Monday, March 23, 2015

My Podcast With People Behind the Science

Just a quick post. I really appreciated the opportunity to record a podcast with People Behind the Science in January; it just posted today. You can read part of the transcript below or listen hereThis podcast series by Dr. Marie McNeely is a wonderful service to science and education as it helps break down the wall of silence between scientists and non-scientists with stories of wit, inspiration, dilemma, light bulb moments and motivation. 



235: Dr. Seth Bordenstein: Seeing Science and Symbiosis Through the Lens of an Evolutionary Microbiologist


Listen to the Episode Here
Dr. Seth Bordenstein is an Associate Professor in the Department of Biological Sciences and in the Department of Pathology, Microbiology, and Immunology at Vanderbilt University. He received his undergraduate, Master’s and PhD degrees from the University of Rochester, receiving his PhD in Evolutionary Genetics. Seth then served as a Postdoctoral Fellow of the National Research Council in the Marine Biological Laboratory in Woods Hole. He worked as an Assistant Research Scientist and Assistant Scientist there and also served as an Adjunct Assistant Professor at Brown University before joining the faculty at Vanderbilt. Among his many honors and awards, Seth has received the Chancellor’s Award for Research and awards for Excellence in research as well as Teaching and Mentoring from Vanderbilt. His research was also featured in as a top story of 2013 in Science News. Seth is here with us today to tell us all about his journey through life and science.
People Behind the Science Podcast Show Notes
Life Outside of Science
When not doing science, Seth spends most of his time with his family. His wife works with him in the lab at Vanderbilt and he has two wonderful daughters.
The Scientific Side
Scientifically, Seth is answering evolutionary biology questions focusing on how one species splits into two, how we achieve the great biodiversity of the planet, and the underlying mechanisms that produce biodiversity.
A Dose of Motivation
“Don’t be trapped by dogma – which is living with the results of other people’s thinking. Don’t let the noise of other’s opinions drown out your own inner voice. And most important, have the courage to follow your heart and intuition.” by Steve Jobs.
“It is a rather startling proposal that bacteria, the organisms which are popularly associated with disease, may represent the fundamental causative factor in the origin of species.” by Ivan E. Wallin
What Got You Hooked on Science?
In college, Seth was struggling to figure out what he wanted to do for a career. However, during his sophomore year, one course in evolutionary biology basically turned him into an evolutionary biologist overnight. This course was taught by two prominent evolutionary biologists Howard Ochman and Allen Orr, and he was immediately fascinated by the field.
The Low Points: Failures and Challenges
Seth’s entire career was on the line when he was nearing the end of his contract at the Marine Biological Laboratory. He was applying for grants with very frustrating results and was beginning to seriously consider alternative career options. Among the options on the table was a career playing poker professionally. Believe it or not, his odds at winning poker were actually higher than the odds for getting a major grant.
A Shining Success!
One science success that Seth has been really excited about examined the role of the gut microbiome in the origin of species. He worked with a talented student to discover that more closely related species have more closely related microbiomes and hybrids can have different microbiomes than either parent. These discoveries were true eureka moments for him and solidified the idea that the pairing of the genome and the microbiome tells a story of ancestry.
Book Recommendations
Symbionticism and the Origin of Species by Ivan Wallin
Most Treasured Travel
In 2009, Seth was able to travel to Japan for an invited lecture. This trip was particularly memorable because Japan was unlike any of the other places he had ever been. He was impressed with the culture, the beauty of the country, and the food. These all left a lasting impact on him.
Quirky Traditions and Funny Memories
As an undergraduate, Seth contributed to some character-building fly room duties that involved cultivating maggots using raw liver. This task was associated with rather unfortunate odors and had to be done even on the weekends. One weekend when Seth went in, the water in the building had been turned off for maintenance, so when he went to clean up and wash dishes afterwards, no water came out. He didn’t learn until later that he had left the sink on with the drain blocked and when the water came back on, the fly room was flooded. This resulted in a big mess including mildew and fungal growth that other lab members had to clean up.
Advice For Us All
Do what you love. This was the single best thing Seth has ever done.
Guest Bio
Seth has broad interests in the role of microbes in animal evolution and health. His lab asks non-linear questions to probe the rules of symbiosis, evolution, and their inseparable connections. They are conducting research to try to uncover the role of the microbiome in the origin of species. Other projects in the lab focus on how viruses subsist in obligate intracellular bacteria. In addition, Seth’s lab is trying to better understand how universal the process of maternal microbial transmission really is. You can learn more about Seth and his research by viewing his lab websitefollowing him on Twitter, or visiting his blog.

Monday, December 29, 2014

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.



Saturday, December 27, 2014

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



Friday, December 26, 2014

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

Sunday, December 21, 2014

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.

Afternoon Symposia

2:00 p.m. – 4:30 p.m.

Special Interest Sessions

4:45 p.m. – 6:30 p.m.

Monday, June 1

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

Afternoon Symposia

2:00 p.m. – 4:30 p.m.

Special Interest Sessions

4:45 p.m. – 6:30 p.m.

Tuesday, June 2

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

Thursday, November 13, 2014

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. 



            
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.