PHYSICAL CONSTRAINTS ON THE SIZE AND SHAPE OF MICROALGAE A DISSERTATION SUBMITTED TO THE DEPARTMENT OF BIOLOGY AND THE COMMITTEE ON GRADUATE STUDIES OF STANFORD UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Kevin Alan Miklasz March 2012 © 2012 by Kevin Miklasz. All Rights Reserved. Re-distributed by Stanford University under license with the author. This work is licensed under a Creative Commons Attribution- Noncommercial-Share Alike 3.0 United States License. http://creativecommons.org/licenses/by-nc-sa/3.0/us/ This dissertation is online at: http://purl.stanford.edu/mz210dd1320 ii I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Mark Denny, Primary Adviser I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Stephen Monismith I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. George Somero I certify that I have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of Doctor of Philosophy. Judith Connor Approved for the Stanford University Committee on Graduate Studies. Patricia J. Gumport, Vice Provost Graduate Education This signature page was generated electronically upon submission of this dissertation in electronic format. An original signed hard copy of the signature page is on file in University Archives. iii Abstract Scaling laws provide a link between biology and physics. They provide a means by which patterns in biology can be quantified and an explanation from physics can be correlated with such patterns. In this thesis, I use scaling laws to look for connections between biology and physics in two systems, diatom frustules and coralline algal reproduction. The first part of this thesis addresses several size and shape related constraints in the unicellular group of phytoplankton known as diatoms. In Chapter 1, an empirically- derived scaling law is related back to theory by modeling how cellular density changes with size. In Chapter 2, several further expressions for sinking speed are derived for various shapes and configurations of diatoms. In Chapter 3, empirical relationships between size and frustule thickness are developed and several hypotheses related to the theoretical basis behind these scaling laws are tested. In Chapter 4, the relationship between carbon flux and diatom size is tested in a theoretical model of diatom bloom dynamics. In the second part of this thesis, I explore patterns with macro-algal spores, an entirely new system for which few scaling laws have been derived. In Chapter 5, I conduct a meta-analysis on one group of macro-algae, coralline algae, to identify empirical scaling laws in the reproductive parameters of this group. In Chapter 6, I report field measurements of reproductive rates of four local species of coralline algae to unravel some of the difficulties encountered in Chapter 5 and noted in the literature. iv Finally in Chapter 7, I compare one component of the fitness between two local species of coralline algae that have different life history strategies. I had various success correlating physics to biology in these two systems through the use of scaling laws. The incomplete success is likely attributed to the fact that the physical explanations were not providing strong constraints on the biological systems and thus were not driving the observed patterns, contrary to expectation. I can thus generally conclude that the geometry of the diatom frustule does not seem to be constrained by sinking speed constraints, and that attachment speed and strength may not be as great a limiting factor on the survival of coralline algal spores as expected. v Acknowledgements It is quite difficult to accomplish any enterprise that takes over five years without the help and support of many people. I am indebted to many people for their support and advice throughout my PhD, and can only barely scratch the surface of the needed thanks here. First and foremost, I want to thank my advisor, Mark Denny. Mark has a natural ability to advise. He has always given his students as much freedom or direction as needed, and knows how to adjust this balance over the course of a thesis. His advice on issues of science or otherwise is always exceptional and greatly appreciated. Over the course of my PhD, I have become convinced that one learns the process of science much as one learns any trade with an apprenticeship, through the example of your mentor. Mark sets an excellent example as a scientist and as an advisor, and I am sure that my growth as a scientist in the past five years is mostly attributed to following his lead and guidance. I can only hope to live up to the example he has set as I continue in my career. I have also been lucky to have an exceptional dissertation committee. George Somero has always been available to offer his abilities as a superb editor, or patiently discuss the nuances of biological terminology that my physics sense has botched. One of my favorite classes at Stanford has been George’s “Philosophy of Science” course, which I still think about today when doing research. Judith Connor has always been both an encouraging positive influence, and harshest critic when needed. Stephen Monismith has offered a helpful hand from my first year on Stanford’s campus when I spent a quarter vi researching in his lab. And Manu Prakash has offered a novel perspective and insight into my thesis. My passion for algae originated in the “Marine Botany” course taught at Friday Harbor Labs by Paul Gabrielson and Charles O’Kelley. I have both of my instructors to thank for such an inspiring course, as well as all of the other students in that course. I’d like to particularly thank Paul, who has graciously put up with my nagging about the California crustose corallines during and after the course. Paul has helped me to figure out how to identify the species used in this thesis, as well as sparking my interest in the nuances of taxonomy. I also want to thank all of the phycologists that have particularly excited my passion for algae, including Kathy Ann Miller, Gayle Hansen, and Tom Mumford. The Denny lab has comprised an exceptional group of people during my time here, and I have them to thank in addition to Mark for my understanding of what it means to be a scientist. Patrick Martone was the first to put the buzz in my ear concerning coralline algae, and is in a large part responsible for my mid-thesis abandonment of diatoms for “pink rocks.” His enthusiasm for corallines is infectious and made my research all that much more exciting. Luke Miller embodies to me a scientist with a balanced life perspective. Luke was never too busy, even when consumed with the end of his thesis, to take the time to build a ridiculously unnecessary device, or to help another labmate with whatever problem they are having. I have tried as best I can to adopt Luke’s example as I’ve gone through my own thesis. I have thoroughly enjoyed the generous lab environment created by everyone I have overlapped with: Mike Boller as my first officemate, Katie Mach as my immediate senior student and an impossible act to follow, vii Anton Staaf’s infinite knowledge in all things engineering, Sarah Tepler’s wit and spite, Megan Jensen as the lab’s other token physicist/engineer, and Tom Hata as both a collaborator on research projects and a co-conspirator on non-research projects. My field work would not be possible without the help of many people who not only helped record my data but also ensured my survival at 3:00 AM on a stormy winter night: James Bohnhoff, Christine O’neill, Kimberly Vincent, Sarah Tepler, Carolyn Tepolt, Alyssa Gehman, Katie Mach, and Hannah Jaris. I want to particularly acknowledge James Bohnhoff, a Stanford undergrad, majoring in chemistry but spending two quarters at Hopkins to broaden his horizons, help out with my research, and undertake a spectacular research project of his own. My knowledge and appreciation for statistics has grown over the course of my PhD, in particular through discussion with Jim Watanabe, our local stats expert. I was always surprised by the hours Jim would put aside when I’d walk into his office, unannounced, to pester him with a complex statistics issue. In addition to Jim, there’s several other people I need to thank for their time and knowledge: Alyssa Gehman, Kristy Kroeker, Alison Haupt, and Chelsea Wood. The staff at Hopkins has made this thesis process much smoother than it would have been otherwise. Chris Patton offered help with a bit of everything from safety issues to acidity sensors to SEM prep work. Judy Thompson generally made everything work out even when you were convinced you did it wrong, and Doreen Zelles would patiently help with any issues that come up (even if you were asking for the fifth time how to send a FedEx package). The main campus staff has been equally vital to the ease of the PhD viii process, in particular Valeria Kizka’s tireless work, but also the help from Jennifer Mason, Dan King, and Matt Pinheiro. I have to acknowledge everyone at Hopkins who has made my thesis a thoroughly fun and enjoyable experience, especially my cohort, Nishad Jayasundara, Jason Ladner, Julie Stewart, Malin Pinsky, and Aaron Carlisle.