Category Archives: science

Congratulations to Molly Shoichet (her hydrogels are used in regenerative medicine and more) for winning the $1 million Gerhard Herzberg Canada Gold Medal

I imagine that most anyone who’s been in contact with Ms. Shoichet is experiencing a thrill on hearing this morning’s (November 10, 2020) news about winning Canada’s highest honour for science and engineering research. (Confession: she, very kindly, once gave me a brief interview for a posting on this blog, more about that later).

Why Molly Shoichet won the Gerhard Herzberg Canada Gold Medal

Emily Chung’s Nov. 10, 2020 news item on the Canadian Broadcasting Corporation (CBC) website announces the exciting news (Note: Links have been removed),

A Toronto chemical engineering professor has won the $1 million Gerhard Herzberg Canada Gold Medal, the country’s top science prize, for her work designing gels that mimic human tissues.

The Natural Sciences and Engineering Research Council of Canada (NSERC) announced Tuesday [Nov. 10, 2020] that Molly Shoichet, professor of chemical engineering and applied chemistry and Canada Research Chair in Tissue Engineering at the University of Toronto is this year’s recipient of the award, which recognizes “sustained excellence” and “overall influence” of research conducted in Canada in the natural sciences or engineering.

Shoichet’s hydrogels are used for drug development and  delivery and regenerative medicine to heal injuries and treat diseases.

NSERC said Shoichet’s work has led to the development of several “game-changing” applications of such materials. They “delivered a crucial breakthrough” by allowing cells to be grown in three dimensions as they do in the body, rather than the two dimensions they typically do in a petri dish.

Hydrogels are polymer materials — materials such as plastics, made of repeating units — that become swollen with water.

“If you’ve ever eaten Jell-o, that’s a hydrogel,” Shoichet said. Slime and the absorbent material inside disposable diapers are also hydrogels.

Shoichet was born in Toronto, and studied science and engineering at the Massachusetts Institute of Technology and the University of Massachusetts Amherst. After graduating, she worked in the biotech industry alongside “brilliant biologists,” she said. She noticed that the biologists’ research was limited by what types of materials were available.

As an engineer, she realized she could help by custom designing materials for biologists. She could make materials specifically suit their needs, to answer their specific questions by designing hydrogels to mimic particular tissues.

Her collaborations with biologists have also generated three spinoff companies, including AmacaThera, which was recently approved to run human trials of a long-acting anesthetic delivered with an injectable hydrogel to deal with post-surgical pain.

Shoichet noted that drugs given to deal with that kind of pain lead to a quarter of opioid addictions, which have been a deadly problem in Canada and around the world.

“What we’re really excited about is not only meeting that critical need of providing people with greater pain relief for a sustained period of time, but also possibly putting a dent in the operation,” she said. 

Liz Do’s Nov. 10, 2020 University of Toronto news release provides more details (Note: Links have been removed),

The  Herzberg Gold Medal is awarded by the Natural Sciences and Engineering Research Council (NSERC) in recognition of research contributions characterized by both excellence and influence.

“I was completely overwhelmed when I was told the good news,” says Shoichet. “There are so many exceptional people who’ve won this award and I admire them. To think of my peers putting me in that same category is really incredible.”

A pioneer in regenerative medicine, tissue engineering and drug delivery, Shoichet and her team are internationally known for their discovery and innovative use of 3D hydrogels.

“One of the challenges facing drug screening is that many of the drugs discovered work well in the lab, but not in people, and a possible explanation for this discrepancy is that these drugs are discovered in environments that do not reflect that of the body,” explains Shoichet.

Shoichet’s team has invented a series of biomaterials that provide a soft, three-dimensional environment in which to grow cells. These hydrogels — water-swollen materials — better mimic human tissue than hard two-dimensional plastic dishes that are typically used. “Now we can do more predictive drug screening,” says Shoichet.

Her lab is using these biomaterials to discover drugs for breast and brain cancer and a rare lung disease. Shoichet’s lab has been equally innovative in regenerative medicine strategies to promote repair of the brain after stroke and overcome blindness.

“Everything that we do is motivated by answering a question in biology, using our engineering and chemistry tools to answer those questions,” says Shoichet.

“The hope is that our contributions will ultimately make a positive impact in the cancer community and in treating diseases for which we can only slow the progression rather than stop and reverse, such as with blindness.”

Shoichet is also an advocate for and advisor on the fields of science and engineering. She has advised both federal and provincial governments through her service on Canada’s Science, Technology and Innovation Council and the Ontario Research Innovation Council. From 2014 to 2018, she was the Senior Advisor to the President on Science & Engineering Engagement at the University of Toronto. She is the co-founder of Research2Reality [emphasis mine], which uses social media to promote innovative research across the country. She also served as Ontario’s first Chief Scientist [emphasis mine], with a mandate to advance science and innovation in the province.

Shoichet is the only person to be elected a fellow of all three of Canada’s National Academies and is a foreign member of the U.S. National Academy of Engineering, and fellow of the Royal Society (UK) — the oldest and most prestigious academic society.

Doug Ford (premier of Ontario) and Molly Shoichet

She did serve as Ontario’s first Chief Scientist—for about six months (Nov. 2017 – July 2018). Molly Shoichet was fired when a new provincial government was elected in the summer of 2018. Here’s more about the incident from a July 4, 2018 article by Ryan Maloney for huffingtonpost.ca (Note: Links have been removed),

New Ontario Premier Doug Ford has fired the province’s first chief scientist.

Dr. Molly Shoichet, a renowned biomedical engineer who teaches at the University of Toronto, was appointed in November [2017] to advise the government and ensure science and research were at the forefront of decision-making.

Shoichet told HuffPost Canada in an email that the she does not believe the decision was about her, and “I don’t even know whether it was about this role.” She said she is disappointed but honoured to have served Ontarians, even for a short time.

Ford’s spokesman, Simon Jefferies told The Canadian Press Wednesday that the government is starting the process of “finding a suitable and qualified replacement.” [emphasis mine]

The move comes just days after Ford’s Progressive Conservatives officially took power in Canada’s largest province with a majority government.

Almost a year later, there was no replacement in sight according to a June 24, 2019 opinion piece by Kimberly Girling (then the Research and Policy Director of the Evidence for Democracy not-for-profit) for the star.com,

Premier Doug Ford, I’m concerned for your government.

I know you feel it too. Last week, one year into your mandate and faced with sharply declining polls after your first provincial budget, you conducted a major cabinet shuffle. This shuffle is clearly an attempt to “put the right people in the right place at the right time” and improve the outcomes of your cabinet. But I’m still concerned.

Since your election, your caucus has made many bold decisions. Unfortunately, it seems many are Ontarians unhappy with most of these decisions, and I’m not sure the current shuffle is enough to fix this.

[] I think you’re missing someone.

What about a Chief Scientist?

It isn’t a radical idea. Actually, you used to have one. Ontario’s first Chief Scientist, Dr. Molly Shoichet, was appointed to advise the government on science policy and champion science and innovation for Ontario. However, when your government was elected, you fired Dr. Shoichet within the first week.

It’s been a year, and so far we haven’t seen any attempts to fill this vacant position. [emphasis mine]

I wonder if Doug Ford and his crew regret the decision to fire Shoichet especially now that the province is suffering from a new peak in rising COVID-19 case numbers. These days government could do with a little bit of good news.

The only way we might ever know is if Doug Ford writes a memoir (in about 20 or 30 years from now).

Molly Shoichet, Research2Reality, and FrogHeart

A May 11, 2015 posting announced the launch of Research2Reality and it’s in this posting that I have a few comments from Molly Shoichet about co-founding a national science communication project. Given how busy she was at the time, I was amazed she took a few minutes to speak to me and took more time to make it possible for me to interview Raymond Laflamme (then director of the Institute for Quantum Computing at the University of Waterloo [Ontario]) and a prominent physicist.

Here are the comments Molly Shoichet offered (from the May 11, 2015 posting),

“I’m very excited about this and really hope that other people will be too,” says Shoichet. The audience for the Research2Reality endeavour is for people who like to know more and have questions when they see news items about science discoveries that can’t be answered by investigating mainstream media programmes or trying to read complex research papers.

This is a big undertaking. ” Mike [Mike MacMillan, co-founder] and I thought about this for about two years.” Building on the support they received from the University of Toronto, “We reached out to the vice-presidents of research at the top fifteen universities in the country.” In the end, six universities accepted the invitation to invest in this project,

Five years later, it’s still going.

Finally: Congratulations Molly Shoichet!

How do viruses and physics go together? Find out at a Nov. 4, 2020 Perimeter Institute (PI) virtual lecture

I got this announcement from an Oct. 29, 2020 Perimeter Institute (PI) Emmy Noether newsletter (received via email),

Catherne Beauchemin

A Physicist’s Adventures in Virology WEDNESDAY, NOVEMBER 4 at 7 pm ET [4 pm PT]

In recent years, there has been a rise in cynicism about many traditionally well-respected institutions – science, academia, news reporting, and even the concepts of experts and expertise more generally. Many people’s primary – or only – exposure to science is through biological or health science, especially during the COVID-19 pandemic.

In health research, rising cynicism has spawned the anti-vaccine movement, and a growing reliance on advice from peer networks rather than experts. In part, such movements are fuelled by several examples of provably false, so-called “scientific results,” coming about either through fraud or incompetence. While skepticism is crucial to science, cynicism rooted in a lack of trust can devalue scientific contributions.

In her lecture webcast, physicist Catherine Beauchemin will explore the erosion of trust in health research, presenting examples from influenza and COVID-19. …

I went to the A Physicist’s Adventures in Virology event and livestrream page to find this,

Two essential ingredients of the scientific method are skepticism and independent confirmation – the ability to glean for oneself whether an established theory or a new hypothesis is true or false. But not everyone has the capacity to perform the experiments to obtain such a confirmation.

Consider, for example, the costs of constructing your own Large Hadron Collider, or your ability as a non-expert to critically read and understand a scientific publication. In practice, acceptance of scientific theories is more often based on trust than on independent confirmation. When that trust is eroded, issues emerge.

Catherine Beauchemin is a Professor of Physics at Ryerson University and a Deputy Program Director in the RIKEN Interdisciplinary Theoretical and Mathematical Sciences Program in Japan. For the last 18 years, she has been developing mathematical and computational descriptions of how viruses spread from cell to cell, a field she calls “virophysics.”

In her November 4 [2020] Perimeter Public Lecture webcast, Beauchemin will highlight some of the issues that have eroded trust in health research, presenting examples from influenza and COVID-19. She will show why she believes many of these issues have their root in the fact that hypotheses in health research are formulated as words rather than mathematical expressions – and why a dose of physics may be just the prescription we need.

Enjoy!

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 in the forest

It seems lignin is a bit of a problem. Its presence in a tree makes processing the wood into various products more difficult. (Of course, some people appreciate trees for other reasons both practical [carbon sequestration?] and/or aesthetic.)

In any event, scientists have been working on ways to reduce the amount of lignin in poplar trees since at least 2014 (see my April 7, 2014 posting titled ‘Good lignin, bad lignin: Florida researchers use plant waste to create lignin nanotubes while researchers in British Columbia develop trees with less lignin’; scroll down about 40% of the way for the ‘less lignin’ story).

(I don’t believe the 2014 research was accomplished with the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 technique as it had only been developed in 2012.)

The latest in the quest to reduce the amount of lignin of poplar trees comes from a Belgian/US team, from an Oct. 6, 2020 news item on ScienceDaily,

Researchers led by prof. Wout Boerjan (VIB-UGent [Ghent University] Center for Plant Systems Biology) have discovered a way to stably finetune the amount of lignin in poplar by applying CRISPR/Cas9 technology. Lignin is one of the main structural substances in plants and it makes processing wood into, for example, paper difficult. This study is an important breakthrough in the development of wood resources for the production of paper with a lower carbon footprint, biofuels, and other bio-based materials. Their work, in collaboration with VIVES University College (Roeselare, Belgium) and University of Wisconsin (USA) appears in Nature Communications.

Picture Tailoring lignin and growth by creating CCR2 allelic variants (From left to right: wild type, CCR2(-/-), CCR2(-/*) line 206, CCR2(-/*) line 12) Courtesy: VIB (Flanders Institute of Biotechnology)

An Oct. 6, 2020 VIB (Vlaams Instituut voor Biotechnologie; Flanders Institute of Biotechnology) press release (also on EurekAlert), which originated the news item, explains the reason for this research and how CRISPR (clustered regularly interspaced short palindromic repeats) technology could help realize it,

Towards a bio-based economy

Today’s fossil-based economy results in a net increase of CO2 in the Earth’s atmosphere and is a major cause of global climate change. To counter this, a shift towards a circular and bio-based economy is essential. Woody biomass can play a crucial role in such a bio-based economy by serving as a renewable and carbon-neutral resource for the production of many chemicals. Unfortunately, the presence of lignin hinders the processing of wood into bio-based products.

Prof. Wout Boerjan (VIB-UGent): “A few years ago, we performed a field trial with poplars that were engineered to make wood containing less lignin. Most plants showed large improvements in processing efficiency for many possible applications. The downside, however, was that the reduction in lignin accomplished with the technology we used then – RNA interference – was unstable and the trees grew less tall.”

New tools

Undeterred, the researchers went looking for a solution. They employed the recent CRISPR/Cas9 technology in poplar to lower the lignin amount in a stable way, without causing a biomass yield penalty. In other words, the trees grew just as well and as tall as those without genetic changes.

Dr. Barbara De Meester (VIB-UGent): “Poplar is a diploid species, meaning every gene is present in two copies. Using CRISPR/Cas9, we introduced specific changes in both copies of a gene that is crucial for the biosynthesis of lignin. We inactivated one copy of the gene, and only partially inactivated the other. The resulting poplar line had a stable 10% reduction in lignin amount while it grew normally in the greenhouse. Wood from the engineered trees had an up to 41% increase in processing efficiency”.

Dr. Ruben Vanholme (VIB-UGent): “The mutations that we have introduced through CRISPR/Cas9 are similar to those that spontaneously arise in nature. The advantage of the CRISPR/Cas9 method is that the beneficial mutations can be directly introduced into the DNA of highly productive tree varieties in only a fraction of the time it would take by a classical breeding strategy.”

The applications of this method are not only restricted to lignin but might also be useful to engineer other traits in crops, providing a versatile new breeding tool to improve agricultural productivity.

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

Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele by Barbara De Meester, Barbara Madariaga Calderón, Lisanne de Vries, Jacob Pollier, Geert Goeminne, Jan Van Doorsselaere, Mingjie Chen, John Ralph, Ruben Vanholme & Wout Boerjan. Nature Communications volume 11, Article number: 5020 (2020) DOI: https://doi.org/10.1038/s41467-020-18822-w Published 06 October 2020

This paper is open access.

Apply for faculty positions or entry to master’s programme at Canada’s Perimeter Institute for Theoretical Physics

I think the title for this post says it all.

Faculty positions

From an Oct. 13, 2020 Perimeter Institute for Theoretical Physics (PI) announcement (received via email),

Perimeter Institute for Theoretical Physics is inviting applications for tenure-track Faculty positions in Quantum Matter and Quantum Information Science. For more information please visit our website.

We would be very grateful if you would circulate this information to outstanding early career candidates who may be interested in this opportunity.

Perimeter Institute offers a dynamic, multi-disciplinary environment with maximum research freedom and opportunity to collaborate. Consideration of applications will begin on December 1, 2020; however, applications will be considered until the positions are filled.

Perimeter Scholars International (PSI) master’s programme

From an Oct. 13, 2020 Perimeter Institute for Theoretical Physics (PI) announcement (received via email),

Perimeter Institute for Theoretical Physics is now accepting applications for the 2021/2022 Perimeter Scholars International (PSI) program. 

PSI is a master’s-level course in theoretical physics designed to bring highly qualified and exceptionally motivated graduate students to the cutting edge of the field in an inclusive training environment. 

This unique Master’s program, in partnership with the University of Waterloo, seeks not only students with stellar undergraduate physics and/or mathematics track records, but also those with diverse backgrounds, collaborative spirit, creativity, and other attributes that will set them apart as future innovators. 

Program features

– Removal of financial barriers: Most students who receive and accept offers of admission to PSI will receive a full scholarship. Perimeter Institute also helps with travel arrangements and any immigration arrangements necessary. 

– Students learn from many of the leading minds in theoretical physics while earning a Master’s degree from the University of Waterloo 

– Collaboration is valued over competition; deep understanding and creativity are valued over rote learning and examination 

– PSI recruits worldwide: 85 percent of students come from outside of Canada

– PSI seeks extraordinary talent who may have non-traditional academic backgrounds, but have demonstrated exceptional scientific aptitude 

Early application deadline: November 15, 2020. 
Final application deadline: February 1, 2021. 

Good luck!

Belated posting for Ada Lovelace Day (it was on Tuesday, Oct. 13, 2020)

For anyone who doesn’t know who Ada Lovelace was (from my Oct. 13, 2015 posting, ‘Ada Lovelace “… manipulative, aggressive, a drug addict …” and a genius but was she likable?‘)

Ada Lovelace was the daughter of the poet Lord Byron and mathematician Annabella Milbanke.

Her [Ada Lovelace’s] foresight was so extraordinary that it would take another hundred years and Alan Turing to recognise the significance of her work. But it was an achievement that was probably as much a product of her artistic heritage as her scientific training.

You can take the title of that October 13, 2015 post as a hint that I was using ‘Ada Lovelace “… manipulative, aggressive, a drug addict …” and a genius but was she likable?‘ to comment on the requirement that women be likable in a way that men never have to consider.

Hard to believe that 2015 was the last time I stumbled across information about the day. ’nuff said. This year I was lucky enough to see this Oct. 13, 2020 article by Zoe Kleinman for British Broadcasting Corporation (BBC) news online,

From caravans [campers] to kitchen tables, and podcast production to pregnancy, I’ve been speaking to many women in and around the technology sector about how they have adapted to the challenges of working during the coronavirus pandemic.

Research suggests women across the world have shouldered more family and household responsibilities than men as the coronavirus pandemic continues, alongside their working lives.

And they share their inspirations, frustrations but also their optimism.

“I have a new business and a new life,” says Clare Muscutt, who lost work, her relationship and her flatmate as lockdown hit.

This Tuesday [Oct. 13, 2020] is Ada Lovelace Day – an annual celebration of women working in the male-dominated science, technology, engineering and maths (Stem) sectors.

And, this year, it has a very different vibe.

Claire Broadley, technical writer, Leeds

Before lockdown, my husband and I ran our own company, producing user guides and written content for websites.

Business income dropped by about two-thirds during lockdown.

We weren’t eligible for any government grants. And because we still had a small amount of work, we couldn’t furlough ourselves.

It felt like we were slowly marching our family towards a cliff edge.

In May [2020], to my astonishment and relief, I was offered my dream job, remote writing about the internet and technology.

Working from home with the children has been the most difficult thing we’ve ever done.

My son is seven. He is very scared.

Sometimes, we can’t spend the time with him that we would like to. And most screen-time rules have gone completely out of the window.

The real issue for us now is testing.

My young daughter caught Covid in July [2020]. And she recently had a temperature again. But it took six days to get a test result, so my son was off school again. And my husband was working until midnight to fit everything in.

There are many other stories in Kleinman’s Oct. 13, 2020 article.

Nancy Doyle’s October 13, 2020 article for Forbes tends to an expected narrative about women in science, technology, engineering, and mathematics (STEM),

“21st century science has a problem. It is short of scientists. Technological innovations mean that the world needs many more specialists in the STEM (Science, Technology, Engineering and Maths) subjects than it is currently training. And this problem is compounded by the fact that women, despite clear evidence of aptitude and ability for science subjects, are not choosing to study STEM subjects, are not being recruited into the STEM workforce, are not staying in the STEM workplace.”

Why Don’t Women Do Science?

Professor Rippon [Gina Rippon, Professor of Neuroscience at Aston University in the UK] walked me through the main “neurotrash” arguments about the female brain and its feebleness.

“There is a long and fairly well-rehearsed ‘blame the brain’ story, with essentialist or biology-is-destiny type arguments historically asserting that women’s brains were basically inferior (thanks, Gustave le Bon and Charles Darwin!) or too vulnerable to withstand the rigours of higher education. A newer spin on this is that female brains do not endow their owners with the appropriate cognitive skills for science. Specifically, they are poor at the kind of spatial thinking that is core to success in science or, more generally, are not ‘hard-wired’ for the necessary understanding of systems fundamental to the theory and practice of science.

The former ‘spatial deficit’ description has been widely touted as one of the most robust of sex differences, quite possibly present from birth. But updated and more nuanced research has not been able to uphold this claim; spatial ability appears to be more a function of spatial experience (think toys, videogames, hobbies, sports, occupations) than sex. And it is very clearly trainable (in both sexes), resulting in clearly measurable brain changes as well as improvements in skill.”

You can find out more about women in STEM, Ada Lovelace, and events (year round) to celebrate her at the Ada Lovelace Day website.

Plus, I found this on Twitter about a new series of films about women in science from a Science Friday (a US National Public Radio podcast) tweet,

Science Friday @scifri

Celebrate #WomenInScience with a brand new season of #BreakthroughFilms, dropping today [October 14, 2020]! Discover the innovative research & deeply personal stories of six women working at the forefront of their STEM fields.

Get inspired at BreakthroughFilms.org

Here’s the Breakthrough Films trailer,

Enjoy!

If you want ‘shredded pecs’, train like a burrowing frog

Caption: Forward burrowers use pointed snouts and powerful forelimbs bolstered by strong pectoral muscles to scrabble into the earth. They’re often orb-shaped to improve their ability to hold water. Credit: Rachel Keeffe

It’s always enjoyable to see the scientific community indulge in a little fun and I’m using that as an excuse for including a frog story here.

From an August 31, 2020 Florida Museum of Natural History news release (also on EurekAlert but published on Sept. 1, 2020) by Halle Marchese announces some research into a little known frog,

You might think the buffest frogs would be high jumpers, but if you want shredded pecs, you should train like a burrowing frog. Though famously round, these diggers are the unsung bodybuilders of the frog world. We bring you tips from frog expert Rachel Keeffe, a doctoral student at the University of Florida, and physical therapist Penny Goldberg to help you get the burrowing body of your dreams.

But first, a caveat: According to Keeffe, no workout regimen can help you train your way into a highly specialized frog physique honed by 200 million years of evolution. To better understand burrowing frog anatomy, Keeffe and her adviser David Blackburn, Florida Museum of Natural History curator of herpetology, analyzed CT scans from all 54 frog families to show these frogs boast a robust and quirky skeleton that is more variable than previously thought.

“People think about frogs as being clean and smooth and slimy, or the classic ‘green frog on a lily pad,’ but a lot of them are dirty – they like to scoot around and be in the dirt,” Keeffe said. “Burrowing frogs are really diverse and can do a lot of cool things. And when you look at the skeletons of known burrowers, they’re very different from what you would call a ‘normal frog.'”

Burrowing frogs are found all over the world from deserts to swamps, but their underground lifestyle makes them difficult to study, Keeffe said. Most tunnel hind end-first with their back legs. But a few species are forward burrowers, using pointed snouts and powerful forelimbs bolstered by strong pectoral muscles to scrabble into the earth.

Keeffe’s sample of 89 frog species revealed radical differences in burrowing bone structure, from clavicles the size of eyelashes to other bones that are unusually thick.

“They’re so diverse that it’s challenging to think about even comparing them. It’s almost a black hole of work that we can do with forward burrowers because we tend to focus on the legs,” she said.

Some burrow to seek refuge, whether from arid temperatures or predators, and underground habitats can be hunting grounds or secluded hiding places. Other burrowing frogs can spend months at a time as deep as 3 feet belowground, surviving on a high-protein diet of termites and ants. The takeaway: If you want to compete for resources with the pros, don’t be afraid to put in the work.

Get the burly burrowing body

To train like a burrowing frog, Goldberg, assistant director of ReQuest Physical Therapy in Gainesville, recommended dedicating time to strengthening your upper back.

“In humans, the most important muscle group to focus on if you were to train like one of these frogs would be the scapular stabilizers,” she said. “These include 17 muscles, such as the lats and rotator cuff, with attachments all the way down to the pelvis that allow the upper back to generate power. To burrow like a forward burrower, you need to strengthen this entire region.”

One strengthening move Goldberg recommended is the “Prone W.” Lie facedown with elbows bent and palms on the floor. Squeeze your shoulder blades down and toward your spine as you lift your arms to the ceiling for a couple seconds at a time.

Like any elite athlete, burrowing frogs also maintain an optimal form. They’re often orb-shaped to improve their ability to hold water.

“Personally, if I were a sphere, I think it would be hard for me to dig, but it doesn’t seem to affect these frogs at all,” Keeffe said. “However, frogs with stumpy legs are definitely worse at jumping, and they tend to stagger when they walk.”

For these frogs, time away from the tunnels might be spent swimming instead, Keeffe said. To compete here, Goldberg recommends the breaststroke, adding that her top training tips for getting the upper back and pecs of a forward burrower would include pullups and pushups to develop the shoulder blade area.

“In my world, we would use resistance bands and pushing or pulling motions to train this area,” Goldberg said. “Anything focusing predominantly on building strength in the upper back region.”

If resistance bands are part of your workout routine, try grasping one with both hands and extending your arms while keeping your elbows straight. For best results, Goldberg recommended starting with three sets of 10.

Burrowing frogs might also hold key answers to gaps in scientists’ understanding of amphibian evolution at large. Keeffe’s analysis also found that forward-burrowing behavior evolved independently at least eight times in about one-fifth of frog families, and the trait’s persistence in the frog family tree suggests it’s a beneficial adaptation. Keeffe also found that forward burrowers tended to have a highly contoured humerus, the bone that connects the shoulder to the elbow in humans.

Understanding how bone shape relates to musculature can help scientists identify which frogs, both modern and extinct, are forward burrowers, a helpful tool given their covert behavior.

“Even though it can be frustrating, I like them because they’re secretive,” Keeffe said. “But the whole thing underlying this study is that frogs can do a lot of cool things – they don’t just jump and they’re not just green.”

CT scans were generated from the National Science Foundation-funded oVert project.

Do take a look at the August 31, 2020 Florida Museum of Natural History news release as the researchers have provided pictures of real ‘forward burrowing frogs’ along with more cartoons and other other images that have been embedded in Marchese’s release.

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

Comparative morphology of the humerus in forward-burrowing frogs by Rachel Keeffe, David C Blackburn. Biological Journal of the Linnean Society, blaa092, DOI: https://doi.org/10.1093/biolinnean/blaa092 Published: 28 August 2020

This paper is behind a paywall.

Congratulations to winners of 2020 Nobel Prize for Chemistry: Dr. Emmanuelle Charpentier & Dr. Jennifer A. Doudna (CRISPR-cas9)

It’s possible there’s a more dramatic development in the field of contemporary gene-editing but it’s indisputable that CRISPR (clustered regularly interspaced short palindromic repeats) -cas9 (CRISPR-associated 9 [protein]) ranks very highly indeed.

The technique, first discovered (or developed) in 2012, has brought recognition in the form of the 2020 Nobel Prize for Chemistry to CRISPR’s two discoverers, Emanuelle Charpentier and Jennifer Doudna.

An October 7, 2020 news item on phys.org announces the news,

The Nobel Prize in chemistry went to two researchers Wednesday [October 7, 2020] for a gene-editing tool that has revolutionized science by providing a way to alter DNA, the code of life—technology already being used to try to cure a host of diseases and raise better crops and livestock.

Emmanuelle Charpentier of France and Jennifer A. Doudna of the United States won for developing CRISPR-cas9, a very simple technique for cutting a gene at a specific spot, allowing scientists to operate on flaws that are the root cause of many diseases.

“There is enormous power in this genetic tool,” said Claes Gustafsson, chair of the Nobel Committee for Chemistry.

More than 100 clinical trials are underway to study using CRISPR to treat diseases, and “many are very promising,” according to Victor Dzau, president of the [US] National Academy of Medicine.

“My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” said Doudna, who is affiliated with the University of California, Berkeley, and is paid by the Howard Hughes Medical Institute, which also supports The Associated Press’ Health and Science Department.

The prize-winning work has opened the door to some thorny ethical issues: When editing is done after birth, the alterations are confined to that person. Scientists fear CRISPR will be misused to make “designer babies” by altering eggs, embryos or sperm—changes that can be passed on to future generations.

Unusually for phys.org, this October 7, 2020 news item is not a simple press/news release reproduced in its entirety but a good overview of the researchers’ accomplishments and a discussion of some of the issues associated with CRISPR along with the press release at the end.

I have covered some CRISPR issues here including intellectual property (see my March 15, 2017 posting titled, “CRISPR patent decision: Harvard’s and MIT’s Broad Institute victorious—for now‘) and designer babies (as exemplified by the situation with Dr. He Jiankui; see my July 28, 2020 post titled, “July 2020 update on Dr. He Jiankui (the CRISPR twins) situation” for more details about it).

An October 7, 2020 article by Michael Grothaus for Fast Company provides a business perspective (Note: A link has been removed),

Needless to say, research by the two scientists awarded the Nobel Prize in Chemistry today has the potential to change the course of humanity. And with that potential comes lots of VC money and companies vying for patents on techniques and therapies derived from Charpentier’s and Doudna’s research.

One such company is Doudna’s Editas Medicine [according to my search, the only company associated with Doudna is Mammoth Biosciences, which she co-founded], while others include Caribou Biosciences, Intellia Therapeutics, and Casebia Therapeutics. Given the world-changing applications—and the amount of revenue such CRISPR therapies could bring in—it’s no wonder that such rivalry is often heated (and in some cases has led to lawsuits over the technology and its patents).

As Doudna explained in her book, A Crack in Creation: Gene Editing and the Unthinkable Power to Control Evolution, cowritten by Samuel H. Sternberg …, “… —but we could also have woolly mammoths, winged lizards, and unicorns.” And as for that last part, she made clear, “No, I am not kidding.”

Everybody makes mistakes and the reference to Editas Medicine is the only error I spotted. You can find out more about Mammoth Biosciences here and while Dr. Doudna’s comment, “My greatest hope is that it’s used for good, to uncover new mysteries in biology and to benefit humankind,” is laudable it would seem she wishes to profit from the discovery. Mammoth Biosciences is a for-profit company as can be seen at the end of the Mammoth Biosciences’ October 7, 2020 congratulatory news release,

About Mammoth Biosciences

Mammoth Biosciences is harnessing the diversity of nature to power the next-generation of CRISPR products. Through the discovery and development of novel CRISPR systems, the company is enabling the full potential of its platform to read and write the code of life. By leveraging its internal research and development and exclusive licensing to patents related to Cas12, Cas13, Cas14 and Casɸ, Mammoth Biosciences can provide enhanced diagnostics and genome editing for life science research, healthcare, agriculture, biodefense and more. Based in San Francisco, Mammoth Biosciences is co-founded by CRISPR pioneer Jennifer Doudna and Trevor Martin, Janice Chen, and Lucas Harrington. The firm is backed by top institutional investors [emphasis mine] including Decheng, Mayfield, NFX, and 8VC, and leading individual investors including Brook Byers, Tim Cook, and Jeff Huber.

An October 7, 2029 Nobel Prize press release, which unleashed all this interest in Doudna and Charpentier, notes this,

Prize amount: 10 million Swedish kronor, to be shared equally between the Laureates.

In Canadian money that amount is $1,492,115.03 (as of Oct. 9, 2020 12:40 PDT when I checked a currency converter).

Ordinarily there’d be a mildly caustic comment from me about business opportunities and medical research but this is a time for congratulations to both Dr. Emanuelle Charpentier and Dr. Jennifer Doudna.

Non-invasive chemical imaging reveals the Eykian Lamb of God’s secrets

Left: color image after the 1950s treatment. The ears of the Eyckian Lamb were revealed after removal of the 16th-century overpaint obscuring the background. Right: color image after the 2019 treatment that removed all of the 16th century overpaint, revealing the face of the Eyckian Lamb. The dotted lines indicate the outline of the head before removal of 16th-century overpaint.

Fascinating, yes? More than one person has noticed that the ‘new’ lamb is “disturbingly human-like.” First, here’s more about this masterpiece and the technology used to restore it (from a July 29, 2020 University of Antwerp (Belgium) press release (Note: I do not have all of the figures (images) described in this press release embedded here),

Two non-invasive chemical imaging modalities were employed to help understand the changes made over time to the Lamb of God, the focal point of the Ghent Altarpiece (1432) by Hubert and Jan Van Eyck. Two major results were obtained: a prediction of the facial features of the Lamb of God that had been hidden beneath non-original overpaint dating from the 16th century (and later), and evidence for a smaller earlier version of the Lamb’s body with a more naturalistic build. These non-invasive imaging methods, combined with analysis of paint cross-sections and magnified examination of the paint surface, provide objective chemical evidence to understand the extent of overpaints and the state of preservation of the original Eyckian paint underneath.

The Ghent Altarpiece is one of the founding masterpieces of Western European painting. The central panel, The Adoration of the Lamb, represents the sacrifice of Christ with a depiction of the Lamb of God standing on an altar, blood pouring into a chalice. During conservation treatment and technical analysis in the 1950s, conservators recognized the presence of overpaint on the Lamb and the surrounding area. But based on the evidence available at that time, the decision was made to remove only the overpaint obscuring the background immediately surrounding the head. As a result, the ears of the Eyckian Lamb were uncovered, leading to the surprising effect of a head with four ears (Figure 1).

Figure 1: Left: Color image after the 1950s treatment. The ears of the Eyckian Lamb were revealed after removal of the 16th century overpaint obscuring the background. (© Lukasweb.be – Art in Flanders vzw). Right: Color image after the 2019 treatment that removed all of the 16th century overpaint, revealing the face of the Eyckian Lamb. The dotted lines indicate the outline of the head before removal of 16th century overpaint. (© Lukasweb.be – Art in Flanders vzw).

During the recent conservation treatment of the central panel, chemical images collected before 16th century overpaint was removed revealed facial features that predicted aspects of the Eyckian Lamb, at that time still hidden below the overpaint. For example, the smaller, v-shaped nostrils of the Eyckian Lamb are situated higher than the 16th century nose, as revealed in the map for mercury, an element associated with the red pigment vermilion (Figure 2, red arrow). A pair of eyes that look forward, slightly lower than the 16th century eyes, can be seen in a false-color hyperspectral infrared reflectance image (Figure 2, right). This image also shows dark preparatory underdrawing lines that define pursed lips, and in conjunction with the presence of mercury in this area, suggest the Eyckian lips were more prominent. In addition, the higher, 16th century ears were painted over the gilded rays of the halo (Figure 2, yellow rays). Gilding is typically the artist’s final touch when working on a painting, which supports the conclusion that the lower set of ears is the Eyckian original. Collectively, these facial features indicate that, compared to the 16th century restorer’s overpainted face, the Eyckian Lamb has a smaller face with a distinctive expression.

Figure 2: Left: Colorized composite elemental map showing the distribution of gold (in yellow), mercury (in red), and lead (in white). The red arrow indicates the position of the Eyckian Lamb’s nostrils. (University of Antwerp). Right: Composite false-color infrared reflectance image (blue – 1000 nm, green – 1350 nm, red – 1650 nm) shows underdrawn lines indicating the position of facial features of the Eyckian Lamb, including forward-gazing eyes, the division between the lips, and the jawline. (National Gallery of Art, Washington). The dotted lines indicate the outline of the head before removal of 16th century overpaint.

The new imaging also revealed previously unrecognized revisions to the size and shape of the Lamb’s body: a more naturalistically shaped Lamb, with slightly sagging back, more rounded hindquarters and a smaller tail. The artist’s underdrawing lines used to lay out the design of the smaller shape can be seen in the false-color hyperspectral infrared reflectance image (Figure 3, lower left, white arrows). Mathematical processing of the reflectance dataset to emphasize a spectral feature associated with the pigment lead white resulted in a clearer image of the smaller Lamb (Figure 3, lower right). Differences between the paint handling of the fleece in the initial small Lamb and the revised area of the larger Lamb also were found upon reexamination of the x-radiograph and the paint surface under the microscope.

Figure 3: Upper left: Color image before removal of all 16th century overpaint. (© Lukasweb.be – Art in Flanders vzw). Upper right: Color image after removal of all 16th century overpaint. (© Lukasweb.be – Art in Flanders vzw). Lower left: False-color infrared reflectance image (blue – 1000 nm, green – 1350 nm, red – 1650 nm) reveals underdrawing lines that denote the smaller hindquarters of the initial Lamb. Lower right: Map derived from processing the infrared reflectance image cube showing the initial Lamb with a slightly sagging back, more rounded hindquarters and a smaller tail. Brighter areas of the map indicate stronger absorption from the -OH group associated with one of the forms of lead white. (National Gallery of Art, Washington).

During the conservation treatment completed in 2019, decisions were informed by well-established conservation methods (high-resolution color photography, X-radiography, infrared imaging, paint sample analysis) as well as the new chemical imaging. In this way, the conservation treatment uncovered the smaller face of the Eyckian Lamb, with forward-facing eyes that meet the viewer’s gaze. Only overpaints that could be identified as being later additions dating from the 16th century onward were carefully and safely removed. The body of the Lamb, however, has not changed. The material evidence indicates that the lead white paint layer used to define the larger squared-off hindquarters was applied prior to the 16th century restoration, but because analysis at the present time cannot definitively establish whether this was a change by the original artist(s) or a very early restoration or alteration by another artist, the enlarged contour of the Lamb was left untouched.

Chemical imaging technologies can be used to build confidence about the state of preservation of original paint and help guide the decision to remove overpaint. Combined with the conservators’ thorough optical examination, informed by years of experience and insights derived from paint cross-sections, chemical imaging methods will no doubt be central to ongoing interdisciplinary research, helping to resolve long-standing art-historical issues on the Ghent Altarpiece as well as other works of art. These findings were obtained by researchers from the University of Antwerp using macroscale X-ray fluorescence imaging and researchers at the National Gallery of Art, Washington using infrared reflectance imaging spectroscopy, interpreted in conjunction with the observations of the scientists and the conservation team from The Royal Institute for Cultural Heritage (KIK-IRPA), Brussels.

A January 22, 2020 British Broadcasting Corporation (BBC) online news item notes some of the response to the ‘new’ lamb (Note: A link has been removed),

Restorers found that the central panel of the artwork, known as the Adoration of the Mystic Lamb, had been painted over in the 16th Century.

Another artist had altered the Lamb of God, a symbol for Jesus depicted at the centre of the panel.

Now conservationists have stripped away the overpaint, revealing the lamb’s “intense gaze” and “large frontal eyes”.

Hélène Dubois, the head of the restoration project, told the Art Newspaper the original lamb had a more “intense interaction with the onlookers”.

She said the lamb’s “cartoonish” depiction, which departs from the painting’s naturalistic style, required more research.

The lamb has been described as having an “alarmingly humanoid face” with “penetrating, close-set eyes, full pink lips and flared nostrils” by the Smithsonian Magazine.

These features are “eye-catching, if not alarmingly anthropomorphic”, said the magazine, the official journal of the Smithsonian Institution.

There was also disbelief on social media, where the lamb was called “disturbing” by some and compared to an “alien creature”. Some said they felt it would have been better to not restore the lamb’s original face.

The painter of the panel, Jan Van Eyck, is considered to be one of the most technical and talented artists of his generation. However, it is widely believed that The Ghent Altarpiece was started by his brother, Hubert Van Eyck.

Taken away by the Nazis during World War Two and Napoleon’s troops in the 1700s, the altarpiece is thought to be one of the most frequently stolen artworks of all time.

If you have the time, do read the January 22, 2020 BBC news item in its entirety as it conveys more of the controversy.

Jennifer Ouellette’s July 29, 2020 article for Ars Technica delves further into the technical detail along with some history about this particular 21st Century restoration. The conservators and experts used artificial intelligence (AI) to assist.

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

Dual mode standoff imaging spectroscopy documents the painting process of the Lamb of God in the Ghent Altarpiece by J. and H. Van Eyck by Geert Van der Snickt, Kathryn A. Dooley, Jana Sanyova, Hélène Dubois, John K. Delaney, E. Melanie Gifford, Stijn Legrand, Nathalie Laquiere and Koen Janssens. Science Advances 29 Jul 2020: Vol. 6, no. 31, eabb3379 DOI: 10.1126/sciadv.abb3379

This paper is open access.

Loop quantum cosmology connects the tiniest with the biggest in a cosmic tango

Caption: Tiny quantum fluctuations in the early universe explain two major mysteries about the large-scale structure of the universe, in a cosmic tango of the very small and the very large. A new study by researchers at Penn State used the theory of quantum loop gravity to account for these mysteries, which Einstein’s theory of general relativity considers anomalous.. Credit: Dani Zemba, Penn State

A July 29, 2020 news item on ScienceDaily announces a study showing that quantum loop cosmology can account for some large-scale mysteries,

While [1] Einstein’s theory of general relativity can explain a large array of fascinating astrophysical and cosmological phenomena, some aspects of the properties of the universe at the largest-scales remain a mystery. A new study using loop quantum cosmology — a theory that uses quantum mechanics to extend gravitational physics beyond Einstein’s theory of general relativity — accounts for two major mysteries. While the differences in the theories occur at the tiniest of scales — much smaller than even a proton — they have consequences at the largest of accessible scales in the universe. The study, which appears online July 29 [2020] in the journal Physical Review Letters, also provides new predictions about the universe that future satellite missions could test.

A July 29, 2020 Pennsylvania State University (Penn State) news release (also on EurekAlert) by Gail McCormick, which originated the news item, describes how this work helped us avoid a crisis in cosmology,

While [2] a zoomed-out picture of the universe looks fairly uniform, it does have a large-scale structure, for example because galaxies and dark matter are not uniformly distributed throughout the universe. The origin of this structure has been traced back to the tiny inhomogeneities observed in the Cosmic Microwave Background (CMB)–radiation that was emitted when the universe was 380 thousand years young that we can still see today. But the CMB itself has three puzzling features that are considered anomalies because they are difficult to explain using known physics.

“While [3] seeing one of these anomalies may not be that statistically remarkable, seeing two or more together suggests we live in an exceptional universe,” said Donghui Jeong, associate professor of astronomy and astrophysics at Penn State and an author of the paper. “A recent study in the journal Nature Astronomy proposed an explanation for one of these anomalies that raised so many additional concerns, they flagged a ‘possible crisis in cosmology‘ [emphasis mine].’ Using quantum loop cosmology, however, we have resolved two of these anomalies naturally, avoiding that potential crisis.”

Research over the last three decades has greatly improved our understanding of the early universe, including how the inhomogeneities in the CMB were produced in the first place. These inhomogeneities are a result of inevitable quantum fluctuations in the early universe. During a highly accelerated phase of expansion at very early times–known as inflation–these primordial, miniscule fluctuations were stretched under gravity’s influence and seeded the observed inhomogeneities in the CMB.

“To understand how primordial seeds arose, we need a closer look at the early universe, where Einstein’s theory of general relativity breaks down,” said Abhay Ashtekar, Evan Pugh Professor of Physics, holder of the Eberly Family Chair in Physics, and director of the Penn State Institute for Gravitation and the Cosmos. “The standard inflationary paradigm based on general relativity treats space time as a smooth continuum. Consider a shirt that appears like a two-dimensional surface, but on closer inspection you can see that it is woven by densely packed one-dimensional threads. In this way, the fabric of space time is really woven by quantum threads. In accounting for these threads, loop quantum cosmology allows us to go beyond the continuum described by general relativity where Einstein’s physics breaks down–for example beyond the Big Bang.”

The researchers’ previous investigation into the early universe replaced the idea of a Big Bang singularity, where the universe emerged from nothing, with the Big Bounce, where the current expanding universe emerged from a super-compressed mass that was created when the universe contracted in its preceding phase. They found that all of the large-scale structures of the universe accounted for by general relativity are equally explained by inflation after this Big Bounce using equations of loop quantum cosmology.

In the new study, the researchers determined that inflation under loop quantum cosmology also resolves two of the major anomalies that appear under general relativity.

“The primordial fluctuations we are talking about occur at the incredibly small Planck scale,” said Brajesh Gupt, a postdoctoral researcher at Penn State at the time of the research and currently at the Texas Advanced Computing Center of the University of Texas at Austin. “A Planck length is about 20 orders of magnitude smaller than the radius of a proton. But corrections to inflation at this unimaginably small scale simultaneously explain two of the anomalies at the largest scales in the universe, in a cosmic tango of the very small and the very large.”

The researchers also produced new predictions about a fundamental cosmological parameter and primordial gravitational waves that could be tested during future satellite missions, including LiteBird and Cosmic Origins Explorer, which will continue improve our understanding of the early universe.

That’s a lot of ‘while’. I’ve done this sort of thing, too, and whenever I come across it later; it’s painful.

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

Alleviating the Tension in the Cosmic Microwave Background Using Planck-Scale Physics by Abhay Ashtekar, Brajesh Gupt, Donghui Jeong, and V. Sreenath. Phys. Rev. Lett. 125, 051302 DOI: https://doi.org/10.1103/PhysRevLett.125.051302 Published 29 July 2020 © 2020 American Physical Society

This paper is behind a paywall.