Monthly Archives: February 2023

Global swarming: getting robot swarms to perform intelligently

This week we have a robotics PhD student, Everardo Gonzalez, joining us to discuss his research on coordinating robots with artificial intelligence (AI). That doesn’t mean he dresses them up in matching bow ties (sadly), but instead he works on how to get a large collective of robots, also called a swarm, to work collectively towards a shared goal.

Why should we care about swarming robots?

Aside from the potential for an apocalyptic robot world domination, there are actually many applications for this technology. Some are just as terrifying. It could be applied to fully automated warfare – reducing accountability when no one is to blame for pulling the trigger (literally).

However, it could also be used to coordinate robots used in healthcare and with organizing fleets of autonomous vehicles, potentially making our lives, and our streets, safer. In the case of the fish-inspired Blue Bots, this kind of coordinated robot system can also help us gather information about our oceans as we try to resolve climate change.

Depiction of how the fish-inspired Blue Bots can observe their surroundings in a shared aquatic space, then send that information and receive feedback from the computer system. Driving the Blue Bots’ behavior is a network model, as depicted in the Agent A square.

#Influencer

Having a group of intelligent robots behaving intelligently sounds like it’s a problem of quantity, however, it’s not that simple. These bots can also suffer from there being “too many cooks in the kitchen”, and, if all bots in the swarm are intelligent, they can start to hinder each other’s progress. Instead, the swarm needs both a few leader bots, that are intelligent and capable of learning and trying new things, along with follower bots, which can learn from their leader. Essentially, the bots play a game of “Follow the Leaders”.

All robots receive feedback with respect to a shared objective, which is typical of AI training and allow the bots to infer which behaviors are effective. In this case, the leaders will get additional feedback on how well they are influencing their followers.

Unlike social media, one influencer with too many followers is a bad thing – and the bots can become ineffective. There’s a famous social experiment in which actors in a busy New York City street stopped to stare at a window to determine if strangers would do the same. If there are not enough actors staring at the window, strangers are unlikely to respond. But as the number of actors increases, the likeness of a stranger stopping to look will also increase. The bot swarms also have an optimal number of leaders required to have the largest influence on their followers. Perhaps we’re much more like robots than the Turing test would have us believe.

Dot to dot

We’re a long way from intelligent robot swarms, though, as Everardo is using simplified 2D particle simulations to begin to tackle this problem. In this case the particles replace the robots, and are essentially just dots (rodots?) in a shared environment that only has two dimensions. The objectives or points of interest for these dot bots are more dots! Despite these simplifications, translating system feedback into a performance review for the leaders is still a challenging problem to solve computationally. Everardo starts by asking the question “what if the leader had not been there”, but then you have to ask “what if the followers that followed that leader did something else?” and then you’ve opened a can of worms reminiscent of Smash Mouth where the “what if”’s start coming and they don’t stop coming.

What if you wanted to know more about swarming robots? Be sure to listen live on Sunday February 26th at 7PM on 88.7FM, or download the podcast if you missed it. To learn a bit more about Everardo’s work with swarms and all things robotics, check out his portfolio at everardog.github.io.

No longer a torrent of salamanders

We are pleased to introduce our upcoming guest, Christopher Cousins, a fourth-year PhD student in the Department of Fisheries and Wildlife, advised by Prof. Tiffany Garcia. Cousins is researching torrent salamanders, a family of small amphibians endemic to the Pacific Northwest.

Chris is also an amateur photographer, check out his Instagram to see more wildlife pics!

The habitat for torrent salamanders stretches from the far north of California up through the Washington coast and includes distinct populations in the Cascade Range and the Oregon Coast Range. Torrent salamanders inhabit cold streams at relatively high altitude — the kind where few or no fish live, leaving the amphibians near or at the top of the local food chain. Such streams can be ephemeral, disappearing at times throughout the year and leaving salamanders vulnerable to desiccation. This problem is only expected to worsen as climate change further upends these water systems. Torrent salamanders are currently candidates for classification under the Endangered Species Act (ESA), the federal law which grants protections to threatened species. Logging presents another danger to salamander habitats, as reduced tree canopy cover can contribute to higher water temperatures. Under the ESA, officials could prohibit logging in buffer zones around small streams, granting salamander habitats the same protection as the larger streams where salmon live.

Chris’s work with salamanders takes many different forms. He has extensive experience in fieldwork, spending six months traveling throughout Oregon and Washington. He has used environmental DNA from water samples to detect torrent salamander populations in various streams. In another project, he collected DNA directly from approximately 150 salamanders. Chris performed both the lab work to process these samples and the bioinformatics analysis to assemble their DNA sequences. This summer, he plans to conduct a detailed survey of the streams of the streams in the H.J. Andrews Experimental Forest. The overarching goal of his PhD is to document the genetic diversity among torrent salamanders and characterize their population structure across the region, which he hopes will help inform the ESA decision-making process.

Chris remembers catching frogs and salamanders as a child – proof of his fascination with amphibians at a young age. His father was in the Navy, so the family moved around repeatedly, but Chris grew up mostly in Japan. Upon moving back to the US, he felt drawn to Oregon and enrolled at Lane community college before transferring to Oregon State to earn his bachelor’s degree as a first-generation college graduate. He remained at OSU for his graduate work due to the community of scientific mentors he had built. To hear more about his journey, what it is like to explore the Mt. St. Helens eruption zone, and what motivates him to work with this threatened species, tune in to KBVR 88.7 FM this this Sunday, Feb 19^th, at 7pm.

Lasers and lipids : in search of a mechanism for dysferlin

This week on Inspiration Dissemination, we are looking forward to chatting with Andrew Carpenter, a postdoctoral fellow working in the lab of Professor Joe Baio in the School of Chemical, Biological, and Environmental Engineering.

Andrew’s research seeks a better understanding of a protein called dysferlin, which plays a critical role in repairing muscle cells. Muscles undergo constant strain as they expand and contract, leading to tears in the sarcolemmas — thin membranes that surround muscle fibers. Dysferlin is responsible for recruiting vesicles to the site of these tears for a process called vesicle fusion to take place. Andrew likens this mechanism to using a denim patch to fix a hole in jeans, if the patch could become fully absorbed into the fabric in the way that vesicles eventually do into sarcolemmas. Dysferlin is clinically important because certain mutations (dysferlinopathies) to the gene encoding dysferlin lead to a disease called muscular dystrophy. The symptoms of dysferlinopathy typically include muscle weakness and damage to the musculoskeletal system, especially in the limbs.

The general importance of dysferlin to cell repair is well-established, but the molecular details of its mechanism of action are relatively unknown. Andrew uses an advanced experimental method called sum-frequency spectroscopy to study the protein at high resolution. This procedure uses two lasers — one infrared and one visible green — and points them at the sample of interest. When the lasers hit the sample, a third beam of light is generated at the surface, carrying information about the vibrations of the molecules. Quantum mechanical calculations are used to examine the intensity of this light as a function of frequency. In Andrew’s research, a synthetic lipid monolayer serves as an in-vitro model of the sarcolemma, and he introduces the dysferlin protein either in its healthy form or with various mutations. Then he uses spectroscopy data to infer changes in protein orientation and binding. In the future, he intends to correlate his experiments with data from live cells.

Sample spectra from Andrew’s recent publication

Andrew first discovered his fascination with laser instrumentation as an undergraduate at Linfield University. After that, he obtained a PhD in Chemistry at the University of Oregon, where he used small oil droplets called nano-emulsions to study the oil-water interface. His background in physical chemistry and expertise in the sum-frequency spectroscopy method have enabled him to readily adapt to studying biological lipid interfaces. His research, including a recent publication, is currently supported by the National Science Foundation.

To hear more about Andrew’s research journey and the differences and similarities in being a postdoc and a graduate student, tune in after the Super Bowl this Sunday, February 12^th, at 7pm on 88.7 FM KBVR.

A Gut Feeling: Examining Whale Ecology Using Number-Two Genetics

This week we have a MS (but soon to be PhD) student from the department of Fisheries and Wildlife, Charles Nye, joining us to discuss their work examining the dietary and environmental DNA of whales. So that begs the question – how exactly does an environment, or a diet, have DNA? Essentially, the DNA of many organisms can be isolated from samples of ocean water near the whales, or in the case of dietary DNA, can be taken from the whales’ fecal matter – that’s right, there’s a lot more you can get from poop than just an unpleasant smell.

Why should we care about what whales eat?

As the climate changes, so too does the composition of creatures and plants in the oceans. Examining environmental DNA gives Charles information on the nearby ecological community – which in turn gives information about what is available for the whale to eat plus what other creatures they may be in resource competition with. He is working to identify the various environmental DNA present to assist with conservation efforts for the right whale near Cape Cod – a whale that they hold as dear to their hearts on the East Coast as the folks of Depoe Bay hold the grey whale to theirs.

By digging into the whale poop to extract dietary DNA, Charles can look into how the whales’ diets shift over seasonal and yearly intervals – and he is doing precisely that with the West Coast grey whales. These dietary shifts may be important for conservation purposes, and may also be applied to studying behavior. For example, by looking at whether or not there are sex differences in diet and asking the ever-important question: do whales also experience bizarre pregnancy cravings?

two people underwater in scuba gear. Some tall kelp in the background. One person is holding a light which emits a beam into the water. — Scuba diving underwater.

How does someone even get to study whales?

Like many careers, it starts with an identity crisis. Charles originally thought they’d go into scientific illustration, but quickly realized that they didn’t want to turn a hobby he enjoyed into a job with deadlines and dread. A fortunate conversation with his ecology professor during undergrad inspired him to join a research lab studying intertidal species’ genetics – and eventually become a technician at the Monterey Bay Aquarium Research Institute.

After a while, simply doing the experiments was not enough and they wanted to be able to ask his own questions like “does all the algae found in a gray whale’s stomach indicate they may actually be omnivores, unlike their carnivorous whale peers?” (mmm, shrimp).

Turns out, in order to study whales all you have to do is start small – tiny turban snail small.

Image of Charles working in the lab and using a micropipette. They are wearing a lab coat and white rubber gloves. He is holding a small tube into which the tip of the micropette is inserted. — Working in the lab.

Excited for more whale tales? Us too. Be sure to listen live on Sunday, February 5th at 7PM on 88.7FM, or download the podcast if you missed it. Want to stay up to date with the world of whales and art? Follow Charles @thepaintpaddock on Twitter/Instagram for his art or @cnyescienceguy on Twitter for his marine biology musings.