Irreversible Processes in Ecological Evolution/RobertMarsland

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Notes by user Robert Marsland (Boston Univ.) for Irreversible Processes in Ecological Evolution

Post-meeting Reflection

1+ paragraphs on any combination of the following:

Presentation highlights

Open questions that came up

How your perspective changed

Impact on your own work

e.g. the discussion on [A] that we are having reminds me of [B] conference/[C] initiative/[D] funding call-for-proposal/[E] research group

Questions from my talk:

True or false?

1. Classical ecological models are inadequate for understanding microbial ecosystems.

2. The large-scale, reproducible patterns we see across microbiomes are emergent features of “typical random ecosystems.”

3. Diverse communities will almost always behave like “random ecosystems.”

Question I want to discuss

Can large-scale ecological changes over time be understood through simple general principles? (Samraat, Jacopo, Priyanga, me: flux balance/metabolic rates, random matrix theory, biochemical and morphological constraints)

Are there ecological summary statistics that change monotonically over time? (Jacopo, and some of my work that I didn't talk about -- see references)

Which properties of individual organisms are essential for predicting large-scale ecological changes?

- Pamela -- why do some vaccines fail to produce large-scale ecological change (i.e., pathogen extinction)?

- Greg -- importance of distribution of susceptibilities to dynamics of epizootic onset.

- Fernanda -- importance of adaptive foraging for understanding why pollinator systems don't collapse -- and why they might under new circumstances.

- Samraat -- taking the mechanics of inter-species interaction seriously, understanding how they affect response of ecosystem to temperature changes.

- Priyanga -- asymmetry of reaction norms for temperature variation.

What do we miss when we focus too much on equilibrium/steady states? (Prevalence of cyclic disturbance/recovery dynamics -- Greg, Samraat)

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Reference material notes

Some examples:

Here is [A] database on [B] that I pull data from to do [C] analysis that might be of interest to this group (insert link).

Here is a free tool for calculating [ABC] (insert link)

This painting/sculpture/forms of artwork is emblematic to our discussion on [X]!

Schwartz et al. 2017 offers a review on [ABC] migration as relate to climatic factors (add the reference as well).

"The Minimum Environmental Perturbation Principle" (Marsland et al. 2019) is some new work I didn't include in my presentation, but which is possibly more relevant to the irreversibility theme. The main result is that a wide class of niche models exhibit monotonic increase in the environmental perturbation under successive invasions/evolution. I would love any feedback from the ecologists about references to add, things that are unclear, etc.

Marsland and England 2017 and Marsland et al. 2015 contain in-depth explanations of the two kinds of “thermodynamic” irreversibility I wrote up on the board.

Mehta et al. 2018 begins with a discussion of the "bias/variance tradeoff", which is extremely relevant to the use of models with many parameters to make predictions. It also has a section on dimensional reduction and clustering that might be useful to people working with high-dimensional phenotype data. (Note that the wiki didn't allow me to enter the whole author list, which should also include Marin Bukov, Charles Fisher and David Schwab.)

Momeni et al. 2017 shows some of the ways in which Lotka-Volterra can fail to capture the population dynamics of a generalized class of consumer-resource models.

Fisher and Mehta 2014 shows how both niche and neutral regimes can arise in Lotka-Volterra dynamics with immigration, depending on the parameter values.

"Available Energy Fluxes..." (Marsland et al. 2019) contains a full explanation of our microbial consumer resource model in the appendix. The Python implementation can be found at our group github: https://github.com/Emergent-Behaviors-in-Biology/community-simulator.

I have also included the original Human Microbiome Project and Earth Microbiome Project data papers, which contain the large-scale patterns I was showing in the presentation.

Gutenknust et al. 2007 explains some of the subtleties of Bayesian model fitting in a very accessible way, and strongly influenced the way I think about many-parameter models.

Goldford et al. 2018 contains some of the patterns I was talking about at the beginning of my talk, which are already captured by a preliminary version of the model.

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Reference Materials

Title	Author name	Source name	Year	Citation count From Scopus. Refreshed every 5 days.	Page views	Related file
Structure, function and diversity of the healthy human microbiome	A. Scott Durkin, Allison Griggs, Alyxandria M. Schubert, Amy L. McGuire, Anthony A. Fodor, Antonio Gonzalez, Anup A. Mahurkar, Ashlee M. Earl, Asif T. Chinwalla, Aye M. Wollam, Barbara A. Methé, Beltran Rodriguez-Mueller, Bo Liu, Bonnie P. Youmans, Brandi Herter, Brandi L. Cantarel, Brian J. Haas, Bruce W. Birren, Candace N. Farmer, Carl C. Baker, Carolyn Deal, Carsten Russ, Catherine A. Lozupone, Catherine C. Davis, Catherine Jordan, Catrina C. Fronick, Cecil M. Lewis, Cesar A. Arze, Chad M. Tomlinson, Chad Nusbaum, Chandri Yandava, Chien Chi Lo, Christian J. Buhay, Christie L. Kovar, Christina Giblin, Christopher S. Smillie, Christopher Wellington, Clinton Howarth, Craig Pohl, Cristyn Kells, Curtis Huttenhower, Dan Knights, Dana A. Busam, Daniel D. Sommer, Daniel McDonald, David J. Dooling, Dawn M. Ciulla, Dennis C. Friedrich, Diana G. Tabbaa, Diane E. Hoffmann, Dirk Gevers, Donna M. Muzny, Doyle V. Ward, Elaine R. Mardis, Elena Deych, Elizabeth A. Lobos, Elizabeth Appelbaum, Emily L. Harris, Emma Allen-Vercoe, Eric J. Alm, Erica J. Sodergren, Floyd E. Dewhirst, Gary Armitage, Gary L. Andersen, George M. Weinstock, Georgia Giannoukos, Gina A. Simone, Granger G. Sutton, Gregory A. Buck, Harindra M. Arachchi, Heather H. Creasy, Heidi H. Kong, Holli A. Hamilton, Hongyu Gao, Huaiyang Jiang, I. Min A. Chen, Indresh Singh, Ioanna Pagani, Irene Newsham, J. Fah Sathirapongsasuti, J. Paul Brooks, Jack D. Sobel, Jacques Izard, Jacques Ravel, James A. Katancik, James R. White, James Versalovic, Jamison M. McCorrison, Jane Peterson, Janet K. Jansson, Jason R. Miller, Jason Walker, Jean McEwen, Jeffery A. Schloss, Jeffrey G. Reid, Jennifer R. Wortman, Jeremy D. Zucker, Jeroen Raes, Johannes Goll, John C. Martin, Jonathan Crabtree, Jonathan Friedman, Jonathan H. Badger, Jonathan M. Goldberg, Jose C. Clemente, Joseph F. Petrosino, Joseph L. Campbell, Joshua Orvis, Julia A. Segre, Karen E. Nelson, Karoline Faust, Karthik C. Kota, Katarzyna Wilczek-Boney, Katherine H. Huang, Katherine P. Lemon, Katherine S. Pollard, Kathie A. Mihindukulasuriya, Kelvin Li, Ken Chu, Kevin P. Riehle, Kim C. Worley, Kimberley D. Delehaunty, Kjersti M. Aagaard, Konstantinos Liolios, Konstantinos Mavromatis, Kris A. Wetterstrand, Krishna Palaniappan, Kristine M. Wylie, Kymberlie Hallsworth-Pepin, Lan Zhang, Larry J. Forney, Laurie Zoloth, Lei Chen, Leslie Foster, Liang Ye, Lisa Begg, Lita M. Proctor, Lora Lewis, Lu Wang, Lucia Alvarado, Lucinda L. Fulton, Lynn Schriml, Makedonka Mitreva, Manolito Torralba, Margaret E. Priest, Maria C. Rivera, Maria Y. Giovanni, Mark A. Watson, Martin J. Blaser, Mary A. Cutting, Mathangi Thiagarajan, Matthew C. Ross, Matthew Pearson, Matthew Scholz, Michael E. Holder, Michael Feldgarden, Michael G. Fitzgerald, Michelle G. Giglio, Michelle Oglaughlin, Mihai Pop, Mina Rho, Mircea Podar, Monika Bihan, Narmada Shenoy, Nathalia Garcia, Niall Lennon, Nicholas B. King, Nicola Segata, Nihar U. Sheth, Nikos C. Kyrpides, Noam J. Davidovics, Olukemi O. Abolude, Omry Koren, Owen White, Pamela McInnes, Pamela Sankar, Patricio S. La Rosa, Patrick D. Schloss, Patrick J. Minx, Patrick S.G. Chain, Paul Spicer, Peter J. Mannon, Qiandong Zeng, R. Dwayne Lunsford, Rachel L. Erlich, Ramana Madupu, Ravi K. Sanka, Rebecca M. Truty, Richard A. Gibbs, Richard K. Wilson, Richard R. Sharp, Rob Knight, Robert C. Edgar, Robert S. Fulton, Rosamond Rhodes, Ruth E. Ley, Ruth M. Farrell, Sahar Abubucker, Sandra L. Lee, Sandra W. Clifton, Sarah K. Highlander, Sarah K. Young, Scott Anderson, Scott T. Kelley, Sean Conlan, Sean M. Sykes, Sergey Koren, Shaila Chhibba, Shane R. Canon, Shannon P. Dugan, Sharvari Gujja, Sheila Fisher, Shibu Yooseph, Shital M. Patel, Susan Kinder Haake, Susan M. Huse, Tatiana A. Vishnivetskaya, Teena Mehta, Tessa Madden, Theresa A. Hepburn, Thomas J. Sharpton, Thomas M. Schmidt, Toby Bloom, Todd J. Treangen, Todd Wylie, Todd Z. Desantis, Tsegahiwot Belachew, Tulin Ayvaz, Valentina Di Francesco, Vandita Joshi, Veena Bhonagiri, Victor M. Felix, Victor M. Markowitz, Vincent Magrini, Vivien Bonazzi, Wendy A. Keitel, Wesley Warren, William D. Shannon, Wm Michael Dunne, Xiang Qin, Yan Ding, Yanjiao Zhou, Yiming Zhu, Yu Hui Rogers, Yuanqing Wu, Yue Liu, Yuzhen Ye, Zhengyuan Wang	Nature	2012	5,565	6
A communal catalogue reveals Earth's multiscale microbial diversity	Aaron Clauset, Aaron R. Jex, Alexandra H. Campbell, Alexandra M. Linz, Allison Berry, Allison E. Williams, Alyssa Cochran, Amnon Amir, Amy Apprill, Andaine Seguinorlando, Anders Karlsson, Andrew P. Rees, Andrew Whitehead, Anna Forsman, Anni Moore, Anson V. Koehler, Antje Gittel, Antonio González, Antonio M. Martín-Platero, Anupriya Tripathi, Asha Rani, Ashish Bhatnagar, Ashley Shade, Aurora MacRae-Crerar, Baddr Shakhsheer, Bazartseren Boldgiv, Beck Wehrle, Benjamin B. Crary, Benjamin D. Shogan, Benjamin L. Turner, Bharath Prithiviraj, Bonnie Laverock, Brenda B. Casper, Brent Stephens, Byron C. Crump, Caitlin Potter, Carol Robinson, Catherine M. Spirito, Catherine Pfister, Cesar Cardona, Chia L. Tan, Chris Freeman, Christopher Quince, Colin J. Brislawn, Colleen T.E. Kellogg, Congcong Shen, D. Lee Taylor, Daniel A. Cristol, Daniel McDonald, Daniel P. Smith, Daniel Van Der Lelie, Daniela Vargas-Robles, Danielle C. Claar, Danilo Ercolini, Dave Shutler, David A. Lipson, David A. Mills, David Armitage, David Garshelis, David Myrold, Diogo Jurelevicius, Dionysios A. Antonopoulos, Donal M. Boyer, Donald A. Walker, Donglai Gong, Donna Berg-Lyons, Douglas C. Woodhams, Duoying Cui, Elizabeth Pilon-Smits, Elliot S. Friedman, Embriette Hyde, Emily M. Landon, Eric A. Dubinsky, Eric Bottos, Eric R. Johnston, Eske Willerslev, Evguenia Kopylova, Ezequiel M. Marzinelli, F. Joseph Pollock, Fabian Michelangeli, Folker Meyer, Forest Rohwer, Francis Q. Brearley, Frédéric Delsuc, Gabriela M. Sheets, Gail Ackermann, Gary M. King, Gavin Collins, George W. Kling, Giancarlo Galindo, Glida Hidalgo, Graeme W. Nicol, Gregory D. Mayer, Gregory Humphrey, Gunnar Gerdts, Haiyan Chu, Hakdong Shin, Hans Peter Grossart, Hebe M. Dionisi, Helen S. Findlay, Hongxia Zhao, Ina Timling, Iratxe Zarraonaindia, Iris I. Levin, Irma D. Fleming, Isaac Gifford, J. Gregory Caporaso, Jack A. Gilbert, Jacob Parnell, Jad Kanbar, James E. McDonald, James T. Morton, Jamie M. McDevitt-Irwin, Janet K. Jansson, Jarrad Hampton-Marcell, Jason Andras, Jed A. Fuhrman, Jeff Hooker, Jeffrey J. Werner, Jeffrey Siegel, Jenni Hultman, Jennifer Defazio, Jennifer F. Biddle, Jeremiah Minich, Jesse Zaneveld, Jessica L. Metcalf, Jiří Bárta, Jo Lynn Carroll, John Alverdy, Jon G. Sanders, Jonathan B. Clayton, Jonathan E. Hickman, Jordan Kueneman, Jose A. Navas-Molina, Jose C. Clemente, Jose L. Agosto Rivera, Joseph R. Mendelson, Josephine Braun, Josh D. Neufeld, Joshua Ladau, Joshua Lefler, Jozef I. Nissimov, Juan Diego Ibáñez-Álamo, Juan J. Soler, Juan M. Peralta-Sánchez, Julia K. Baum, Julie D. Jastrow, Julie LaRoche, Karen Noyce, Karen Tait, Karl J. Rockne, Kate Ballantine, Katherine D. McMahon, Katherine R. Amato, Katherine S. Pollard, Kefeng Niu, Kelly D. Goodwin, Kelly Lanede Graaf, Kenneth J. Locey, Kim M. Handley, Kim Miller, Kirsten S. Hofmockel, Krista L. McGuire, Kristin West, Kristina Guyton, L. Margarita Martínez, L. Scott Johnson, Largus T. Angenent, Lauren M. Seyler, Lee J. Kerkhof, Liliana Davalos, Linda A. Whittingham, Lingjing Jiang, Lisa Al-Moosawi, Liza Garcia, Lucas Moitinho-Silva, Lucie Bittner, Lucy Seldin, Ludovic Orlando, Lukas Van Zwieten, Luke K. Ursell, Luke R. Thompson, Magda Magris, Manuel E. Lladser, Manuel Martín-Vivaldi, Manuel Martínez-Bueno, Maria Alexandra Garcia-Amado, Maria Gloria Dominguez-Bello, Mariana Lozada, Mark D. Schrenzel, Martin Sperling, Matthew J. Nolan, Matthew Schrenk, Maureen L. Coleman, Melita A. Stevens, Miguel Lentino, Miles Richardson, Mohamed F. Haroon, Molly K. Gibson, Monica Bhatnagar, Monika Krezalek, Mónica Contreras, Mónica Medina, Naseer Sangwan, Nathalie Fenner, Neslihan Taş, Nicholas A. Bokulich, Nicole M. Scott, Nicole S. Webster, Noah Fierer, Noriko Okamoto, Nur A. Hasan, Olayinka Osuolale, Olivia U. Mason, Pamela Weisenhorn, Paola Piombino, Paola Vitaglione, Paul Munroe, Peter D. Steinberg, Peter Golyshin, Peter Larsen, Peter O. Dunn, Peter Petraitis, Pierre Liancourt, Qikun Zhang, Qiyun Zhu, Rachael M. Morgan-Kiss, Ravi Ranjan, Rebecca J. Safran, Rebecca Vega Thurber, Regina Lamendella, Rick L. Stevens, Rita L. Seger, Rita R. Colwell, Rob Knight, Robert E. Espinoza, Robert G. Clark, Robert J. Prill, Robin B. Gasser, Robin Dowell, Roger Karlsson, Ross Stephen Hall, Russell D. Dawson, Ryan McMinds, Ryan T. Gill, S. Craig Cary, Safiyh Taghavi, Sara Sjöling, Sarah E. Daly, Sarah Jane Haig, Sarah L. O'Brien, Sarah M. Owens, Se Jin Song, Sean M. Gibbons, Selena Marie Rodriguezl, Seth Kauppinen, Shane R. Haydon, Shaun Nielsen, Shi Wang, Siavash Mirarab, Simon Creer, Simon Lax, Sophie Weiss, Stefan Hulth, Stefan Janssen, Stefano Mocali, Stephanie D. Jurburg, Stephen A. Wood, Stephen B. Pointing, Stephen Joseph, Steve Simmons, Steven J. Hallam, Subramanya Rao, Susan R. Whitehead, Suzanne J. Kennedy, Tao Wang, Tim Urich, Tom Weaver, Tomasz Kosciolek, Torsten Thomas, Trevor C. Charles, Tugrul Giray, Ulf Riebesell, Valerie McKenzie, Vanessa Ezenwa, Vanessa Hale, Vera Tai, Vincenzo Fogliano, Virginia Sanz, Walter P. MacCormack, Wayne Roundstone, Wenju Liang, William A. Walters, William Brazelton, William Van Treuren, Wyatt Oswald, Yadira Ortiz Castellano, Yeqin Yang, Yingying Ni, Yongqin Liu, Yoshiki Vázquez-Baeza, Yu Shi, Zhenjiang Zech Xu	Nature	2017	718	6
Universally sloppy parameter sensitivities in systems biology models	Christopher R. Myers, Fergal P. Casey, James P. Sethna, Joshua J. Waterfall, Kevin S. Brown, Ryan N. Gutenkunst	PLoS Computational Biology	2007	700	6
Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics	Alex Betts, Alex H. Lang, Amrita Kar, Brian R. Granger, Christopher J. Marx, Daniel Segrè, Gracia Bonilla, Ilija Dukovski, Nicholas Leiby, Pankaj Mehta, William J. Riehl, William R. Harcombe	Cell Reports	2014	264	4
Emergent simplicity in microbial community assembly	Alicia Sanchez-Gorostiaga, Alvaro Sanchez, Daniel Segrè, Djordje Bajić, Joshua E. Goldford, Mikhail Tikhonov, Nanxi Lu, Pankaj Mehta, Sylvie Estrela	Science	2018	225	11
Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions	Babak Momeni, Li Xie, Wenying Shou	eLife	2017	79	0
A high-bias low-variance introduction to machine learning for physicists	Alexandre G. R. Day, Ching-Hao Wang, Clint Richardson, Pankaj Mehta		2018	0	9	Download
Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities	Alvaro Sanchez, Joshua Goldford, Kirill Korolev, Pankaj Mehta, Robert Marsland III, Wenping Cui	PLoS Computational Biology	2019	0	1
The Minimum Environmental Perturbation Principle: A New Perspective on Niche Theory	Pankaj Mehta, Robert Marsland III, Wenping Cui		2019	0	1
Time and Irreversibility in axiomatic thermodynamics	Giovanni Valente, Harvey R. Brown, Robert Marsland III	American Journal of Physics	2015	0	0
Limits of Prediction in thermodynamic systems: a review	Jeremy England, Robert Marsland III	Reports on Progress in Physics	2017	0	1
The transition between the niche and neutral regimes in ecology	Charles K. Fisher, Pankaj Mehta	Proceedings of the National Academy of Sciences	2014	0	2
Statistical physics of self-replication				0	7