Here's a page to share important papers, review articles, relevant news, etc.

Additional Classes to study evolution of multicellularity ?

Volvox was intensively discussed during the workshop. In the Ulvophyceae (green seaweeds)
one finds other examples, including very large uni-cellular organisms (up to 8 meters!) with multiple nuclei and also
multi-cellular forms. The following paper I just came across might be of interest to some of you...

"Evolution and Cytological Diversification of the Green Seaweeds (Ulvophyceae)"
http://www.ncbi.nlm.nih.gov/pubmed/20368268

I would be happy to discuss more...
Christoph



Liyan Ping's talk on division of labor in a bacterial swarm


Here are the references:

1. Chemotaxis in Escherichia coli analysed by three-dimensional tracking
http://www.nature.com/nature/journal/v239/n5374/abs/239500a0.html
2. Swimming behavior of the monotrichous bacterium Pseudomonas fluorescens SBW25
http://onlinelibrary.wiley.com/doi/10.1111/1574-6941.12076/abstract
3. three-dimensional tracking of motile bacteria near a solid planar surface
http://www.pnas.org/content/92/13/6195
4. Bacterial motility on a surface: many ways to a common goal
http://www.annualreviews.org/doi/full/10.1146/annurev.micro.57.030502.091014
5. Dynamics of bacterial swarming
http://www.sciencedirect.com/science/article/pii/S0006349510002183
6. Visualization of flagella during bacterial swarming
http://jb.asm.org/content/192/13/3259
7. Microbubbles reveal chiral fluid flows in bacterial swarms
http://www.pnas.org/content/108/10/4147.full
8. Water reservoir maintained by cell growth fuels the spreading of a bacterial swarm
http://www.pnas.org/content/109/11/4128.full



Here are are a few classic and more recent papers that KITP journalist-in-residence Peter Byrne finds useful in defining the territory of the evolution of multicellarity and cooperation:

The Spandrels of San Marcos:
http://www.jstor.org/stable/77447

The Confusions of Fitness:
http://docencia.med.uchile.cl/evolucion/pdf2005/LEWONTIN2004-fitness.pdf

Complexity and Evolution-What Everybody Knows:
https://www.eeb.ucla.edu/Faculty/Jacobs/gold/Home/Classes_files/McShea.pdf

The Evolution of Eusociality:
http://www.nature.com/nature/journal/v466/n7310/full/nature09205.html

Evolutionary Explanations for Cooperation:
http://www.ncbi.nlm.nih.gov/pubmed/17714660

Towards a General Theory of Group Selection:
http://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2012.01835.x/abstract

Life is Physics: evolution as a collective phenomenon far from equilibrium:
http://arxiv.org/abs/1011.4125

Against Growth: http://www.eurozine.com/articles/2012-11-30-farley-en.html
An economist uses advances in evolutionary biology to argue for abandoning competition-based neo-classical economics (and Prisoner's Dilemma-type models) in favor of making room for the emergence of a more rational socio-economic system based upon group cooperation.

After 8 weeks here, I see an important role for (some of the less-windy) philosophers to synthesize and clarify the ground-breaking work of more narrowly-focused scientists. Peter Godfrey Smith has made a major contribution. The reviews of his 2009 book "Darwinian Populations and Natural Selection" are worth reading and sum up his work: http://www.petergodfreysmith.com/Dpops_Main.html

Here are some awesome publications be a newly minted Philosopher of Biology -- Ellen Clarke -- who argues that multilevel selection need not be predicated on conflict suppression at the lower levels. She also has a wonderful piece on the problem of trying to justify the social welfare state with Tit For Tat:
https://sites.google.com/site/ellenlclarke/publications



Mogens Jensen talk on biological oscillators

Inducing phase-locking and chaos in cellular oscillators by modulating the driving stimuli
Modeling oscillatory control in NF-κB, p53 and Wnt signaling
Global and Local: Synchronization and Emergence



Material related to Michael Doebeli's talk on kin vs. group selection

Wine/Water Mixing Problem, Wikipedia
Altruism Researchers Must Cooperate, Samir Okasha, Nature (2010)
Towards a General Theory of Group Selection, Simon et al, Evolution, 2013
Group selection video I (PDE)
Group selection video II (stochastic version)
Hamilton’s rule in multi-level selection models, Simon et al, Journal of Theoretical Biology, 2012
Some correspondence about the paper by Nowak et al, Nature, 2010
Group selection and inclusive fitness are not equivalent; the Price equation vs. models and statistics




Basics of game theory

The logic of animal conflict (Maynard-Smith & Price, Nature 1973)
Evolution and the Theory of Games (Maynard-Smith, Cambridge Press 1982)
Evolutionary Games and Population Dynamics (Hofbauer & Sigmund, Cambridge Press 1998)
Models of cooperation based on the Prisoner's Dilemma and the Snowdrift game (Doebeli & Hauert, Ecology Letters 2005)
Snowdrift game dynamics and facultative cheating in yeast (Gore et al., Nature 2009)
Prisoner's dilemma in an RNA virus (Turner & Chao, Nature 1999)
Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors (Kerr et al., Nature 2002)

Papers and thoughts on somatic evolution in cancer progression

Modelling: Computing cancer, Neil Savage Nature 491, S62–S63 (2012)


Stuff to go w Murray Multicellularity Talk
Talk file as PPT

Talk file as PDF
Multicellularity Conceptual Big.pdf
Koschwanez Engineered Multicellularity Paper
Koschwanez Evolved Multicellularity Paper (in revision eLife)

References related to Mimi Koehl's talk on chonaoflagellates:

You can link to or download my papers on from my website: http://ib.berkeley.edu/labs/koehl/

BASIC APPROACH TO PRODUCING FIELD FLOW CONDITIONS IN THE LAB ON THE SCALE OF MICROSCOPIC ORGANISMS:
Koehl, M. A. R. and M. A. Reidenbach. (2007) Swimming by microscopic organisms in ambient water flow. Experiments in Fluids 43: 755-768.

ROMAN STOCKER'S MICROFLUIDICS DEVICE TO MAKE A PATCH OF NUTRIENTS OR PREY:
Seymour J.R., Ahmed T., Marcos & Stocker R., 2008, “A microfluidic chemotaxis assay to study microbial behaviour in diffusing nutrient patches”, Limnology and Oceanography: Methods, 6, 477-488.

Here are some references about the molecular and cell biology of choanoflagellates that you were asking about during my talk on Thursday. You can link to most of these papers via Nicole King's website: http://kinglab.berkeley.edu/

MOLECULAR PHYLOGENY AND COMPARATIVE GENOMIC ANALYSES --RELATIONSHIP OF CHOANOFLAGELLATES TO METAZOA:
King, N. and Carrroll, S.B. (2001) A receptor tyrosine kinase from choanoflagellates: Molecular insights into early animal evolution. PNAS. 98(26): 15032–15037.

Steenkamp, E. T., Wright, J. and Baldauf, S. L. (2006) The protistan origins of animals and fungi. Mol. Biol. Evol. 23: 93-106.

Nicole King, M. Jody Westbrook*, Susan L. Young*, Alan Kuo, Monika Abedin, Jarrod Chapman, Stephen Fairclough, Uffe Hellsten, Yoh Isogai, Ivica Letunic, Michael Marr, David Pincus, Nicholas Putnam, Antonis Rokas, Kevin J. Wright, Richard Zuzow, William Dirks, Matthew Good, David Goodstein, Derek Lemons, Wanqing Li, Jessica Lyons, Andrea Morris, Scott Nichols, Daniel J. Richter, Asaf Salamov, JGI Sequencing, Peer Bork, Wendell A. Lim, Gerard Manning, W. Todd Miller, William McGinnis, Harris Shapiro, Robert Tjian, Igor V. Grigoriev, Daniel Rokhsar. (2008) The genome of the choanoflagellateMonosiga brevicollis and the origin of metazoans.Nature. 451: 783-788.

HOW CELL DIVISION PRODUCES A MULTICELLULAR COLONY:
Fairclough SR, Dayel MJ, and King N (2010) Multicellular development in a choanoflagellate. Current Biology 20:R875-6.

COLONY AND SINGLE-CELLED FORMS OF S. ROSETTA:
Dayel MJ, Alegado RA‡, Fairclough SR‡, Levin TC, Nichols SA, McDonald K and King N (2011) Cell differentiation and morphogenesis in the colony-forming choanoflagellate Salpingoeca rosetta. Developmental Biology. 357:73-82.

THE INDUCTION OF COLONY FORMATION BY ALGORIPHAGUS BACTERIA:
Alegado RA*, Brown LW*, Cao S, Dermenjian RK, Zuzow R, Fairclough SR, Clardy J§ and King N§ (2012) Bacterial regulation of colony development in the closest living relatives of animals.**eLife. 1: e00013.

CADHERINS IN CHOANOFLAGELLATES:
Monika Abedin and Nicole King. (2008)The premetazoan ancestry of cadherins.Science. 319(5865):946-948

Hamilton and May 1977 paper on evolution of dispersal



Paul Rainey's talk on transitions (in individuality) and levels (of selection)

Paul gave us a chalk talk on 31 January 2013. Below are images of the board at the conclusion of his talk.

Board 1: Road Map - topics we covered.
1) from here (individual particles) to there (groups of particles)
2) abstract formalism of Darwinism
3) Darwinian individuality
4) units/levels of selection
5) transitions in Darwinian individuality
6) hierarchical organisation
7) what needs explaining? (reproduction, "De-Darwinisation")
8) cooperation/conflict
9) MLS1/2
10) fitness decoupling
11) chicken & egg
12) solutions/proto-multicellular forms
20130131_Rainey1.jpg


Board 2: "MLS1": multi-level selection 1 - individual particles (x) as units of selection with their accompanying fitness/selective properties. they might "come together" in various ways (dotted circle). however, no emergent fitness/selective properties of the "group" are present.
20130131_Rainey2.jpg

Board 3: "MLS2" - collections of individual particles (within solid circles) are units of selection, with selective properties that are not simply the sum of the selective properties of the particles. List at left are some things that we know are features of extant multicellularity, that we would like to explain/understand the evolution of.
20130131_Rainey3.jpg

Board 4: Proposed Solutions
20130131_Rainey4.jpg




Time lapse video of the ichthyosporean Sphaeroforma arctica -

Iñaki Ruiz-Trillo

http://www.youtube.com/watch?v=NwQk6xsqLJo

for more picture of Capsaspora and ichthyosporeans, check
http://www.multicellgenome.com/photos/index.html

for more info on the development of Creolimax fragrantissima as a new model organism see
http://www.sciencedirect.com/science/article/pii/S0012160613000146

Jorge M. Pacheco's talk on stochastic effects in hematopoiesis


During the talk, there were suggestions that Chronic Myeloid Leukemia (CML) does not originate in hematopoietic stem cells but further downstream (from myeloid progenitors).
To clarify this issue, here I upload several references that report the experimental findings which show the presence of the
Ph-chromossome in cells from the myeloid, erythroid, megakaryocytic, and B-lymphoid lineages in humans.

When taken in the context of our current understanding of hematopoiesis, this data proves that the cell of origin of CML must be a Hematopoietic Stem Cell.










The references below, in turn, discuss reports on patients who did not relapse from Major Molecular Response (MMR)
after stopping their treatment employing TKIs. This is a hot subject under active debate in most oncology meetings devoted to CML,
and new and exciting data is expected shortly.






Evolution through the lens of synthetic biology


Synthetic gene circuit for tuning gene expression uniformly in all cells, with linear dependence on the extracellular inducer concentration:


Synthetic gene circuit for controlling the time scales of bet hedging (stochastic switching):

CompuCell3D mini workshop


Simple Yeast-like simulation


Solari's talk relevant papers



I just realized the model paper has been published.


Some relevant papers for Simpson's Macroevolution of Individuality talk

My slides:


My papers on transitions:



Related Van Valen paper:


Rice's stochastic Price equation:


Some papers of interest for Brad Olson's and Cristian Solari's talks

This is a comprehensive review that I wrote with Jim Umen on the Volvocales, biology and their genomes