations, can we affect what they do, and can we begin to communicate with them? Those are really exciting ideas.”

You can go here for the April 12, 2021 ‘Making music from spider webs’ ACS press conference’ it runs about 30 mins. and you will hear some ‘spider music’ played.

Getting back to the image and spider webs in general, we are most familiar with orb webs (in the part of Canada where I from if nowhere else), which look like spirals and are 2D. There are several other types of webs some of which are 3D, like tangle webs, also known as cobwebs, funnel webs and more. See this March 18, 2020 article “9 Types of Spider Webs: Identification + Pictures & Spiders” by Zach David on Beyond the Treat for more about spiders and their webs. If you have the time, I recommend reading it.

I’ve been following Buehler’s spider web/music work for close to ten years now; the latest previous posting is an October 23, 2019 posting where you’ll find a link to an application that makes music from proteins (spider webs are made up of proteins; scroll down about 30% of the way; it’s in the 2nd to last line of the quoted text about the embedded video).

Here is a video (2 mins. 17 secs.) of a spider web music performance that Buehler placed on YouTube,

Feb 3, 2021

Markus J. Buehler

Spider’s Canvas/Arachonodrone show excerpt at Palais de Tokyo, Paris, on November 2018. Video by MIT CAST. More videos can be found on www.arachnodrone.com. The performance was commissioned by Studio Tomás Saraceno (STS), in the context of Saraceno’s carte blanche exhibition, ON AIR. Spider’s Canvas/Arachnodrone was performed by Isabelle Su and Ian Hattwick on the spider web instrument, Evan Ziporyn on the EWI (Electronic Wind Instrument), and Christine Southworth on the guitar and EBow (Electronic Bow)

You can find more about the spider web music and Buehler’s collaborators on http://www.arachnodrone.com/,

Spider’s Canvas / Arachnodrone is inspired by the multifaceted work of artist Tomas Saraceno, specifically his work using multiple species of spiders to make sculptural webs. Different species make very different types of webs, ranging not just in size but in design and functionality. Tomas’ own web sculptures are in essence collaborations with the spiders themselves, placing them sequentially over time in the same space, so that the complex, 3-dimensional sculptural web that results is in fact built by several spiders, working together.

Meanwhile, back among the humans at MIT, Isabelle Su, a Course 1 doctoral student in civil engineering, has been focusing on analyzing the structure of single-species spider webs, specifically the ‘tent webs’ of the cyrtophora citricola, a tropical spider of particular interest to her, Tomas, and Professor Markus Buehler. Tomas gave the department a cyrtophora spider, the department gave the spider a space (a small terrarium without glass), and she in turn built a beautiful and complex web. Isabelle then scanned it in 3D and made a virtual model. At the suggestion of Evan Ziporyn and Eran Egozy, she then ported the model into Unity, a VR/game making program, where a ‘player’ can move through it in numerous ways. Evan & Christine Southworth then worked with her on ‘sonifying’ the web and turning it into an interactive virtual instrument, effectively turning the web into a 1700-string resonating instrument, based on the proportional length of each individual piece of silk and their proximity to one another. As we move through the web (currently just with a computer trackpad, but eventually in a VR environment), we create a ‘sonic biome’: complex ‘just intonation’ chords that come in and out of earshot according to which of her strings we are closest to. That part was all done in MAX/MSP, a very flexible high level audio programming environment, which was connected with the virtual environment in Unity. Our new colleague Ian Hattwick joined the team focusing on sound design and spatialization, building an interface that allowed him the sonically ‘sculpt’ the sculpture in real time, changing amplitude, resonance, and other factors. During this performance at Palais de Tokyo, Isabelle toured the web – that’s what the viewer sees – while Ian adjusted sounds, so in essence they were together “playing the web.” Isabelle provides a space (the virtual web) and a specific location within it (by driving through), which is what the viewer sees, from multiple angles, on the 3 scrims. The location has certain acoustic potentialities, and Ian occupies them sonically, just as a real human performer does in a real acoustic space. A rough analogy might be something like wandering through a gothic cathedral or a resonant cave, using your voice or an instrument at different volumes and on different pitches to find sonorous resonances, echoes, etc. Meanwhile, Evan and Christine are improvising with the web instrument, building on Ian’s sound, with Evan on EWI (Electronic Wind Instrument) and Christine on electric guitar with EBow.

For the visuals, Southworth wanted to create the illusion that the performers were actually inside the web. We built a structure covered in sharkstooth scrim, with 3 projectors projecting in and through from 3 sides. Southworth created images using her photographs of local Lexington, MA spider webs mixed with slides of the scan of the web at MIT, and then mixed those images with the projection of the game, creating an interactive replica of Saraceno’s multi-species webs.

If you listen to the press conference, you will hear Buehler talk about practical applications for this work in materials science.

Antikythera’s (a 2,000 year old computer) secrets unlocked?

The Antikythera Mechanism is fascinating and a March 12, 2021 University College London (UCL) press release (also on EurekAlert) reveals the reason for the fascination before announcing the latest research into this ‘celestial’ object,

Known to many as the world’s first analogue computer, the Antikythera Mechanism is the most complex piece of engineering to have survived from the ancient world. The 2,000-year-old device was used to predict the positions of the Sun, Moon and the planets as well as lunar and solar eclipses.

Exploded model of the Cosmos gearing of the Antikythera Mechanism. ©2020 Tony Freeth.

Continuing on from the March 12, 2021 University College London (UCL) press release,

Published in Scientific Reports, the paper from the multidisciplinary UCL Antikythera Research Team reveals a new display of the ancient Greek order of the Universe (Cosmos), within a complex gearing system at the front of the Mechanism.

Lead author Professor Tony Freeth (UCL Mechanical Engineering) explained: “Ours is the first model that conforms to all the physical evidence and matches the descriptions in the scientific inscriptions engraved on the Mechanism itself.

“The Sun, Moon and planets are displayed in an impressive tour de force of ancient Greek brilliance.”

The Antikythera Mechanism has generated both fascination and intense controversy since its discovery in a Roman-era shipwreck in 1901 by Greek sponge divers near the small Mediterranean island of Antikythera.

The astronomical calculator is a bronze device that consists of a complex combination of 30 surviving bronze gears used to predict astronomical events, including eclipses, phases of the moon, positions of the planets and even dates of the Olympics.

Whilst great progress has been made over the last century to understand how it worked, studies in 2005 using 3D X-rays and surface imaging enabled researchers to show how the Mechanism predicted eclipses and calculated the variable motion of the Moon.

However, until now, a full understanding of the gearing system at the front of the device has eluded the best efforts of researchers. Only about a third of the Mechanism has survived, and is split into 82 fragments – creating a daunting challenge for the UCL team.

The biggest surviving fragment, known as Fragment A, displays features of bearings, pillars and a block. Another, known as Fragment D, features an unexplained disk, 63-tooth gear and plate.

Previous research had used X-ray data from 2005 to reveal thousands of text characters hidden inside the fragments, unread for nearly 2,000 years. Inscriptions on the back cover include a description of the cosmos display, with the planets moving on rings and indicated by marker beads. It was this display that the team worked to reconstruct.

Two critical numbers in the X-rays of the front cover, of 462 years and 442 years, accurately represent cycles of Venus and Saturn respectively. When observed from Earth, the planets’ cycles sometimes reverse their motions against the stars. Experts must track these variable cycles over long time-periods in order to predict their positions.

“The classic astronomy of the first millennium BC originated in Babylon, but nothing in this astronomy suggested how the ancient Greeks found the highly accurate 462-year cycle for Venus and 442-year cycle for Saturn,” explained PhD candidate and UCL Antikythera Research Team member Aris Dacanalis.

Using an ancient Greek mathematical method described by the philosopher Parmenides, the UCL team not only explained how the cycles for Venus and Saturn were derived but also managed to recover the cycles of all the other planets, where the evidence was missing.

PhD candidate and team member David Higgon explained: “After considerable struggle, we managed to match the evidence in Fragments A and D to a mechanism for Venus, which exactly models its 462-year planetary period relation, with the 63-tooth gear playing a crucial role.”

Professor Freeth added: “The team then created innovative mechanisms for all of the planets that would calculate the new advanced astronomical cycles and minimize the number of gears in the whole system, so that they would fit into the tight spaces available.”

“This is a key theoretical advance on how the Cosmos was constructed in the Mechanism,” added co-author, Dr Adam Wojcik (UCL Mechanical Engineering). “Now we must prove its feasibility by making it with ancient techniques. A particular challenge will be the system of nested tubes that carried the astronomical outputs.”

h/t BBC (British Broadcasting Corporation) March 12, 2021 article about the Anitikythera Mechanism, which includes another image and an embedded video. The March 12, 2021 University College London (UCL) press release includes links to more information about the Antikythera Mechanism, the research, and Dr. Tony Freeth.

For the insatiably curious, I have an October 2, 2012 posting and an August 3, 2016 posting with what was the latest information at the time.

Here’s a link to and a citation for the latest paper,

A Model of the Cosmos in the ancient Greek Antikythera Mechanism by Tony Freeth, David Higgon, Aris Dacanalis, Lindsay MacDonald, Myrto Georgakopoulou & Adam Wojcik. Scientific Reports volume 11, Article number: 5821 (2021) DOI: https://doi.org/10.1038/s41598-021-84310-w Published 12 March 2021

This paper is open access and, as these things go, it’s fairly accessible reading, i.e., even someone like me who has no interest in astronomy can understand enough to enjoy the article.

Today’s post falls, thematically speaking, into similar territory as yesterday’s (March 16, 2021) posting where in addition to celebrating Urania Day I included information about astronomy and some of its history.

mRNA, COVID-19 vaccines, treating genetic diseases before birth, and the scientist who started it all

This post was going to be about new research into fetal therapeutics and mRNA.But, since I’ve been very intrigued by the therapeutic agent, mRNA, which has been a big part of the COVID-19 vaccine story; this seemed like a good opportunity to dive a little more deeply into that topic at the same time.

It’s called messenger ribonucleic acid (mRNA) and until seeing this video I had only the foggiest idea of how it works, which is troubling since at least two COVID-19 vaccines are based on this ‘new’ technology. From a November 10, 2020 article by Damian Garde for STAT,

Garde’s article offers detail about mRNA along with fascinating insight into how science and entreneurship works.

mRNA—it’s in the details, plus, the loneliness of pioneer researchers, a demotion, and squabbles

Garde’s November 10, 2020 article provides some explanation about how mRNA vaccines work and it takes a look at what can happen to pioneering scientists (Note: A link has been removed),

For decades, scientists have dreamed about the seemingly endless possibilities of custom-made messenger RNA, or mRNA.

Researchers understood its role as a recipe book for the body’s trillions of cells, but their efforts to expand the menu have come in fits and starts. The concept: By making precise tweaks to synthetic mRNA and injecting people with it, any cell in the body could be transformed into an on-demand drug factory. [emphasis mine]

But turning scientific promise into medical reality has been more difficult than many assumed. Although relatively easy and quick to produce compared to traditional vaccine-making, no mRNA vaccine or drug has ever won approval [until 2021].

Whether mRNA vaccines succeed or not, their path from a gleam in a scientist’s eye to the brink of government approval has been a tale of personal perseverance, eureka moments in the lab, soaring expectations — and an unprecedented flow of cash into the biotech industry.

Before messenger RNA was a multibillion-dollar idea, it was a scientific backwater. And for the Hungarian-born scientist behind a key mRNA discovery, it was a career dead-end.

Katalin Karikó spent the 1990s collecting rejections. Her work, attempting to harness the power of mRNA to fight disease, was too far-fetched for government grants, corporate funding, and even support from her own colleagues.

It all made sense on paper. In the natural world, the body relies on millions of tiny proteins to keep itself alive and healthy, and it uses mRNA to tell cells which proteins to make. If you could design your own mRNA, you could, in theory, hijack that process and create any protein you might desire — antibodies to vaccinate against infection, enzymes to reverse a rare disease, or growth agents to mend damaged heart tissue.

In 1990, researchers at the University of Wisconsin managed to make it work in mice. Karikó wanted to go further.

The problem, she knew, was that synthetic RNA was notoriously vulnerable to the body’s natural defenses, meaning it would likely be destroyed before reaching its target cells. And, worse, the resulting biological havoc might stir up an immune response that could make the therapy a health risk for some patients.

It was a real obstacle, and still may be, but Karikó was convinced it was one she could work around. Few shared her confidence.

“Every night I was working: grant, grant, grant,” Karikó remembered, referring to her efforts to obtain funding. “And it came back always no, no, no.”

By 1995, after six years on the faculty at the University of Pennsylvania, Karikó got demoted. She had been on the path to full professorship, but with no money coming in to support her work on mRNA, her bosses saw no point in pressing on.

She was back to the lower rungs of the scientific academy.

“Usually, at that point, people just say goodbye and leave because it’s so horrible,” Karikó said.

There’s no opportune time for demotion, but 1995 had already been uncommonly difficult. Karikó had recently endured a cancer scare, and her husband was stuck in Hungary sorting out a visa issue. Now the work to which she’d devoted countless hours was slipping through her fingers.

“I thought of going somewhere else, or doing something else,” Karikó said. “I also thought maybe I’m not good enough, not smart enough. I tried to imagine: Everything is here, and I just have to do better experiments.”

In time, those better experiments came together. After a decade of trial and error, Karikó and her longtime collaborator at Penn — Drew Weissman, an immunologist with a medical degree and Ph.D. from Boston University — discovered a remedy for mRNA’s Achilles’ heel.

The stumbling block, as Karikó’s many grant rejections pointed out, was that injecting synthetic mRNA typically led to that vexing immune response; the body sensed a chemical intruder, and went to war. The solution, Karikó and Weissman discovered, was the biological equivalent of swapping out a tire.

Every strand of mRNA is made up of four molecular building blocks called nucleosides. But in its altered, synthetic form, one of those building blocks, like a misaligned wheel on a car, was throwing everything off by signaling the immune system. So Karikó and Weissman simply subbed it out for a slightly tweaked version, creating a hybrid mRNA that could sneak its way into cells without alerting the body’s defenses.

“That was a key discovery,” said Norbert Pardi, an assistant professor of medicine at Penn and frequent collaborator. “Karikó and Weissman figured out that if you incorporate modified nucleosides into mRNA, you can kill two birds with one stone.”

That discovery, described in a series of scientific papers starting in 2005, largely flew under the radar at first, said Weissman, but it offered absolution to the mRNA researchers who had kept the faith during the technology’s lean years. And it was the starter pistol for the vaccine sprint to come.

Entrepreneurs rush in

Garde’s November 10, 2020 article shifts focus from Karikó, Weissman, and specifics about mRNA to the beginnings of what might be called an entrepreneurial gold rush although it starts sedately,

Derrick Rossi [emphasis mine], a native of Toronto who rooted for the Maple Leafs and sported a soul patch, was a 39-year-old postdoctoral fellow in stem cell biology at Stanford University in 2005 when he read the first paper. Not only did he recognize it as groundbreaking, he now says Karikó and Weissman deserve the Nobel Prize in chemistry.

“If anyone asks me whom to vote for some day down the line, I would put them front and center,” he said. “That fundamental discovery is going to go into medicines that help the world.”

But Rossi didn’t have vaccines on his mind when he set out to build on their findings in 2007 as a new assistant professor at Harvard Medical School running his own lab.

He wondered whether modified messenger RNA might hold the key to obtaining something else researchers desperately wanted: a new source of embryonic stem cells [emphasis mine].

In a feat of biological alchemy, embryonic stem cells can turn into any type of cell in the body. That gives them the potential to treat a dizzying array of conditions, from Parkinson’s disease to spinal cord injuries.

But using those cells for research had created an ethical firestorm because they are harvested from discarded embryos.

Rossi thought he might be able to sidestep the controversy. He would use modified messenger molecules to reprogram adult cells so that they acted like embryonic stem cells.

He asked a postdoctoral fellow in his lab to explore the idea. In 2009, after more than a year of work, the postdoc waved Rossi over to a microscope. Rossi peered through the lens and saw something extraordinary: a plate full of the very cells he had hoped to create.

Rossi excitedly informed his colleague Timothy Springer, another professor at Harvard Medical School and a biotech entrepreneur. Recognizing the commercial potential, Springer contacted Robert Langer, the prolific inventor and biomedical engineering professor at the Massachusetts Institute of Technology.

On a May afternoon in 2010, Rossi and Springer visited Langer at his laboratory in Cambridge. What happened at the two-hour meeting and in the days that followed has become the stuff of legend — and an ego-bruising squabble.

Langer is a towering figure in biotechnology and an expert on drug-delivery technology. At least 400 drug and medical device companies have licensed his patents. His office walls display many of his 250 major awards, including the Charles Stark Draper Prize, considered the equivalent of the Nobel Prize for engineers.

As he listened to Rossi describe his use of modified mRNA, Langer recalled, he realized the young professor had discovered something far bigger than a novel way to create stem cells. Cloaking mRNA so it could slip into cells to produce proteins had a staggering number of applications, Langer thought, and might even save millions of lives.

“I think you can do a lot better than that,” Langer recalled telling Rossi, referring to stem cells. “I think you could make new drugs, new vaccines — everything.”

Within several months, Rossi, Langer, Afeyan [Noubar Afeyan, venture capitalist, founded and runs Flagship Ventures], and another physician-researcher at Harvard formed the firm Moderna — a new word combining modified and RNA.

Springer was the first investor to pledge money, Rossi said. In a 2012 Moderna news release, Afeyan said the firm’s “promise rivals that of the earliest biotechnology companies over 30 years ago — adding an entirely new drug category to the pharmaceutical arsenal.”

But although Moderna has made each of the founders hundreds of millions of dollars — even before the company had produced a single product — Rossi’s account is marked by bitterness. In interviews with the [Boston] Globe in October [2020], he accused Langer and Afeyan of propagating a condescending myth that he didn’t understand his discovery’s full potential until they pointed it out to him.

Garde goes on to explain how BioNTech came into the mRNA picture and contrasts the two companies’ approaches to biotechnology as a business. It seems BioNTech has not cashed in the same way as has Moderna. (For some insight into who’s making money from COVID-19 check out Giacomo Tognini’s December 23, 2020 article (Meet The 50 Doctors, Scientists And Healthcare Entrepreneurs Who Became Pandemic Billionaires In 2020) for Forbes.)

Garde ends his November 10, 2020 article on a mildly cautionary note,

“You have all these odd clinical and pathological changes caused by this novel bat coronavirus [emphasis mine], and you’re about to meet it with all of these vaccines with which you have no experience,” said Paul Offit, an infectious disease expert at Children’s Hospital of Philadelphia and an authority on vaccines.

What happened to Katalin Karikó?

Matthew Rosza’s January 25, 2021 article about Karikó and her pioneering work features an answer to my question and some advice,

“I want young people to feel — if my example, because I was demoted, rejected, terminated, I was even subject for deportation one point — [that] if they just pursue their thing, my example helps them to wear rejection as a badge,” Karikó, who today is a senior vice president at BioNTech RNA Pharmaceuticals, told Salon last month when discussing her story. “‘Okay, well, I was rejected. I know. Katalin was rejected and still [succeeded] at the end.’ So if it helps them, then it helps them.”

Despite her demotion, Karikó continued with her work and, along with a fellow immunologist named Dr. Drew Weissman, penned a series of influential articles starting in 2005. These articles argued that mRNA vaccines would not be neutralized by the human immune system as long as there were specific modifications to nucleosides, a compound commonly found in RNA.

By 2013, Karikó’s work had sufficiently impressed experts that she left the University of Pennsylvania for BioNTech RNA Pharmaceuticals.

Karikó tells Salon that the experience taught her one important lesson: In life there will be people who, for various reasons, will try to hold you back, and you can’t let them get you down.

“People that are in power, they can help you or block you,” Karikó told Salon. “And sometimes people select to make your life miserable. And now they cannot be happy with me because now they know that, ‘Oh, you know, we had the confrontation and…’ But I don’t spend too much time on these things.”

Before moving onto the genetic research which prompted this posting, I have an answer to the following questions:

Could an mRNA vaccine affect your DNA (deoxyribonucleic acid) and how do mRNA vaccines differ from the traditional ones?

No, DNA is not affected by the COVID-19 mRNA vaccines, according to a January 5, 2021 article by Jason Murdock for Newsweek,

The type of vaccines used against COVID-19 do not interact with or alter human genetic code, also known as DNA, scientists say.

In traditional vaccines, a piece of a virus, known as an “antigen,” would be injected into the body to force the immune system to make antibodies to fight off future infection. But mRNA-based methods do not use a live virus, and cannot give someone COVID.

Instead, mRNA vaccines give cells the instructions to make a “spike” protein also found on the surface of the virus that causes COVID. The body kickstarts its immune response by creating the antibodies needed to combat those specific virus proteins.

Once the spike protein is created, the cell breaks down the instructions provided by the mRNA molecule, leaving the human immune system prepared to combat infection. The mRNA vaccines are not a medicine—nor a cure—but a preventative measure.

Gavi, a vaccine alliance partnered with the World Health Organization (WHO), has said that mRNA instructions will become degraded in approximately 72 hours.

It says mRNA strands are “chemical intermediaries” between DNA in our chromosomes and the “cellular machinery that produces the proteins we need to function.”

But crucially, while mRNA vaccines will give the human body the blueprints on how to assemble proteins, the alliance said in a fact-sheet last month that “mRNA isn’t the same as DNA, and it can’t combine with our DNA to change our genetic code.”

It explained: “Some viruses like HIV can integrate their genetic material into the DNA of their hosts, but this isn’t true of all viruses… mRNA vaccines don’t carry these enzymes, so there is no risk of the genetic material they contain altering our DNA.”

The [US] Centers for Disease Control and Prevention (CDC) says on its website that mRNA vaccines that are rolling out don’t “interact with our DNA in any way,” and “mRNA never enters the nucleus of the cell, which is where our DNA (genetic material) is kept.”

Therapeutic fetal mRNA treatment

Rossi’s work on mRNA and embryonic stem cells bears a relationship of sorts to this work focusing on prebirth therapeutics. (From a January 13, 2021 news item on Nanowerk), Note: A link has been removed,

Researchers at Children’s Hospital of Philadelphia and the School of Engineering and Applied Science at the University of Pennsylvania have identified ionizable lipid nanoparticles that could be used to deliver mRNA as part of fetal therapy.

The proof-of-concept study, published in Science Advances (“Ionizable Lipid Nanoparticles for In Utero mRNA Delivery”), engineered and screened a number of lipid nanoparticle formulations for targeting mouse fetal organs and has laid the groundwork for testing potential therapies to treat genetic diseases before birth.

A January 13, 2021 Children’s Hospital of Philadelphia (CHOP) news release (also on EurekAlert), which originated the news item, delves further into the research,

“This is an important first step in identifying nonviral mediated approaches for delivering cutting-edge therapies before birth,” said co-senior author William H. Peranteau, MD, an attending surgeon in the Division of General, Thoracic and Fetal Surgery and the Adzick-McCausland Distinguished Chair in Fetal and Pediatric Surgery at CHOP. “These lipid nanoparticles may provide a platform for in utero mRNA delivery, which would be used in therapies like fetal protein replacement and gene editing.”

Recent advances in DNA sequencing technology and prenatal diagnostics have made it possible to diagnose many genetic diseases before birth. Some of these diseases are treated by protein or enzyme replacement therapies after birth, but by then, some of the damaging effects of the disease have taken hold. Thus, applying therapies while the patient is still in the womb has the potential to be more effective for some conditions. The small fetal size allows for maximal therapeutic dosing, and the immature fetal immune system may be more tolerant of replacement therapy.

Of the potential vehicles for introducing therapeutic protein replacement, mRNA is distinct from other nucleic acids, such as DNA, because it does not need to enter the nucleus and can use the body’s own machinery to produce the desired proteins. Currently, the common methods of nucleic acid delivery include viral vectors and nonviral approaches. Although viral vectors may be well-suited to gene therapy, they come with the potential risk of unwanted integration of the transgene or parts of the viral vector in the recipient genome. Thus, there is an important need to develop safe and effective nonviral nucleic acid delivery technologies to treat prenatal diseases.

In order to identify potential nonviral delivery systems for therapeutic mRNA, the researchers engineered a library of lipid nanoparticles, small particles less than 100 nanometers in size that effectively enter cells in mouse fetal recipients. Each lipid nanoparticle formulation was used to encapsulate mRNA, which was administered to mouse fetuses. The researchers found that several of the lipid nanoparticles enabled functional mRNA delivery to fetal livers and that some of those lipid nanoparticles also delivered mRNA to the fetal lungs and intestines. They also assessed the lipid nanoparticles for toxicity and found them to be as safe or safer than existing formulations.

Having identified the lipid nanoparticles that were able to accumulate within fetal livers, lungs, and intestines with the highest efficiency and safety, the researchers also tested therapeutic potential of those designs by using them to deliver erythropoietin (EPO) mRNA, as the EPO protein is easily trackable. They found that EPO mRNA delivery to liver cells in mouse fetuses resulted in elevated levels of EPO protein in the fetal circulation, providing a model for protein replacement therapy via the liver using these lipid nanoparticles.

“A central challenge in the field of gene therapy is the delivery of nucleic acids to target cells and tissues, without causing side effects in healthy tissue. This is difficult to achieve in adult animals and humans, which have been studied extensively. Much less is known in terms of what is required to achieve in utero nucleic acid delivery,” said Mitchell. “We are very excited by the initial results of our lipid nanoparticle technology to deliver mRNA in utero in safe and effective manner, which could open new avenues for lipid nanoparticles and mRNA therapeutics to treat diseases before birth.”

Here’s a link to and a citation for the paper,

Ionizable lipid nanoparticles for in utero mRNA delivery by Rachel S. Riley, Meghana V. Kashyap, Margaret M. Billingsley, Brandon White, Mohamad-Gabriel Alameh, Sourav K. Bose, Philip W. Zoltick, Hiaying Li, Rui Zhang, Andrew Y. Cheng, Drew Weissman, William H. Peranteau, Michael J. Mitchell. Science Advances 13 Jan 2021: Vol. 7, no. 3, eaba1028 DOI: 10.1126/sciadv.aba1028

This paper appears to be open access. BTW, I noticed Drew Weissman’s name as one of the paper’s authors and remembered him as one of the first to recognize Karikó’s pioneering work. I imagine that when he co-authored papers with Karikó he was risking his reputation.

Funny how a despised field of research has sparked a ‘gold rush’ for research and for riches, yes?.

A quantum phenomenon (Kondo effect) and nanomaterials

This is a little outside my comfort zone but here goes anyway. From a December 23, 2020 news item on phys.org (Note: Links have been removed),

Osaka City University scientists have developed mathematical formulas to describe the current and fluctuations of strongly correlated electrons in quantum dots. Their theoretical predictions could soon be tested experimentally.

Theoretical physicists Yoshimichi Teratani and Akira Oguri of Osaka City University, and Rui Sakano of the University of Tokyo have developed mathematical formulas that describe a physical phenomenon happening within quantum dots and other nanosized materials. The formulas, published in the journal Physical Review Letters, could be applied to further theoretical research about the physics of quantum dots, ultra-cold atomic gasses, and quarks.

At issue is the Kondo effect. This effect was first described in 1964 by Japanese theoretical physicist Jun Kondo in some magnetic materials, but now appears to happen in many other systems, including quantum dots and other nanoscale materials.

A December 23, 2020 Osaka City University press release (also on EurekAlert), which originated the news item, provides more detail,

Normally, electrical resistance drops in metals as the temperature drops. But in metals containing magnetic impurities, this only happens down to a critical temperature, beyond which resistance rises with dropping temperatures.

Scientists were eventually able to show that, at very low temperatures near absolute zero, electron spins become entangled with the magnetic impurities, forming a cloud that screens their magnetism. The cloud’s shape changes with further temperature drops, leading to a rise in resistance. This same effect happens when other external ‘perturbations’, such as a voltage or magnetic field, are applied to the metal. 

Teratani, Sakano and Oguri wanted to develop mathematical formulas to describe the evolution of this cloud in quantum dots and other nanoscale materials, which is not an easy task. 

To describe such a complex quantum system, they started with a system at absolute zero where a well-established theoretical model, namely Fermi liquid theory, for interacting electrons is applicable. They then added a ‘correction’ that describes another aspect of the system against external perturbations. Using this technique, they wrote formulas describing electrical current and its fluctuation through quantum dots. 

Their formulas indicate electrons interact within these systems in two different ways that contribute to the Kondo effect. First, two electrons collide with each other, forming well-defined quasiparticles that propagate within the Kondo cloud. More significantly, an interaction called a three-body contribution occurs. This is when two electrons combine in the presence of a third electron, causing an energy shift of quasiparticles. 

“The formulas’ predictions could soon be investigated experimentally”, Oguri says. “Studies along the lines of this research have only just begun,” he adds. 

The formulas could also be extended to understand other quantum phenomena, such as quantum particle movement through quantum dots connected to superconductors. Quantum dots could be a key for realizing quantum information technologies, such as quantum computers and quantum communication.

Here’s a link to and a citation for the paper,

Fermi Liquid Theory for Nonlinear Transport through a Multilevel Anderson Impurity by Yoshimichi Teratani, Rui Sakano, and Akira Oguri. Phys. Rev. Lett. 125, 216801 (Issue Vol. 125, Iss. 21 — 20 November 2020) DOI: https://doi.org/10.1103/PhysRevLett.125.216801 Published Online: 17 November 2020

This paper is behind a paywall.

A better quality of cultivated meat from McMaster University?

This could be a bit stomach-churning for some folks.

Researchers at Canada’s McMaster University have developed and are commercializing a technique for cultivated meat (the first experiment involved mouse meat). (You could call it vat-grown meat.) A January 19, 2021 news item on phys.org makes the announcement (Note: Links have been removed),

McMaster researchers have developed a new form of cultivated meat using a method that promises more natural flavor and texture than other alternatives to traditional meat from animals.

Researchers Ravi Selvaganapathy and Alireza Shahin-Shamsabadi, both of the university’s School of Biomedical Engineering, have devised a way to make meat by stacking thin sheets of cultivated muscle and fat cells grown together in a lab setting. The technique is adapted from a method used to grow tissue for human transplants.

A January 19, 2021 McMaster University news release (also on EurekAlert) by Wade Hemsworth, which originated the news item, offers more details,

The sheets of living cells, each about the thickness of a sheet of printer paper, are first grown in culture and then concentrated on growth plates before being peeled off and stacked or folded together. The sheets naturally bond to one another before the cells die.

The layers can be stacked into a solid piece of any thickness, Selvaganapathy says, and “tuned” to replicate the fat content and marbling of any cut of meat – an advantage over other alternatives.

“We are creating slabs of meat,” he says. “Consumers will be able to buy meat with whatever percentage of fat they like – just like they do with milk.”

As they describe in the journal Cells Tissues Organs, the researchers proved the concept by making meat from available lines of mouse cells. Though they did not eat the mouse meat described in the research paper, they later made and cooked a sample of meat they created from rabbit cells.

“It felt and tasted just like meat,” says Selvaganapathy.

There is no reason to think the same technology would not work for growing beef, pork or chicken, and the model would lend itself well to large-scale production, Selvaganapathy says.

The researchers were inspired by the meat-supply crisis in which worldwide demand is growing while current meat consumption is straining land and water resources and generating troubling levels of greenhouse gases.

“Meat production right now is not sustainable,” Selvaganapathy says. “There has to be an alternative way of creating meat.”

Producing viable meat without raising and harvesting animals would be far more sustainable, more sanitary and far less wasteful, the researchers point out. While other forms of cultured meat have previously been developed, the McMaster researchers believe theirs has the best potential for creating products consumers will accept, enjoy and afford.

The researchers have formed a start-up company to begin commercializing the technology.

The researchers have included a picture of the ‘meat’,

Caption: A sample of meat cultivated by researchers at Canada’s McMaster University, using cells from mice. Credit: McMaster University

Here’s a link to and a citation for the paper,

Engineering Murine Adipocytes and Skeletal Muscle Cells in Meat-like Constructs Using Self-Assembled Layer-by-Layer Biofabrication: A Platform for Development of Cultivated Meat by Alireza Shahin-Shamsabadi and P. R. (Ravi) Selvaganapathy. Cells Tissues Organs (2021). DOI: 10.1159/000511764

This paper is behind a paywall.

1st biohybrid artificial retina built with silk fibroin & retinal cells

A December 12, 2020 news item on Nanowerk announces a step forward in the development of artificial retinas,

“The biohybrid retina is a cell therapy for the reconstruction of the damaged retina by implanting healthy cells in the patient’s eye,” says Fivos Panetsos, director of the Neuro-computation and Neuro-robotics Group of the UCM and member of the Institute of Health Research of the Hospital Clínico San Carlos de Madrid (IdISSC).

A December 11, 2020 Universidad Complutense de Madrid (UCM) press release on EurekAlert, which originated the news item, delves further,

The cells of the artificial retina adhere to very thin silk fibroin biofilms – a biomaterial 100% biocompatible with human tissue – and covered by a gel which protects them during eye surgery and allows them to survive during the time they need to get integrated with the surrounding tissue after transplantation.

“The transplanted retina also contains mesenchymal cells that function as producers of neuroprotective and neuroreparative molecules and facilitate functional integration between implanted and patient cells”, adds UCM’s researcher and director of the study, published in the Journal of Neural Engineering .

One more step in a problem with more than 196 million affected

To build this artificial retina, researchers have developed silk fibroin films with mechanical characteristics similar to Bruch’s membrane – the layer of cells that supports the neural retina. Then, they have biofunctionalized them so that retinal cells could adhere, and on them they have grown epithelial and neural cells. Finally, they have carried out an in vitro study of the structural and functional characteristics of the biohybrid.

Age-Related Macular Degeneration (AMD) is a neurodegenerative disease that causes a progressive loss of central vision and even blindness in its most advanced stage. Triggered by heterogeneous, complex and still poorly understood mechanisms, it is the leading cause of irreversible vision loss in people over 65 years of age and affects more than 196 million people worldwide.

AMD is an incurable disease, and current treatments can only alleviate symptoms and slow down the progression of the disease. “This research is an important step towards solving the problem of blindness faced by AMD patients”, concludes Panetsos.

Here’s a link to and a citation for the paper,

First steps for the development of silk fibroin-based 3D biohybrid retina for age-related macular degeneration (AMD) by Nahla Jemni-Damer, Atocha Guedan-Duran, Jasmin Cichy, Paloma Lozano-Picazo, Daniel Gonzalez-Nieto, José Perez-Rigueiro, Francisco Rojo, Gustavo V. Guinea, Assunta Virtuoso, Giovanni Cirillo, Michele Papa, Félix Armada-Maresca, Carlota Largo-Aramburu, Salvador D Aznar-Cervantes, José L Cenis, and Fivos Panetsos.Journal of Neural Engineering, Volume 17, Number 5 (or 2020 Neural Eng. 17 055003) DOI: doi: 10.1088/1741-2552/abb9c0 Published 28 October 2020 • © 2020 IOP Publishing Ltd

This paper is behind a paywall.