Thoughts on Survival/Success in The New Era of Academia - Part 1

Considering what has transpired in my career thus far and its still a career in its early phases, I have accrued just a few nuggets of wisdom that are useless if they are not shared. Let's start with the obvious. A career in the life sciences has its bountiful share of stress, which can frequently limit passion. Im not optimistic for the future of science if passion continues to dwindle for young scientists given the current funding climate. Take this observation for instance. Students in bio (red line) lose their interest in academic research jobs as they spend more time in grad school. Wow. Are PIs that bad at training their students to enjoy the job? Are we not taking in qualified enough students who can find strength through the struggles?

Citation: Sauermann H, Roach M (2012) Science PhD Career Preferences: Levels, Changes, and Advisor Encouragement. PLoS ONE 7(5): e36307. doi:10.1371/journal.pone.0036307

As a graduate student, I wished that I had a better idea of what it took to be successful in academia; I was told not to worry - that there would be plenty of jobs because the baby boomers would be retiring. That led to some false hopes. Fortunately, few students are being told this today. Not so fortunately, the latest stats indicate that 14% of life science phd land an academic job. As a postdoc, I wondered what it took to secure an academic job in a highly competitive environment. What was I supposed to do different than grad school? As a beginning investigator, I wondered how to get funded? This happened to be right around the time federal funding percentages were plummeting to historical lows (whoops). I wrote six grants before I got my first NSF grant. The answer to all these questions is the same. DO NOT TAKE NO FOR AN ANSWER. Perseverance is what make the difference. We can persevere if we imagine what excellence is and pull our future forward to meet that excellence. Excellence is always ahead of us and can always be attained by any of us. Just dont give up.

Success, which is what we are talking about here, is a state of mind more than a thing. In this light, I started tweeting nuggets of wisdom under the Twitter hashtag #tosrb for thoughts of my initials. I have heard from some colleagues and students that these shots of insight are useful. That is my hope, that I can pass on some insight to those that are just beginning. By doing so, by coaching through accrued wisdom, we may speed up the pace of excellence in science for future trail blazers, rather than waiting for people to learn these things themselves over a long career. 

Over this coming week, I will post several of these tweets on a daily basis. Red highlights indicate ones that I think rise about the rest. As always, comments and questions are encouraged!

1. 1/23/13: If u dont train your students to be better than u, then u are failing them and the society who benefits from future scientists #tosrb
2. 1/23/13: Most grad students transform in grad school. Fewer transcend. 14% ultimately get academic jobs. We need to talk about why. #tosrb
3. 1/23/13: Grad school is not a right of passage once students enter it, but rather the beginning of a 5 year boot camp. No guarantees at end. #torso
4. 1/23/13: Only 14% of life science PhDs in US get tenure track jobs in comparison to 55% of law students becoming lawyers. Change is needed #tosrb
5. 1/24/13: PI's must recognize that any recognition imparted to them is because of their students. Anything else is a failure in leadership #tosrb

3 Facts You May Not Know About Bees and Colony Collapse Disorder

We need bees for our future. They are essential for 130 crops and command 16 billion dollars of industry value. Yet bees are disappearing from the bizarre phenomenon of Colony Collapse Disorder without signs of an obvious disease. Several of my colleagues in the insect and microbiome fields are working hard to better understand and solve this major problem, including Jay Evans, Nancy Moran and Irene Newton. It seems as if not just one infectious agent causes colony collapse disorder but rather it arises as a tragedy of diverse reasons.

I came across the talk below and received a major upgrade in my knowledge on Colony Collapse Disorder. Noah Wilson-Rich's Tedx Boston talk raises several counter-intuitive facts about urban beekeeping and its impact on the colony collapse mystery. The 3 most salient facts he describes are below, followed by his full Ted talk.

• Colony Collapse Disorder is not a new problem. Say what... that's not what Ive been aware of.   Yet Noah shows at 6:03 in his talk that bee die offs have occurred periodically over the last 1000 years.

• Survival of bees is greater in urban beekeeping (62.5%) than the more traditional rural beekeeping (40%). Can we get some microbiome folks working on this please? Do bees reared on city roof tops have a better microbial community than those reared rurally? Noah's Best Bees Company uses a probiotic nutritious blend (Apivax) to inhibit fungal infections and upregulate the bee immune system.

• Honey yield is greater in urban beekeeping (26.25%) versus rural beekeeping (16.75%). Here honey yield is measured as average pounds for first year.

I like Noah's approach. He is trying to figure out ways to increase bee health as a complement to others focussed on figuring out how Colony Collapse Disorders arise. The merger of these two paths will undoubtedly be fruitful when it occurs in the future.

Diet Cures Multiple Sclerosis

Source

I am fascinated by how changes in the gut microbiome can alter the course and even reverse human disease. Take the recent surge of fecal transplants for instance to treat chronic diseases such as IBD, Clostridium difficile, Crohn's, and multiple sclerosis (blog post). I am also intrigued by how plant strong and paleo diets seem to be increasingly beneficial for health.

Here is an inspirational TEDx talk by Dr. Terry Wahls (@TerryWahls) on how she used pubmed.gov to research and develop a hunter gatherer diet rich in phytonutrients that cured her multiple sclerosis - an autoimmune disease of the central nervous system. Note that her approach focussed on the beneficial vitamins and phytonutrients from these foods. She did not mention the changes in the gut bacteria that are also occurring on this diet and that can have positive repercussions on the body's metabolites. I hope her message helps others.

Diet changes the gut microbiome, which in turn changes the metabolic, neuronal, and inflammatory networks that may cause or cure many chronic 'Western' diseases. Nothing short of awesome. The regenerative power of the gut microbiome is akin to stem cells and here to stay.

The Robogut: Bring Your Insides Out [video]

This state-of-the-art Robogut at the University of Guelph is used to simulate the inner workings of the human gut with bottles, gas chambers, and tubes. Amazing research. The goal is to mine the liquid gold products of the human microbiome and use them for applications to human health. Who would have thought to turn the complexity of the intestine into an in vitro culturing system. Im inspired by the creativity and applications here. I imagine some of you out there might have some fresh ideas for what you'd like to do with such an apparatus. Leave your comments below.

Apparently, this same lab just used the apparatus to grow a cocktail of good bacteria to treat patients with Clostridium difficile. Link to cbcnews story from today.

                         

Source: thestar.com

Related Blog Post:

Can a fecal transplant cure IBD, Colitis, Crohn's, C. difficle, Multiple Sclerosis..?

The Superorganism - Vlog 3

In this video blog, I use the analogy of Superman to describe the Superorganism - a collection of organisms that together gives powers (i.e., fitness) to a single animal or plant. Other similar terms such as Bosch & McFall-Ngai's metaorganism and Rosenbergs' hologenome are pulled together to discuss what it will take to know if these terms are real evolutionary units of Life, real entities that the frontier of Biology must confront. As mentioned previously, I view these vlogs so far as experiments that will only survive or not with your feedback. I look forward to your criticisms or support on the video blogging vs. text blogging and the concepts in the videos. Thanks a bunch, Seth

Related vlog or blog posts:

1. Phylosymbiotic Vlog 1
2. The Large Immune Effect Vlog 2
3. Science of the Superorganism
4. The Story Behind Speciation By Symbiosis

Microbiology / Science Trends in Web Search (2004-2012)

Just caught wind of this Google Trends tool that shows you the worldwide web search interest in any term you give it from the period 2004-2012. It then scales the data over time as a percentage from 0 to 100%, with 100% being the peak of the search intensity.

So I dipped into some science words. Interesting trends below...

MICROBIOME

-reassuring but no surprise here. Looks like we're now in an exponential growth phase

MICROBIOTA

- odd oscillations that I cant quite put a finger on, but note increasing trend over time

MICROBIAL DIVERSITY

-Note how popular this term was 8 years ago, prior to rush of studies on microbial diversity in hosts, now referred to as microbiome and microbiota

MICROBIAL ECOLOGY

-same problem as microbial diversity, above

DARWIN, EVOLUTION

-Yowza, trend seems to show pretty big decline with a flatline now. Is this correlated to rise of anti-evolution bills, I wonder.

SCIENCE

-again, I take this as a concerning sign. Sigh

SCIENCE EDUCATION

-uggghh, more sighs

FACEBOOK

-positive control in this experiment works!

Grant Writing Inspiration [picture]

Bringing out the big guns for a dose of grant writing inspiration today

Coffee, check

Spicy hot cocoa to add kick, check

Candle (and cello music) ambiance, check

Darwin bobble, check

Matryoshka doll for symbiosis, check

Foam earth ball to toss against wall, check

Brain upgrade initiating....

"The Large Immune Effect" - Vlog 2

In this 2nd video blog (vlog), I introduce the concept of the Large Immune Effect - a colloquial term first introduced in our Speciation by Symbiosis Review in Trends in Ecology and Evolution 27(8):443. The Large Immune Effect refers to the collection of evolution studies that provide evidence that immune genes are the most rapidly evolving in human and other animal's genomes and undergo the most adaptive evolution. As a result, immune genes are agents of change that can drive population shifts in the microbiome which may parallel the evolutionary history of the host. Its interconnections with Phylosymbiosis are presented, which is a term that was previous discussed in video blog (vlog) 1. As mentioned previously, I view these vlogs so far as experiments that will only survive or not with your feedback. I look forward to your criticisms or support on the video blogging vs. text blogging and the concepts in the videos. Thanks, Seth

"Phylosymbiotic" - Vlog 1

I've decided to incorporate video blogs in order to make some of the information exchange here more immersive and interactive. While I can't see the others watching or reading these blogs, I do know that I appreciate video over reading myself. Scientists are often out of the comfort zone on video, and stick to what they know best - writing. But in my opinion we need not worry so much as the point of social media, blogging, and microblogging is to connect. Video blogging can be easier and more immersive, thus establishing better connections. Through video and the general media, science has a better opportunity to increase scientific literacy. So here goes jumping into the video blogosphere head first. Hope others consider doing this too -Seth

The Digitization of Education: What is all the fuss about MOOC?

Have you heard the buzz around Massive Open Online Education (MOOC) over the last year? How much do you really know? From the Khan Academy videos to the water cooler talk among department colleagues who are rightfully concerned about the future of their profession, there is a tidal wave of change potentially coming to Universities. 


Information technology has changed every industry it has touched and it is currently in the nascent stages of changing academia. Ten years from now if information technology has its way, education will be far different, more immersive, and hopefully more beneficial to the masses than it is today. The division of student and professor will possibly be blurred as the conventional rules of linear lecturing will be decommissioned to an academic world that the student hasn't created, but nonetheless gets to affect through their own online learning.

I have been looking for a good article or video on MOOCs to brush up on my basic understanding of them. This one is it. Coursera co-founder Daphne Koller gives a perfect 20 minute breakdown via her TED talk. It touches on the need, promise, opportunities, and fears of MOOCs.

For a critique of the MOOC movement, see this recently published article.  The MOOC movement is not an indicator of educational evolution.

The Science of The Superorganism: Host-Microbiota Specificity, Again

What determines the constituents and abundance of microbes in a host? 

A critical question emerging in the science of the Superorganism (our genes + microbial symbionts) is how exactly does the microbial symbiont community inside us assemble? Is it random? Do we just acquire the bacteria that are around us when we're born? Does our diet affect which bacteria thrive in our guts? Do our genes interact with the admixture of microbes in the environment to select for specific ones that confer beneficial traits?

Numerous studies show the influence of diet on the assemblage of the microbial community. But emerging studies in the past year, which have received less attention, indicate the host selects for specific species of bacteria as well. Here are three highlight stories:

1. Hawlena et al (2012) show that in fleas and ticks, the composition of the microbial symbiont community is not determined by their vertebrate host (rodents) or environment, but by their arthropod host. Specifically, ticks have different communities of microbes than fleas, and species of ticks share more similar microbial communities than species of fleas. Other factors such as rodent host did not matter as much.

2. Salem et al (2012) show in firebugs that the "fitness of symbiont deprived bugs could be completely restored by re-infection with the original microbiota, while reciprocal cross-infections of microbial communities across both pyrrhocorid species only partically rescued fitness, demonstrating a high degree of host-symbiont specificity" In particular, survivorship decreases and nymphal development time to adulthood increases in aposymbiotic and cross-infected species, but not control or re-inoculated species. Even mating frequency is reduced. This study has a really beautiful set of functional data.

3. Engel and Moran (2013) describe a specific and stable microbial community of honey bees, suggesting long-term coevolution between bee-specific bacteria and bees.

If anyone has any important studies to highlight on this topic, please let me know so I can post them.

Note: we also found species-specific microbiotas that changed in constituents and abundance in parallel with the speciation events of their Nasonia wasp hosts. Related blog posts on this work:

• The story behind Speciation by Symbiosis (April 26, 2012)
• Is the microbiome part of the organism or the environment? (May 11, 2012)
• Is the microbiota species specific? (June 23, 2012)
• ASM's Small Things Considered Spotlights Our Article (August 16, 2012)

Neil Degrasse Tyson | Video from Vanderbilt Lecture

Scientists and educators do not frequently achieve celebrity status. But shouldn't they? Shouldn't we live in a society where we have more science rock stars like Neil Tyson or the late Carl Sagan. Part of the decline of scientific literacy in America is due to the fact that scientists are not made more visible to the public, that politics trumps facts and smart policy, and that scientists are not valued equally to sports stars or media celebrities.

The media needs to buy into this concept so that science advances as fast as fashion and special effects in our culture. 

Last night, Neil Degrasse Tyson visited Vanderbilt. His visit inspired these brief remarks shared above. I recorded a few snippets of his opening remarks and views on science education. 

Dr. Neil Degrasse Tyson, an American astrophysicist and science communicator, discusses his arrival to Nashville, his talk, twitter, and his books in a very humorous way.

Tyson discusses the difficulties in advancing science education in America, the consequences it has on society, one way in which the fall of American science education can be reversed, and his responsibilities to educating the public, not congress.

Tyson discusses the decreasing trend line of American scientific literacy, the forces that want to change the science curriculum, and the national imperative in science literacy that his new show, COSMOS, will bring to Fox watchers.

Animated 3D Video of Human Microbiome

A quick post on a really good video from the Knight Lab on how the Human Microbiome (wiki) varies across body space (skin, mouth, vagina, gut) and across time (from infant to adult). Its a really nice way to sum up years of data in three minutes! I can also imagine that we all can immediately use this video in teaching the microbiome. Hence, this is why I am posting to the blog rather than twitter, where it may get lost in the twittersphere feed.

What is Open Access Publishing & Why Is It Important?

Answer: Open Access Publishing is the future.

This video should be mandatory watching for all scientists, students, and anyone remotely interested in using research to make decisions about your health and future.

Open Access Publishing allows you to read the articles you want for free. Afterall, you probably paid for some portion of the research through your tax dollars going to fund the federal science budgets.

The bearded guy with the plad shirt is Jonathan Eisen, who I credit for getting me interested in social media and open access publishing. He and others have done the same for countless other scientists. His Ted Talk on the ubiquity of microbes is worth a watch.

Animated Doodle Video of Wolbachia | Eliminate Dengue Project

As many readers of this blog know, the Wolbachia | Eliminate Dengue Project is a Bill and Melinda Gates Foundation project spearheaded by Scott O'Neill at Monash University in Melbourne.  Ive posted on it recently here. Yesterday, they posted this great animated doodle video for everyone to understand how Wolbachia, a bacterial infection of arthropods, is being used to stop mosquito transmission of dengue virus, the causative agent of Dengue (a.k.a bone break) fever.

Is this serious? You betcha. The World Health Organization estimates that over 40% of the world's population is at risk and a whopping 100 million dengue virus infections occur worldwide each year. Numbers of infection are also on the rise.

Symbiotic Control: Vietnam is next for Wolbachia-based eradication of Dengue

Source: ABC News 

Vietnam to replicate Cairns dengue project

By Brad Ryan

Updated Thu Oct 18, 2012 1:36pm AEDT

PHOTO: The project involves releasing mosquitoes after infecting them with the 'wolbachia' bacteria, which blocks the spread of the virus. (ABC TV News - file image)

MAP: Cairns 4870

Researchers trialling a technique to stop dengue fever transmission around Cairns in far north Queensland will replicate the experiment in Vietnam.

The Eliminate Dengue project involves releasing mosquitoes into communities after infecting them with the 'wolbachia' bacteria, which blocks the spread of the virus.

Vietnam's Ministry of Health has approved a trial on the small island of Tri Nguyen.

Program manager Dr Peter Ryan says it should begin in March.

"In Vietnam, particularly in the health system, the community is very involved in health programs there," he said.

"Essentially they're setting up the equivalent of a Neighbourhood Watch system for wolbachia.

"Representatives from the community will actually undertake releases of mosquitoes in their own and the neighbours' yards."

Dr Ryan says Vietnamese researchers have been involved in the program for several years.

"Scientists from Vietnam have visited Cairns and actually participated in some of the trials," he said.

"The Ministry of Health in Vietnam has just approved a field trial which will be undertaken in a small island called Tri Nguyen Island [with] about 700 households."

Topics: infectious-diseases-other, research, medical-research, invertebrates---insects-and-arachnids, cairns-4870, vietnam

First posted Thu Oct 18, 2012 10:49am AEDT

My talk at the University of Idaho

Earlier this week, I had the pleasure of visiting a talented group of biologists who are passionate and collaborative about evolution, microbial ecology, genomics, phylogenetics, mobile elements, theoretical modeling of coevolution, statistics, mathematics, and programming. Its an evolution commune dream - like the Woods Hole of the Northwest. If you're interested in any of these topics, you need to visit them or check them out on the web. The Department of Biological Sciences and the IBEST institute at the University of Idaho are top notch. The director of the IBEST institute, Prof. Larry Forney, invited me out for a seminar. Below is the talk nearly in full on the genomics of microbial symbionts (1st half, up to 35:43) and symbiont-induced speciation (2nd half, starting at 35:44). The instant start into Slide 2 is part of the video.

Symbionts as Targets and Agents of Change - October 16, 2012

Below are pictures taken along the way between Salt Lake City and Moscow, Idaho. The landscape is beautiful. The first one is courtesy of the Facebook page of the University of Idaho. While I was there, there was a campus-wide email alert of a moose on the loose on campus. They are aggressive but thankfully no harm was done and it made for a good chuckle. The second picture is a shot of Salt Lake.

Can A Fecal Transplant Cure IBD, Colitis, Crohn's, C. difficile, Multiple Sclerosis..?

Some call it a fecal transplantation. Others, fecal bacteriotherapy. Call it what you want, but there is regenerative power in poop for severe, bowel problems. Seriously? Yes. Cure rates are generally above 90% for Clostridium difficile; treatments for Crohn's Disease and Multiple Sclerosis are not as well studied, but appear promising. Everyone should know about fecal transplants as C. difficile infections have risen 400% since 2000 (largely due to hospitals spreading them). Just in the past year, I have had one family member and one friend come down with C. diff infection. Doctors are recalcitrant to prescribe fecal transplants, but that appears to be due to lack of knowledge rather than success.

1. CNN raised the profile of fecal transplants a trillion fold when it posted this article on the front page of its website a couple of days ago: Little known fecal transplant cures woman's bacterial infection. If anyone was previously skeptical, this article basically legitimizes fecal transplantation.
2. The Henry Ford Hospital in Detroit, MI recently found that 43/49 patients with C. difficile infections were cured after fecal transplants; they had no problems up to three months later. Fecal transplant from mom cures ailing toddler.
3. A 2011 literature review found that 92% of 317 patients with recurrent C. difficile infection or pseudomembranous colitis had disease resolution upon fecal transplant. 
4. Clinics and retreats are offered! For instance in the US, the Bright Medicine Clinic in Portland, Oregon performs Fecal Transplants for many conditions discussed below.
5. There's a blog called Fecal Microbiota Transplant that reports seemingly unpublished data on transplants improving Multiple Sclerosis in patients with bowel syndromes. At a minimum, patients were able to walk again!
6. Two papers on inflammatory bowel disease indicate that of nine patients who were non-responsive to standard treatment, all nine of them responded dramatically well to fecal transplant therapy.  Bacteriotherapy Using Fecal Flora (2004) and Treatment of Ulcerative Colitis Using Fecal Bacteriotherapy (2003)
7. We NEED a site that provides location information on fecal transplants. I can not seem to find one and people will clearly be asking for more information. Googling around appears to come up with specific instances, so if you search hard enough, you may find something in your neck of the woods. (There is a partial list of USA fecal transplant places here); if you're in TN, Vanderbilt's clinical chief, Dr. Michael Vaezi of Gastroenterology is doing fecal transplants in response to refractory Clostridium difficult; In Virginia at the Virginia Commonwealth University, Dr. Michael Edmond is doing fecal transplants for C. diff [news link]; In Nevada, Gastroenterology Consultants in Carson City offers fecal transplantation for C. diff
8. There's a Facebook Page that appears to be a good social media resource, aptly named Fecal Bacteriotherapy is "The Bomb"
9. There are reports on the internet of do-it-yourself fecal transplants. Clinics can be hard to find and the treatment is not typically covered under insurance, especially for IBD. Understandably, these barriers to a treatment have led some to pursue self-treatment with enema kits. Probiotic Therapy Home Infusion Protocol and Success of Self-Administered Home Fecal Transplantation for C. difficile Infection. 
10. A University of Guelph lab in Canada has developed a Robogut machine to simulate the human gut conditions in vitro. They have successfully used it to grow a cocktail of bacteria that cured C. diff infections from two elderly patients. What a breakthrough! Symbionticism Blog Post Link

Background: Despite the conventional lexicon that poop is dirty, an agent of infection, and should be left for one place and one place only - the toilet, poop may be as powerful in its regenerative capacity as stem cells. Perhaps better. Roughly 40% of your feces is made up of bacteria living inside and shed from your gut. These species help us digest food, develop intestinal tissue, and fight off infections among many other things.

Disease: The bacteria in your gut are as much a part of you as your genes. The fact that some fraction of them come out in your waste is fortunate because these symbiotic bacteria can be used in the purest form of recycling that humans may ever know. Friends or family that are suffering month-to-month, or year-to-year, with debilitating or deadly diseases such as Crohn's disease, ulcerative colitis (these first two are often referred to as IBD or inflammatory bowel disease), Clostridium difficile, etc know all too well the long and painful aspects of these diseases. In many cases, antibiotics are prescribed over and over, with each one that fails leading to more expensive ones that are also more difficult to get. The irony of the antibiotic ferris wheel is that antibiotics may be buying a little more time or even exacerbating the problem, while the solution happens to be right in front of us, or behind us to be technically accurate. The healthy bacteria in poop from a friend or family member can be "transplanted" into the gut of a sick patient and fully cure them in many cases.

Professor Thomas Borody (MD, PhD) is one of the leading physician scientists in this area and this video is definitely worth watching and sharing to classrooms, friends, and family.

Further Reading: Fecal Microbiota Transplantation and Emerging Applications. Borody and Khoruts 2012. Nature Reviews Gastroenterology and Hepatology 9: 88-96.

Update from O'Neill Lab on Wolbachia / Eliminate Dengue Project

This news just in from the Eliminate Dengue project in Australia (NPR story and audio). As Ive tweeted and blogged about many times, Scott O'Neill's lab has been leading a Gates Foundation funded effort to introduce Wolbachia-infected mosquitoes into Australian suburbs in the fight to replace uninfected mosquitoes that are competent to transmit dengue virus with Wolbachia-infected ones that are incompetent to harbor and transmit dengue virus. The science has been remarkably fruitful and the project's success appears to be positioning the program to do releases in other countries, such as Thailand and Brazil. Here we get an update letter from the Team. The key updates are:

• Wolbachia inhibits growth of Dengue virus in mosquitoes.
• Release 1: Of the massive releases of wMel Wolbachia-infected mosquitoes performed 16 months ago, a whopping 97% of mosquitoes harbor Wolbachia. That's staying power!
• Release 2: A second trial is ongoing to test if wMelPop Wolbachia can do the same as wMel. The difference between the two strains is that while wMelPop has stronger inhibition of Dengue virus growth in mosquitoes, it can not invade mosquito populations as efficiently as wMel.
• Release 3: Mysterious - they are currently working with a 3rd strain that combines the best of wMel and wMelPop. I have not heard about this yet in the literature but it is tantalizing.
• If you live in Australia, the Project needs you. Home owners in Edge Hill, Cairns North, Whitfield, Parramatta Park, Manunda, Westcourt, and Stratford, Australia should contact 1-800-811-054.

Seminar Teaser

Update: September 1, 2012 - Two more teaser slides for my Labor Day Seminar to the Department. Hopefully this will help the crowd grow from nobody attending to ten people, maybe? These questions are what the seminar will be on.

Original Post:

I am putting together a seminar for Monday and I am kinda proud of this opening slide. Nice to see all the young people and furry animals we've worked with over the past few years. I recommend all PIs do this because rarely do we see the lab family all together, and in one place, unless its for our retirement :) As I said earlier on Twitter two days ago:

One of the top things about being a scientist is watching students become better scientists than you at the same stage.

&

Training students to be better than you at the same stage = progress = 

brighter future for all.  

Photo of bacteria man altered from The Economist, Microbes Maketh Man, Jon Berkeley/SPL

Wall Street Journal on Wolbachia & Selfish DNA

When Genes/Microbes Look Out Only for Themselves

Wow. Its a fun week for science in the press. First, the Economist cover features the study of the microbiome, and today the Wall Street Journal's Matt Ridley picked up the theme of selfish DNA with a highlight on Wolbachia, cytoplasmic male sterility, and selfish mitochondria. Check out the big link above.

ASM's "Small Things Considered" Spotlights Our Article, Speciation By Symbiosis

Over at ASM's Small Things Considered Blog, a very popular blog on all things microbes, Elio Schaechter discusses our recent review entitled Speciation by Symbiosis. I'll start this post by saying that I think the review (coauthored by my student Rob Brucker, @liveinsymbiosis) is one of the most important pieces that Ive contributed to. I'll explain more about that opinion below. Elio is favorable to the article. He highlights some of the key aspects of the review, including:

1. Some of the examples they cite are startling. For one, Wolbachia, like some other bacterial symbionts of insects, induces parthenogenesis in the insect host, a form of asexual reproduction that does not involve fertilization and leads to what is called “asexual speciation

2. For another, Drosophila flies reared on different diets house different microbiota, and show strong mating discrimination; ergo, the symbionts dictate who mates with whom. 

3. Bacterial symbionts that we could classify as vertically-transmitted, nutritional mutualists (e.g., insect symbionts in the genus Buchnera) assist in resource exploitation, thereby creating new ecological opportunities for their host

4. Endosymbionts can also induce cytoplasmic incompatibility.  Here the offspring of infected males and uninfected females are sterile, therefore, unproductive. 

5. In other cases, the offspring of hybrid matings become more susceptible to infection than non-hybrids, which may reduce their fertility and viability. We are working on this very issue right now and plan to have a paper ready in the next few weeks.

This review article was actually a decade in the making for me. Speciation by symbiosis was the topic of my Ph.D. thesis at the University of Rochester and along with Jack Werren, we helped put Wolbachia on the map as one of the first cases by which symbionts drive the evolution of reproductive isolation between species. This work was later followed by several other important studies on Wolbachia and speciation and came on the heels of intense evangelizing by Lynn Margulis that symbionts were important to speciation; though I contend that she actually provided little evidence that directly linked symbionts to speciation. In my opinion, Lynn was more interested in showing that symbionts drive adaptations, an undeniable legacy that she has left behind.

After the Wolbachia-associated speciation work came out, there seemed to be a lull in the pace of work on symbionts and speciation. Within the last few years however and the uptick in microbiome studies in all organisms, it has since become clearer that speciation by symbionts in general is a robust field with many new insights to be gleaned in the future. Symbionts drive mate discrimination in Drosophila, rapid evolution of immune genes that in turn cause hybrid maladies in plants, and directly prevent gene flow between closely related species - all discussed in the paper. Our hope is that the review revitalizes the topic for new and old investigators alike, and that as the merger between speciation genetics and symbiosis become seamless, the pioneer of the idea that symbionts drive speciation, Ivan Wallin, be formally recognized. More on Ivan in our article and ASM Small Things Considered Blog.

Finally, we tried to publish this article as open access at various journals, but it ended up in TREE's hands. If anyone needs a full copy of the pdf, do not hesitate to email me. My email is readily available by google search or the lab home page.

Related blog posts:
1. The story behind Speciation by Symbiosis? (April 26, 2012)
2. Is the microbiome part of the organism or the environment?
3. Is the microbiota species specific? (June 23, 2012)

Quantified Self and The Microbiome One Year in The Making

With a custom iPhone app and a year of daily gut microbiome data from Eric Alm et al. at MIT, this video from the 2012 GET Conference (recorded April 25, 2012) shows:

• His human microbiome is stable over a year
• Temporal variation within his microbiome is lower than human-to-human variation
• Fiber has an effect on microbial community structure
• Travel affects gut microbiome 

A panel of pioneers in "The Quantified Self" movement (self-tracking of health/disease) then meet at the GET Conference to talk about what they have done and learned in the process of self-tracking, including Eric and Larry Smarr. Eric talks more about how the gut microbiome surprisingly stays stable over time. Its resilient. One of the most interesting points in the panel discussion occurs at 7:57 by Larry. He raises the prospect that self-tracking can become the norm and its benefit is that we'll see the onset of disease way before symptoms ever occur. I agree with this. The microbial flora will unquestionably show changes prior to our body ever feeling the negative outcomes. The upshot is that this could lead to preventive medicine in which doctors and patients tweek the microbiome back to normal before something makes us feel ill. Fascinating.

After watching this, you will see that "Medicine 2.0" (web 2.0 + participatory, self-tracking + doctors) is on the horizon.

Bordenstein Lab Online and Social Media Resources

         Wolbachia (1-5), Nasonia (6-7), & Lab Sites (8-16)

1. Discover the Microbes Within! The Wolbachia Project, Discovery-based project on Wolbachia symbiosis for precollege and college science education; includes labs, videos, and lectures, and other resources
2. Discover the Microbes Within! The Wolbachia Project Facebook Page, Social media outlet updated weekly (and sometimes daily) to disseminate outreach activities, new Wolbachia papers or news stories, history facts, and conferences 
3. Wolbachia pipientis, An Exemplar Species Page for the Encyclopedia of Life
4. Wolbachia, A Heritable Pandemic, Online resources to informational websites, news releases, primary literature, WebQuest, and educational modules 
5. Bioinformatics, Online educational modules for undergraduate and high school students, Microbial Life Educational Resources
6. Nasonia Facebook Page, Social media outlet to disseminate Nasonia papers, news stories, history facts, and conferences. Nasonia is a genus of parasitoid wasps that is frequently used in high schools, university labs, and biocontrol companies. 
7. Nasonia Posterous Page, listserv and blog for Nasonia researchers and educators to email each  other on new tools to the community, collaborative projects, conferences, and more..
8. Blog, Symbionticism – A blog about symbiosis, science, and science education. 
9. YouTube One Channel - videos and video blogs by Seth on research and science education
10. Vimeo - videos on research and science education
11. Insect Innate Immunity Database, an online database and annotation tool of insect immunity genes
12. Bordenstein lab website, Description of the lab’s research, education, pics, and links to pubs
13. Twitter, @Symbionticism, Microblogging news stories about symbiosis, genomics, science, education, new Wolbachia papers, and conferences 
14. Lab Twitter Feeds: @liveinsymbiosis (Robert Brucker, Postdoc), @dnadiva87 (Lisa Funkhouser, Ph.D. student), @JMetcalfVU (Jason Metcalf, M.D./Ph.D. student),  @lifelovescience (Kristin Jernigan, postdoc), @skotomorph, (Joey Simmons, Research Assistant), @lepage_d (Daniel LePage, Ph.D. student)
15. Lab Blogs: Live In Symbiosis (Robert Brucker, Ph.D.)
16. Hologenome Facebook Page, Community venue to track the history and future of innate interactions between the microbiome and animal genome.