Podcasts about theoretical biology

About our Guest:Judith Donathhttps://cyber.harvard.edu/people/jdonathKey Discussion Points:Understanding Signaling Theory:The foundation of signaling theory in communication.The balance between honest and deceptive signals.Evolutionary Biology and Communication:Darwin's insights on animal communication.Zahavi's Handicap Principle and its role in ensuring signal honesty.Maynard Smith's Index Signals and their reliability without cost.AI and the Evolution of Communication:The impact of AI on the reliability of communication signals.Challenges posed by deepfakes in video and audio.The arms race between deception technologies and verification methods.Cultural and Institutional Roles:How culture and institutions uphold the reliability of signals.The interplay between technological advancements and societal norms.Future of Communication in the Digital Age:Strategies for developing secure communication channels.Balancing privacy with the need for verification.The role of trusted sources in maintaining signal integrity.Papers and Books Mentioned:Turing, A. M. (1950). Computing machinery and intelligence. Mind, 59(236), 433-460. https://doi.org/10.1093/mind/LIX.236.433Zahavi, A. (1975). Mate selection—a selection for a handicap. Journal of Theoretical Biology, 53(1), 205-214. https://doi.org/10.1016/0022-5193(75)90111-3Veblen, T. (1899). The Theory of the Leisure Class. New York: Macmillan.https://moglen.law.columbia.edu/LCS/theoryleisureclass.pdfhttps://dn720401.ca.archive.org/0/items/theoryofleisurec01vebl/theoryofleisurec01vebl.pdfWeizenbaum, J. (1966). ELIZA—A computer program for the study of natural language communication between man and machine. Communications of the ACM, 9(1), 36-45. https://doi.org/10.1145/365153.365168Donath, J. S. (2002). Identity and deception in the virtual community. In Communities in cyberspace (pp. 37-68). Routledge.https://vivatropolis.com/papers/Donath/IdentityDeception/IdentityDeception.pdfCurrent Progress on the forthcoming book: Signals, Truth & Designhttps://vivatropolis.com/judith/signalsTruthDesign.htmlDonath, J. (2014). The social machine: designs for living online. MIT Press.https://direct.mit.edu/books/monograph/4037/The-Social-MachineDesigns-for-Living-OnlineOther:The Story about the Ferrari executive Deepfake attempthttps://www.carscoops.com/2024/07/ferrari-ceo-impersonator-uncovered-by-colleague-in-deepfake-call/We geeked out for a moment on Programming languages. Learn about them here.The C languagehttps://en.wikipedia.org/wiki/C_(programming_language)Introduction to Chttps://www.w3schools.com/c/c_intro.phpAPL Languagehttps://en.wikipedia.org/wiki/APL_(programming_language)Learn APLhttps://xpqz.github.io/learnapl/intro.htmlTry APLhttps://tryapl.orgLISP Languagehttps://en.wikipedia.org/wiki/Lisp_(programming_language)Learn LISPhttps://www.geeksforgeeks.org/introduction-to-lisp/

Uma associação a longo prazo entre dois organismos de espécies diferentes. Separe trinta minutinhos do seu dia e descubra, com a Mila Massuda, o que é simbiose e a notícia de um evento simbiótico raríssimo, a simbiose primária. Apresentação: Mila Massuda (@milamassuda) Roteiro: Mila Massuda (@milamassuda) e Emilio Garcia (@emilioblablalogia) Edição: Clayton Heringer (@tocalivros) e Juscelino Filho (@canalmusicalia) Produção: Prof. Vítor Soares (@profvitorsoares) @Matheus_Heredia e BláBláLogia (@blablalogia) Gravado e editado nos estúdios TocaCast REFERÊNCIAS: COALE, T. H. et al. Nitrogen-fixing organelle in a marine alga. Science, v. 384, n. 6692, p. 217–222, 12 abr. 2024. CORNEJO-CASTILLO, F. M. et al. Metabolic trade-offs constrain the cell size ratio in a nitrogen-fixing symbiosis. Cell, 1 mar. 2024. MARTIN, W. F.; GARG, S.; ZIMORSKI, V. Endosymbiotic theories for eukaryote origin. Philosophical Transactions of the Royal Society B: Biological Sciences, v. 370, n. 1678, p. 20140330, 2015. SAGAN, L. On the origin of mitosing cells. Journal of Theoretical Biology, v. 14, n. 3, p. 225-IN6, mar. 1967. STEPHENS, T. G. et al. Why is primary endosymbiosis so rare? The New Phytologist, v. 231, n. 5, p. 1693–1699, 1 set. 2021. Quer ir além dos trinta minutinhos e se aprofundar no mundo da Ecologia? CURSO DE ECOLOGIA POR APENAS R$42,00 https://cursosdebiologia.hotmart.host/

Découvrez le livre NEUROSAPIENS, sorti le 26 janvier aux éditions Les Arènes !  Pour apprendre à créer rapidement et à moindre coût son podcast, c'est par ici !  Pourquoi pleurons-nous ? Déjà, cette question pourrait faire tout l'épisode parce que les larmes sont un véritable mystère ! L'homme est la seule espèce caractérisée par des larmes émotionnelles ! D'autres animaux sont susceptibles de gémir ou de crier, mais aucun ne verse des larmes d'émotion – pas même nos plus proches cousins primates. Les primates, et d'autres animaux, libèrent des larmes, certes, mais leur fonction se limite à humidifier les yeux, à les nettoyer, voire à les soigner. Nous allons aussi répondre aux questions suivantes : combien de types de larmes existe-t-il ? Ont-elles réellement un effet cathartique ? Comment fonctionnent mécaniquement les larmes ? Que se passe-t-il pour les personnes qui ne pleurent jamais ? Production, animation, réalisation et illustration : Anaïs Roux Instagram : https://www.instagram.com/neurosapiens.podcast/ neurosapiens.podcast@gmail.com Produit et distribué en association avec LACME Production. _________ Musique  KEEP ON GOING Musique proposée par La Musique Libre Joakim Karud - Keep On Going : https://youtu.be/lOfg0jRqaA8 Joakim Karud : https://soundcloud.com/joakimkarud ONE NIGHT AWAY Musique de Patrick Patrikios _________ Sources :  Bylsma LM, Gračanin A, Vingerhoets AJJM. The neurobiology of human crying. Clin Auton Res. 2019 Feb;29(1):63-73. doi: 10.1007/s10286-018-0526-y. Epub 2018 Apr 23. PMID: 29687400; PMCID: PMC6201288. Rottenberg, J., Bylsma, L. M., & Vingerhoets, A. J. J. M. (2008). Is Crying Beneficial? Current Directions in Psychological Science, 17(6), 400–404. https://doi.org/10.1111/j.1467-8721.2008.00614.x T. LUTZ, Crying : a natural and cultural history of tears, W. W. Norton, 2001. Biological Signals as Handicaps. A. Grafen in Journal of Theoretical Biology, Vol. 144, No. 4, pages 517–546; June 21, 1990. Hendriks, Michelle & Nelson, Judith & Cornelius, Randolph & Vingerhoets, Ad. (2008). Why Crying Improves Our Well-being: An Attachment-Theory Perspective on the Functions of Adult Crying. 10.1007/978-0-387-29986-0_6.  The Science of Emotion: Research and Tradition in the Psychology of Emotion. Randolph R. Cornelius. Prentice-Hall, 1995. The Handicap Principle: A Missing Piece of Darwin's Puzzle. Amotz Zahavi et al. Oxford University Press, 1997. The Symbolic Species: The Co-Evolution of Language and the Brain. Terrence W. Deacon. W. W. Norton, 1998. Crying: A Natural and Cultural History of Tears. Tom Lutz. W. W. Norton, 2001. A Darwinian Look at a Wailing Baby. Carl Zimmer in New York Times; March 8, 2005. Maternal Effects in Mammals. Edited by Dario Maestripieri and Jill M. Mateo. University of Chicago Press (in press).

Fyodor Kondrashov, scientist and educator. Ph.D. from the University of California at San Diego. Professor at the Institute of Science and Technology (IST), Austria. Scientific director of the School of Molecular and Theoretical Biology. How did living organisms become the way we know them today? The Kondrashov lab is focused on understanding the natural world in an evolutionary context, typically focusing on studying genetic information due to the abundance of DNA and protein sequence data. Kondrashov and his group do not restrict themselves to studying specific functions or phenotypes, instead, a staple feature of their research is a focus on how functions and phenotypes change over time. Therefore, their research is inherently interdisciplinary, grounded in classical evolutionary fields of population genetics and molecular evolution while drawing from other fields, such as cell and molecular biology, bioinformatics, and biophysics. Recently, the group has become increasingly interested in the experimental assay of fitness landscapes. Combining experiments, theory, and computational biology, they query how changes in the genotype affect fitness or specific phenotypes. In the near future, they hope to expand their experimental capabilities in order to query a wider range of interesting phenotypes in a high-throughput manner. FIND FYODOR ON SOCIAL MEDIA Facebook | Instagram | Twitter ================================ SUPPORT & CONNECT: Support on Patreon: https://www.patreon.com/denofrich Twitter: https://twitter.com/denofrich Facebook: https://www.facebook.com/denofrich YouTube: https://www.youtube.com/denofrich Instagram: https://www.instagram.com/den_of_rich/ Hashtag: #denofrich © Copyright 2022 Den of Rich. All rights reserved.

Fyodor Kondrashov, scientist and educator. Ph.D. from the University of California at San Diego. Professor at the Institute of Science and Technology (IST), Austria. Scientific director of the School of Molecular and Theoretical Biology.How did living organisms become the way we know them today? The Kondrashov lab is focused on understanding the natural world in an evolutionary context, typically focusing on studying genetic information due to the abundance of DNA and protein sequence data.Kondrashov and his group do not restrict themselves to studying specific functions or phenotypes, instead, a staple feature of their research is a focus on how functions and phenotypes change over time. Therefore, their research is inherently interdisciplinary, grounded in classical evolutionary fields of population genetics and molecular evolution while drawing from other fields, such as cell and molecular biology, bioinformatics, and biophysics. Recently, the group has become increasingly interested in the experimental assay of fitness landscapes. Combining experiments, theory, and computational biology, they query how changes in the genotype affect fitness or specific phenotypes. In the near future, they hope to expand their experimental capabilities in order to query a wider range of interesting phenotypes in a high-throughput manner.FIND FYODOR ON SOCIAL MEDIAFacebook | Instagram | Twitter================================PODCAST INFO:Podcast website: https://www.uhnwidata.com/podcastApple podcast: https://apple.co/3kqOA7QSpotify: https://spoti.fi/2UOtE1AGoogle podcast: https://bit.ly/3jmA7ulSUPPORT & CONNECT:Support on Patreon: https://www.patreon.com/denofrichTwitter: https://www.instagram.com/denofrich/Instagram: https://www.instagram.com/denofrich/Facebook: https://www.facebook.com/denofrich

This week we conclude our two-part discussion with ecologist Mark Ritchie of Syracuse University on how he and his SFI collaborators are starting to rethink the intersections of thermodynamics and biology to better fit our scientific models to the patterns we observe in nature. Most of what we know about the enzymatic processes of plant and animal metabolisms comes from test tube experiments, not studies in the context of a living organism. What changes when we zoom out and think about life's manufacturing and distribution in situ?Starting where we left off in in Episode 62, we tour the implications of Mark's biochemistry research and ask: What can studying the metabolism of cells tell us about economics? How does a better model of photosynthesis change the way we think about climate change and the future of agriculture? Why might a pattern in the failure of plant enzymes help biologists define where to direct the search for life in space?A better theory of the physics of biomolecules — and the networks in which they're embedded — provides a clearer understanding of the limits for all living systems, and how those limits shape effective strategies for navigating our complex world.Welcome to COMPLEXITY, the official podcast of the Santa Fe Institute. I'm your host, Michael Garfield, and every other week we'll bring you with us for far-ranging conversations with our worldwide network of rigorous researchers developing new frameworks to explain the deepest mysteries of the universe.If you value our research and communication efforts, please subscribe, rate, and review this show at Apple Podcasts, and/or consider making a donation at santafe.edu/give. You can find numerous other ways to engage with us at santafe.edu/engage. Thank you for listening!Join our Facebook discussion group to meet like minds and talk about each episode.Follow us on social media:Twitter • YouTube • Facebook • Instagram • LinkedInRelated Reading & Listening:Ritchie Lab at Syracuse University | Mark's Google Scholar Page | Mark's soil ecology startupReaction and diffusion thermodynamics explain optimal temperatures of biochemical reactionsby Mark Ritchie in Scientific ReportsThermodynamics Of Far From Equilibrium Systems, Biochemistry, And Life In A Warming World [Mark Ritchie's 2021 SFI Seminar + @SFIscience Twitter thread on Mark's talk]Scale and information-processing thresholds in Holocene social evolutionby Jaeweon Shin, Michael Holton Price, David H. Wolpert, Hajime Shimao, Brendan Tracey & Timothy A. KohlerGeneralized Stoichiometry and Biogeochemistry for Astrobiological Applicationsby Christopher P. Kempes, Michael J. Follows, Hillary Smith, Heather Graham, Christopher H. House & Simon A. Levin Complexity 4: Luis Bettencourt on The Science of CitiesComplexity 5: Jennifer Dunne on Food Webs & ArchaeoEcologyComplexity 17: Chris Kempes on The Physical Constraints on Life & EvolutionComplexity 35: Scaling Laws & Social Networks in The Time of COVID-19 with Geoffrey WestComplexity 41: Natalie Grefenstette on Agnostic Biosignature DetectionAlien Crash Site 15: Cole Mathis on Pathway Assembly and AstrobiologyPodcast theme music by Mitch Mignano.Cover artwork adapted from photos by Peter Nguyen and Torsten Wittmann (UCSF).

Location: Champ's Clock Shop, Douglasville, GA Dr Rob describes a contentious idea: the Waiting Time Problem. Mathematical simulations tells us that the rise of specific new mutations would take a fantastically long time. This is a serious challenge to evolution. Yet, most people misunderstand the problem. We are not talking about the time it takes for a new mutation to appear but the time it takes a new mutation to appear multiple times (because most new mutations are lost to genetic drift) plus the time it takes the lucky surviving mutation to spread through the entire population and completely replace the original variant. The numbers are shocking. Even the simplest 1-letter change would take longer than evolution allows, but 2-letter and longer combinations are orders of magnitude worse. Notes and links: Sanford et al. 2015. The waiting time problem in a model hominin population. Theoretical Biology and Medical Modelling 12:18. Carter R 2019. A successful decade for Mendel's Accountant. Journal of Creation 33(2):51–56. The Antikythera Mechanism Harrison' clocks and the Longitude problem Rupe and Sanford. 2013. Using numerical simulation to better understand fixation rates, and establishment of a new principle: Haldane's Ratchet. Proceedings of the 7th International Conference on Creationism, Article 32. Batten D. 2005. Haldane's Dilemma has not been solved. Journal of Creation 19(1):20–21. ReMine W. 2010. Cost theory and the cost of substitution—a clarification. Journal of Creation 19(1):113–125.

Location: Champ's Clock Shop, Douglasville, GA Dr Rob describes a contentious idea: the Waiting Time Problem. Mathematical simulations tells us that the rise of specific new mutations would take a fantastically long time. This is a serious challenge to evolution. Yet, most people misunderstand the problem. We are not talking about the time it takes for a new mutation to appear but the time it takes a new mutation to appear multiple times (because most new mutations are lost to genetic drift) plus the time it takes the lucky surviving mutation to spread through the entire population and completely replace the original variant. The numbers are shocking. Even the simplest 1-letter change would take longer than evolution allows, but 2-letter and longer combinations are orders of magnitude worse. Notes and links: Sanford et al. 2015. The waiting time problem in a model hominin population. Theoretical Biology and Medical Modelling 12:18. Carter R 2019. A successful decade for Mendel's Accountant. Journal of Creation 33(2):51–56. The Antikythera Mechanism Harrison' clocks and the Longitude problem Rupe and Sanford. 2013. Using numerical simulation to better understand fixation rates, and establishment of a new principle: Haldane's Ratchet. Proceedings of the 7th International Conference on Creationism, Article 32. Batten D. 2005. Haldane's Dilemma has not been solved. Journal of Creation 19(1):20–21. ReMine W. 2010. Cost theory and the cost of substitution—a clarification. Journal of Creation 19(1):113–125.

En este capítulo, hablamos con: -Marta del Olmo, PhD en Theoretical Chronobiology en el Institute of Theoretical Biology of Charite, Humbolft-Universität zu Berlin. ¿Qué son los ritmos circadianos? ¿Podemos modelizar nuestro reloj interno? ¿Hay restaurantes en Berlin para comer decentemente algo que no sean die Hamburguer? Para contactarnos: Email: phdtalks.es@gmail.com Instagram: @phdtalks_ Mucho love, amigos.

« Homo Fabulus, pourquoi tu utilises parfois du langage finaliste dans tes vidéos ? ». Aujourd'hui je vous dis pourquoi ! Mes experts, Pierrick Bourrat : https://pierrickbourrat.com/ Et Jean-Baptiste André : http://jb.homepage.free.fr/ 00:00 Introduction 00:58 Le finalisme classique 07:14 Le finalisme de la sélection naturelle 10:20 Le finalisme des individus 14:11 Le finalisme des adaptations Ce n'est que grâce à votre soutien que je peux affecter mes gènes à la production de vidéos ! Si vous aimez leur travail et souhaitez qu'il continue, faites augmenter ma fitness sur uTip ou Tipeee : https://utip.io/homofabulus https://tipeee.com/homofabulus/ Facebook : https://www.facebook.com/H0moFabulus/ Twitter : https://twitter.com/homofabulus pour les infos strictement liées à la chaîne et https://twitter.com/stdebove pour mon compte perso alimenté plus régulièrement Insta : https://www.instagram.com/stephanedebove/ Références : 1. Plato. Timaeus and Critias (ed Johansen, T. K.)trans. by Lee, D. (). 2. Paley, W. Natural Theology: Or, Evidences of the Existence and Attributes of the Deity, Collected from the Appearances of Nature Sixth. isbn: 978-1-108-00355-1 (Cambridge University Press, Cambridge, 1802). 3. Ariew, A. in The Cambridge Companion to the Philosophy of Biology (eds Hull, D. L. & Ruse, M.) (Cambridge University Press, 2007). 4. Williams, G. C. Adaptation and Natural Selection Reprint edition. English. isbn: 978-0- 691-02615-2 (Princeton University Press, Princeton, NJ, 1966). 5. Okasha, S. Agents and Goals in Evolution isbn: 978-0-19-881508-2 (Oxford University Press, Oxford, New York, July 2018). 6. Darwin. L'origine Des Espèces (1859). 7. Dennett, D. C. The Intentional Stance (1989). 8. Rice, S. H. Evolutionary Theory: Mathematical and Conceptual Foundations (2004). 9. Mayr, E. Toward a New Philosophy of Biology: Observations of an Evolutionist (1988). 10. Monod, J. Le Hasard et La Necessite - Essai Sur La Philosophie Naturelle de La Biologie Moderne (1970). 11. Pittendrigh, C. in Behavior and Evolution (1958). 12. Grafen, A. Optimization of Inclusive Fitness. en. Journal of Theoretical Biology 238, 541–563. issn: 0022-5193 (Feb. 2006). 13. Lehmann, L. & Rousset, F. When Do Individuals Maximize Their Inclusive Fitness? The American Naturalist 195, 717–732. issn: 0003-0147 (2020). 14. Maynard-Smith, J. Evolution and the Theory of Games (1982). 15. Millikan, R. G. In Defense of Proper Functions. Philosophy of Science 56, 288–302. issn: 0031-8248 (1989). 16. Lecointre, G. Le Hasard Dans l'évolution de La Vie Apr. 2020. 17. Grafen, A. The Formal Darwinism Project in Outline. en. Biology and Philosophy, 1–20 (2014/??/??).

Merhabalar. Bugün sizlere, başımdan geçen bir olaydan esinlenerek, zoraki atıf (coercive citation) ile ilgili öğrendiklerimi yazmak istedim. Olay şu şekilde; bir yazımızı, bu yılın başında, bir dergiye gönderdik. Hakemlerden revizyon isteği geldi. Ancak hakemlerden biri, yazıya kendi belirlediği referansları da (3 adet) eklememizi istiyordu. Referansların üçü de aynı ülkedendi, ve yazarlarına baktığımızda ise üç makalede de var olan ortak isimler mevcuttu. Diğer düzeltmeleri yaptıktan sonra, söz konusu makalelerin yazıya bir katkı sağlamayacağını düşünerek, hakemin bu isteğini uygun görmedik ve kibarca teşekkür ederek yazıyı revize edilmiş haliyle tekrar yükledik. İkinci revizyon isteğinde, hakem kendi belirlediği referanslara atıf isteğini yeniledi. Diğer revizyonları halledip, atıf isteğine teşekkür ederek yazıyı tekrar yükledik. Üçüncü revizyon mailinde, artık diğer hakemlerin aradan çıktığını ve bizden atıf isteyen hakemin revizyon (ve atıf) isteklerinin kaldığını gördük. Bu konuda duruşumuz netti ancak bu mail süreci de can sıkıcı bir hal almaya başlamıştı. Görünen o ki, bu atıfları yapmazsak bu hakemden geçemeyecektik. Bu sefer durumu editöre bildirmeye karar verdik. Yine de, daha deneyimli insanlar için minik görünen ve bir maille halledilebilecek bu problemin, benim gibi yeni yetme bir araştırmacı için artık ete kemiğe bürünmüş bir probleme dönüşmesi, çok heves kırıcı ve dikkat dağıtıcı bir hal almıştı. Bir noktada, yazarımız İbrahim Sarbay’dan esinlenerek, biraz da farkındalık oluşturmak amacıyla, Twitter’da 24 saat süren bir anket başlattım. Anket sonucunda kazanan taraf beliydi ancak oy kullanan 147 kişiden 60 kişi de “bırak lanet olsun, referansları koy da başın ağrımasın, sırada bekleyen diğer işlerine bak” diyordu. Yani durum biraz da kanıksanmıştı. 60 kişi (%41) pek de azımsanmayacak bir rakamdı. Anket devam ederken, Haldun abi de bana mesaj üzerinden bunun neden ve nasıl uygunsuz olduğu ile ilgili referanslar göndermekteydi. Bunun üzerine, hazır elimde bununla ilgili seçkin referanslar varken, durumu derlemeye karar verdim. Twitter Anketi Öncelikle, Kuo-Chen Chou ile tanışalım.. Kendisi, 1938 doğumlu, Amerikan biyofizik ve biyobilişimci. Halen Boston’da, kar amacı gütmeyen bir araştırma örgütünde görevli. Chou’nun bu yazıda olmasının sebebi ise şu, Chou’nun h indeksi 135 ve 2014-2018 arası çeşitli kuruluşlar tarafından en yüksek atıf alan araştırmacılar arasında gösterilmiş. Chou’nun birçok dergide editör ve hakemliği bulunuyor. Bunlardan bazıları The Open Bioinformatics Journal, (Baş editör, 2008–2019),  Journal of Theoretical Biology (yayın kurulu 2005–2019), Journal of Biomedicine and Biotechnology (2008–2014) ve The Open Biochemistry Journal (2007–2019). Kuo-Chen Chau https://en.wikipedia.org/wiki/Kuo-Chen_Chou 2019’da, Bioinformatics dergisi, zoraki atıf ile bağlantısı olan bir hakemleri ile ilgili bir editöryel yayınlıyor. 2020’de ise, Journal of Theoretical Biology dergisi de, kendi editör kurulunda da olan, aynı hakemin, kendilerinde de zoraki atıf ile bağlantısı olduğuna dair bir editöryel yayınlıyor. Daha sonraları, Nature dergisi, ismi verilmeyen bu kişinin Chou olduğunu ortaya çıkartıyor. Günün sonunda, Chou Journal of Theoretical Biology editöryel kurulundan ve Bioinformatics hakemliğinden çıkartılıyor.​1​ Akademik yayıncılıkta zoraki atıf Burada, iki çeşit zoraki atıftan bahsedebiliriz. Birincisi, hakemin kendi önceki makalelerine istediği atıf, diğeri ise editörün kendi dergisine istediği atıf. Günümüz şartlarında, ortak dilde, bilimin “niteliğini niceliklemeye” yarayan belli bazı parametreler var. Bunun sonucu olarak, kabaca, hakemin kendi makalesine istediği atıf hakem kişisinin h indeksini, dergiye istenen atıf ise derginin impakt faktörünü yükseltecek diyebiliriz. Dergiler için talep edilen zoraki atıflarda genelde eklenmesi istenen referansın makaleye katkısı gözetilmez. Yazarı belirli bir makaleye yönlendirmek yerine,

Merhabalar. Bugün sizlere, başımdan geçen bir olaydan esinlenerek, zoraki atıf (coercive citation) ile ilgili öğrendiklerimi yazmak istedim. Olay şu şekilde; bir yazımızı, bu yılın başında, bir dergiye gönderdik. Hakemlerden revizyon isteği geldi. Ancak hakemlerden biri, yazıya kendi belirlediği referansları da (3 adet) eklememizi istiyordu. Referansların üçü de aynı ülkedendi, ve yazarlarına baktığımızda ise üç makalede de var olan ortak isimler mevcuttu. Diğer düzeltmeleri yaptıktan sonra, söz konusu makalelerin yazıya bir katkı sağlamayacağını düşünerek, hakemin bu isteğini uygun görmedik ve kibarca teşekkür ederek yazıyı revize edilmiş haliyle tekrar yükledik. İkinci revizyon isteğinde, hakem kendi belirlediği referanslara atıf isteğini yeniledi. Diğer revizyonları halledip, atıf isteğine teşekkür ederek yazıyı tekrar yükledik. Üçüncü revizyon mailinde, artık diğer hakemlerin aradan çıktığını ve bizden atıf isteyen hakemin revizyon (ve atıf) isteklerinin kaldığını gördük. Bu konuda duruşumuz netti ancak bu mail süreci de can sıkıcı bir hal almaya başlamıştı. Görünen o ki, bu atıfları yapmazsak bu hakemden geçemeyecektik. Bu sefer durumu editöre bildirmeye karar verdik. Yine de, daha deneyimli insanlar için minik görünen ve bir maille halledilebilecek bu problemin, benim gibi yeni yetme bir araştırmacı için artık ete kemiğe bürünmüş bir probleme dönüşmesi, çok heves kırıcı ve dikkat dağıtıcı bir hal almıştı. Bir noktada, yazarımız İbrahim Sarbay’dan esinlenerek, biraz da farkındalık oluşturmak amacıyla, Twitter’da 24 saat süren bir anket başlattım. Anket sonucunda kazanan taraf beliydi ancak oy kullanan 147 kişiden 60 kişi de “bırak lanet olsun, referansları koy da başın ağrımasın, sırada bekleyen diğer işlerine bak” diyordu. Yani durum biraz da kanıksanmıştı. 60 kişi (%41) pek de azımsanmayacak bir rakamdı. Anket devam ederken, Haldun abi de bana mesaj üzerinden bunun neden ve nasıl uygunsuz olduğu ile ilgili referanslar göndermekteydi. Bunun üzerine, hazır elimde bununla ilgili seçkin referanslar varken, durumu derlemeye karar verdim. Twitter Anketi Öncelikle, Kuo-Chen Chou ile tanışalım.. Kendisi, 1938 doğumlu, Amerikan biyofizik ve biyobilişimci. Halen Boston’da, kar amacı gütmeyen bir araştırma örgütünde görevli. Chou’nun bu yazıda olmasının sebebi ise şu, Chou’nun h indeksi 135 ve 2014-2018 arası çeşitli kuruluşlar tarafından en yüksek atıf alan araştırmacılar arasında gösterilmiş. Chou’nun birçok dergide editör ve hakemliği bulunuyor. Bunlardan bazıları The Open Bioinformatics Journal, (Baş editör, 2008–2019),  Journal of Theoretical Biology (yayın kurulu 2005–2019), Journal of Biomedicine and Biotechnology (2008–2014) ve The Open Biochemistry Journal (2007–2019). Kuo-Chen Chau https://en.wikipedia.org/wiki/Kuo-Chen_Chou 2019’da, Bioinformatics dergisi, zoraki atıf ile bağlantısı olan bir hakemleri ile ilgili bir editöryel yayınlıyor. 2020’de ise, Journal of Theoretical Biology dergisi de, kendi editör kurulunda da olan, aynı hakemin, kendilerinde de zoraki atıf ile bağlantısı olduğuna dair bir editöryel yayınlıyor. Daha sonraları, Nature dergisi, ismi verilmeyen bu kişinin Chou olduğunu ortaya çıkartıyor. Günün sonunda, Chou Journal of Theoretical Biology editöryel kurulundan ve Bioinformatics hakemliğinden çıkartılıyor.​1​ Akademik yayıncılıkta zoraki atıf Burada, iki çeşit zoraki atıftan bahsedebiliriz. Birincisi, hakemin kendi önceki makalelerine istediği atıf, diğeri ise editörün kendi dergisine istediği atıf. Günümüz şartlarında, ortak dilde, bilimin “niteliğini niceliklemeye” yarayan belli bazı parametreler var. Bunun sonucu olarak, kabaca, hakemin kendi makalesine istediği atıf hakem kişisinin h indeksini, dergiye istenen atıf ise derginin impakt faktörünü yükseltecek diyebiliriz. Dergiler için talep edilen zoraki atıflarda genelde eklenmesi istenen referansın makaleye katkısı gözetilmez. Yazarı belirli bir makaleye yönlendirmek yerine,

Pandemic viruses are deadly, but over time they should weaken as they pick up mutations. Will this happen with the pandemic coronavirus? We can only hope. But has it ever happen before? Yes, between 1917 and 2009, the human H1N1 virus picked up thousands of mutations and eventually went extinct (twice). Yet if this virus does not get us, something else will! How does this affect our view of eternity? Links Genetic entropy information Genetic Entropy and the Mystery of the Genome (available on Creation.com) Carter RW, Sanford, JC (2012) A new look at an old virus: mutation accumulation in the human H1N1 influenza virus since 1918. Theoretical Biology and Medical Modelling 9:42 | doi:10.1186/1742-4682-9-42. Carter RW, More evidence for the reality of genetic entropy, Journal of Creation 28(1):16–17, 2014. Carter RW, More evidence for the reality of genetic entropy—update, Journal of Creation 33(1):3–4, 2019. Mendel's Accountant evolution simulation software The 1917 "Spanish flu" may have started in China The Gospel of John on Bible Gateway.com, English Standard Version Intro Music by Xihcsr Intro Graphics by MattWalkerVideo Additional imagery from Pixabay.com (and, no, I don't know what the words in German mean)  

Tema ove epizode je Gaia hipoteza i pitanje njene komplementarnosti sa teorijom evolucije.Pričali smo o tome šta su osnovni principi Gaia hipoteze, kako su James Lovelock i Lynn Margulis došli do tih ideja, a onda smo se fokusirali na kritike Gaia hipoteze, pre svega na rad "Darwinizing Gaia" Freda Doolittlea. Gosti:dr Milan M. Ćirković, Astronomska opservatorija Beograddr Srđa Janković, Univerzitetska dečija klinika & Radio Beograd (emisija Solaris) Preporučena literatura za dalje istraživanje: James Lovelock, Gaia: A New Look at Life on Earth (2000) [1979]Lynn Margulis, Symbiotic Planet: A New Look at Evolution (1998)Lynn Margulis & Dorian Sagan, Slanted Truths: Essays on Gaia, Symbiosis, and Evolution (1997)Doolittle, F. 2017. Darwinizing Gaia, Journal of Theoretical Biology 434, 11-19

Gudrun talks with Changjing Zhuge. He is a guest in the group of Lennart Hilbert and works at the College of applied sciences and the Beijing Institute for Scientific and Engineering Computing (BISEC) at the Beijing University of Technology. He is a mathematician who is interested in system biology. In some cases he studies delay differential equations or systems of ordinary differential equations to characterize processes and interactions in the context of cancer research. The inbuilt delays originate e.g. from the modeling of hematopoietic stem cell populations. Hematopoietic stem cells give rise to other blood cells. Chemotherapy is frequently accompanied by unwished for side effects to the blood cell production due to the character of the drugs used. Often the production of white blood cells is hindered, which is called neutropenia. In an effort to circumvent that, together with chemotherapy, one treats the patient with granulocyte colony stimulating factor (G-CSF). To examine the effects of the typical periodic chemotherapy in generating neutropenia, and the corresponding response of this system to given to G-CSF Changjing and his colleagues studied relatively simple but physiologically realistic mathematical models for the hematopoietic stem cells. And these models are potential for modeling of other stem-like biosystems such as cancers. The delay in the system is related to the platelet maturation time and the differentiation rate from hematopoietic stem cells into the platelet cell. Changjing did his Bachelor in Mathematics at the Beijing University of Technology (2008) and continued with a PhD-program in Mathematics at the Zhou-Peiyuan Center for Applied Mathematics, Tsinghua University, China. He finished his PhD in 2014. During his time as PhD student he also worked for one year in Michael C Mackey's Lab at the Centre for Applied Mathematics in Bioscience and Medicine of the McGill University in Montreal (Canada). References C. Zhuge, M.C. Mackey, J. Lei: Origins of oscillation patterns in cyclical thrombocytopeniaJournal of Theoretical Biology 462,432-445, 2019. C. Zhuge, X. Sun, J. Lei: On positive solutions and the Omega limit set for a class of delay differential equations. Discrete and Continuous Dynamical Systems - Series B, 18(9), 2487~2503, 2013. C. Zhuge, M.C. Mackey, J. Lei: Neutrophil dynamics in response to chemotherapy and G-CSF Journal of Theoretical Biology 293, 111-120 2012.Podcasts L. Hilbert, G. Thäter: Zellkerne, Gespräch im Modellansatz Podcast, Folge 206, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2019. M. Gonciarz, G. Thäter: Portrait of Science, Gespräch im Modellansatz Podcast, Folge 197, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2019. G. Thäter, K. Page: Embryonic Patterns, Gespräch im Modellansatz Podcast, Folge 161, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2018. L. Adlung, G. Thäter, S. Ritterbusch: Systembiologie, Gespräch im Modellansatz Podcast, Folge 39, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2016. Omega Tau-Podcast 072: Forschung in der Zellbiologie, 2011. J. Schmoranze, I. Wessolowski: Beim Herrn der Mikroskope – AMBIO Core Facility, Sciencekompass Podcast, Episode 009 B, 2017.

Gudrun talks with Changjing Zhuge. He is a guest in the group of Lennart Hilbert and works at the College of applied sciences and the Beijing Institute for Scientific and Engineering Computing (BISEC) at the Beijing University of Technology. He is a mathematician who is interested in system biology. In some cases he studies delay differential equations or systems of ordinary differential equations to characterize processes and interactions in the context of cancer research. The inbuilt delays originate e.g. from the modeling of hematopoietic stem cell populations. Hematopoietic stem cells give rise to other blood cells. Chemotherapy is frequently accompanied by unwished for side effects to the blood cell production due to the character of the drugs used. Often the production of white blood cells is hindered, which is called neutropenia. In an effort to circumvent that, together with chemotherapy, one treats the patient with granulocyte colony stimulating factor (G-CSF). To examine the effects of the typical periodic chemotherapy in generating neutropenia, and the corresponding response of this system to given to G-CSF Changjing and his colleagues studied relatively simple but physiologically realistic mathematical models for the hematopoietic stem cells. And these models are potential for modeling of other stem-like biosystems such as cancers. The delay in the system is related to the platelet maturation time and the differentiation rate from hematopoietic stem cells into the platelet cell. Changjing did his Bachelor in Mathematics at the Beijing University of Technology (2008) and continued with a PhD-program in Mathematics at the Zhou-Peiyuan Center for Applied Mathematics, Tsinghua University, China. He finished his PhD in 2014. During his time as PhD student he also worked for one year in Michael C Mackey's Lab at the Centre for Applied Mathematics in Bioscience and Medicine of the McGill University in Montreal (Canada). References C. Zhuge, M.C. Mackey, J. Lei: Origins of oscillation patterns in cyclical thrombocytopeniaJournal of Theoretical Biology 462,432-445, 2019. C. Zhuge, X. Sun, J. Lei: On positive solutions and the Omega limit set for a class of delay differential equations. Discrete and Continuous Dynamical Systems - Series B, 18(9), 2487~2503, 2013. C. Zhuge, M.C. Mackey, J. Lei: Neutrophil dynamics in response to chemotherapy and G-CSF Journal of Theoretical Biology 293, 111-120 2012.Podcasts L. Hilbert, G. Thäter: Zellkerne, Gespräch im Modellansatz Podcast, Folge 206, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2019. M. Gonciarz, G. Thäter: Portrait of Science, Gespräch im Modellansatz Podcast, Folge 197, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2019. G. Thäter, K. Page: Embryonic Patterns, Gespräch im Modellansatz Podcast, Folge 161, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2018. L. Adlung, G. Thäter, S. Ritterbusch: Systembiologie, Gespräch im Modellansatz Podcast, Folge 39, Fakultät für Mathematik, Karlsruher Institut für Technologie (KIT), 2016. Omega Tau-Podcast 072: Forschung in der Zellbiologie, 2011. J. Schmoranze, I. Wessolowski: Beim Herrn der Mikroskope – AMBIO Core Facility, Sciencekompass Podcast, Episode 009 B, 2017.

Scientists are trying to figure out if they can predict big earthquakes by simulating small quakes in labs and studying big quakes under the ocean. Thanks to the University of Rhode Island for sponsoring this video. Thanks also to our Patreon patrons https://www.patreon.com/MinuteEarth and our YouTube members. ___________________________________________ To learn more, start your googling with these keywords: Earthquake: A violent shaking of the earth, usually due to movements of tectonic plates under the earth’s crust. Seismometer: An instrument that detects changes in the up-down motion of the earth. Seismic body waves: Higher frequency waves released by earthquakes that can move through solid rock. Seismic surface waves: Lower frequency waves released by earthquakes that move along the ground and cause most damage. Earthquake Early Warning System: A network of strategically placed seismometers that trigger emergency warning systems in particular areas when they detect large seismic body waves. Evacuation Clearance Time: The time needed to evacuate a particular population to safety. Earthquake Precursor: An anomalous event that gives an effective warning of an impending earthquake. Transform Faults: Faults where two tectonic plates slide past each other. ___________________________________________ Subscribe to MinuteEarth on YouTube: http://goo.gl/EpIDGd Support us on Patreon: https://goo.gl/ZVgLQZ And visit our website: https://www.minuteearth.com/ Say hello on Facebook: http://goo.gl/FpAvo6 And Twitter: http://goo.gl/Y1aWVC And download our videos on itunes: https://goo.gl/sfwS6n ___________________________________________ Credits (and Twitter handles): Script Writer: David Goldenberg (@dgoldenberg) Script Editor, Video Director & Narrator: Alex Reich (@alexhreich) Video Illustrator: Jesse Agar (@JesseAgarYT) With Contributions From: Henry Reich, Kate Yoshida, Ever Salazar, Emily Elert, Peter Reich Music by: Nathaniel Schroeder: http://www.soundcloud.com/drschroeder ___________________________________________ This material is based upon work supported by the National Science Foundation under Grant 1654416. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. ___________________________________________ References: Geller, R. (1997). Earthquake Prediction: A Critical Review. Geophysical Journal International. 131 (425-450). Retrieved from: https://academic.oup.com/gji/article/131/3/425/2138719 Wei, M. (2018). Seismic Behavior on Oceanic Transform Faults at the East Pacific Rise. Transform Plate Boundaries and Fracture Zones. Elsevier. Retrieved from: https://www.elsevier.com/books/transform-plate-boundaries-and-fracture-zones/duarte/978-0-12-812064-4 Hsu, Y., and Peeta, S. (2015). Clearance Time Estimation for Incorporating Evacuation Risk in Routing Strategies for Evacuation Operation. Networks and Spatial Economics. 15 (743-764). Retrieved from: https://link.springer.com/article/10.1007/s11067-013-9195-5 Kucken, M. and Newell, A. (2005). Fingerprint Formation. Journal of Theoretical Biology. 235 (71-83). Retrieved from: https://www.ncbi.nlm.nih.gov/pubmed/15833314. Wei, M. (2019). Personal Communication. Graduate School of Oceanography. University of Rhode Island.

Try Dashlane Premium free for 30 days: https://www.dashlane.com/MinuteEarth. Use the coupon code ‘MinuteEarth’ to get 10% off Dashlane Premium. Because of the chaotic way fingerprints develop and the multiplying effect of compound probability, it's basically impossible for any two fingers to have matching prints. Thanks also to our Patreon patrons https://www.patreon.com/MinuteEarth and our YouTube members. ___________________________________________ To learn more, start your googling with these keywords: Fingerprint: The markings on the skin on the last joint of the thumb or finger. Fingerprint Ridges: The raised lines on the fingerprint. Fingerprint Pattern: The main design in the middle of the fingerprint; usually a loop, whorl, or arch. Volar Pad: The mass of stem cells that grows under the fingers during a particular time during fetal development that is responsible for determining the pattern of the fingerprint. Fingerprint Minutiae: The various tiny points in each fingertip where the ridgelines get blocked or split. Compound Probability: The likelihood that independent events will occur simultaneously. ___________________________________________ Subscribe to MinuteEarth on YouTube: http://goo.gl/EpIDGd Support us on Patreon: https://goo.gl/ZVgLQZ And visit our website: https://www.minuteearth.com/ Say hello on Facebook: http://goo.gl/FpAvo6 And Twitter: http://goo.gl/Y1aWVC And download our videos on itunes: https://goo.gl/sfwS6n ___________________________________________ Credits (and Twitter handles): Script Writer, Video Director, and Narrator: David Goldenberg (@dgoldenberg) Video Illustrator: Arcadi Garcia & Ever Salazar With Contributions From: Henry Reich, Alex Reich, Kate Yoshida, Peter Reich Music by: Nathaniel Schroeder: http://www.soundcloud.com/drschroeder ___________________________________________ References: Kucken, M. and Newell, A. (2005). Fingerprint Formation. Journal of Theoretical Biology. 235 (71-83). Retrieved from: https://www.ncbi.nlm.nih.gov/pubmed/15833314. Kucken, M. (2007). Models for Fingerprint Pattern Formation. Forensic Science International. 171 (85-96). Retrieved from: https://www.ncbi.nlm.nih.gov/pubmed/17459625. Kucken, Michael (2018). Personal Communication. Center of Information Services and High Performance Computing. TU Dresden. Wertheim, K. (2011). Fingerprint Sourcebook: Embryology and Morphology of the Friction Skin Ridge. Retrieved from: https://www.ncjrs.gov/App/Publications/abstract.aspx?ID=247303