The Urge to Merge: Towards a Unified Theory on the Origin of Species

Above is my keynote lecture from Dalhousie University, Nova Scotia from a workshop on the Evolutionary Genomics of Symbiosis (Recorded December 2nd, 2014).  Part historical, part philosophical, part research, the lecture discusses the history of evolution and symbiosis (from Darwin to today), the culture divide that polarizes to a certain degree contemporary studies of speciation, and the prospects going forward for unifying evolution, genetics and symbiosis into a coherent theory on species formation.

I specifically review our work on F1 and F2 hybrid lethality induced by Wolbachia endosymbionts and the gut microbiome. With regards to the universality of symbiosis in speciation, I end by asking whether our study system of Nasonia wasps is just hyper-prone to symbionts causing reproductive isolation, or instead have we and others just experimentally asked the question of whether symbionts can drive the origin of species where others have not. Often the difference comes down to simply remeasuring the isolation trait after the microbiome is removed. I suggest that the answer is squarely in the latter category. A speciation geneticist will tend to find the nuclear genes underlying speciation. The speciation microbiologist will tend to find the microbes that cause speciation. Combining these approaches together will give the life sciences a more holistic understanding how new animal and plant species arise. We are not yet there, but the horizon is unfolding for the community to watch and join.

In attendance at this workshop were stellar scientists including Margaret Mcfall-Ngai, Ford Doolittle, John Archiblad, Thomas Bosch, Andrew Roger, Rob Beiko, etc. It appears that Dalhousie and Kiel Universities are on a path to merge their graduate training programs into a beacon of symbiosis scholarship. Keep an eye out for it - it will be a good example to follow.

Tales from the Biosphere with Ed Yong

Science writer Ed Yong talks about Wolbachia, other symbioses, and the modern science communication ecosystem in this podcast. His story-based approach to Wolbachia biology and science in general is natural, entertaining, and understanding of the general audience who he is writing to. Ed has told a few stories about our research here (speciation) and here (antibiotic gene transfer), but you really get to know him in a speaking setting like this podcast. It's like your sitting in the room and getting an insight on Wolbachia biology and the dynamic job of a serious science journalist who thinks deliberately about how to write. Do listen for a few minutes...

"Communicating Science In The Social Media Age: No-One Has To Read This... " 30th October 2014, University College Cork

Ed Yong - Communicating Science In The Social Media Age NoOne Has To Read This By Pharmabiotic On Mixcloud

Family-friendly travel policies at universities

This post is inspired by the increasing and welcome trend of large academic conferences that provide onsite childcare services. There is good news and some bad news about this service.

The good news is that faculty, staff, and students who take advantage of this relatively new service at meetings now have a way to attend conferences and advance their careers as single parents or dual-career parents. Without such a service, it fair to say their professional development and networking would be (and has been for some) hampered. Reduced opportunities to speak about your work, meet colleagues, and hear about the latest greatest work in the field translates for many to reduced career growth.

The bad news is that the childcare services are heavily overpriced for reasons that probably relate to the observation that the companies have large expenses of their own. Some of them travel around the country to conferences, essentially offering a mobile unit of childcare. They also clearly have a monopoly on the price of care as they are the only service at the conference site. No competition breeds hefty prices. Moreover, bringing children to conferences is bad news for the travelers as the children's airfare has to be covered somehow.

About a year ago, I asked the twitterverse if any universities have family friendly policies that support the costs of child airfare or childcare services at conferences. It just seemed like a natural thing to provide yet my own institution did not. I got one reply, and that one was enough to launch a search for how common this service is. Since then, Ive noticed a number of universities that provide such a service. They are listed below.

If you don't have a family friendly travel policy at your own academic institution, well hopefully you now have some motivation to write your Faculty Senate about driving the change. I am going to do so right away (example letter to Vanderbilt below). If you do have a family friendly travel policy that isn't on this list yet, let me know and Ill add it.

Cornell University | Faculty Dependent Care Travel Fund | $1500 per year
Northwestern University | Dependent Care Professional Travel Grant Program | $750 per year
University of Michigan | Child Travel Expense Policy | $1000 per year
Brown University | Dependent Care Travel Fund | $750 per year
UC Berkeley | Dependent Care Travel Policy | In development

EXAMPLE LETTER

December 27, 2014                                                                          

Dear Paul and Colleagues:

Thank you for taking the time to read this proposal on behalf of Vanderbilt University's single and dual-career parents. From research staff to faculty, parents in academia often struggle to find the work-life balance and financial resources to attend national and international meetings because the costs of airfare and childcare services are near prohibitive. Indeed, childcare is an increasing and welcome trend at large meetings, yet without the support to travel to conferences, staff and faculty parents must restrict their professional development and networking. As a result, their (and Vanderbilt's) scholarship is at a disadvantage relative to parents who are not juggling a single or dual career in academia.

In response to this escalating demand, universities are launching Family-Friendly Travel Policies. I have listed five examples below with web links in red. Each of them support parents with financial assistance for airfare and/or childcare services to attend meetings. At a time when single and dual-career parents are rising, it seems that a similar policy at Vanderbilt would not only lift the burden of current employees, but serve as a recruiting tool for those that consider family policies in the job search. A reduced opportunity to speak about your work, meet colleagues, and hear about the latest work in the field translates for many to reduced career growth. We can eliminate this bias and at the same time lift the spirit around family-friendly policies at Vanderbilt. 

Ø  Cornell University | Faculty Dependent Care Travel Fund | $1500 per year

Ø  Northwestern University | Dependent Care Professional Travel Grant Program | $750 per year

Ø  University of Michigan | Child Travel Expense Policy | $1000 per year

Ø  Brown University | Dependent Care Travel Fund | $750 per year

Ø  UC Berkeley | Dependent Care Travel Policy | In development

Thank you very much for considering this Faculty Life principle.

Sincerely,

Seth Bordenstein

Should you consider attending ASM 2015 this spring?

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The general program for the 2015 American Society of Microbiology meeting in New Orleans is out, and registration is now open. The sessions look incredible, and I've listed them below as I imagine they might resonate with many of the readers of this blog. The bolded sessions look particularly interesting for scholars of symbiosis or host-microbe interactions. This is one conference that makes a daring attempt to cover the many exciting developments in all of microbiology, including a major focus on eukaryotic-microbe symbioses.

I've had the great pleasure of attending two other general ASM conferences in the past few years and am always deeply impressed with 1) gender balance of speakers 2) career development stage of speakers 3) the opportunity to meet those people you've always wanted to 4) the high quality of the lectures 5) the vendor booths (ton of free science schwag) 6) the remarkable organization. This is a PROFESSIONAL meeting in every sense of the word. Do consider coming and if it is your first time, I promise that you will not be disappointed. Hope to see you there.

If you have kids, ASM is very good about offering onsite childcare services. More info here.

(disclaimer: I am hosting the session on Holobionts and Their Hologenomes in which the following people are scheduled to speak: Eugene and Ilana Rosenberg (Tel Aviv University), Jonathan Klassen (U. Connecticut), and Nicole Webster (Australian Institute of Marine Science)). 

Sunday, May 31

Plenary Sessions
8:00 a.m. – 10:30 a.m.

• Engineering Microbial Communities
• Healthy Waters, Healthy People: A Tribute to Rita Colwell
• Metabolism at the Host-Bacterial Interface
• Phages through the Ages: Celebrating the Centennial Anniversary of Phage Discovery and Outlining Research Avenues for the Next 100 Years

Afternoon Symposia
2:00 p.m. – 4:30 p.m.

• Context Is Everything
• Dangerous Cargo of Bacterial Translocation Systems
• En-Lightened Microorganisms: What's New with Phototrophic Microbes?
• Evolutionary Forecasting and Infectious Disease: A New Hammer in the Epidemiological Toolbox
• Life after Death
• Metabolism in Microbial Symbioses
• Microbes in Microbes (Russian Dolls)
• Mobile DNA and Genome Plasticity
• New Approaches for Natural Product Prospecting and Discovery
• Next Generation Microbiology Education: Tried and True Evidence-Based Learning Strategies and Outcomes
• Pre-Existing Conditions: Roles for the Microbiome and Host Genetics in Shaping the Response to Diet and Pathogens
• Single Cell Dynamics

Special Interest Sessions
4:45 p.m. – 6:30 p.m.

• Annual History of Microbiology Lecture – From Humor to Virus: The Microbiology of Yellow Fever in Historical Perspective
• Contributions to "Extreme" Microbiology by Female Scientists
• Immunology Issues and Infection in Hemoglobinopathy Populations with Health Disparities
• Update on NIH's Grant Application Submission and Peer Review Process

Monday, June 1

Plenary Sessions
8:00 a.m. – 10:30 a.m.

• Emerging Infectious Diseases (Preliminary)
• The Envelope, Please
• (R)evolutionary Crosstalk between Microbes and Planet Earth
• Zombie Microbes: Dormancy, Latency, and Persistence

Afternoon Symposia
2:00 p.m. – 4:30 p.m.

• Antigenic Variation, Vaccine-Driven Evolution
• ASM Lecturer's Choice: Recent Developments in Microbiome Research
• Benefits and Risks of Fresher and More Natural Food Trends
• Evolution, Adaptation, and RNA Viral Scape to Insect and Human Sensing
• General Motors
• Holobionts and Their Hologenomes
• Making a Happy Home: New Concepts in Niche Modulation by Microbial Pathogens
• Oceans Alive: Marine Microbes in Action
• Pathogen Population Dynamics within the Host
• Polymicrobial Community Development and Evolution
• Real-Time Microbiology
• Unearthing the Dark Matter of Microbial Metabolism and Diversity

Special Interest Sessions
4:45 p.m. – 6:30 p.m.

• Making Your Presence Known
• Using an IDP to Plan a Successful Scientific Career

Tuesday, June 2

Plenary Sessions
8:00 a.m. – 10:30 a.m.

• Blooming Microbes: Communities in Flux (Preliminary)
• The Third Age of Antimicrobials
• Cellular Decision Making
• The Quest for Causality: How to Get at the Role of the Microbiota in Host Health?
• Afternoon Symposia
  2:00 p.m. – 4:30 p.m.
  • The Dark Biochemistry of Microbial Genomes: Unexpected Enzyme Reactions of "Genetic False Friends"
  • Designer Therapeutics: Novel Approaches for Thwarting Specific Pathogens
  • Emerging Frontiers in the Microbiology of Oil and Gas Degradation in Terrestrial and Marine Environments
  • Fungi and Their Role in Ecosystems
  • Innate Immunity at the Host-Microbe Interface
  • Integrative 'Omics Approaches in Model Human Host-Microbiome Systems
  • Life in the Extreme
  • New Life for an Old Regulator: New Developments in ppGpp Research
  • Patho-Epigenetics
  • Shifting Paradigms: Diversity in Chemotaxis Signling Systems
  • Small Genetic Change: Large Impact
  • Stem Cells and Microbial Reprogramming of Host Cells and Tissues

My Book Review of The Hologenome Concept by the Rosenbergs

"Holos" means whole in Greek and genome is of course all of the DNA in an organism. Thus, hologenome is the term that captures the intergenomic networkism present in every animal and plant and parallels the term holobiont - the sum of all organisms present in an animal or plant.

Microbe magazine published my book review of the Hologenome Concept: Human, Animal and Plant Microbiota. As good friend Dr. Laura Williams pointed out to me, the review is unfortunately under a paywall. I believe this book will strike a chord with everyone interested in the life sciences. It is a form of heightened pattern recognition in biology. Hence, I'm posting the original text of the review here. 

The Hologenome Concept: Human, Animal and Plant Microbiota              Eugene Rosenberg and Ilana Zilber-Rosenberg (ed.). Springer, New York, 2014, 178 p., $149 (eBook) or $189 (hardcover). “So, like it or not, microbiology is going to be in the center of evolutionary study in the future—and vice versa.” -Carl Woese, The Hologenome Concept, pg. 109 In The Hologenome Concept: Human, Animal and Plant Microbiota, Eugene Rosenberg and Ilana Zilber-Rosenberg methodically advance the postmodern synthesis in which the holobiont — the host plus its associated microorganisms— forge a unique biological entity subject to the fundamental tenets of biological evolution. This book is based on the popular idea that no “individual” plant or animal, including Homo sapiens, exists independently of microbes. The authors were in fact among the fırst serious advocates of this view and have published a number of conceptual papers on the hologenome. Now backed by a symphonic-like arrangement of hard evidence, The Hologenome Concept is poised to be an influential piece of literature that encompasses biology’s most signifıcant developments in the last decade. What has led Rosenberg and Zilber-Rosenberg to this inflection point? Looking back in history, the germ theory of disease is a perfect starting point to put The Hologenome Concept in context. The germ theory left two lasting legacies on biology. First, it massively widened the focus of biology on diagnosing, treating, and eradicating infectious diseases. Second, it narrowed biology’s focus on microbes to such an extent that all host-associated microbes were essentially viewed as harmful and thus extrinsic entities to animals and plants. Today, there are of course a myriad of reasons to doubt that all microbes are bad (indeed quite the opposite), and this shift in thinking gained notable momentum in the mid- 20th century. Ivan Wallin’s and Lynn Margulis’s plights in convincing biologists that mitochondria were bacterially derived were among the seminal turning points in adjusting perceptions toward the broader nature of evolution. In the last few decades, microbiology has made revolutionary contributions to all disciplines of biology. From Carl Woese’s evolutionary tree of life to the universality of microbiomes in plants and animals, there is a tangible sense that something substantial is affecting how we study, understand, apply, and teach the life sciences. More than just advances in technology and more than realizing the central importance of microbiology in shaping life, the postmodern synthesis that we are now witnessing is tackling additions and upgrades to theories that seem untouchable, including the Darwin and Wallace theory of evolution by natural selection. Rosenberg and Zilber-Rosenberg demonstrate with precision that this inflection point in the history of biology is not just a common sense issue, but one that is scientifıcally grounded in a treasure of data. Chapters are devoted to illustrating how the canonical mechanisms of evolutionary change seamlessly fıt into a hologenomic unit of selection, namely genetic variation in the hologenome, maternal transmission between holobiont generations, and multi-level selection theory and fıtness. They bring together a vivid recipe for how variation in plants and animals exists beyond the nuclear genome, spanning microbial amplifıcation, acquisition of novel microbes, and horizontal gene transfer. In particular, genetic variation of complex organisms is not restricted to the nuclear genome and cytoplasm, but to the general microbiome as well. This variation encodes phenotypes subject to natural selection. Thus, the central tenet of the book is that the hologenome is a newly appreciated unit of variation and evolution in which the amalgam of genomes in the host and symbionts collectively are a target of natural selection. For those that have seen the central role of symbiosis in biology, this book will be an essential reference of key papers, defınitions, teaching, inspiration, and future discourse. It was for me. For others that doubt the emerging horizon of the microbiome’s role in evolution, this book will fuse their familiarities with frontier research to form a new appreciation on how variation and selection on the host-associated microbiota is equal to these same forces acting on the nuclear genome. Indeed in my own analysis of the book, I have found it most helpful to ask, when are the evolutionary properties of a nuclear gene any different than those of a microbe in the microbiome? I have not yet been able to discriminate the two, and this simple exercise is the essence of The Hologenome Concept. The book is written exceptionally clearly and provides bullet points at the end of each chapter to emphasize key themes in the text. The fırst chapter is one of the most important of the book because it frames the concepts and definitions in such a clear manner that confusion over nomenclature, which can be widespread in the early phases of introducing new concepts, is erased in favor of a vibrant appreciation for a hologenomic level of selection. What is and is not the hologenome makes the rest of the arguments seamlessly fall into place. The hologenome is not a metagenome, superorganism, organ, or the singular unit of selection in evolution. It is a body of scholarship that fıts squarely into genetics and multilevel selection theory in which the genome, DNA-containing organelles, and microbiome cooperate and clash to forge a source of variation for evolution by natural selection and the origin of species. The Hologenome Concept: Human, Animal and Plant Microbiota brings forth an upgraded “grandeur in this view of life.” Seth Bordenstein Vanderbilt University Nashville, Tenn.

Claire Fraser TEDx: "Im a microbiologist; I love Bacteria"

Just found this video which was posted today by the Institute for Genome Sciences. It appears to be a TEDx Mid Atlantic 2013 lecture by Dr. Claire Fraser.

Dr. Fraser, Director of the Institute for Genome Sciences at the University of Maryland, is a big deal in the science of genomics and microbiology. Her lecture is an introduction of ~17 minutes in length. It is worthy of your attention, especially if you need an introductory refresher on the microbiome or are just a fan of Dr. Fraser's science.

The only thought I'd add is that while ecology is a persistent theme in this talk, there is also an evolutionary story to be told as well. More to come on this later as our lab delves into the microbiome-evolution axis.

Congratulations to the 2014 Golden Goose Awardees

In 2012 I happened to sit on a plane next to Congressman Jim Cooper from Nashville, TN, where I learned of his brainchild, the Golden Goose Awards, to honor the serendipity of how basic federally funded research significantly impacts our daily lives (blog link).

The award program is first rate and has honored some notable scientists. Congrats to the 2014 awardees! Here is a well-done video of their stories.

A small investment in science brigs us the vastness of tomorrow.

ABOUT THE GOLDEN GOOSE AWARD

What: The purpose of the “Golden Goose” award is to demonstrate the human and economic benefits of federally funded research by highlighting examples of seemingly obscure studies that have led to major breakthroughs and resulted in significant societal impact.  Such breakthroughs include development of life-saving medicines and treatments; game-changing social and behavioral insights; and major technological advances related to national security, energy, the environment, communications, and public health. Such breakthroughs may also have resulted in economic growth through the creation of new industries or companies.

Congressman Jim Cooper (D-TN) originally conceived of the Golden Goose award as a means of educating Members of Congress and the general public about the value of federal funding of basic scientific research. The name of the award is a play on the “Golden Fleece” awards issued between 1975 and 1988 by Senator William Proxmire (D-WI), which targeted specific federally funded research grants as examples of government waste. The name also alludes to the fable of the goose that laid the golden eggs. Researchers who have used federal funding to make their research breakthroughs constitute the “goose,” and the innovations stemming from their work are the “golden eggs.” The Golden Goose Award explicitly links the two.