‘Necrobotic’ spiders as mechanical grippers

A July 25, 2022 news item on ScienceDaily describes research utilizing dead spiders,

Spiders are amazing. They’re useful even when they’re dead.

Rice University mechanical engineers are showing how to repurpose deceased spiders as mechanical grippers that can blend into natural environments while picking up objects, like other insects, that outweigh them.

Caption: An illustration shows the process by which Rice University mechanical engineers turn deceased spiders into necrobotic grippers, able to grasp items when triggered by hydraulic pressure. Credit: Preston Innovation Laboratory/Rice University

A July 25, 2022 Rice University news release (also on on EurekAlert but published August 4, 2022), which originated the news item, explains the reasoning, Note: Links have been removed,

“It happens to be the case that the spider, after it’s deceased, is the perfect architecture for small scale, naturally derived grippers,” said Daniel Preston of Rice’s George R. Brown School of Engineering. 

An open-access study in Advanced Science outlines the process by which Preston and lead author Faye Yap harnessed a spider’s physiology in a first step toward a novel area of research they call “necrobotics.”

Preston’s lab specializes in soft robotic systems that often use nontraditional materials, as opposed to hard plastics, metals and electronics. “We use all kinds of interesting new materials like hydrogels and elastomers that can be actuated by things like chemical reactions, pneumatics and light,” he said. “We even have some recent work on textiles and wearables. 

“This area of soft robotics is a lot of fun because we get to use previously untapped types of actuation and materials,” Preston said. “The spider falls into this line of inquiry. It’s something that hasn’t been used before but has a lot of potential.”

Unlike people and other mammals that move their limbs by synchronizing opposing muscles, spiders use hydraulics. A chamber near their heads contracts to send blood to limbs, forcing them to extend. When the pressure is relieved, the legs contract. 

The cadavers Preston’s lab pressed into service were wolf spiders, and testing showed they were reliably able to lift more than 130% of their own body weight, and sometimes much more. They had the grippers manipulate a circuit board, move objects and even lift another spider.  

The researchers noted smaller spiders can carry heavier loads in comparison to their size. Conversely, the larger the spider, the smaller the load it can carry in comparison to its own body weight. Future research will likely involve testing this concept with spiders smaller than the wolf spider, Preston said

Yap said the project began shortly after Preston established his lab in Rice’s Department of Mechanical Engineering in 2019.

“We were moving stuff around in the lab and we noticed a curled up spider at the edge of the hallway,” she said. “We were really curious as to why spiders curl up after they die.”

A quick search found the answer: “Spiders do not have antagonistic muscle pairs, like biceps and triceps in humans,” Yap said. “They only have flexor muscles, which allow their legs to curl in, and they extend them outward by hydraulic pressure. When they die, they lose the ability to actively pressurize their bodies. That’s why they curl up. 

“At the time, we were thinking, ‘Oh, this is super interesting.’ We wanted to find a way to leverage this mechanism,” she said.

Internal valves in the spiders’ hydraulic chamber, or prosoma, allow them to control each leg individually, and that will also be the subject of future research, Preston said. “The dead spider isn’t controlling these valves,” he said. “They’re all open. That worked out in our favor in this study, because it allowed us to control all the legs at the same time.”

Setting up a spider gripper was fairly simple. Yap tapped into the prosoma chamber with a needle, attaching it with a dab of superglue. The other end of the needle was connected to one of the lab’s test rigs or a handheld syringe, which delivered a minute amount of air to activate the legs almost instantly. 

The lab ran one ex-spider through 1,000 open-close cycles to see how well its limbs held up, and found it to be fairly robust. “It starts to experience some wear and tear as we get close to 1,000 cycles,” Preston said. “We think that’s related to issues with dehydration of the joints. We think we can overcome that by applying polymeric coatings.”

What turns the lab’s work from a cool stunt into a useful technology?

Preston said a few necrobotic applications have occurred to him. “There are a lot of pick-and-place tasks we could look into, repetitive tasks like sorting or moving objects around at these small scales, and maybe even things like assembly of microelectronics,” he said. 

“Another application could be deploying it to capture smaller insects in nature, because it’s inherently camouflaged,” Yap added. 

“Also, the spiders themselves are biodegradable,” Preston said. “So we’re not introducing a big waste stream, which can be a problem with more traditional components.”

Preston and Yap are aware the experiments may sound to some people like the stuff of nightmares, but they said what they’re doing doesn’t qualify as reanimation. 

“Despite looking like it might have come back to life, we’re certain that it’s inanimate, and we’re using it in this case strictly as a material derived from a once-living spider,” Preston said. “It’s providing us with something really useful.”

Co-authors of the paper are graduate students Zhen Liu and Trevor Shimokusu and postdoctoral fellow Anoop Rajappan. Preston is an assistant professor of mechanical engineering.

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

Necrobotics: Biotic Materials as Ready-to-Use Actuators by Te Faye Yap, Zhen Liu, Anoop Rajappan, Trevor J. Shimokusu, Daniel J. Preston. Advanced Science
DOI: https://doi.org/10.1002/advs.202201174 First published: 25 July 2022

As noted in the news release, this paper is open access.

Diagnosing diseases by using nanomembranes to isolate biomarkers in tears

How are they planning to make people cry on command or use a swab on your eyeball? In general, I like the idea of using tears instead of other bodily secretions but it’s the practicalities that have me questioning how this kind of diagnostic test could be implemented. In any event, here’s more from a July 20, 2022 news item on phys.org,

Going to the doctor might make you want to cry, and according to a new study, doctors could someday put those tears to good use. In ACS Nano, researchers report a nanomembrane system that harvests and purifies tiny blobs called exosomes from tears, allowing researchers to quickly analyze them for disease biomarkers. Dubbed iTEARS, the platform could enable more efficient and less invasive molecular diagnoses for many diseases and conditions, without relying solely on symptoms.

A July 20, 2022 American Chemical Society (ACS) news release (also on EurekAlert), which originated the news item, explains the work in more detail,

Diagnosing diseases often hinges on assessing a patient’s symptoms, which can be unobservable at early stages, or unreliably reported. Identifying molecular clues in samples from patients, such as specific proteins or genes from vesicular structures called exosomes, could improve the accuracy of diagnoses. However, current methods for isolating exosomes from these samples require long, complicated processing steps or large sample volumes. Tears are well-suited for sample collection because the fluid can be collected quickly and non-invasively, though only tiny amounts can be harvested at a time. So, Luke Lee, Fei Liu and colleagues wondered if a nanomembrane system, which they originally developed for isolating exosomes from urine and plasma, could allow them to quickly obtain these vesicles from tears and then analyze them for disease biomarkers.

The team modified their original system to handle the low volume of tears. The new system, called “Incorporated Tear Exosomes Analysis via Rapid-isolation System” (iTEARS), separated out exosomes in just 5 minutes by filtering tear solutions over nanoporous membranes with an oscillating pressure flow to reduce clogging. Proteins from the exosomes could be tagged with fluorescent probes while they were still on the device and then transferred to other instruments for further analysis. Nucleic acids were also extracted from the exosomes and analyzed. The researchers successfully distinguished between healthy controls and patients with various types of dry eye disease based on a proteomic assessment of extracted proteins. Similarly, iTEARS enabled researchers to observe differences in microRNAs between patients with diabetic retinopathy and those that didn’t have the eye condition, suggesting that the system could help track disease progression. The team says that this work could lead to a more sensitive, faster and less invasive molecular diagnosis of various diseases — using only tears.

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

Discovering the Secret of Diseases by Incorporated Tear Exosomes Analysis via Rapid-Isolation System: iTEARS by Liang Hu, Ting Zhang, Huixiang Ma, Youjin Pan, Siyao Wang, Xiaoling Liu, Xiaodan Dai, Yuyang Zheng, Luke P. Lee, and Fei Liu. ACS Nano 2022, XXXX, XXX, XXX-XXX DOI: https://doi.org/10.1021/acsnano.2c02531 Publication Date:July 20, 2022 © 2022 American Chemical Society

This paper appears to be open access.

Stifle the noise with seaweed

The claim that most spaces are now designed with sound-absorption in mind seems a little overblown to me but judge for yourself, from a July 14, 2022 news item on phys.org,

From airplanes to apartments, most spaces are now designed with sound-absorbing materials that help dampen the droning, echoing and murmuring sounds of everyday life. But most of the acoustic materials that can cancel out human voices, traffic and music are made from plastic foams that aren’t easily recycled or degraded. Now, researchers reporting in ACS Sustainable Chemistry & Engineering have created a biodegradable seaweed-derived film that effectively absorbs sounds in this range.

A July 14, 2022 American Chemical Society (ACS) news release (also on EurekAlert), which originated the news item, describes the work in more detail,

Controlling and optimizing the way sound moves throughout a room is key to creating functional spaces. Foam acoustic panels are a common solution, and they come in a variety of materials and thicknesses tailored to specific sound requirements. Most of these foams, however, are made from polyurethane and other polymers that are derived from crude oil or shale gas. To avoid petrochemicals, researchers have explored more renewably sourced and biodegradable sound-absorbing alternatives. But many current options are made from plant fibers that don’t effectively dampen noises in the most useful range of sound frequencies, or they are too thick or unwieldy to fabricate. So, Chindam Chandraprakash and colleagues wanted to develop a plant-derived, biodegradable material that would be simple to manufacture and that could absorb a range of sounds.

The team created thin films of agar, a jelly-like material that comes from seaweed, along with other plant-derived additives and varied both the thickness and porosity of the films. After running the materials through a battery of tests, the researchers measured how well the films dampened sound across a range of frequencies — from a bass hum to a shrill whine. To do this, the team created a sound tube in which a speaker is placed at one end, and the test film is fitted over the other end. Microphones in the middle of the tube measured the amount of sound emitted by the speaker and the amount of sound reflected off the film. These experiments showed that porous films made with the highest concentrations of agar had the greatest sound-absorbing qualities and performed similarly to traditional acoustic foams. The researchers plan to explore ways to modify the agar films to give them other desirable properties, such as flame resistance, and will explore other biologically derived film materials.

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

Agar-Based Composite Films as Effective Biodegradable Sound Absorbers by Surendra Kumar, Kousar Jahan, Abhishek Verma, Manan Agarwal, and C. Chandraprakash. ACS Sustainable Chem. Eng. 2022, 10, 26, 8242–8253 DOI: https://doi.org/10.1021/acssuschemeng.2c00168 Publication Date: June 23, 2022 Copyright © 2022 American Chemical Society

This paper is behind a paywall.

Artificial graphene with buckyballs

A July 21, 2022 news item on Nanowerk describes graphene in its ‘natural’ state and explains what ‘artificial’ graphene is although there is no mention of why variants are a hot topic,

Graphene consists of carbon atoms that crosslink in a plane to form a flat honeycomb structure. In addition to surprisingly high mechanical stability, the material has exciting electronic properties: The electrons behave like massless particles, which can be clearly demonstrated in spectrometric experiments.

Measurements reveal a linear dependence of energy on momentum, namely the so-called Dirac cones – two lines that cross without a band gap – i.e. an energy difference between electrons in the conduction band and those in the valence bands.

Variants in graphene architecture

Artificial variants of graphene architecture are a hot topic in materials research right now. Instead of carbon atoms, quantum dots of silicon have been placed, ultracold atoms have been trapped in the honeycomb lattice with strong laser fields, or carbon monoxide molecules have been pushed into place on a copper surface piece by piece with a scanning tunneling microscope, where they could impart the characteristic graphene properties to the electrons of the copper.

A July 21, 2022 Helmholtz-Zentrum Berlin (HZB) press release (also on EurekAlert), which originated the news item, describes research into whether or not layering buckyballs onto gold would result in artificial graphene,

Artificial graphene with buckyballs?

A recent study suggested that it is infinitely easier to make artificial graphene using C60 molecules called buckyballs [or buckminsterfullerenes or, more generically, fullerenes]. Only a uniform layer of these needs to be vapor-deposited onto gold for the gold electrons to take on the special graphene properties. Measurements of photoemission spectra appeared to show a kind of Dirac cone.

Analysis of band structures at BESSY II

“That would be really quite amazing,” says Dr. Andrei Varykhalov, of HZB, who heads a photoemission and scanning tunneling microscopy group. “Because the C60 molecule is absolutely nonpolar, it was hard for us to imagine how such molecules would exert a strong influence on the electrons in the gold.” So Varykhalov and his team launched a series of measurements to test this hypothesis.

In tricky and detailed analyses, the Berlin team was able to study C60 layers on gold over a much larger energy range and for different measurement parameters. They used angle-resolved ARPES spectroscopy at BESSY II [third-generation synchrotron radiation source], which enables particularly precise measurements, and also analysed electron spin for some measurements.

Normal behavior

“We see a parabolic relationship between momentum and energy in our measured data, so it’s a very normal behavior. These signals come from the electrons deep in the substrate (gold or copper) and not the layer, which could be affected by the buckyballs,” explains Dr. Maxim Krivenkov, lead author of the study. The team was also able to explain the linear measurement curves from the previous study. “These measurement curves merely mimic the Dirac cones; they are an artifact, so to speak, of a deflection of the photoelectrons as they leave the gold and pass through the C60 layer,” Varykhalov explains. Therefore, the buckyball layer on gold cannot be considered an artificial graphene.

Caption: Measurement data from BESSY II before and after deposition of C60 molecules demonstrate the replication of the band structure and the emergence of cone-like band crossings. A scanning electron microscopy of the buckyballs on gold is superimposed in the centre. Credit: HZB

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

On the problem of Dirac cones in fullerenes on gold by M. Krivenkov, D. Marchenko, M. Sajedi, A. Fedorov, O. J. Clark, J. Sánchez-Barriga, E. D. L. Rienks, O. Rader and A. Varykhalov. Nanoscale, 2022,14, 9124-9133 First published: 23 May 2022

This paper is open access.

Five 2023 events: SCWIST (Society for Canadian Women in Science and Technology) and SFU’s (Simon Fraser University) Café Scientifique

I have one January 2023 event for the Society for Canadian Women in Science and Technology (SCWIST) and four Simon Fraser University (SFU) Café Scientifique events, one each month, for January through April 2023.

SCWIST and Canada’s Department of National Defence

From a January 2023 SCWIST newsletter (received via email),

Defense [sic] is a Place for STEM [science, technology, engineering, and mathematics] Women

Have you always wondered about where STEM fits within the area of defense? Or are you curious about where a STEM career can lead you within defense?

SCWIST and the Department of National Defense [sic] have partnered to bring you an exciting panel presentation and discussion on these questions and more. Join our speakers as they highlight the challenges and accomplishments of being STEM women in the area of National Defense [sic]. Online seats available [emphasis mine]

Based on that last phrase, I believe this is a hybrid event.

Here is logistical and biographical information for the event and its speakers and moderators from the Event registration page, Note 1: The event is being held on one of the city of Vancouver campuses (and possibly online), Note 2: I have made some changes to the formatting.

Date and time

Tue, 24 January 2023, 3:30 PM – 5:00 PM PST

Location

SFU VentureLabs 555 West Hastings Street #Suite #1200 Vancouver, BC V6B 4N6

SPEAKERS

Captain Kalina Yurick joined the military in 2011 and attended the Royal Military College of Canada to earn her degree in Aeronautical Engineering. Throughout her time at school, Kalina fenced for the RMC varsity team. Some highlights included captaining for her last two years and representing Canada at the World Military games in South Korea.

After school Kalina began her flight training in Moose Jaw, Saskatchewan. She completed her Phase 3 training on the CT-140 Harvard II and transitioned to Qualified Flight Instructor at the school for her first posting. Kalina earned her Masters of Science in Aeronautics education throughout her instructor tour.

Kalina’s current posting is with 407 Long Range Patrol Squadron in Comox, British Columbia. She currently flies the CP-140 Aurora, which is a platform used for anti-submarine warfare and surveillance.

Kalina’s husband is also a pilot at 407 Squadron, where they are fortunate to work and fly together. They tackle the challenges of maintaining a healthy work-life balance as a team while progressing through their careers.

Lieutenant-Colonel Melissa Reyes has served over thirty-three years as a Canadian Armed Forces (CAF) officer, and is now specializing in space-related capabilities and tasks for the CAF. Her various military experiences, around the world and Canada, have given her a sound knowledge of satellites and space systems, operations, and management.

Among her many assignments, Melissa has worked at the Canadian Space Agency, 12th Space Warning Squadron Greenland, North American Aerospace Defense (NORAD) Headquarters, and Kandahar Air Field (Afghanistan). She is presently employed as the Section Head for Intelligence, Surveillance, and Reconnaissance Space Systems, within the Royal Canadian Air Force.

Melissa received her Master of Sciences Degree, specializing in Remote Sensing, from the University of Colorado (2008), and completed the International Space University / Space Studies Program (2012). Melissa has been involved in various Science, Technology, Engineering and Mathematics (STEM) initiatives and employment equity groups throughout her career and is honoured to be part of this event for the Society for Canadian Women in Science and Technology.

Lieutenant Commander Calley Gray has served 18 years in the Royal Canadian Navy as a Marine Systems Engineer. She has a degree in Mechanical Engineering from the Royal Military College of Canada and a double masters from the Massachusetts Institute of Technology in Mechanical Engineering and Naval Architecture.

LCdr Gray spent 4 years serving onboard various Canadian Patrol Frigates culminating in her appointment as Head of the Marine Systems Engineering Department on HMCS WINNIPEG. She deployed with the Canadian Navy to South America and South-East Asia, participating in detection and monitoring operations to facilitate the interdiction of illicit drug trafficking. Her naval deployments also included conducting training, exercises and engagements with foreign navies and other international security partners, and providing security for the Vancouver 2010 Olympics.

As a strong advocate for women in engineering, she championed institutional change within the naval engineering occupation by helping to remove barriers for women’s career progression. In December 2020, she deployed to Iraq as the Gender Advisor for NATO Mission Iraq. During her 9 month deployment, she contributed to advancements in Iraq’s Second National Action Plan on Women, Peace and Security by working with international experts and the Iraqi Ministry of Defence to open various educational and professional development opportunities to women.

Now back in Canada, LCdr Gray is the Gender Advisor for Chief Professional Conduct and Culture which has been stood up to lead a fundamental transformation in the way in which system misconduct (sexual misconduct, hateful conduct, systemic barriers, harassment, violence, discrimination, employment inequity, unconscious biases, and abuse of power in the workplace) is understood and addressed in the Canadian Department of National Defence and the Canadian Armed Forces.

CO-MODERATORS

Dr. Poh Tan, SCWIST President (co-moderator) is an entrepreneur, stem cell scientist, educator, 2x TEDx speaker, and mother of two boys. With a Ph.D in stem cell biology, Poh is currently completing a second PhD with a focus in science education. She is the founder and CEO of STEMedge Academy where she creates programs to support high school students develop research capacity in STEM. She returns to the Board of Directors as SCWIST’s President.

Ms. Avneet Sandhu (co-moderator) works as a communications officer for the Department of National Defence and is responsible for assisting with diversity and inclusion files. She supports the Advisory Council on Diversity to Commander of the Royal Canadian Navy Maritime Forces Pacific Formation (MARPAC) and Joint Task Force Pacific (JTFP), and the Advisory Group on Intersectionality to the Commander of Military Personnel Generation.

Avneet also supports announcements and engagements for senior officers and connects women-led organizations, university faculty, and students with the Department of National Defence and the Canadian Armed Forces. Avneet graduated from Simon Fraser University in 2019 with a Bachelor of Arts degree in International Studies and a minor in Education. Avneet is an incoming JD candidate and is the co-founder, vice-president, and director of external relations for She Connects – a nationwide mentorship program for girls in high school.

Simon Fraser University’s (SFU) Café Scientifique January – April 2023 events

I received (via email) a January 12, 2023 notice from Simon Fraser University’s (SFU) Café Scientifique about their Winter/Spring 2023 events, Note: I have made some changes to the formatting by adding descriptive text from the event pages,

Welcome to a brand new year of SFU Cafe Scientifique discussions.  We have put together an amazing line-up of speakers and topics for January-April 2023.  Below are some details and registrations links.  Zoom invites will be sent to those who register.  We look forward to engaging with you then.

All sessions are on Tuesdays 5:00-6:30pm PST over Zoom

January 31, 2023

So you think you can forge? with Dr. Nabyl Merbouh, SFU Chemistry

[Join Dr. Nabyl Merbouh as he discusses how to spot art forgeries using electron microscopy and X-ray spectroscopy tools and techniques.

Forgeries are often only discernible by the keen eye of a trained expert. Sometimes, even a keen eye cannot be adequate. Join Dr. Nabyl Merbouh as he discusses how electron microscopy-based and X-ray spectroscopy-based tools and techniques are being used for identifying microscopic to atomic-scale differences in samples to identify real vs. fake art.]

*ETA January 30, 2023: Dr. Byron Gates, Associate Chair, Department of Chemistry
Canada Research Chair, Tier II in Surface Chemistry (2005-2014) will be co-presenting.*

February 21, 2023

Watermelon Snow: Science, Art and a lone polar bear with Dr. Lynne Quarmby, SFU Molecular Biology and Biochemistry

[Dr. Lynne Quarmby speaks on her personal journey and concerns about climate change that led to her interest in watermelon snow.

Watermelon-red snow is a tell-tale sign of springtime blooms of microscopic algae on alpine and arctic snow. Under the microscope, the algae are stunningly beautiful, but still, why study them? Dr. Lynne Quarmby will take us on a journey from molecular biology to the high Arctic and home again, illuminating the science of cells, of the climate, and of snow algae, while offering a reminder that much about the human experience is beyond reason. In this talk, we will hear about one scientist’s search for what it means to live a good life at a time of increasing desperation about the future.]

March 28, 2023

What should we know about Quantum Technologies? with Dr. Kero Lau, SFU Physics

[Join Dr. Kero Lau as he explains how quantum technologies work and how we use them in our daily lives

About two decades ago scientists realized that using the quantum properties of fundamental particles has the potential to dramatically improve the performance of our technology. Since then, significant progress has been made towards using quantum systems, and we are now very close to realizing practical quantum devices. In this talk, Dr. Kero Lau will give us a scientific overview of the principle behind quantum technologies, and how they could impact our day-to-day life.]

April 25, 2023

The Pathways from our DNA to our Brain with Dr. Lloyd Elliott, SFU Statistics and Actuarial Science

[Dr. Lloyd Elliott explains how our DNA affects brain function and neurodegenerative diseases.]

Quite a start to 2023!

A robot with body image and self awareness

This research is a rather interesting direction for robotics to take (from a July 13, 2022 news item on ScienceDaily),

As every athletic or fashion-conscious person knows, our body image is not always accurate or realistic, but it’s an important piece of information that determines how we function in the world. When you get dressed or play ball, your brain is constantly planning ahead so that you can move your body without bumping, tripping, or falling over.

We humans acquire our body-model as infants, and robots are following suit. A Columbia Engineering team announced today they have created a robot that — for the first time — is able to learn a model of its entire body from scratch, without any human assistance. In a new study published by Science Robotics,, the researchers demonstrate how their robot created a kinematic model of itself, and then used its self-model to plan motion, reach goals, and avoid obstacles in a variety of situations. It even automatically recognized and then compensated for damage to its body.

Courtesy Columbia University School of Engineering and Applied Science

A July 13, 2022 Columbia University news release by Holly Evarts (also on EurekAlert), which originated the news item, describes the research in more detail, Note: Links have been removed,

Robot watches itself like an an infant exploring itself in a hall of mirrors

The researchers placed a robotic arm inside a circle of five streaming video cameras. The robot watched itself through the cameras as it undulated freely. Like an infant exploring itself for the first time in a hall of mirrors, the robot wiggled and contorted to learn how exactly its body moved in response to various motor commands. After about three hours, the robot stopped. Its internal deep neural network had finished learning the relationship between the robot’s motor actions and the volume it occupied in its environment. 

“We were really curious to see how the robot imagined itself,” said Hod Lipson, professor of mechanical engineering and director of Columbia’s Creative Machines Lab, where the work was done. “But you can’t just peek into a neural network, it’s a black box.” After the researchers struggled with various visualization techniques, the self-image gradually emerged. “It was a sort of gently flickering cloud that appeared to engulf the robot’s three-dimensional body,” said Lipson. “As the robot moved, the flickering cloud gently followed it.” The robot’s self-model was accurate to about 1% of its workspace.

Self-modeling robots will lead to more self-reliant autonomous systems

The ability of robots to model themselves without being assisted by engineers is important for many reasons: Not only does it save labor, but it also allows the robot to keep up with its own wear-and-tear, and even detect and compensate for damage. The authors argue that this ability is important as we need autonomous systems to be more self-reliant. A factory robot, for instance, could detect that something isn’t moving right, and compensate or call for assistance.

“We humans clearly have a notion of self,” explained the study’s first author Boyuan Chen, who led the work and is now an assistant professor at Duke University. “Close your eyes and try to imagine how your own body would move if you were to take some action, such as stretch your arms forward or take a step backward. Somewhere inside our brain we have a notion of self, a self-model that informs us what volume of our immediate surroundings we occupy, and how that volume changes as we move.”

Self-awareness in robots

The work is part of Lipson’s decades-long quest to find ways to grant robots some form of self-awareness.  “Self-modeling is a primitive form of self-awareness,” he explained. “If a robot, animal, or human, has an accurate self-model, it can function better in the world, it can make better decisions, and it has an evolutionary advantage.” 

The researchers are aware of the limits, risks, and controversies surrounding granting machines greater autonomy through self-awareness. Lipson is quick to admit that the kind of self-awareness demonstrated in this study is, as he noted, “trivial compared to that of humans, but you have to start somewhere. We have to go slowly and carefully, so we can reap the benefits while minimizing the risks.”  

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

Fully body visual self-modeling of robot morphologies by Boyuan Chen, Robert Kwiatkowski, Carl Vondrick and Hod Lipson. Science Robotics 13 Jul 2022 Vol 7, Issue 68 DOI: 10.1126/scirobotics.abn1944

This paper is behind a paywall.

If you follow the link to the July 13, 2022 Columbia University news release, you’ll find an approximately 25 min. video of Hod Lipson showing you how they did it. As Lipson notes discussion of self-awareness and sentience is not found in robotics programmes. Plus, there are more details and links if you follow the EurekAlert link.

Augmented reality and the future of paper books

I’ve started to think that paper books will be on an ‘endangered species’ list in the not too distant future. Now, it seems researchers at the University of Surrey (UK) may have staved off that scenario according to an August 3, 2022 news item on ScienceDaily,

Augmented reality might allow printed books to make a comeback against the e-book trend, according to researchers from the University of Surrey.

An August 3, 2022 University of Surrey press release (also on EurekAlert), which originated the news item, describes the idea and the research in more detail,

Surrey has introduced the third generation (3G) version of its Next Generation Paper (NGP) project, allowing the reader to consume information on the printed paper and screen side by side.  

Dr Radu Sporea, Senior lecturer at the Advanced Technology Institute (ATI), comments: 

“The way we consume literature has changed over time with so many more options than just paper books. Multiple electronic solutions currently exist, including e-readers and smart devices, but no hybrid solution which is sustainable on a commercial scale.  

“Augmented books, or a-books, can be the future of many book genres, from travel and tourism to education. This technology exists to assist the reader in a deeper understanding of the written topic and get more through digital means without ruining the experience of reading a paper book.” 

Power efficiency and pre-printed conductive paper are some of the new features which allow Surrey’s augmented books to now be manufactured on a semi-industrial scale. With no wiring visible to the reader, Surrey’s augmented reality books allow users to trigger digital content with a simple gesture (such as a swipe of a finger or turn of a page), which will then be displayed on a nearby device.  

George Bairaktaris, Postgraduate researcher at the University of Surrey and part of the Next Generation Paper project team, said: 

“The original research was carried out to enrich travel experiences by creating augmented travel guides. This upgraded 3G model allows for the possibility of using augmented books for different areas such as education. In addition, the new model disturbs the reader less by automatically recognising the open page and triggering the multimedia content.” 

“What started as an augmented book project, evolved further into scalable user interfaces. The techniques and knowledge from the project led us into exploring organic materials and printing techniques to fabricate scalable sensors for interfaces beyond the a-book”.

…  

Caption: Next Generation Paper book example Credit: Courtesy of Advanced Technology Institute at the University of Surrey

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

Augmented Books: Hybrid Electronics Bring Paper to Life by Georgios Bairaktaris, Brice Le Borgne, Vikram Turkani, Emily Corrigan-Kavanagh, David M. Frohlich, Radu A. Sporea. IEEE Pervasive Computing (early access) PrePrints pp. 1-8, DOI: 10.1109/MPRV.2022.3181440 Published: July 12, 2022

This paper is behind a paywall.

For better science literacy change science education

Zahilyn D. Roche Allred’s July 12, 2022 essay for The Conversation (h/t July 13, 2022 news item on phys.org) suggests that even people with undergraduate science degrees have some issues with science literacy (Note: Links have been removed),

To graduate with a science major, college students must complete between 40 and 60 credit hours of science coursework. That means spending around 2,500 hours in the classroom throughout their undergraduate career.

However, research has shown that despite all that effort, most college science courses give students only a fragmented understanding of fundamental scientific concepts. The teaching method reinforces memorization of isolated facts, proceeding from one textbook chapter to the next without necessarily making connections between them, instead of learning how to use the information and connect those facts meaningfully.

The ability to make these connections is important beyond the classroom as well, because it’s the basis of science literacy: the ability to use scientific knowledge to accurately evaluate information and make decisions based on evidence.

As a chemistry education researcher, I have been working since 2019 with my colleague Sonia Underwood to learn more about how chemistry students integrate and apply their knowledge to other scientific disciplines.

A large body of research shows that traditional science education, for both science majors and non-majors, doesn’t do a good job of teaching science students how to apply their scientific knowledge and explain things that they may not have learned about directly.

With that in mind, we developed a series of cross-disciplinary activities guided by a framework called “three-dimensional learning.”

In short, three-dimensional learning, known as 3DL, emphasizes that the teaching, learning and assessing of college students should involve the use of fundamental ideas within a discipline. It should also involve tools and rules that support students in making connections within and between disciplines. Finally, it should engage students in the use of their knowledge. The framework was developed on the basis of how people learn as a way to help all students gain a deep understanding of science.

Allred goes on to describe a piece of previously published research. Here’s a link to and citation for that work

Students’ use of chemistry core ideas to explain the structure and stability of DNA by Zahilyn D. Roche Allred, Anthony J. Farias, Alex T. Kararo, Kristin N. Parent, Rebecca L. Matz, Sonia M. Underwood. Biochemistry and Molecular Biology Education Volume 49, Issue 1 (January/February 2021) Pages 55-68 DOI: https://doi.org/10.1002/bmb.21391 First published: 09 September 2020

This paper is behind a paywall.

A CRISPR (clustered regularly interspaced short palindromic repeats) anniversary

June 2022 was the 10th anniversary of the publication of a study the paved the way for CRISPR-Cas9 gene editing and Sophie Fessl’s June 28, 2022 article for The Scientist offers a brief history (Note: Links have been removed),

Ten years ago, Emmanuelle Charpentier and Jennifer Doudna published the study that paved the way for a new kind of genome editing: the suite of technologies now known as CRISPR. Writing in [the journal] Science, they adapted an RNA-mediated bacterial immune defense into a targeted DNA-altering system. “Our study . . . highlights the potential to exploit the system for RNA-programmable genome editing,” they conclude in the abstract of their paper—a potential that, in the intervening years, transformed the life sciences. 

From gene drives to screens, and diagnostics to therapeutics, CRISPR nucleic acids and the Cas enzymes with which they’re frequently paired have revolutionized how scientists tinker with DNA and RNA. … altering the code of life with CRISPR has been marred by ethical concerns. Perhaps the most prominent example was when Chinese scientist He Jiankui created the first gene edited babies using CRISPR/Cas9 genome editing. Doudna condemned Jiankui’s work, for which he was jailed, as “risky and medically unnecessary” and a “shocking reminder of the scientific and ethical challenges raised by this powerful technology.” 

There’s also the fact that legal battles over who gets to claim ownership of the system’s many applications have persisted almost as long as the technology has been around. Both Doudna and Charpentier’s teams from the University of California, Berkeley, and the University of Vienna and a team led by the Broad Institute’s Feng Zhang claim to be the first to have adapted CRISPR-Cas9 for gene editing in complex cells (eukaryotes). Patent offices in different countries have reached varying decisions, but in the US, the latest rulings say that the Broad Institute of MIT [Massachusetts Institute of Technology] and Harvard retains intellectual property of using CRISPR-Cas9 in eukaryotes, while Emmanuelle Charpentier, the University of California, and the University of Vienna maintain their original patent over using CRISPR-Cas9 for editing in vitro and in prokaryotes. 

Still, despite the controversies, the technique continues to be explored academically and commercially for everything from gene therapy to crop improvement. Here’s a look at seven different ways scientists have utilized CRISPR.

Fessl goes on to give a brief overview of CRISPR and gene drives, genetic screens, diagnostics, including COVID-19 tests, gene therapy, therapeutics, crop and livestock improvement, and basic research.

For anyone interested in the ethical issues (with an in depth look at the Dr. He Jiankui story), I suggest reading either or both Eben Kirksey’s 2020 book, “The Mutant Project; Inside the Global Race to Genetically Modify Humans,”

An anthropologist visits the frontiers of genetics, medicine, and technology to ask: Whose values are guiding gene editing experiments? And what does this new era of scientific inquiry mean for the future of the human species?

“That rare kind of scholarship that is also a page-turner.”
—Britt Wray, author of Rise of the Necrofauna

At a conference in Hong Kong in November 2018, Dr. He Jiankui announced that he had created the first genetically modified babies—twin girls named Lulu and Nana—sending shockwaves around the world. A year later, a Chinese court sentenced Dr. He to three years in prison for “illegal medical practice.”

As scientists elsewhere start to catch up with China’s vast genetic research program, gene editing is fueling an innovation economy that threatens to widen racial and economic inequality. Fundamental questions about science, health, and social justice are at stake: Who gets access to gene editing technologies? As countries loosen regulations around the globe, from the U.S. to Indonesia, can we shape research agendas to promote an ethical and fair society?

Eben Kirksey takes us on a groundbreaking journey to meet the key scientists, lobbyists, and entrepreneurs who are bringing cutting-edge genetic engineering tools like CRISPR—created by Nobel Prize-winning biochemists Jennifer Doudna and Emmanuelle Charpentier—to your local clinic. He also ventures beyond the scientific echo chamber, talking to disabled scholars, doctors, hackers, chronically-ill patients, and activists who have alternative visions of a genetically modified future for humanity.

and/or Kevin Davies’s 2020 book, “Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing,”

One of the world’s leading experts on genetics unravels one of the most important breakthroughs in modern science and medicine. 

If our genes are, to a great extent, our destiny, then what would happen if mankind could engineer and alter the very essence of our DNA coding? Millions might be spared the devastating effects of hereditary disease or the challenges of disability, whether it was the pain of sickle-cell anemia to the ravages of Huntington’s disease.

But this power to “play God” also raises major ethical questions and poses threats for potential misuse. For decades, these questions have lived exclusively in the realm of science fiction, but as Kevin Davies powerfully reveals in his new book, this is all about to change.

Engrossing and page-turning, Editing Humanity takes readers inside the fascinating world of a new gene editing technology called CRISPR, a high-powered genetic toolkit that enables scientists to not only engineer but to edit the DNA of any organism down to the individual building blocks of the genetic code.

Davies introduces readers to arguably the most profound scientific breakthrough of our time. He tracks the scientists on the front lines of its research to the patients whose powerful stories bring the narrative movingly to human scale.

Though the birth of the “CRISPR babies” in China made international news, there is much more to the story of CRISPR than headlines seemingly ripped from science fiction. In Editing Humanity, Davies sheds light on the implications that this new technology can have on our everyday lives and in the lives of generations to come.

Kevin Davies is the executive editor of The CRISPR Journal and the founding editor of Nature Genetics. He holds an MA in biochemistry from the University of Oxford and a PhD in molecular genetics from the University of London. He is the author of Cracking the Genome, The $1,000 Genome, and co-authored a new edition of DNA: The Story of the Genetic Revolution with Nobel Laureate James D. Watson and Andrew Berry. In 2017, Kevin was selected for a Guggenheim Fellowship in science writing.

I’ve read both books and while some of the same ground is covered, the perspectives diverge somewhat. Both authors offer a more nuanced discussion of the issues than was the case in the original reporting about Dr. He’s work.

Tissue nanotransfection

I’m wondering how I missed the research from last year (2021) which foregrounds this latest work. Ah well. It happens. Making up for lost time, here’s a July 18, 2022 news item on phys.org about tissue nanotransfection, Note: Links have been removed,

The Indiana Center for Regenerative Medicine and Engineering (ICRME) at Indiana University School of Medicine is home to tissue nanotransfection (TNT) regenerative medicine technology that achieves functional tissue reprogramming in the live body. Last year, ICRME researchers published on how to manufacture the TNT 2.0 silicon chip hardware in Nature Protocol. Now, their research demonstrates for the first time that TNT can serve as a non-viral, topical gene-editing delivery device.

TNT is a minimally invasive device that can reprogram tissue function in the live body by applying pulses of harmless, electric sparks to deliver specific genes of interest to the skin.

“TNT-based delivery can achieve cell-specific gene editing,” said corresponding author Chandan K. Sen, Ph.D., the J. Stanley Battersby Chair and distinguished professor of surgery, director of the ICRME at IU School of Medicine and executive director of the Indiana University Health Comprehensive Wound Care Center. “Your skin has thousands of genes and in chronic wounds many key genes are silenced by DNA methylation. TNT-based gene editing technology can remove that barrier.”

A July 18, 2022 Indiana University School of Medicine news release (also on EurekAlert), which originated the news item, updates the information with some of the latest research, Note: Links have been removed,

In this study, genome-wide methylation was observed in the chronic wound tissue of patients. This was reproduced in an experimental murine model. TNT-based, cell-specific gene editing rescued wound healing. Results were published recently [July 12, 2022] in the Journal of Clinical Investigation.

Previous TNT application studies reported on the rescue of injured legs, diabetic neuropathy, crushed nerve and the stroke-affected brain. This is the first time promoter methylation of genes is recognized as a critical barrier to wound healing. In this study, ICRME investigators found that P53 methylation and gene silencing as a critical barrier to cutaneous wound epithelial-to-mesenchymal transition (EMT), a mechanism that is necessary to close skin wounds. TNT based non-viral keratinocyte-specific demethylation of P53 gene rescued EMT and achieved wound closure.

Chronic wounds can result in serious and sometimes life-threatening complications from an abundance of dying and necrotic tissue, such as cellulitis, lower-extremity amputation and sepsis. Treating chronic wounds is estimated to cost the United States health care system $28 billion annually, which amplifies the need to test novel treatments to prevent amputation, save lives and lower health care costs.

“Inspired by observations in chronic wound patients, this work has achieved an important milestone highlighting the need to de-silence genes at the wound-site,” said first author Kanhaiya Singh, PhD, assistant professor of surgery and an investigator at the ICRME.

Here are two links and citations. First, the earlier work,

Fabrication and use of silicon hollow-needle arrays to achieve tissue nanotransfection in mouse tissue in vivo by Yi Xuan, Subhadip Ghatak, Andrew Clark, Zhigang Li, Savita Khanna, Dongmin Pak, Mangilal Agarwal, Sashwati Roy, Peter Duda & Chandan K. Sen. Nature Protocols volume 16, pages 5707–5738 (2021) DOI: https://doi.org/10.1038/s41596-021-00631-0 Published: 26 November 2021 Issue Date: December 2021

This paper is behind a paywall.

Now, the latest work

Genome-wide DNA hypermethylation opposes healing in chronic wound patients by impairing epithelial-to-mesenchymal transition by Kanhaiya Singh, Yashika Rustagi, Ahmed S. Abouhashem, Saba Tabasum, Priyanka Verma, Edward Hernandez, Durba Pal, Dolly K. Khona, Sujit K. Mohanty, Manishekhar Kumar, Rajneesh Srivastava, Poornachander R Guda, Sumit S. Verma, Sanskruti Mahajan, Jackson A. Killian, Logan A. Walker, Subhadip Ghatak, Shomita S. Mathew-Steiner, Kristen Wanczyk, Sheng Liu, Jun Wan, Pearlly Yan, Ralf Bundschuh, Savita Khanna, Gayle M. Gordillo, Michael P. Murphy, Sashwati Roy, and Chandan K. Sen. J Clin Invest. DOI: https://doi.org/10.1172/JCI157279 Published: July 12, 2022 Version 1 (In-Press Preview) Version 2: J Clin Invest. 2022;132(17):e157279. https://doi.org/10.1172/JCI157279. Volume 132, Issue 17 Published September 1, 2022

This paper is open access.