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Scholar Profile: Roman Bauer Page 3 CRYONICS 2nd Quarter 2020 | Vol 41, Issue 2 www.alcor.org Scholar Profile: Roman Bauer page 3 Mathematics and Modeling 2019 Aging Conferences in Cryonics page 33 page 16 CRYONICS Editorial Board Saul Kent Ralph C. Merkle, Ph.D. Contents Max More, Ph.D. R. Michael Perry, Ph.D. 3 Scholar Profile: Roman Bauer, Ph.D. Editor Computational biologist and interdisciplinary research Aschwin de Wolf team leader, Dr. Roman Bauer, explains the promise of Contributing Writers computational modeling to the future of biology. Currently Roman Bauer based at Newcastle University, Dr. Bauer leads a team of Ben Best experimental researchers and computational experts in David Brandt-Erichsen cryopreservation research focused on retinal tissue. He is also Max More, Ph.D. R. Michael Perry, Ph.D. the creative mind behind the open-source biology dynamics Nicole Weinstock modeler BioDynaMo, a powerful resource in his work and Aschwin de Wolf quite possibly, the future of cryonics. Copyright 2020 by Alcor Life Extension Foundation 15 Pro-Death Philosophy in Star Trek Picard All rights reserved. Most filmed science fiction is really “anti-science” fiction. Reproduction, in whole or part, David Brandt-Erichsen reviews Star Trek Picard. without permission is prohibited. 16 Mathematics and Modeling in Cryonics: Cryonics magazine is published quarterly. Some Historical Highlights Please note: If you change your address We survey, at layman’s level, some of the remarkable uses of less than a month before the magazine is mathematics modeling that have occurred in cryonics stretching mailed, it may be sent to your old address. back to the early 1970s. Topics include modelling heat transfer during perfusion, mathematical analysis of re-circulating closed- Address correspondence to: Cryonics Magazine circuit perfusion systems, quantification of ischemia, and predicting 7895 East Acoma Drive, Suite 110 cryoprotectant toxicity. Scottsdale, Arizona 85260 Phone: 480.905.1906 33 2019 Aging Conferences Toll free: 877.462.5267 Report on notable 2019 aging conferences by Ben Best. Fax: 480.922.9027 42 Fight Aging! Letters to the Editor welcome: Reports from the front line in the fight against aging [email protected] Advertising inquiries: 48 Membership Statistics 480.905.1906 x113 How many members, associate members, and patients does Alcor [email protected] have and where do they live? ISSN: 1054-4305 Visit us on the web at www.alcor.org 50 Revival Update Mike Perry surveys the news and research to report on new Alcor News Blog http://www.alcor.org/blog/ developments that bring us closer to the revival of cryonics patients. 2 Cryonics / 2nd Quarter 2020 www.alcor.org Scholar Profile: Roman Bauer, Ph.D. By Nicole Weinstock he recent coronavirus Discovering Neuroinformatics Tpandemic has spurred a number of comparisons and Dr. Bauer was born in Zürich, Switzerland to a Turkish artist historical coverage of the and art therapist, and a Swiss computer programmer. “I think 1918 influenza pandemic my current work as a computational biologist combines the two that swept the globe just main features of my parents’ work quite well,” Bauer observes, over a century ago. Though “namely, creativity and the usage of computers.” both events inspire(d) a Though he grew up in a small town in northeast Switzerland, sense of solidarity and he returned to urbanity to pursue his B.Sc., followed by his collaboration across the M.Sc. and Ph.D., at the acclaimed public research university, sciences, this latest test ETH Zürich. Bauer arrived with a deep-seated interest in of innovation carries artificial intelligence (AI), but the university had no official AI the distinctive force of course. He pursued the Computational Science and Engineering computational modeling. (CSE) course, focusing on robotics and theoretical physics. For computational biologist An important turning point emerged when he discovered a Dr. Roman Bauer and cryopreservation re- collaboration between ETH Zürich and the University of Zürich, searcher, Dr. Roman Bauer, called the Institute of Neuroinformatics. Considered a cutting- this moment serves to underscore the power of computational edge collaboration, it was founded in late 1995, just a couple models in a broad range of biological research, including years after the field of its naming was coined. cryonics: The union of neuroscience and information science, It can be brains, cryopreservation of biological tissues, neuroinformatics is principally concerned with the development the spreading of pandemics – if we can collect data, of modern computational tools and databases capable of model based on this data, make predictions, and then managing, analyzing, modeling, and sharing vast amounts test those predictions, then we can get a much better of high-dimensional neuroscience data.1,2 It relies heavily on insight on what’s going on. computational models: mathematical models generated by With a robust background in computer science and computers that simulate and study complex systems ranging 3 neuroinformatics, Bauer has dedicated his career to the anywhere from weather to infectious diseases. In the case of advancement of computational modeling in experimental neuroinformatics, these systems relate to the brain. biology. He is best known for his initiation and ongoing Given his enduring interest in AI, Bauer saw a unique leadership of the BioDynaMo cohort. A free accessible software, opportunity at the institute, which eventually supported the BioDynaMo platform allows computer science experts his CSE master’s thesis. It investigated how complex and non-experts alike to create, run, and visualize 3D agent- networks develop in the brain, drawing from the theory of based biological simulations from a simple laptop. If Bauer’s morphogenesis by British mathematician, Alan Turing. vision comes to fruition, the platform will eventually become a Though widely regarded as the father of theoretical computer formidable nexus of agent-based modeling where users will be science and artificial intelligence, Turing also made significant able to freely share models and test for reproducibility around contributions to biology and chemistry. In his 1952 article, the globe. The Chemical Basis of Morphogenesis, Turing discussed the Bauer has relied on BioDynaMo for a number of past projects, biological processes that give rise to an organism’s particular 4 in addition to his current research focus on the cryopreservation shape and form, e.g., stripes, spots, tails, etc. He coined the of neural tissue. Based on results thus far, he and his team term “morphogen” to refer to the specific chemical agents that 5 are optimistic about the value of their computational tools in initiate or dictate morphogenesis. Bauer’s thesis examined optimizing cryopreservation protocols, a potentially significant these morphogens to determine whether or not they could benefit for cryonics. exist in the brain – they can and there is strong evidence that www.alcor.org Cryonics / 2nd Quarter 2020 3 they do – using computers to simulate the development of computer, but still within a reasonable amount of time. He knew biologically plausible networks. that kind of advancement could not be achieved alone. It would require outside expertise in not just computational excellence, “My master’s thesis was really the first time that I directly but more precisely, computational efficiency. Who had the looked at AI from a biological point of view,” says Bauer. resources and reputation for the job? He was drawn to the interdisciplinary nature of the study and resolved to lean into it. In the fall of 2009, he began his Ph.D. In 2013, Bauer began a Research Associateship under Professor in Neuroinformatics under the guidance of Professor Rodney of Neuroinformatics, Marcus Kaiser, at Newcastle University Douglas, a pioneer in neuromorphic computation and co- (NU) in England. Concurrent with his research, he continued founder of the institute. to chip away at his ABM software idea. With encouragement from his friend and co-founder of SCImPULSE Foundation, Dr. Creating BioDynaMo Marco Manca, Bauer pitched it to the European Organization for Nuclear Research (CERN). Bauer’s Ph.D. stemmed from an interesting comparison between neurons and genes. He explains: The birthplace of the World Wide Web, CERN is an international collaboration of 23 member states that unites some of the most The human brain has 86 billion neurons, and about 1015 brilliant scientific minds to conduct world-class research in synapses, so it’s extremely large and very specifically fundamental physics.8 The organization uses the world’s largest connected...We have about 20,000 protein coding and most powerful particle accelerator, the Large Hadron genes, and in total about 60,000 genes, which is much Collider (LHC). The accelerator’s 16.5-mile ring-shaped form smaller than the number of neurons or synapses in the straddles the border of its French-Swiss headquarters.9 brain. Somehow this genetic code manages to specify our brain, and computers are a great way to explore CERN accepted Bauer’s proposal and in 2018 the first working how this works. version of the aptly named open-source biology dynamics modeler “BioDynaMo” was launched. Thanks to their efforts, That was the objective of Bauer’s Ph.D. thesis, which and those of a growing number of collaborators like the culminated in the first model of cortical neural network self- University of Cyprus and GSI Darmstadt, BioDynaMo can organization in 3D space. This “first” was significant not just now simulate tens of millions of neurons from a simple laptop for the outcome but for the means as well. Bauer used a specific around the globe. Though that may seem tremendous – and it class of computational modeling called agent-based modeling is, relatively speaking – Bauer reminds us that it is still short (ABM) or individual-based modeling (IBM) – something that of the 86 billion neurons that exist in the brain. Nevertheless, has become a foundational tool in his current work. he estimates that if the project continues at its current rate of Though quite complex, ABMs are models that simulate a certain progress, this goal will be fulfilled in approximately seven years.
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