Research

Overview: Evolutionary Theory

I am an evolutionary theorist. My research involves devising testable hypotheses. This is one of the two sides of Popper’s coin; the other side being testing of hypotheses, which is the purview of empirical science. The biological questions I address are firmly grounded in evolutionary biology. Evolution provides a unifying framework upon which all other biology is built.

I ascribe to the modern economic mantra of using micro primitives to explain macro phenomena. For example, how can a simple molecular such as a methyl group added to DNA nucleotides result in enormous evolutionary changes? The combination of bottom-up and top-down approaches has proven especially useful in my research. I also espouse a mathematician’s predilection for keeping a myriad of useful counterexamples in my backpocket. To that end, I spend a lot of timing learning about fascinating organisms (which, after all, motivate all of our work), their ecological contexts, and molecular idiosyncrasies. In depth knowledge of natural history goes a long way in readily discerning whether a theory is bogus.

What is sex?

What exactly is sex and how did it originate? What exactly is meiosis? What is fertilization/syngamy? Is syngamy a modified form of meiosis? Does self-fertilization count as sex? Does meiotic recombination really matter? Are there any eukaryotes that are truly asexual or lack meiosis? Why has sex not disappeared from most eukaryotic lineages? What is a eukaryote? Why do eukaryotic organisms age? Surprisingly, these questions may all be closely intertwined, if not equivalent. Was the original or current function of really to increase genetic variation? Instead, I am pursuing whether the function of sex was and still is to decrease epigenetic variation, as well as decreased variance in ploidy.

Typically, questions regarding maintenance of sex (or maintenance of any form of genetic variation) are best answered using population genetics. However, population genetics is generally acknowledged to be inadequate for explaining origins of variation. Origins of evolutionary variation are largely the bailiwick of evolutionary developmental (evo-devo) biologists, which falls under the aegis of epigenetics. The core of my research is an attempt to unify the study of maintenance and origins of evolutionary variation by applying classical population genetic techniques to epigenetic phenomena. I am also conducting research in other aspects of evolutionary origins of sex, such as origins of sex determination, sex chromosomes, and sexual dimorphism.

Sexuality studies

We are investigating whether there are universal differences between females and males, including in humans. For individuals that have pairs of chromosomes per nucleus, the answer is clearly that a continuum exists between the sexes. But what about individuals with only one of each chromosome per nucleus, which in humans means eggs and sperm? Here the answer is much less obvious. We have proposed that only sperm cells have nuclei that lack pores and only male meiosis produces four functional and symmetrical products (four sperm in humans). But these notions have not been tested.

This work has many interesting sociological implications. Are animals eggs and sperm really individuals? What does it mean to be an individual? This may help determine the grey dividing line between cooperation and competition. Why do textbooks only depict (symmetrical) male meiosis and not (asymmetrical) female meiosis? We have been applying sexuality, feminist, and queer studies to biology, but can we return the favour and apply biology to those other fields?

Patterns of biodiversity

Modern patterns of biodiversity largely seem idiosyncratic. Why are most plants flowering plants? Why are most animals insects? Why have vertebrates radiated into so many difficult niches, such as their many independent transitions from terrestrial/freshwater to marine environments? We are investigating the roles of polyploidy (doubling of all chromosomes) and chromosomal fissioning in radiations. In particular, we are seeing whether polyploidy induces epigenetic changes which in turn result in non-adaptive radiations, while chromosomal fissioning results in adaptive non-radiations.

Epigenetics

Evolution of sex and patterns of biodiversity both appear to depend on evolutionary epigenetics. Epigenetic signals are literally heritable signals on top of DNA nucleotides. There is enormous untapped potential in applying population and quantitative genetics to epigenetic signals, with applications ranging from epidemiology to evolutionary ecology. This aspect of my work is highly philosophical (what exactly is a gene?) and is often highly mathematical. But, herein lies the possibility of unifying the various definitions of epigenetic, a term that spans everything from classic developmental biology to transposons to chromatin remodeling and cytosine methylation. Epigenetic phenomena may also provide the crucial link between evolution and ecology insofar as epigenetic signals are both heritable and malleable by environmental perturbations. Evolution truly looks different once one dons epigenetically-coloured glasses!

Quantifying diversity

There has been surprisingly little theoretical work done in quantifying biological diversity. I am using information theory and number theory to quantify diversity, especially of multiple (vice pairwise) interactions. I would also like to begin using graph theory. Are different mathematical methods for quantifying diversity commensurate with one another? Which method is most appropriate for a given application? In addition to obvious conservation and bioinformatic implications, this work is applicable in other contexts, such as measuring interactions between multiple genes (linkage disequilibrium and epistasis), measuring interactions between multiple individuals in sociobiology (division of labour), quantifying levels of promiscuity, and quantifying diversity in hiring of human workers that is sensitive to tokenism.

History and Philosophy

We are pursuing fundamental concepts in evolution, such as (1) What does it mean for something to be genetic? (2) What does it mean to be sexual? Does sex with ones self count? (3) What is a gamete if it is not haploid and if haploid stages are never unicellular? (4) What is theory? (5) Do there exist feminist and queer perspectives on epigenetics and evolution of sex? (6) What is an individual? Definitions are arbitrary and only as good as the conceptual simplifications that derive from them. How has our historical view of the above concepts changed and how can we best define terms so as to get the most powerful and testable theories?

Classical botany and natural history

My own theoretical work is motivated by a strong and continuing devotion to natural history and classical botany. There is nothing more valuable than a litany of real world examples at one’s fingertips to quickly test theories. Thus, there is nothing better for a theorist than to have a deep understanding of as many organisms as possible, from molecular details all the way to population level details. I work with cacti, cycads, gnetophytes, and other non-flowering seed plants. My natural history work has largely been in Arizona and New Mexico, although is expanding to cover local regions as well as other deserts.

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