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 synthetic biology


Engineering Microbial Symbiosis for Mars Habitability

Correll, Randall R., Worden, Simon P.

arXiv.org Artificial Intelligence

The colonization of Mars presents extraordinary challenges, including radiation exposure, low atmospheric pressure, and toxic regolith. Recent advancements in synthetic biology and genetic engineering offer unprecedented opportunities to address these obstacles by utilizing terrestrial extremophiles and engineered organisms. This paper examines the potential for creating symbiotic relationships between terrestrial microbes and hypothetical Martian life forms, should they exist, to support a sustainable human presence on Mars. Inspired by natural examples of endosymbiosis, such as mitochondria and chloroplasts, we propose methods to engineer life forms capable of enduring Martian conditions. Key components include experimental designs, laboratory simulations, and bioengineering approaches essential to this endeavor. The ethical, political, and technological challenges of introducing engineered life to Mars are critically evaluated, with an emphasis on international collaboration and robust planetary protection policies. This research underscores engineered symbiosis as a transformative strategy for enabling life to adapt and thrive on Mars while advancing humanity's aspirations for interplanetary habitation and exploration. By addressing these challenges, this work highlights a path toward sustainable life on Mars, reflecting both scientific ingenuity and ethical stewardship.


Biocomputation: Moving Beyond Turing with Living Cellular Computers

Communications of the ACM

It is a well-known story that theoretical computer science and biology have been drawing inspiration from each other for decades. While computer science has tried to mimic the functioning of living systems to develop computing models, including automata, artificial neural networks, and evolutionary algorithms, biology has used computing as a metaphor to explain the functioning of living systems.4 For example, biologists have used Boolean logic to conceptualize gene regulation since early 1970s, when Jacques Monod wrote the inspirational statement "… like the workings of computers."40 This article contends that information processing is the link between computer science and molecular biology. In computer science, a model of computation such as finite state machines or Turing machines defines how to generate output from a set of inputs and a set of rules or instructions.


The whack-a-mole governance challenge for AI-enabled synthetic biology: literature review and emerging frameworks

Undheim, Trond Arne

arXiv.org Artificial Intelligence

AI-enabled synthetic biology has tremendous potential but also significantly increases biorisks and brings about a new set of dual use concerns. The picture is complicated given the vast innovations envisioned to emerge by combining emerging technologies, as AI-enabled synthetic biology potentially scales up bioengineering into industrial biomanufacturing. However, the literature review indicates that goals such as maintaining a reasonable scope for innovation, or more ambitiously to foster a huge bioeconomy don't necessarily contrast with biosafety, but need to go hand in hand. This paper presents a literature review of the issues and describes emerging frameworks for policy and practice that transverse the options of command-and control, stewardship, bottom-up, and laissez-faire governance. How to achieve early warning systems that enable prevention and mitigation of future AI-enabled biohazards from the lab, from deliberate misuse, or from the public realm, will constantly need to evolve, and adaptive, interactive approaches should emerge. Although biorisk is subject to an established governance regime, and scientists generally adhere to biosafety protocols, even experimental, but legitimate use by scientists could lead to unexpected developments. Recent advances in chatbots enabled by generative AI have revived fears that advanced biological insight can more easily get into the hands of malignant individuals or organizations. Given these sets of issues, society needs to rethink how AI-enabled synthetic biology should be governed. The suggested way to visualize the challenge at hand is whack-a-mole governance, although the emerging solutions are perhaps not so different either.


Can We Program Our Cells?

#artificialintelligence

Making living cells blink fluorescently like party lights may sound frivolous. But the demonstration that it's possible could be a step toward someday programming our body's immune cells to attack cancers more effectively and safely. That's the promise of the field called synthetic biology. While molecular biologists strip cells down to their component genes and molecules to see how they work, synthetic biologists tinker with cells to get them to perform new feats -- discovering new secrets about how life works in the process. Listen on Apple Podcasts, Spotify, Google Podcasts, Stitcher, TuneIn or your favorite podcasting app, or you can stream it from Quanta. Steve Strogatz (00:03): I'm Steve Strogatz, and this is The Joy of Why, a podcast from Quanta Magazine that takes you into some of the biggest unanswered questions in science and math today. In this episode, we're going to be talking about synthetic biology. Simply put, we could say that synthetic biology is a fusion of biology, especially molecular biology, and engineering. The distinctive thing about it is that it treats cells as programmable devices. It's a kind of tinker toy approach that builds circuits, but not out of wires and switches like we're used to, but rather out of biological components, like proteins and genes. But also, the approach holds promise for illuminating how life works at the deepest level. It's one thing to strip cells apart to see how they work. But it's another thing to tinker with cells to try to get them to perform new tricks, which is something that my guest, Michael Elowitz, does. For example, a while back, he engineered cells to blink on and off like Christmas lights. Michael Elowitz is a professor of biology and biological engineering at Caltech and Howard Hughes Medical Institute. It's great to be here. Strogatz (01:53): So let's talk about the foundational idea of synthetic biology. I mentioned it in the intro, that's -- that living cells, we could think of as programmable devices. The field, synthetic biology, it seems like you guys have this philosophy that you can learn about cells by building functionality into cells yourself.


Destruction Democratised - Farsight

#artificialintelligence

Some technological advances are so great that they create ruptures in our understanding of what is possible. Eighty years ago, such a rift took place via the invention of the atom bomb, transforming the way we conceive of warfare and global order. From artificial intelligence to synthetic biology, experts and policymakers are beginning to dissect the potential consequences of adding unfamiliar, highly advanced, and potentially devastating new additions to the toolboxes of adversarial powers. When referring to world order, we often operate within a'Great Power' discourse and assume that geopolitical disruptions require geopolitical might. The democratisation of destructive technologies, however, will likely create the conditions for smaller non-state actors, and even individuals, to have a greater impact on an international level.


Origin of life from a maker's perspective -- focus on protocellular compartments in bottom-up synthetic biology

Ivanov, Ivan, Smoukov, Stoyan K., Nourafkan, Ehsan, Landfester, Katharina, Schwille, Petra

arXiv.org Artificial Intelligence

The origin of life is shrouded in mystery, with few surviving clues, obscured by evolutionary competition. Previous reviews have touched on the complementary approaches of top-down and bottom-up synthetic biology to augment our understanding of living systems. Here we point out the synergies between these fields, especially between bottom-up synthetic biology and origin of life research. We explore recent progress made in artificial cell compartmentation in line with the crowded cell, its metabolism, as well as cycles of growth and division, and how those efforts are starting to be combined. Though the complexity of current life is among its most striking characteristics, none of life's essential features require it, and they are unlikely to have emerged thus complex from the beginning. Rather than recovering the one true origin lost in time, current research converges towards reproducing the emergence of minimal life, by teasing out how complexity and evolution may arise from a set of essential components.


AI as a 'wise counsel' for synthetic biology

#artificialintelligence

Machine learning is transforming all areas of biological science and industry, but is typically limited to a few users and scenarios. A team of researchers at the Max Planck Institute for Terrestrial Microbiology led by Tobias Erb has developed METIS, a modular software system for optimizing biological systems. The research team demonstrates its usability and versatility with a variety of biological examples. Though engineering of biological systems is truly indispensable in biotechnology and synthetic biology, today machine learning has become useful in all fields of biology. However, it is obvious that application and improvement of algorithms, computational procedures made of lists of instructions, is not easily accessible.


Developing an NLP-based Recommender System for the Ethical, Legal, and Social Implications of Synthetic Biology

Dablain, Damien, Huang, Lilian, Sepulvado, Brandon

arXiv.org Artificial Intelligence

Synthetic biology is an emerging field that involves the engineering and re-design of organisms for purposes such as food security, health, and environmental protection. As such, it poses numerous ethical, legal, and social implications (ELSI) for researchers and policy makers. Various efforts to ensure socially responsible synthetic biology are underway. Policy making is one regulatory avenue, and other initiatives have sought to embed social scientists and ethicists on synthetic biology projects. However, given the nascency of synthetic biology, the number of heterogeneous domains it spans, and the open nature of many ethical questions, it has proven challenging to establish widespread concrete policies, and including social scientists and ethicists on synthetic biology teams has met with mixed success. This text proposes a different approach, asking instead is it possible to develop a well-performing recommender model based upon natural language processing (NLP) to connect synthetic biologists with information on the ELSI of their specific research? This recommender was developed as part of a larger project building a Synthetic Biology Knowledge System (SBKS) to accelerate discovery and exploration of the synthetic biology design space. Our approach aims to distill for synthetic biologists relevant ethical and social scientific information and embed it into synthetic biology research workflows.



We Are Entering A New Era Of Innovation. Here's What We Need To Do:

#artificialintelligence

There’s no doubt that digital technology has been highly disruptive. In industry after industry, from retail to media to travel and hospitality, nimble digital upstarts have set established industries on their head, completely changing the basis upon which firms compete. Many incumbents haven’t survived. Many others are greatly diminished. Still, in many ways, the digital revolution has been a huge disappointment. Besides the meager productivity gains, we’ve seen a ​​global rise in authoritarian populism, stagnant wages, reduced productivity growth and weaker competitive markets, not to mention an anxiety epidemic, increased obesity and, at least in the US, decreased life expectancy. We can—and must—do better. We can learn from the mistakes we made during the digital revolution and shift our mindset from disrupting markets to tackling grand challenges. This new era of innovation will give us the ability to shape the world around us like never before, at a molecular level and achieve incredible things. Yet we can’t just leave our destiny to the whims of market and technological forces. We must actually choose the outcomes we prefer and build strategies to achieve them. The possibilities that we will unlock from new computing architectures, synthetic biology, advanced materials science, artificial intelligence and other things will give us that power. What we do with it is up to us.