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Biology

Artificial Intelligence and Synthetic Biology Are Not Harbingers of … – Stimson Center

Are AI and biological research harbingers of certain doom or awesome opportunities?

Contrary to the reigning assumption that artificial intelligence (AI) will super-empower the risks of misuse of biotech to create pathogens and bioterrorism, AI holds the promise of advancing biological research, and biotechnology can power the next wave of AI to greatly benefit humanity. Worries about the misuse of biotech are especially prevalent, recently prompting the Biden administration to publish guidelines for biotech research, in part to calm growing fears.

The doomsday assumption that AI will inevitably create new, malign pathogens and fuel bioterrorism misses three key points. First, the data must be out there for an AI to use it. AI systems are only as good as the data they are trained upon. For an AI to be trained on biological data, that data must first exist which means it is available for humans to use with or without AI. Moreover, attempts at solutions that limit access to data overlook the fact that biological data can be discovered by researchers and shared via encrypted form absent the eyes or controls of a government. No solution attempting to address the use of biological research to develop harmful pathogens or bioweapons can rest on attempts to control either access to data or AI because the data will be discovered and will be known by human experts regardless of whether any AI is being trained on the data.

Second, governments stop bad actors from using biotech for bad purposes by focusing on the actors precursor behaviors to develop a bioweapon; fortunately, those same techniques work perfectly well here, too. To mitigate the risks that bad actors be they human or humans and machines combined will misuse AI and biotech, indicators and warnings need to be developed. When advances in technology, specifically steam engines, concurrently resulted in a new type of crime, namely train robberies, the solution was not to forego either steam engines or their use in conveying cash and precious cargo. Rather, the solution was to employ other improvements, to later include certain types of safes that were harder to crack and subsequently, dye packs to cover the hands and clothes of robbers. Similar innovations in early warning and detection are needed today in the realm of AI and biotech, including developing methods to warn about reagents and activities, as well as creative means to warn when biological research for negative ends is occurring.

This second point is particularly key given the recent Executive Order (EO) released on 30 October 2023 prompting U.S. agencies and departments that fund life-science projects to establish strong, new standards for biological synthesis screening as a condition of federal funding . . . [to] manage risks potentially made worse by AI. Often the safeguards to ensure any potential dual-use biological research is not misused involve monitoring the real world to provide indicators and early warnings of potential ill-intended uses. Such an effort should involve monitoring for early indicators of potential ill-intended uses the way governments employ monitoring to stop bad actors from misusing any dual-purpose scientific endeavor. Although the recent EO is not meant to constrain research, any attempted solutions limiting access to data miss the fact that biological data can already be discovered and shared via encrypted forms beyond government control. The same techniques used today to detect malevolent intentions will work whether large language models (LLMs) and other forms of Generative AI have been used or not.

Third, given how wrong LLMs and other Generative AI systems often are, as well as the risks of generating AI hallucinations, any would-be AI intended to provide advice on biotech will have to be checked by a human expert. Just because an AI can generate possible suggestions and formulations perhaps even suggest novel formulations of new pathogens or biological materials it does not mean that what the AI has suggested has any grounding in actual science or will do biochemically what the AI suggests the designed material could do. Again, AI by itself does not replace the need for human knowledge to verify whatever advice, guidance, or instructions are given regarding biological development is accurate.

Moreover, AI does not supplant the role of various real-world patterns and indicators to tip off law enforcement regarding potential bad actors engaging in biological techniques for nefarious purposes. Even before advances in AI, the need to globally monitor for signs of potential biothreats, be they human-produced or natural, existed. Today with AI, the need to do this in ways that still preserve privacy while protecting societies is further underscored.

Knowledge of how to do something is not synonymous with the expertise in and experience in doing that thing: Experimentation and additional review. AIs by themselves can convey information that might foster new knowledge, but they cannot convey expertise without months of a human actor doing silica (computer) or in situ (original place) experiments or simulations. Moreover, for governments wanting to stop malicious AI with potential bioweapon-generating information, the solution can include introducing uncertainty in the reliability of an AI systems outputs. Data poisoning of AIs by either accidental or intentional means represents a real risk for any type of system. This is where AI and biotech can reap the biggest benefit. Specifically, AI and biotech can identify indicators and warnings to detect risky pathogens, as well as to spot vulnerabilities in global food production and climate-change-related disruptions to make global interconnected systems more resilient and sustainable. Such an approach would not require massive intergovernmental collaboration before researchers could get started; privacy-preserving approaches using economic data, aggregate (and anonymized) supply-chain data, and even general observations from space would be sufficient to begin today.

Setting aside potential concerns regarding AI being used for ill-intended purposes, the intersection of biology and data science is an underappreciated aspect of the last two decades. At least two COVID-19 vaccinations were designed in a computer and were then printed nucleotides via an mRNA printer. Had this technology not been possible, it might have taken an additional two or three years for the same vaccines to be developed. Even more amazing, nuclide printers presently cost only $500,000 and will presumably become less expensive and more robust in their capabilities in the years ahead.

AI can benefit biological research and biotechnology, provided that the right training is used for AI models. To avoid downside risks, it is imperative that new, collective approaches to data curation and training for AI models of biological systems be made in the next few years.

As noted earlier, much attention has been placed on both AI and advancements in biological research; some of these advancements are based on scientific rigor and backing; others are driven more by emotional excitement or fear. When setting a solid foundation for a future based on values and principles that support and safeguard all people and the planet, neither science nor emotions alone can be the guide. Instead, considering how projects involving biology and AI can build and maintain trust despite the challenges of both intentional disinformation and accidental misinformation can illuminate a positive path forward.

The concerns regarding the potential for AI and biology to be used for ill-intended purposes should not overshadow the present conversations about using technologies to address important regional and global issues.

Specifically, in the last few years, attention has been placed on the risk of an AI system training novice individuals how to create biological pathogens. Yet this attention misses the fact that such a system is only as good as the data sets provided to train it; the risk already existed with such data being present on the internet or via some other medium. Moreover, an individual cannot gain from an AI the necessary experience and expertise to do whatever the information provided suggests such experience only comes from repeat coursework in a real-world setting. Repeat work would require access to chemical and biological reagents, which could alert law enforcement authorities. Such work would also yield other signatures of preparatory activities in the real world.

Others have raised the risk of an AI system learning from biological data and helping to design more lethal pathogens or threats to human life. The sheer complexity of different layers of biological interaction, combined with the risk of certain types of generative AI to produce hallucinated or inaccurate answers as this article details in its concluding section makes this not as big of a risk as it might initially seem. Specifically, the risks from expert human actors working together across disciplines in a concerted fashion represent a much more significant risk than a risk from AI, and human actors working for ill-intended purposes together (potentially with machines) presumably will present signatures of their attempted activities. Nevertheless, these concerns and the mix of both hype and fear surrounding them underscore why communities should care about how AI can benefit biological research.

The merger of data and bioscience is one of the most dynamic and consequential elements of the current tech revolution. A human organization, with the right goals and incentives, can accomplish amazing outcomes ethically, as can an AI. Similarly, with either the wrong goals or wrong incentives, an organization or AI can appear to act and behave unethically. To address the looming impacts of climate change and the challenges of food security, sustainability, and availability, both AI and biological research will need to be employed. For example, significant amounts of nitrogen have already been lost from the soil in several parts of the world, resulting in reduced agricultural yields. In parallel, methane gas is a pollutant that is between 22 and 40 times worse depending on the scale of time considered than carbon dioxide in terms of its contribution to the Greenhouse Effect impacting the planet. Bacteria generated through computational means can be developed through natural processes that use methane as a source of energy, thus consuming and removing it from contributing to the Greenhouse Effect, while simultaneously returning nitrogen from the air to the soil, thereby making the soil more productive in producing large agricultural yields.

The concerns regarding the potential for AI and biology to be used for ill-intended purposes should not overshadow the present conversations about using technologies to address important regional and global issues. To foster global activities to help both encourage the productive use of these technologies for meaningful human efforts and ensure ethical applications of the technologies in parallel an existing group, namely the international Genetically Engineered Machine (iGEM) competition, should be expanded. Specifically, iGEM represents a global academic competition, which started in 2004, aimed at improving understanding of synthetic biology while also developing an open community and collaboration among groups. In recent years, over 6,000 students in 353 teams from 48 countries have participated. Expanding iGEM to include a track associated with categorizing and monitoring the use of synthetic biology for good as well as working with national governments on ensuring that such technologies are not used for ill-intended purposes would represent two great ways to move forward.

As for AI in general, when considering governance of AIs, especially for future biological research and biotechnology efforts, decisionmakers would do well to consider both existing and needed incentives and disincentives for human organizations in parallel. It might be that the original Turing Test designed by computer science pioneer Alan Turing intended to test whether a computer system is behaving intelligently, is not the best test to consider when gauging local, community, and global trust. Specifically, the original test involved Computer A and Person B, with B attempting to convince an interrogator, Person C, that they were human, and that A was not. Meanwhile, Computer A was trying to convince Person C that they were human.

Consider the current state of some AI systems, where the benevolence of the machine is indeterminate, competence is questionable because some AI systems are not fact-checking and can provide misinformation with apparent confidence and eloquence, and integrity is absent. Some AI systems can change their stance if a user prompts them to do so.

However, these crucial questions regarding the antecedents of trust should not fall upon these digital innovations alone these systems are designed and trained by humans. Moreover, AI models will improve in the future if developers focus on enhancing their ability to demonstrate benevolence, competence, and integrity to all. Most importantly, consider the other obscured boxes present in human societies, such as decision-making in organizations, community associations, governments, oversight boards, and professional settings such as decision-making in organizations, community associations, governments, oversight boards, and professional settings. These human activities also will benefit by enhancing their ability to demonstrate benevolence, competence, and integrity to all in ways akin to what we need to do for AI systems as well.

Ultimately, to advance biological research and biotechnology and AI, private and public-sector efforts need to take actions that remedy the perceptions of benevolence, competence, and integrity (i.e., trust) simultaneously.

David Bray is Co-Chair of the Loomis Innovation Council and a Distinguished Fellow at the Stimson Center.

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Artificial Intelligence and Synthetic Biology Are Not Harbingers of ... - Stimson Center

Biology

Multiomic analysis of cervical squamous cell carcinoma identifies … – Nature.com

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Biology

Future House wants to build an AI biologist. They’re looking to a … – Chemistry World

A 10-year mission to build an AI biologist has just launched. The team from US not-for-profit moonshot Future House wants to create an autonomous research assistant to accelerate the speed of scientific discovery and help tackle the key challenges facing humanity including antibiotic resistance, food security and climate change.

The fundamental bottleneck in biology today is not just data or computational power, but human effort, too: no individual scientist has time to design tens of thousands of individual hypotheses, or to read the thousands of biology papers that are published each day, explained Sam Rodriques, chief executive of the Future House project.

The ultimate aim of the Future House project is to produce an AI scientist capable of autonomously completing routine tasks of varying complexity, from designing DNA primers to troubleshooting experimental problems. Such a system must be able to reason scientifically: to make predictions, design experiments and analyse outcomes, something which is beyond the scope of current AI systems. However, the multidisciplinary team, including biologists, biochemists and AI researchers, plan to build upon recent advances in AIs for science, most significantly the chemistry large language model (LLM) ChemCrow. Released in April, this LLM already exhibits many of the characteristics of a future AI scientist and could act as a blueprint for the Future House project.

The performance of LLMs in chemistry to date have been notoriously poor. LLM systems are trained on huge amounts of text, allowing them to predict the next logical response with increasing accuracy as the training set is broadened. But lack of reasoning and critical thinking capabilities mean these models typically provide nonsense answers to even the most simple chemical questions.

The problem is theres not enough data in chemistry, explains Andrew White, one of the developers behind ChemCrow and now head of science at Future House. A lot of the data is programmatically generated (ie chemical names) so not that rich, and many papers are hidden behind paywalls and therefore not accessible for training. A lot of chemical data is also locked up in pictures of structures which cant easily be converted into language.

This question of training data access is not easily resolved but White, alongside fellow developer Philippe Schwaller, circumvented part of this crucial data acquisition process by combining the LLM directly with a collection of useful chemical tools including LitSearch, Name2SMILES and ReactionPlanner. Instead of trying to have the LLM operate directly on chemicals, what we did with ChemCrow is to give access to tools, says White. The LLM is acting one level higher and orchestrating these tools together to accomplish open-ended complex chemistry tasks.

Users can enter a question or instruction in natural language and the system will work through the problem using a combination of the different available tools to complete each step in the overall task. For example, in their preliminary studies, the ChemCrow team asked the system to make an insect repellent. The AI was able to perform a web search to determine what an insect repellent is, conduct a literature review to find examples, convert compound names to SMILES structures, design a synthesis, then operate the robotic laboratory system at IBM to produce a physical sample of a known insect repellent.

One of the really exciting parts is that the synthesis pipelining tool is combined with the IBM RoboRXN so theres that conversion to an actual synthesis procedure, explains Schwaller. ChemCrow was one of the first connections to the physical world enabling us to do an actual synthesis from a large language model.

The system is also able to respond to feedback and errors reported by the robotic system, iteratively modifying and validating its work sequence to allow the AI to fix problems autonomously without human input.

But White and Schwaller are keen to emphasise that ChemCrow is about augmenting the work already done by chemists rather than replacing them. There are certain problems where you just need to scale, to do more experiments and generate new compounds faster, says White. ChemCrow is not going to be inventing new reactions or catalysts but scaling up routine tasks. I hope its viewed as empowering.

Through ChemCrow, those tools which are usually hard to set up and maybe not accessible to an experimental chemist become much more accessible using natural language. Its an assistant, not a replacement, adds Schwaller.

The enhanced capabilities of this LLM have already been well-received by the community. ChemCrow is a cool idea. It augments the LLM performance in chemistry and new capabilities emerge by the integration of the 18 expert-designed tools, says Andr Silva Pimentel, a chemical AI researcher at the Pontifical Catholic University of Rio de Janeiro in Brazil. [However], the effectiveness of ChemCrow is also related to the quality and quantity of the tools it uses. ChemCrow improves the reasoning process, but it cannot fully rectify flawed reasoning.

The ChemCrow team are already addressing these limitations, both by enhancing the number of tools available and probing how the system responds to failure and works through unexpected problems. But solutions to these limitations also have wider implications for the future of AI as an assistant to scientists.

Large language models really arent optimised for structure recognition, says White. Theres this gap right now between the AI work going on in Silicon Valley and whats needed to do science. To move forward we need to give these models the ability to really see and look directly at these objects (chemical structures, proteins, genomes) and were trying to bridge that gap at Future House.

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Future House wants to build an AI biologist. They're looking to a ... - Chemistry World

Biology

From French literature to the lab: Biochem grad finds true passion in … – ASU News Now

November 20, 2023

Editors note:This story is part of a series of profiles of notable fall 2023 graduates.

Bethany Kolbaba Kartchner is by all accounts a true Renaissance woman. She has a master's degree in French literature and is about to graduate from ASUs School of Molecular Scienceswith a PhD in biochemistry. Bethany Kolbaba Kartchner Download Full Image

But before her journey started at ASU, when she decided she wanted a science degree, it had been more than 10 years since she had completed the basic science classes necessary to enroll in a graduate program. In addition, she had a family who needed her. Kartchner spent a month researching ASU's biochemistry programs, strategizing how she could take classes and still be the primary caretaker of her children.

It was very important to me that their lives would not be affected by my new pursuit, stated Kartchner. I enrolled in one online class at Rio Salado every four months until I had taken all the necessary classes they offered. Then, I took higher-level, in-person classes and labs at Mesa Community College because they had an excellent preschool program for my youngest child. Once I had taken all of the classes I could at the community college level, I applied to ASU to complete my second bachelors degree, in biochemistry.

When Kartchner came to ASU, she was incredibly nervous. The school seemed so big, and she wasn't sure shed be accepted as a nontraditional student, as most of her classmates were decades younger than her.

I needn't have worried, explained Kartchner. Everyone was very welcoming, and the professors were incredibly accessible. I quickly found study partners and settled into a nice routine.

One of her professors, Marcia Levitus, took a special interest in Kartchner and helped her to hone her interests and identify a lab where she could gain experience to apply to the doctoralprogram. She found a position in Professor Jeremy Mills lab working with proteins. She was especially attracted to professor Mills' work due to the range in research from designing proteins on a computer to putting the gene that encodes that protein intoE. coli,characterizing the protein and solving its structure using X-ray crystallography.

His lab really does everything and I've been fortunate to gain experience in all aspects of the protein design workflow, said Kartchner.

In the laboratory, Beth was far more than simply an excellent researcher, said Mills. Rather, Beth served as a manager, mentor and confidant to her colleagues and at times her advisor and was always incredibly generous with her time.

Beth was often the first person I would introduce new students to because I was certain that she would make them feel welcome in the laboratory regardless of their experience or background, Mills continued. As much as Id like to have Beth in the laboratory still, I am so excited that she has moved on to bigger and better things. I can say without hesitation that having Beth in our laboratory for the last few years has shaped how we do things in ways that will continue for years to come. I am so grateful to Beth that she gave me the privilege of being able to work with and learn from her.

During 2021, Kartchner worked remotely for Moderna in the Computational Sciences and Molecular Engineering Division, where she implemented the Rosetta RNA tertiary structure prediction platform.

Editor's note: Answers may have been edited for length or clarity.

Question: What was your aha moment when you realized you wanted to study the field you majored in?

Answer: I was driving my children to their activities and listening to Science Friday on NPR. Ira Flatow, the host, was interviewing J. Craig Venter about his book "Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life."In the interview, they discussed a field that was completely new to me synthetic biology, which is basically reengineering biology for human purposes. I was immediately intrigued and I knew that I wanted to become proficientin this field.

Preparing to come to ASU took me about four years. I studied every weekday from 46 a.m. while the children slept, and on Sunday afternoons, I would go to the public library from 15 p.m. When we went on family vacations, I kept up my regime, often studying in closets because they were the only place where turning on a light wouldn't wake the family. I have a very special memory of studying biology in a closet in an Airbnb in Nevada. I was learning about ribosomes and how they translate mRNA into proteins, and this feeling of complete joy swept over me. I absolutely loved what I was doing. It was so exciting to learn about the world.

Q:Whats something you learned while at ASU in the classroom or otherwise that surprised you or changed your perspective?

A: I expected my graduate work to challenge me academically, so when I struggled with an abstract concept, that didn't surprise me. What I didn't expect was that graduate work would challenge me personally. I didn't know that the struggles that I would go through would change the way I see myself and my world. I've become a much stronger person and a much more critical thinker because of my studies at ASU.

Q: Whats the best piece of advice youd give to those still in school?

A: School is hard and can be overwhelming at times. Break down big projects into smaller steps and work on them methodically. All the small daily steps move you closer to your goals.

Q: What advice would you give anyone who is contemplating taking on a big project or working toward a long-term goal?

A: Don't be afraid of really long-term goals. When I was 36 and contemplating whether I should pursue my doctorate degree in biochemistry, I knew that the path would be long and that I would be 47 years old when I finished. Initially, that thought was very daunting. However, I knew that eventually, I would be 47 and I'd either be 47 with a doctorate or 47 without one. I decided that I wanted to be 47 with a doctorate so I got started.

Q: What are your plans aftergraduation?

A: I'm working as a scientist of computational biology for a biotech startup (FL83) in the Flagship Pioneering ecosystem based inBoston. I work remotely and travel to Boston every few months to work on site. I love what I'm doing.

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From French literature to the lab: Biochem grad finds true passion in ... - ASU News Now

Biology

Revisiting the Pioneering Work of India’s Women Wildlife Biologists … – The Wire Science

At a time when the ascendency of women is being celebrated with the role of women scientists in the Chandrayaan Mission, the introduction of the Womens Reservation Bill in parliament, and the array of medals that Indian women have brought home from the Asian Games, the book, Women in the Wild,throws light on some remarkable achievements done by some of women wildlife biologists. The book throws light on their struggles in the remotest corners of the country.

Published by Juggernaut, editor Anita Mani points out that the field of biology as a discipline attracted few women until the 1980s. The Wildlife Institute of India and The Salim Ali School of Ecology and Environmental Sciences, affiliated with Pondicherry University, were among the first to open their doors to women for postgraduate programmes in wildlife science. Eminent writers, many of them environmentalists themselves, have portrayed the trials and triumphs of these pioneering women wildlife biologists, in this book.

Pioneers and pathbreakers

Jamal Ara, considered Indias first woman ornithologist, had no formal academic education in wildlife biology but taught herself in the field. As Raza Kazmi, who has written the chapter about her, points out, unlike the ornithologists of her era, this first lady of Indian ornithology did not come from a royal background or a merchant background. She was an educated Muslim woman, travelling, working, and excelling all on her own. From the Chota Nagpur plateau of todays Jharkhand, her work on the ornithology of the plateau remains the only comprehensive study of birds of the region. Both Salim Ali and Zafar Futehally, pioneering naturalists and ornithologists, who corresponded with her regularly, held her in high esteem.

Jamal Ara wrote prolifically from 1949 to 1988. Her first paper in the Bombay Natural History Society Journal in 1949 was on the wildlife reserves of Bihar. There were more than 60 papers and popular articles in her name, including a booklet for children on birds, published by the National Book Trust in 1970. She also gave regular talks on All India Radio on the vanishing birds and animals of Bihar. Then she disappeared from the scene of Indian ornithology. But her bird book for children, in its 13th edition, continues to regale kids. There is a beautiful garden in her home in Ranchi where, her daughter points out, most of her bird observations were made. This is the centenary year of her birth and the lead article on her, inWomen in the Wildis a fitting tribute to the countrys first bird woman.

Particularly moving is the story of turtle girl, J. Vijaya, poignantly narrated by Zia Whitaker, daughter of renowned ornithologist Zafar Futehally and a founder of the Madras Crocodile Bank. Vijaya led a brief but rich life conserving Indias freshwater turtles and, in the process, rediscovering the Cochin forest cane turtle. Also profiled is the work ofAyushi Jain, a young biologist from Uttar Pradesh, who has been conserving the critically endangered Cantors giant softshell turtle in Kasargod district of Kerala. With community support, she hopes to revive the turtle and its habitat and ensure co-existence with humans.

The planet has lost more than 80% of its freshwater aquatic life and a third of its wetlands since 1970. More than 50% of the worlds freshwater turtles, like the Cantors giant softshell turtle, are on the verge of extinction.

Wildcards and wildcats

Vidya Athreya was one of the first women in India to conduct long-term research on big cats using radio collars. At the time of writing Athreyas story on unlocking the secret lives of leopards, Ananda Banerjee found she had collared 11 leopards and one tiger. It was only after her collaring of the leopards and other wildlife that the scientific community started believing that leopards do live in human-dominated landscapes. Athreya points out, In a country where people and their livestock are everywhere, wild animals do not understand borders, or whether an area is a sanctuary or not.

In the early 2000s, while working in the Nashik and Pune districts of Maharashtra, she found leopards and hyenas in well-irrigated areas. Before irrigation reached, wolves lived in these dry, arid areas. Athreyas studies showed that substantial populations of leopards, hyenas, jackals, wolves, jungle cats, and foxes lived in rural habitations and their diet included domestic animals and rodents.

Trapping leopards and relocating them to forest areas does not work. With great homing instincts, they return to the area they have been moved from. This was proved by radio-collaring a large old leopard called Ajoba, rescued from a well near Pune and released in a forested area. Ajoba travelled 120 km to return to Sanjay Gandhi National Park (SGNP), Mumbai, which was believed to have been home.

Though not all farmers are comfortable with leopards, they accept them. In 2011, after several encounters between humans and leopards around SGNP, its field director started the Mumbaikars for SGNP project to generate awareness of human-leopard interactions. Athreya collared leopards and opened doors for understanding them. The leopard population went up from 22 to 47 in 2018. Athreya collaborated with journalists and the articles written changed public perception of the big cat. A Marathi film was made on the collared cat Ajoba with Urmila Matondkar playing the role of Athreya.

Uma Ramakrishnan, a scientist, molecular ecologist, and wildlife detective, has specialised in the study of scat, especially that of the tiger. In the world of wildlife biologists turd is a treasure, almost like gold, she maintains. Professor of ecology and evolution with the National Centre for Biological Sciences, Bengaluru, she travels thousands of kilometers through forests and protected areas to collect and analyse the biological material tigers leave in faecal matter, hair scrapped from scratch marks on trees, and even traces of saliva, retrieved from a prey. It enables her to understand the ecology of endangered species.

Wild animals live secretive lives and are shy. Observing the rarely-sighted pangolin is difficult, and so is counting tigers whose movements are camouflaged. Poop is one way of researching and knowing the big cat. Like blood, scat contains DNA that scientists study. In addition to clues about the individual identity of a tiger, genetic material tells you where the tiger is from, what it is eating, whether it is healthy, how fast it travels, and its mating patterns.

For her Masters at Pune University, she worked for a year in the elephant scientist R. Sukumars laboratory. Her fieldwork took her to Periyar Tiger Reserve, Kerala, where she investigated if being tuskless impacted their reproduction. Was being makhna(tuskless) a disadvantage as far as the opposite sex was concerned?

Since Indian tiger reserves are modest in size and isolated, she wanted to understand what was happening with wild tigers. Along with Ph.D. student Prachi Thatte, she mapped the genetic landscape of Indian tigers in protected areas to figure out if they are genetically distinct or mixed. She found the intermingling of tiger populations in different reserves in Central India though connectivity was impeded by heavy traffic and pockets of human population. Presented as evidence in the Supreme Court, it led to the provision of an underpass that enabled the movement of wildlife between Kanha and Pench tiger reserves.

In Ranthambhore Tiger Reserve, lack of connectivity was leading to inbreeding in the tiger population. In Odishas Similipal, pseudo-melanism was traced to a single mutation in the genome of unusually high frequency. With the broad stripes of the tigers spreading into the pelt, the Odisha tigers were often referred to as black tigers. Prolonged isolation from tigers in other reserves had caused the cats to change their stripes. Since the closest population of tigers is about 800 km from Similipal, Ramakrishnan predicts all tigers of Similipal could become black. Her path-breaking work on tigers has been presented by Prerna Bindra, a writer and wildlife conservationist.

Dealing with difficulties

Neha Sinhas chapterThe Oak Calls Her Homeon Ghazala Shahabuddin and her study of the oak forests of the Himalayas reads like poetry. The trees stand like monuments, their bark full of lichen, their trunks complex and knotted. These arent knots of sorrow but binds of togetherness. The branches of oaks are festooned with ferns. The trunks of the tree are mushy with deep, luscious moss near whorls of lichen. Under the oaks, numerous seedlings and shrubs push towards the sun.

Shahabuddin says no two oak forests look the same. They have many tiers of complex vegetation. Banj oaks have leaves with silver underneath, and Tilonj oaks have twisted, convoluted boughs. The pine and oak trees look different and have different impacts on the ecosystem. Oaks germinate and thrive in moist areas and maintain soil moisture, often with streams emerging from these forests. She is excited by the diversity of these forests and the number of birds they harbour.

Oak forests are hotspots for biodiversity and birds. In a 2017 study with Rajkamal Goswami and Munish Gupta, she found 136 bird species from 42 sites in the mid-elevation Himalayas, around Mukteshwar. Another 80 species have been added by other team members all unique to the ecological richness of these mountains.

In many parts of the Himalayas, Shahabuddin found chir pine were invading oak stands. With people collecting biomass and other products, forests had degraded and the chir, which needs less water but more sun than the oak, established itself. Pine forests have less bird life than oak forests and are more susceptible to forest fires.

Among the many wonders of the oak forests is theToona ciliata, a sub-tropical tree punctured artistically with holes made by the only sap-sucking woodpecker of Asia and one of the four sapsucker species in the world. The rufous-bellied woodpecker drills holes before drinking deeply. Shahabuddins intuition about wild spaces is as important as her scientific knowledge. She worries that the recession of the oak forests will impact birds like the rufus-bellied woodpecker. Since 2014, she has been setting up bird-based tourism for Uttarakhand youth.

Divya Mudappa of the Nature Conservation Foundations Western Ghats program tries to make life safer for the endangered macaques, giant Malabar squirrels, and other animals that live in the 220 sq km Valparai Plateau and are killed by speeding vehicles. In addition to physically signaling drivers to slow down, activists have put up sign boards, canopy crossings with ropes, old fire hoses, and rubberized tarpaulin so that these animals use the skyway instead of roads. This has had mixed success because many animals may prefer the road. Though the authorities have put speed breakers, road kills continue. Tying up with local companies like Parry Agro, Mudappa and her team have restored degraded forests with native trees, providing crucial corridors for birds, bees, and other wildlife transiting downslope.

The women profiled in the book have worked in diverse landscapes, covering the Indian subcontinent. Nandini Velho and Usha Lachunga have worked extensively in the Eastern Himalayas, Ghazala Shahabuddin in the mid-elevation western Himalayas, and Divya Mudappa in the cool slopes of the southern Western Ghats. The biologists have a strong emotional connection to the landscape as well as the species they are helping conserve. The message that comes through strongly is that biodiversity conservation has to be in sync with local communities.

Women featured in the book have dealt with sexism from colleagues, seniors, and local people. As Anita Mani points out they have gone through incidents from fending off men on lonely beaches at night to locking themselves in rooms in remote forest quarters to keep predatory officials at bay. Despite these hurdles, women biologists have made great strides. What is heartening is the crop of young women field biologists now coming forward for nature conservation.

This article first appeared on Mongabay. Read the original piece here.

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Biology

UofA researcher states biology is behind the enjoyment of the safe … – ktlo.com

Roller coasters. Scary movies. Bungee jumping. Why do we like the things that scare us?

One researcher at the University of Arkansas, Dr. Brittany Schrick, believes she has it figured out.

Listen:

click to download audio

Schrick says, at the bottom of it all, is biology.

Listen:

click to download audio

Endorphins are hormones that can give us a sense of well-being.

That rush of fear followed by a sense of relief has social effects as well, Schrick said.

Listen:

click to download audio

However, the tolerance for fun fear isnt the same for everyone.

Listen:

click to download audio

Schrick said that some people seem to have a higher threshold for risk taking than others, and it often shows up at an early age. They are the ones likely to look for thrilling activities because they like how they feel being on the edge of safety.

And, interestingly, the fun of the safe scare often starts with infants.

Listen:

click to download audio

So why not be scared sometimes when we know everything will end up OK?

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UofA researcher states biology is behind the enjoyment of the safe ... - ktlo.com

Biology

US (AL): Grant awarded to study tomato-killer pathogen – Verticalfarmdaily.com: global indoor farming news

Dr. Tuan Tran, assistant professor of biology at the University of South Alabama, describes Ralstonia solananacearum as something like a supervillain in the world of plant pathogens.

The soil-based bacterium causes wilt in crops such as tomatoes, peppers and potatoes. Scientists around the world have been studying it for years, but so far its been difficult to eradicate the pathogen.

Its an important disease, said Tran. It damages a wide variety of crops. Not just ones we eat, but flowers as well. And once its there, you cannot get rid of it. So crop rotation basically doesnt work. Farmers would just abandon a field when they got bacterial wilt.

Ralstonia is relevant everywhere you go on every continent. From Asia and Africa to North and South America. If were not careful, it can get out and destroy other plants, and theres no effective way to control them. Ralstonia can live in water for decades.

Dr. Tuan Tran, assistant professor of biology at the University of South Alabama, was awarded a $40,000 grant by the USDA and the Alabama Department of Agriculture and Industries to study a soil-based bacterium that causes wilt in crops such as tomatoes, peppers and potatoes.

This year, Tran was awarded a $40,000 grant to study the genetic diversity of Ralstonia by the USDA and the Alabama Department of Agriculture and Industries.

He was also part of an international team that published a recent article in Plant Physiology, a leading research journal in the field of plant biology. His work for that study focused on Xanthomonas campetris, a bacterium that causes black rot in crucifers such as cabbage and lettuce.

Dr. Kelly Major, interim chair for the Department of Biology at the University of South Alabama, praised his research and work with students.

Dr. Trans expertise is in the molecular and biochemical aspects of plant pathology, Major said. Specifically, he has been using novel microscopic and molecular approaches toward understanding how plants and plant membranes interact with both pathogenic and beneficial microbes. His work is timely and of great interest, particularly here in Alabama, where agriculture is such an important sector of the economy. Moreover, his work has attracted the interest of undergraduate and graduate students alike. He offers USA biology students authentic, invaluable research experience at the lab bench that is critical to the training of our future scientists.

Tran earned a bachelors degree in biotechnology from the Ho Chi Minh City University of Science. He earned a Vietnam Education Foundation fellowship to pursue a Ph.D. in plant pathology at the University of Wisconsin-Madison. Then he spent five years as a research fellow at Nanyang Technological University in Singapore. In 2021, he accepted a faculty position at the University of South Alabama.

In his Plant-Microbe Interactions Research Group at South, Tran has 10 undergraduate and graduate students. He hopes to inspire them the way he was inspired. His former students and those he's mentored include Ph.D. candidates at the University of Wisconsin-Madison, lecturers at the University of Science in Vietnam, graduate students at Nanyang Technological University in Singapore and a postdoctoral researcher at the Tokyo University of Agriculture and Technology.

The main focus of his South lab is the intersection of plant immunity and bacterial pathogenesis. Research looks at how plant membrane composition effects surface immune receptors in plants, as well as how bacterial virulence factors compromise plant defense by interfering with membrane dynamics.

Tran also collaborates with Dr. Jonathon Audia, a professor of microbiology and immunology in the Frederick P. Whiddon College of Medicine to study plant interaction with the foodborne pathogen Salmonella enterica.

For his Ralstonia research, Tran works with common Roma and Bonny Best tomatoes. Each year he holds a research presentation for Mobile middle school students when they comes to South for GEMS: Go Explore Math and Science!

Using a popular fruit helps students understand what hes describing. They recognize seedlings from gardens and backyards.

Who doesnt like tomatoes? Tran asked. I usually just cook them in a soup or have them on a sandwich.

Source: southalabama.edu

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US (AL): Grant awarded to study tomato-killer pathogen - Verticalfarmdaily.com: global indoor farming news

Biology

Evolutionary biologists put the ‘manosphere’ on notice The Medical … – The Medical Republic

Evolutionary scholars want you to stop mis-using their concepts. Those theories dont mean what you think they mean.

There are perfectly legitimate reasons for taking a deep interest in the evolutionary psychology of human female mating strategies. Perhaps youre an anthropology student, a historical novelist, a psychologist, or a reality TV producer.

But some have nefarious intentions, according to research published in the journal of Evolutionary Human Sciences.

[E]volutionary hypotheses on female mating strategies are routinely invoked among the antifeminist online communities, collectively known as the manosphere, the authors from Kent, UK, and Lille, France, warn.

And frankly, theyre sick of it.

Evolutionary scholars might be surprised to see sexist worldviews reinforced by the dual mating strategy and sexy son hypotheses, or by the latest research on the ovulatory cycle, they write.

The manosphere has its own version of evolutionary psychology, mingling cutting-edge scientific theories and hypotheses with personal narratives, sexual double standards and misogynistic beliefs. After analysing this phenomenon, this article suggests ways to mitigate it.

Of course, internet misogynists are not the first to manipulate evolutionary approaches to human behaviour for their own ends.

Everyone likes to claim Darwin for their own 19th century feminists used sexual selection through female choice to bolster the campaign for womens autonomy, and survival of the fittest is an unshakeable ideological pillar for fiscal libertarians, the authors point out, so the manosphere cant be accused of originality. But that doesnt mean it shouldnt be taken seriously.

These (mis)understandings of evolutionary psychology (EP) should be extremely concerning to those working in the field because legitimate scientific hypotheses are routinely used to justify disdain towards women, they say.

And theyre looking at you, incels (involuntary celibates), the Red Pill (TRP), Pickup-Artists (PUAs), Mens Rights Activists (MRAs), and Men Going Their Own Way (MGTOW).

The Back Page will refrain from providing links, for obvious reasons. Muck up your own search history and leave us out of it thank you very much.

You really dont have to go there though, because the authors bravely delved into three decades of manosphere online discourse (from 1993-2022). And they found that, yep, evolutionary psychology was pretty popular on those pages, mainly because of the obsession with sex.

Because evolutionary psychology is, well, huge, the authors had to narrow it down, concentrating specifically on references to female mating strategies (just as quite a lot of the manosphere does too).

Theories on female mating strategies have grown in number since the 1970s. Its a veritable smorgasbord of ideas. Macaques and bonobos have really shown us the way when it comes to realising that not all women are coy or lacking in eagerness to mate, nor necessarily very selective and sometimes monogamous but sometimes not. Females can, you know, have varied behaviours according to circumstances. This is all very good for biological sciences and for feminism, say the authors.

Given this legacy, evolutionary scholars might be quite surprised to see evolutionary research on female mating strategies appropriated in misogynistic ways, the authors say.

The dual mating hypothesis is particularly popular, they found, and the basis of a lot of Ah-ha moments like this one from an MGTOW thread on the social media platform Reddit:

Its 2019, we all know the secret females have been hiding for over a million years now. DUAL MATING STRATEGY. F&*k the alphas [alpha males], suck resources and attention from all others.

And another on the same platform from a Red Pill thread:

There is an observed dualistic mating strategy observed in primates and anecdotally in humans. Women have two motives for using sex. Primal: in an intimate reproductive urge to obtain genes from a partner. Passion and horniness. Transactional: in a survivalist exchange to obtain resources from a partner. Female Bonobos will trade sex for food, and women will marry rich men they are not sexually attracted to.

In this world, there is no grey area of hypotheses, just the hard world of facts, along with citations that dont in fact back up the argument, the researchers found. And, oh yes, its deliberate.

People do not consciously act in their genes best interests. Yet, the use of the term strategy in the evolutionary literature misleadingly reinforces that impression, the authors say.

Hence the conclusion that feminism is, you guessed it, a sexual strategy.

Other theories-as-facts are around extra pair mating, used to assert that all women are cheaters because its a biological drive (and your girlfriend definitely will, especially if youre not an alpha male).

Our analysis revealed a lot of subtle and not-so-subtle shifts occur between EP and its manosphere version, the authors write.

Mostly gone are the marks of hypothesising. So are the precautions about using the genes eye view shortcut, or about the conditional nature of instincts. The timeline also changes: while academic hypotheses dwell on the aggregate behaviour of our ancestors over millennia, their manosphere versions are more unclear on that aspect.

Of course, this is coupled with a total absence of discussion on male sexuality and its evolutionary underpinnings.

Evolutionary biology scholars cant do much to stop their work being misinterpreted in hateful ways, the authors admit.

But they can make it harder to do, starting with ditching the morally loaded terms cuckold and infidelity and promiscuity. Language matters, the authors stress.

Secondly, you might think you dont need to state the obvious in a scientific paper, because your readers are colleagues who know all about the ultimate/proximate distinction and that behaviours from the distant past are not necessarily still with us.

What our analysis reveals however, is that these articles are also routinely read, shared and discussed by online communities. Moreover, in abstracts, titles and conclusions, academic publishing also encourages the communication of results in very definite terms, the authors point out.

Finally, go on, engage, call it out. Write a paper like this one, they say.

Ultimately, this might not contribute to mitigating the prevalence of EP in manosphere communities after all, EP is a rich and blossoming discipline.

However, it would at least make it harder for serious scholarship to get assimilated by the general public to reactionary and misogynistic discourse.

Evolutionary Human Sciences (2023), online 30 August

Send story ideas to cate@medicalrepublic.com.au. You never know wholl end up reading them

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Evolutionary biologists put the 'manosphere' on notice The Medical ... - The Medical Republic

Biology

Unearthing how a carnivorous fungus traps and digests worms – EurekAlert

image:

Glowing traps.

Credit: Hung-Che Lin (CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/)

A new analysis sheds light on the molecular processes involved when a carnivorous species of fungus known as Arthrobotrys oligospora senses, traps and consumes a worm. Hung-Che Lin of Academia Sinica in Taipei, Taiwan, and colleagues present these findings November 21st in the open access journal PLOS Biology.

A. oligospora usually derives its nutrients from decaying organic matter, but starvation and the presence of nearby worms can prompt it to form traps to capture and consume worms. A. oligospora is just one of many species of fungi that can trap and eat very small animals. Prior research has illuminated some of the biology behind this predator-prey relationship (such as certain genes involved in A. oligospora trap formation) but for the most part, the molecular details of the process have remained unclear.

To boost understanding, Lin and colleagues performed a series of lab experiments investigating the genes and processes involved at various stages of A. oligospora predation on a nematode worm species called Caenorhabditis elegans. Much of this analysis relied on a technique known as RNAseq, which provided information on the level of activity of different A. oligospora genes at different points in time. This research surfaced several biological processes that appear to play key roles in A. oligospora predation.

When A. oligospora first senses a worm, the findings suggest, DNA replication and the production of ribosomes (structures that build proteins in a cell) both increase. Next, the activity increases of many genes that encode proteins that appear to assist in the formation and function of traps, such as secreted worm-adhesive proteins and a newly identified family of proteins dubbed trap enriched proteins (TEP).

Finally, after A. oligospora has extended filamentous structures known as hyphae into a worm to digest it, the activity is boosted of genes coding for a variety of enzymes known as proteasesin particular, a group known as metalloproteases. Proteases break down other proteins, so these findings suggest that A. oligospora uses proteases to aid in worm digestion.

These findings could serve as a foundation for future research into the molecular mechanisms involved in A. oligospora predation and other fungal predator-prey interactions.

The authors add, Our comprehensive transcriptomics and functional analyses highlight the role of increased DNA replication, translation, and secretion in trap development and efficacy. Furthermore, a gene family that is largely expanded in the genomes of nematode-trapping fungi were found to be enriched in traps and critical for trap adhesion to nematodes. These results furthered our understanding of the key processes required for fungal carnivory.

#####

In your coverage, please use this URL to provide access to the freely available paper in PLOS Biology: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002400

Citation: Lin H-C, de Ulzurrun GV-D, Chen S-A, Yang C-T, Tay RJ, Iizuka T, et al. (2023) Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. PLoS Biol 21(11): e3002400. https://doi.org/10.1371/journal.pbio.3002400

Author Countries: Taiwan, United States

Funding: Funding for this work was provided by the Academia Sinica Investigator Award AS-IA-111-L02 and the Ministry of Science and Technology MOST grant 110-2311-B-001-047-MY3 to Y.-P.H. Computing was also supported by a research allocation from NSF XSEDE (TG-MCB190010) to E.M.S. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Experimental study

Cells

Competing interests: The authors have declared that no competing interests exist.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Unearthing how a carnivorous fungus traps and digests worms - EurekAlert

Biology

Space Biology Research Wraps Up Crew’s Work Week – NASA Blogs

The suns first rays begin illuminating Earths atmosphere as the space station orbited 260 miles above the central United States.

Bacteria, brain aging, and gravity-sensing cells were the main research subjects aboard the International Space Station on Friday. The seven Expedition 70 crew members also worked on computers, communications gear, and life support maintenance to wrap up the work week.

NASA Flight Engineer Loral OHara explored how microorganisms grow in microgravity, the potential damage they cause to spacecraft, and ways to disinfect the harmful bacteria. She inoculated microbe samples inside the Life Science Glovebox that will be compared to uninoculated samples. The NASA-sponsored Bacteria Adhesion and Corrosion study takes place in the Kibo laboratory module and aims to keep space crews and humans on Earth healthy.

Commander Andreas Mogensen from ESA (European Space Agency) viewed cell samples under a microscope for the Cerebral Ageing experiment. The study looks at brain cell-like samples to understand accelerated aging symptoms seen in patients on Earth and observed in astronauts on long-term space missions.

Astronaut Satoshi Furukawa from JAXA (Japan Aerospace Exploration Agency) prepared different cell samples for observation inside the Confocal Microscope then closed out the Cell Gravisensing biology Investigation. Earlier in the day, he swapped hard drives on a laptop computer then assisted OHara continuing to unpack the SpaceX Dragon cargo spacecraft.

NASA Flight Engineer Jasmin Moghbeli spent her day in the Harmony module configuring a variety of NASA and Roscosmos hardware. She first calibrated an ultrasonic inspection device that uses high-frequency sound waves to analyze materials, Afterward, Moghbeli checked space-to-ground, VHF, and inter-module communication systems.

Roscosmos cosmonaut Oleg Kononenko researched 3D printing techniques to learn how to manufacture tools and supplies in space and reduce dependence on cargo missions from Earth. Cosmonaut Nikolai Chub spent his day on life support and electronics maintenance. Cosmonaut Konstantin Borisov configured Soyuz crew ship and Progress resupply ship laptop computers then continued his photographic analysis of the stations Roscosmos modules.

Learn more about station activities by following thespace station blog,@space_stationand@ISS_Researchon X, as well as theISS FacebookandISS Instagramaccounts.

Get weekly video highlights at:https://roundupreads.jsc.nasa.gov/videoupdate/

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Space Biology Research Wraps Up Crew's Work Week - NASA Blogs