Friday, July 25, 2014


AAM Link
This new report on the charted and uncharted viral world (what it was tentatively called last year) is now out from the American Academy of Microbiology and a group of virologists (including me). We met last summer in Washington, DC, stuck ourselves in a room for a few days, and had a fun mind jam. Here's what we and the excellent team at AAM came up with. The steering committee for the meeting included Curtis Suttle, Marilyn Roossinck, and Willie Wilson. 

Link to page:

Abstract: In contrast to their negative reputation as disease causing agents, some viruses can perform crucial biological and evolutionary functions that help to shape the world we live in today, according to Viruses Throughout Life & Time: Friends, Foes, Change AgentsViruses Throughout Life & Time: Friends, Foes, Change Agents is based on the deliberation of a group of scientific experts who gathered for two days in San Francisco, CA in July 2013 to answer a series of questions regarding the variety of roles that viruses play in the natural world.

Executive Summary: In contrast to their negative reputation as disease causing agents, some viruses can perform crucial biological and evolutionary functions that help to shape the world we live in today, according to a new report by the American Academy of Microbiology.

“Viruses participate in essential Earth processes and influence all life forms on the planet, from contributing to biogeochemical cycles, shaping the atmospheric composition, and driving major speciation events,” states Marilyn Roossinck of Pennsylvania State University, a member of the steering committee that helped to organize the colloquium.

The report, Viruses Throughout Life & Time: Friends, Foes, Change Agents, is based on the deliberation of a group of scientific experts who gathered for two days in San Francisco, CA in July 2013 to answer a series of questions regarding the variety of roles that viruses play in the natural world.

“The inspiration for holding the colloquium was that recent metagenomics studies of viruses have indicated we know very little about the real world of viruses. Almost all published research is about the viruses that cause disease in humans and their domesticated plants and animals. This certainly represents only a very small fraction of the viruses that really exist,” says Roossinck. “It is very important to understand the real world of viruses, as this can inform our basic understanding of life and its origins, as well as major earth phenomena like carbon cycling.” 

Beyond their pathogenic impact, the report examines in depth the size of the virosphere, the origin of viruses, the overlooked biological and microbial ecological role of viruses, and how these live forms have contributed to evolution. Additional highlights from the report explain how some viruses are commensal organisms or symbionts, their functioning in microbial communities, and their role in maintaining the biosphere. The array of responsibilities taken on by viruses is due to their incredible sequence diversity and genomic plasticity, referred to as “viral dark matter”.

The report concludes by stimulating the readers to think about key questions: “What if viruses had never existed on Earth? Would life have evolved quite differently”? Continued viral research will help to answer these enticing questions.

Links to papers and talks on endosymbiont phage from our lab:
3. Seminar at University of Illinois | Phage section starts at ~31 minute mark

Sunday, July 20, 2014

The Ten Principles of the Hologenome

Source: Charis Tsevis, Science News
(Update - June 12, 2015: For newly updated principles, see this blog post - What are Holobionts and Hologenomes?)

So recently I've been thinking a lot about the principles of the hologenome. From a summer workshop at the Munster Graduate School of Evolution in Germany to various dialogues with luminaries, there is a palpable interest in what is and what is not the hologenome. From reading The Hologenome Concept by the Rosenbergs and their conceptual papers to a coming NESCENT workshop on the ecology and evolution of the host-associated microbiota, I am now taking stock of what I've stored in the attic thus far and trimming it down to make it useful for everyone. I have also set up a FaceBook community page on the Hologenome for anyone who would like to join the discussion. I anticipate that Ill publish this list in a journal at some point, but for now it is most valuable here and at once.

These are my Ten Principles of the Hologenome.

1. The hologenome is a unit of selection that incorporates the genomes of the holobiont - host genome, cytoplasmic organelles, and host-associated microbiome. These three compartments of variation can cooperate or clash to forge a unit of selection whose importance grows as we probe the functions and specificity of the host-associated microbiome. 

2. The hologenome is comprised of microbial parasites, mutualists, and commensals - all sources of variation that selection can act against or with.

3. The hologenome is best understood in terms of equating a microbe in the microbiome to a gene in the genome - if a gene can be selected for in the genome, a host-associated microbe can too. If a gene is neutral, a microbe can be too. If a gene comes and goes in the genome (i.e., recombination), a microbe can too.

4. The hologenome is not a superorganism, metagenome, organ, or the only unit of selection. It is an assembly of genomes of diverse organisms, some of which is essential to holobiont fitness.

5. The hologenome is a body of scholarship that fits squarely into genetics and multi-level selection theory.

6. The hologenome does not change evolutionary biology, but upgrades it to incorporate the microbiome as part of the genetic variation subject to selection.

7. The hologenome fits seamlessly into all canonical mechanisms of evolutionary change, namely genetic variation, intergenomic disequilibria (i.e., mitochondria and host genome), maternal transmission to some extent, and selection.

8. The hologenome reboots Lamarckian evolution (microbial acquisition) into neo-Darwinian evolution.

9. The hologenome variation arises not only from genetic variation, recombination, mutation, but also new microbial acquisition, microbe amplification, and extensive horizontal gene transfer.

10. The hologenome exemplifies the postmodern synthesis of various disciplines, including the unification of evolutionary biology, genetics, and microbiology. 


Wednesday, July 16, 2014

Out with the mosquitoes. In with the Wolbachia!

A University of Kentucky professor (disclaimer: good friend), Dr. Stephen Dobson, and his former student have teamed up to form MosquitoMate - a company aimed at using a unique approach to getting rid of mosquitoes and their transmitted viruses. Many of the readers of this blog will be familiar with the Eliminate Dengue project in which mosquitoes infected with bacterium Wolbachia are released with the aim of replacing uninfected populations that can transmit human disease agents with Wolbachia-infected ones that can not transmit the disease. 

This new approach aims to release just Wolbachia-infected males to sterilize female mosquitoes in nature. By doing so, the mosquito population size can be crashed, if not eliminated wholesale. A great video and some selected quotes below:

"Most mosquito control companies use chemical pesticides which are sprayed out of trucks and planes, or maybe out of a backpack sprayer," Dobson said. "Ours is a very different approach. By using a natural bacterium called Wolbachia and the mosquitoes' innate ability to find mates, we are applying an approach which does not require chemicals."

"A big advantage to our method is that the male mosquitoes are 'self-delivering.' We don't need to devote hours in finding and treating all the mosquitoes in your yard. The male mosquitoes find the females for us," Mains said.

I really like this work! Good luck to the team. 

Monday, July 7, 2014

Scientists: How can you afford to not be on social media?

It's no secret anymore. Science has embraced social media in a way that will have many early adopters saying "I knew this was going to happen" and those yet to adopt it saying "What's all the fuss about? How can I get involved?

Using social media for science is like any other aspect of life that needs diligence and training. If you don't care about it or don't know what to care about, you'll be missing all the fun and rewards. I had the same journey. I questioned the value of spending bits of time on twitter or why people would blog - that seemed like a major time sink. But when scientists that i respected were so involved with social media, i felt compelled to figure out what they got out of it. There are far more virtues of social media that one could list in a short blurb about it. So I will boil some of my favorite aspects of social media down to three key points.

1. Staying in touch with the current literature - If you don't use twitter, then you likely stay on top of new articles by pubmed searches, table of content emails, and word of mouth. Twitter makes these methods seem archaic as following experts and their tweets brings the literature directly to you rather than you searching for it. It also comes filtered directly from the experts rather than through luck of finding the articles in a random search. Many tweets are just links to really cool articles that you would have seen six months later in a pubmed search; but because luminary X on twitter caught it first, you get to see it and integrate it into your science far faster. Also, sometimes the tweets to publications come with a fatal criticism or major complement - helping you to see where the community places the work. 

2. Staying in touch with conferences - It seems like there are more and more conferences that we all want to go to every year, but we don't have the budget to attend all of them. Twitter users will use hashtags (i.e., #ASM2014 for this year's American Society of Microbiology meeting) that you can click on and follow the conference in a virtual way that brings you the most exciting talks and key points right to your desktop or phone. Following conference hashtags has been of such tremendous value to me that I have at times questioned the need to go to conferences all that often. Moreover, if you're not at a conference, you can interject into conference happenings by tweeting to conference goers or using the hashtag to virtually place your ideas and "self" in the conference.

3. Giving your research wings - Both twitter and blogs are venues to disseminate research and the stories behind that research to those that care. You can hope that someone reads a table of contents and finds your most recent publication or they search for your work in pubmed, but why not cast your paper into their world directly through social media. In this fast-moving and competitive world of science, getting your student's work out there is important. Or for the assistant professor, how about expediting the growth of your international reputation by connecting with tweeters from across the world? It is lab policy that all students join twitter. Some use it more than others, but at least it is something they can test out and come back to if they don't like it at first. 

I like to think that twitter is my Department of the World in which collegiality by proximity is replaced by collegiality without borders. I can tweet research questions, follow my peer's work, go to conference seminars, talk about latest results, promote students all in the social media world. It takes far less time that non-users think, it is far more valuable too, and the only question left to ask is "How can you afford to not be on social media?"

Seth Bordenstein

Twitter: @Symbionticism

Thursday, July 3, 2014

Homo evolutis: Faster than Moore's Law?

Stop what you're doing and take a moment to be inspired. We all need a little bit of it every now and then - no matter how fleeting the inspiration is. It is a bit out there but within the realm of speculation.

Let's talk about a mind-expanding idea on the future of us. Its about what Homo sapiens is about to become through the exponential growth of nanotechnology, artificial intelligence, and genomics.

With this long view of so-called "Homo evolutis" by Juan Enqriquez (TEDx talk here) in mind, the philosophical futurist Jason Silva, aka The Timothy Leary of the Viral Video Age, reminds us below of E.O. Wilson's quote:

"Homo sapiens, the first truly free species, is about to decommission natural selection, the force that made us…Soon, we must look deep within ourselves and decide what we wish to become". Here is Silva's cinematic trailer-like video "To Be Human is To Be Transhuman".

Ok. Back to reality and go have a great July 4th! But if you'd rather stay in the moment, watch this next one on "Awe".

Tuesday, July 1, 2014

What do evolutionary biologists talk about at their annual conference?

If you're like me and did not make it to Raleigh, NC this past month for the annual Evolution 2014 Conference, well there's good news. I'm jazzed to see there are a plethora of lectures online at their Evolution 2014 YouTube Channel. This meeting is one of the premier venues to share scientific research related to evolutionary biology.

Most talks are short (15 minutes) and you can get a sense of the topic and the speaker in the title of each presentation. Be sure to click the "Load More" button as you scroll to the bottom to load all the seminars. I haven't watched all the ones that I wanted to yet, but Ive saved them to my "Watch Later" bin. Anyone can do this if they have a YouTube Channel (mine is here). I highly recommend starting a professional channel as a venue to store your talks online and disseminate them to the community. Like all forms of social media in science, these tools are taking off and good ways to advance the open access nature of your science across the world, to the few people who may actually care to watch.

As an example, here's a recent talk by senior graduate student in our lab, Lisa Funkhouser-Jones. In her research, the key question is how many animal genes does it take to tame maternally transmitted bacteria (Wolbachia)?