Symbionticism

Science PIs Fail If They Are So Ego-Driven That They Stand in Front of Their Students

2013-06-14T15:01:00.000-05:00

The title of this post is adapted from a quote from one of the most important Chinese philosophers, Lao Tzu, circa 6th century BCE. I saw it on Friday and it reminded me of a tweet that Ive been meaning to write. The Lao Tzu quote is:

"A leader is not a good leader if he is so ego-driven that he is always standing in front of his team"

My tweet would have been something like this (and yes tweeter aficionados, it is less than 140 characters):

"Scientists fail what they stand for if they do not acknowledge their students at the beginning, during, and end of every talk they give."

Here's what is easy to forget. PIs get the big corner office, the love and admiration from the group, the rush from the applause of a seminar crowd. But leaders must sacrifice themselves for those that produce the work. PIs are leaders of their team. But it is not leadership for them, but for their students.

Remember this - Scientists should choose to be lab team leaders because they want to nurture the next generation just as much as they nurture their own children. Indeed, scientists were once students themselves who needed their own leaders.

But perhaps the need for scientists to promote their students is even more paramount today than generations before, because the scientist pool is bigger than ever (only 14% of life science phds get tenure-track jobs), the competition is stiff, and the grant money is tight.

Put your students first in every thing we do. We are here to service them.

What are your thoughts?

Francis Collins Performs "The Sequester Blues"

2013-06-10T10:04:00.002-05:00

Quick thought here...the NIH director Francis Collins has the coolest double helix on the neck of his guitar. Definitely a must see. But perhaps the NIH Director should, respectfully, stick to his day job and claw us out of the sequester. Or maybe collaborate with BB King to amp up his performance. Now that could get some dollars flowing back at science. Here he is singing "The Sequester Blues" to commiserate with US scientists. Click this link to see the video.

http://bcove.me/12fospdu

This Is a Time of Connection & Creative Collaboration - Let Students Embrace It.

2013-05-30T21:39:00.001-05:00

What happens when students teach project-based learning in science to each other?

Five high school seniors who call themselves WIN (Wolbachia in Nashville website) wanted to find out and their experience was stunning. This story begins with them - they all participate in the School for Science and Math at Vanderbilt, a magnet school which uses project-based laboratory learning year round with select students from the Metropolitan Nashville High School. Here's what they set out to achieve in their own words.

"As our participation in the School for Science and Math at Vanderbilt has promoted our interest in science, we hoped to share this enthusiasm with the students while also fostering their own personal development and outlook on science. We hoped that the students will feel comfortable asking questions and getting help from us because we are also high school students." Project Report Quote

The WIN team students, along with Angela Eeds (director of the SSMV) and I, partnered up this past year to use Discover the Microbes Within! The Wolbachia Project lab series as a scaffold for tethering integrative, real-world scientific research into a Metropolitan Nashville high school biology class (Overton High School freshmen and sophomores taught by Adam Taylor). The Wolbachia Project engages high school and college students in nature and inquiry and contributes new scientific data on bacterial endosymbionts (Wolbachia, Encylopedia of Life) all across the world. The WIN team students comment..

"As the project progressed, we continually showed them how their results were applicable to the real-world, beneficial to the addition to scientific knowledge, and impactful on the scientific community. We made efforts to stress the validity of their participation in the project by paralleling their work with the Wolbachia project which is conducted not only on a national level but on an international level." Project Report Quote

There's so much Id like to say about these students and their experiences, but most of all, as I listened to the WIN team speak after they completed their project in the spring, their comments made it joyfully clear that they did something that mattered - that gave them all a sense of meaning. First, they transcended into education role models for their peers. The WIN student scientists were seen as big shots, perhaps where star athletes, cheerleaders, and popular kids reign supreme. Second, the WIN team also pointed out that for the freshmen and sophomore students, there was an unexpected aura of comfortability among them. It sprouted specifically because of the peer-to-peer learning. It seems to me that both of these outcomes are what makes project-based learning and peer-to-peer learning work so well independently, but together they form a symbiosis that is more powerful than each one alone.

We do not speak about it, but there is often a social gap in high school classes between the student young adults / teenagers and the teacher "big" adults. But with teacher students as young as the learners in this case, that social gap shrunk for the benefit of all. Its like science 2.0 for education. Just as social media undoubtedly connects these students as friends, social peer-to-peer learning offers an extra dose of comfortability for teaching and learning. Further empowerment ensues with the hands-on learning of project-based science. It was an epic win / win for the WIN team.

Below is how the WIN team assessed their efforts in improving science education. Metrics from surveys taken by the 26 student learners before and after implementation of the Wolbachia Project all go up. Perhaps most significant in looking at the numbers is that these freshman and sophomore students are in Mr. Taylor's honors class and already receive extensive training in hands-on research in biology. The students put it best...

"The results from the two surveys showed our project and interactions with the students had a general positive influence on the classroom in terms of their view of and aptitude towards science. Their desire for a hands-on learning style, as shown in the surveys, suggests that the heavy rotation of labs and experiments emphasized in this project are key to generating interest in science and educating youth about STEM fields.

Let's keep improving High School education with the help of our students. Here is a 23 minute video of the WIN students (apologies in advance for the shaky recording on my phone).

A little bit of news on our lab's research system

2013-05-21T10:34:00.001-05:00

Thanks to Popular Science for picking up our research system

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FYI: Do Parasites Get Parasites?

By Daniel Engber Posted 05.20.2013 at 10:00 am

Parasites of Parasites Science picture co/ Getty Images

Parasites of parasites—sometimes called hyperparasites—seem to be quite common. In fact, parasites of parasites are themselves prone to parasites, leading to what might appear to be an endless progression of interspecies abuse.

Studies in the lab and field have identified some of these elaborate, nested relationships. Last November, a team of researchers in the Netherlands published research on a wasp that lays its eggs inside a caterpillar, which in turn feeds on cabbage leaves. That means the nutrients and energy pass through three distinct organisms, and the same lab has documented related systems with even more layers of interaction.

Seth Bordenstein, a microbiologist at Vanderbilt University, studies a five-tiered system that starts with a fledgling bird. Blowflies infest the bird’s underside with bloodsucking larvae, which then drop off and fall prey to hyperparasitic wasps. The wasps, in turn, carry a parasitic bacterium called Wolbachia, which has evolved to modify its host’s reproductive system. The bacteria are subject to their own invasion, though, from tiny viruses known as bacteriophages, which hijack Wolbachia’s cellular machinery to expand their population.

Just how small can parasites get? The final layer of these systems might be the transposon, which is a roving bit of nucleic acid—a single, parasitic gene. Transposons have been discovered inside viruses that infect other viruses, which in turn infect amoebas that infect human beings. “I think it’s difficult to see where one organism begins and another one ends,” Bordenstein says. “We are only beginning to appreciate how intertwined these layers of organisms are in large flora and fauna.”

Have a burning science question you'd like to see answered in our FYI section? Email it tofyi@popsci.com or tweet @popsci hashtag #PopSciFYI.

ASM 2013 LINKS

2013-05-19T20:46:00.004-05:00

A brief post that the American Society for Microbiology Meeting | Final Program PDF is happening now in Denver. The latest science in microbiology can be tracked on

twitter with hashtag #ASM2013 or
videos through the YouTube Channel hosted by Stanley Maloy

There was a blow out session on "Citizen Science" tonight (chaired by David Coil and Jonathan Eisen, blog post here), which inspired many. The key tweets from that session can be seen through this excellent storify by @Sponch2. I highly recommend a scan of these tweets for anyone interested in microbiology, discovery-based science, and project-based research in and outside the classroom. Rumor has it that even da Wolbachia Project (pdf of article in American Biology Teacher) got a shout out.

Trailer video for Wolbachia Project in Nashville

Those who can, DO. Those who understand, TEACH.

2013-05-13T20:28:00.003-05:00

"You must have the zeal of a missionary....You need to find satisfaction in your actions and you need to find satisfaction in your results. That will make you a great teacher" - George Wolfe

Here is a brief post on my good friend and Emmy Award Winner George Wolfe and his TEDx talk. George is director of the magnet high school - the Loudon Academy of Science, which was established in partnership with the Howard Hughes Medical Institute in 2005. His bio is ridiculously extensive, including hosting a PBS show called Homework Hotline, and I encourage you to read his list of accomplishments by clicking the link associated with his name.

In the TEDx talk, he reminds us that we are all teachers at some point in our lives, if not our profession. You teach your children, peers, and colleagues, and thus he states that there is no more important job than teaching. "Where would we be without teaching?", he asks.

George is one of the main brains behind Discover the Microbes Within! The Wolbachia Project that we formalized at an international national level about eight years ago. He is also a pure inspiration in the truest sense. His TEDx-talk is called the Power of One. I thank George for this talk and wish that we had more access to his passion on a daily basis. I have learned a tremendous amount from him.

The History of Science: When Was The Word "Scientist" First Used?

2013-04-29T15:37:00.001-05:00

As a scientist, I found Prof. Laura Snyder's TED talk fascinating. I suspect her narrative on the history of science will have wide appeal, which is why Im sharing it here as a blog post rather than tweet.

Prof. Laura Synder is a Fulbright Scholar and Professor of Philosophy at St. John's University. In her talk, she illuminates to me and I suspect to you as well that the word "scientist" was shockingly first used in 1833, not that long ago! We owe its origins to a poet's inquisitiveness. Ultimately, it was the scientist William Whewell who coined the term scientist in response to the poet's plea that "natural philosophers" upgrade the name of their profession. How could it be that the word scientist was invented so recently?

She gives flesh to four Cambridge University students who in 1812 formed the "Philosophical Breakfast Club" to talk about the state of science in Britain and the world. In ushering in a new scientific revolution that even reached to Charles Darwin, the Philosophical Breakfast Club rapturously changed science. She also reminds us loud and clear that "science is not just for scientists". These six words spoken at the end of her talk resonate boldly with me. They are an anthem for science communication and outreach and for social media platforms like Twitter and Blogging that build bridges between scientists and those interested in science.

And for those that prefer reading over watching, here is Laura Snyder's TED talk transposed to text. Ive highlighted in blue some key sections that stand out to me.

"I'd like you to come back with me for a moment to the 19th century, specifically to June 24, 1833. The British Association for the Advancement of Science is holding its third meeting at the University of Cambridge. It's the first night of the meeting, and a confrontation is about to take place that will change science forever.

An elderly, white-haired man stands up. The members of the Association are shocked to realize that it's the poet Samuel Taylor Coleridge, who hadn't even left his house in years until that day. They're even more shocked by what he says.

"You must stop calling yourselves natural philosophers."

Coleridge felt that true philosophers like himself pondered the cosmos from their armchairs. They were not mucking around in the fossil pits or conducting messy experiments with electrical piles like the members of the British Association.

The crowd grew angry and began to complain loudly. A young Cambridge scholar named William Whewell stood up and quieted the audience. He politely agreed that an appropriate name for the members of the association did not exist.

"If 'philosophers' is taken to be too wide and lofty a term," he said, "then, by analogy with 'artist,' we may form 'scientist.'" This was the first time the word scientist was uttered in public, only 179 years ago.

I first found out about this confrontation when I was in graduate school, and it kind of blew me away. I mean, how could the word scientist not have existed until 1833? What were scientists called before? What had changed to make a new name necessary precisely at that moment? Prior to this meeting, those who studied the natural world were talented amateurs. Think of the country clergyman or squire collecting his beetles or fossils, like Charles Darwin, for example, or, the hired help of a nobleman, like Joseph Priestley, who was the literary companion to the Marquis of Lansdowne when he discovered oxygen. After this, they were scientists, professionals with a particular scientific method, goals, societies and funding.

Much of this revolution can be traced to four men who met at Cambridge University in 1812: Charles Babbage, John Herschel, Richard Jones and William Whewell. These were brilliant, driven men who accomplished amazing things. Charles Babbage, I think known to most TEDsters, invented the first mechanical calculator and the first prototype of a modern computer. John Herschel mapped the stars of the southern hemisphere, and, in his spare time, co-invented photography. I'm sure we could all be that productive without Facebook or Twitter to take up our time. Richard Jones became an important economist who later influenced Karl Marx. And Whewell not only coined the term scientist, as well as the words anode, cathode and ion, but spearheaded international big science with his global research on the tides. In the Cambridge winter of 1812 and 1813, the four met for what they called philosophical breakfasts. They talked about science and the need for a new scientific revolution. They felt science had stagnated since the days of the scientific revolution that had happened in the 17th century. It was time for a new revolution, which they pledged to bring about, and what's so amazing about these guys is, not only did they have these grandiose undergraduate dreams, but they actually carried them out, even beyond their wildest dreams. And I'm going to tell you today about four major changes to science these men made.

About 200 years before, Francis Bacon and then, later, Isaac Newton, had proposed an inductive scientific method. Now that's a method that starts from observations and experiments and moves to generalizations about nature called natural laws, which are always subject to revision or rejection should new evidence arise. However, in 1809, David Ricardo muddied the waters by arguing that the science of economics should use a different, deductive method. The problem was that an influential group at Oxford began arguing that because it worked so well in economics, this deductive method ought to be applied to the natural sciences too. The members of the philosophical breakfast club disagreed. They wrote books and articles promoting inductive method in all the sciences that were widely read by natural philosophers, university students and members of the public. Reading one of Herschel's books was such a watershed moment for Charles Darwin that he would later say, "Scarcely anything in my life made so deep an impression on me. It made me wish to add my might to the accumulated store of natural knowledge." It also shaped Darwin's scientific method, as well as that used by his peers. [Science for the public good]

Previously, it was believed that scientific knowledge ought to be used for the good of the king or queen, or for one's own personal gain. For example, ship captains needed to know information about the tides in order to safely dock at ports. Harbormasters would gather this knowledge and sell it to the ship captains. The philosophical breakfast club changed that, working together. Whewell's worldwide study of the tides resulted in public tide tables and tidal maps that freely provided the harbormasters' knowledge to all ship captains. Herschel helped by making tidal observations off the coast of South Africa, and, as he complained to Whewell, he was knocked off the docks during a violent high tide for his trouble. The four men really helped each other in every way. They also relentlessly lobbied the British government for the money to build Babbage's engines because they believed these engines would have a huge practical impact on society. In the days before pocket calculators, the numbers that most professionals needed -- bankers, insurance agents, ship captains, engineers — were to be found in lookup books like this, filled with tables of figures. These tables were calculated using a fixed procedure over and over by part-time workers known as -- and this is amazing -- computers, but these calculations were really difficult. I mean, this nautical almanac published the lunar differences for every month of the year. Each month required 1,365 calculations, so these tables were filled with mistakes. Babbage's difference engine was the first mechanical calculator devised to accurately compute any of these tables. Two models of his engine were built in the last 20 years by a team from the Science Museum of London using his own plans. This is the one now at the Computer History Museum in California, and it calculates accurately. It actually works. Later, Babbage's analytical engine was the first mechanical computer in the modern sense. It had a separate memory and central processor. It was capable of iteration, conditional branching and parallel processing, and it was programmable using punched cards, an idea Babbage took from Jacquard's loom. Tragically, Babbage's engines never were built in his day because most people thought that non-human computers would have no usefulness for the public. [New scientific institutions]

Founded in Bacon's time, the Royal Society of London was the foremost scientific society in England and even in the rest of the world. By the 19th century, it had become a kind of gentleman's club populated mainly by antiquarians, literary men and the nobility. The members of the philosophical breakfast club helped form a number of new scientific societies, including the British Association. These new societies required that members be active researchers publishing their results. They reinstated the tradition of the Q&A after scientific papers were read, which had been discontinued by the Royal Society as being ungentlemanly. And for the first time, they gave women a foot in the door of science. Members were encouraged to bring their wives, daughters and sisters to the meetings of the British Association, and while the women were expected to attend only the public lectures and the social events like this one, they began to infiltrate the scientific sessions as well. The British Association would later be the first of the major national science organizations in the world to admit women as full members. [External funding for science]

Up to the 19th century, natural philosophers were expected to pay for their own equipment and supplies. Occasionally, there were prizes, such as that given to John Harrison in the 18th century, for solving the so-called longitude problem, but prizes were only given after the fact, when they were given at all. On the advice of the philosophical breakfast club, the British Association began to use the extra money generated by its meetings to give grants for research in astronomy, the tides, fossil fish, shipbuilding, and many other areas. These grants not only allowed less wealthy men to conduct research, but they also encouraged thinking outside the box, rather than just trying to solve one pre-set question. Eventually, the Royal Society and the scientific societies of other countries followed suit, and this has become -- fortunately it's become -- a major part of the scientific landscape today.

So the philosophical breakfast club helped invent the modern scientist. That's the heroic part of their story. There's a flip side as well. They did not foresee at least one consequence of their revolution. They would have been deeply dismayed by today's disjunction between science and the rest of culture. It's shocking to realize that only 28 percent of American adults have even a very basic level of science literacy, and this was tested by asking simple questions like, "Did humans and dinosaurs inhabit the Earth at the same time?" and "What proportion of the Earth is covered in water?" Once scientists became members of a professional group, they were slowly walled off from the rest of us. This is the unintended consequence of the revolution that started with our four friends.

Charles Darwin said, "I sometimes think that general and popular treatises are almost as important for the progress of science as original work." In fact, "Origin of Species" was written for a general and popular audience, and was widely read when it first appeared. Darwin knew what we seem to have forgotten, that science is not only for scientists."

Thank you.

Via Source

Social Media for Scientists: YouTube One Channel

2013-04-25T16:16:00.000-05:00

If you have videos posted to youtube, then you should definitely check out the new layout design. In the span of ten minutes, you can customize your "YouTube One Channel" as they now call it with a banner from your gallery or theirs, feature video, and a list of videos that you can customize according to theme, recency, popularity, etc. If you do not post videos to youtube, then you should. Its a great way to give wings to your science to other scientists and the public. Consider it a broader impact if you will. Video pages are on the rise, like twitter and facebook. They are here to stay as an online footprint of your life or profession, whatever you may choose. For scientists or educators, lectures, seminars, news features, TED talks, etc are all great things to post. Ive gotten immense benefit from watching research seminars on youtube because there are always meetings that you miss or talks you would like to hear twice. If you set up a channel, let me know so I can subscribe to it!

http://www.youtube.com/user/sbordenstein

The Microbiome Blurs the Lines Between Genes and Environment

2013-04-25T14:30:00.004-05:00

On the lecture circuit this past couple of months, Ive given talks about the hologenome (link to video post), which is the term being used by

From Wikicommons

some to refer to the collection of eukaryotic cells and microbial cells that make up the organism. By far, the most common and intriguing question I get is whether the microbiome is a (i) phenotype, (ii) genotype, or the (iii) environment. Quite honestly, its more complicated than you might think at first. Genes involved in immunity select for the presence of certain microbes, making the microbiome almost like a phenotype that is encoded for. Microbes are also genotypes themselves with their genomes providing life-serving functions that our genome does not encode for. Finally, microbes are in and part of the external environment, and the nuclear genome could live with a microbiome much like the organism lives with a certain ph or moisture. This question is a rabbit hole that we can go deep into. To my surprise, Science 2.0 just recently posted this excellent article below on the very issue raised here. It's well worth a read, a nap, and then another read. Then read the comments section as well. What do you think? As always, I welcome your thoughts on how far down the rabbit hole we can go.

Natural Selection And Microbiota

There is no question that Darwin's tremendous insight into the mechanisms by which evolution occurred was one of the singularly most significant events in biology. Similarly with the discovery of DNA and genetics, the processes by which organisms were formed received a similar boost. So the purpose of this article is not to argue that Darwin or genetics is wrong. Instead, the point is to suggest that it is necessarily incomplete. In the same way that Darwin's work was incomplete because he lacked the necessary information about genetics. The modern evolutionary synthesis is also incomplete, because it fails to extend the issues of natural selection in an organism's development to their co-evolutionary partners; the microbes.

"Evolution is cleverer than you are" Orgel's rule.

Nowhere does this ring more true than in examining the incompleteness of what we understand about the process of life perpetuating itself.

Naive group selection gave rise to gene-centricism, from which we acquired kin selection and inclusive fitness theories. Every one of which takes an essentially linear view of natural selection. Parents pass on their genes to offspring, which are selected for, in turn passing on their traits. The gene is considered the unit of selection, so that it is characterized, metaphorically, as being "selfish" in its interest of having greater representation in future generations. Behavioral traits, such as cooperation and altruism, are explained by suggesting that we benefit by assisting other genes to be passed into future generations, as long as we are related in some fashion. As a result, there is a supposed genetic explanation for every permutation of traits that exists, even those that have zero biological fitness. Hopefully an alternative view may offer a different perspective on such thinking.

This all presents a nice concise package, except that it isn't the full story and it may not even be fully true.

http://www.biology-direct.com/content/2/1/30

In the first place, we have to recognize that this entire story presumes a level of biological isolation that simply doesn't exist. Every organism must cope with the environment that it exists in, while simultaneously serving as an environment for many other creatures. Each exerts an influence on its environment, as well as the environment exerting influences in return.

There is no isolation.

Therefore, one of the first problems we encounter is the notion that the gene is the unit of selection. Certainly recent work in epigenetics has demonstrated that there are other influences that can determine whether a gene is expressed or not, so it is clear that the gene cannot singularly be responsible for the traits an organism exhibits, if it can't actually ensure that it is expressed, or how it is expressed. Moreover, the concept of "selfishness" is demonstrably wrong because every instance where such behavior manifests, results in the destruction of the organism (segregator distorter genes, carcinomas, etc.). Therefore, we should dispense with the notion of the gene being the singular unit of selection, and simply concede that it is a means of selection. In other words, it simply carries the "message" which may be utilized or ignored as determined by other processes.

This has already largely been recognized, since genetic expression may be influenced by environmental factors, but nevertheless, the persistent view that the genes are the "blueprint"pervades most views of evolution. There is no question that the gene is the means by which information is replicated and passed between generations. That isn't in dispute. However, this is only one stage of a multi-stage operation that will ultimately result in a viable organism that is capable of competing and whose fitness will determine "success" or "failure".

However, we have some new insights to consider and they are quite radical. In the first place, we are not the "owners" of our bodies. We are outnumbered in our own bodies, by microbes by a ratio of over 10 to 1. The genomes represented by these microbes outnumbers our own by 100 to 1.

In studying germ-free (GF) mice we can now see that genes are insufficient to produce a viable organism. Of course, there have already been strong hints of that in many other animal species. After all, what does it mean to produce a termite genetically, if one doesn't account for the symbiotic protozoans necessary to digest its food? There are many other such relationships, that are conveniently termed symbiotic, but in truth represent absolutely essential traits on which the creature has evolved to depend on.

Therefore, one of the first conditions we must recognize is that we do not evolve alone, nor does natural selection work solely on the products of our genes. We are dependent on our microbes for survival and selection as they are on us for their environment.

Moreover, these microbes can't just be arbitrarily introduced whenever we choose. They are specific to individual species and even individuals within a species and must be present/introduced at critical stages of development (1). This indicates that these microbes aren't merely some external presence that exerts an influence (2). They are part of the process, as inextricably linked to our development as are the regulatory signals to our own cells. Even something that is so fundamentally related to fitness, such as pregnancy, requires the involvement of microbes for success.

[NOTE: It also doesn't appear that there is any particular uniformity of microbes to any individual beyond providing assistance in similar metabolic ways]

Failure to adhere to these developmental requirements, produces difficulty for the organism in question.

Similarly one has to consider the role of these commensal organisms and their influence on an organism's genes, because if an organism can exploit a trait that already exists, then it reduces or even eliminates the selection pressure for such a trait to be manifest in the genome.

As a result, there are traits that exist for which the genome has no "knowledge".
http://www.sciencemag.org/content/338/6104/198.short
http://www.sciencecodex.com/new_studies_reveal_connections_between_animals_microbial_communities_and_behavior-100019

This raises the question of how much of our survival and response to natural selection is due to micro-organisms stepping into the breach to provide a critical service for which our genome was unprepared?

Whatever else we may think, it is clear that viewing an organism and natural selection, from the pureperspective of genes is incomplete (3). Therefore it may be more precise to say that genes provide the basic environment, while microbes manipulate and refine to produce a working ecosystem. As a result, as goes their success, so goes our.

Of course, it is too simple to begin thinking that these microbes are the "heroes" of our scenario, since it is equally important to note that many of the diseases that humans experience are equally the result of such microbes (4). No matter how one wishes to view this; "friend or foe", the truth is that we're all in this together.

Additional references:
http://www.nature.com/nature/journal/v486/n7402/pdf/nature11234.pdf
http://news.wustl.edu/news/Pages/23956.aspx /JR-Review-RoundandMazmanian.pdf

=======================================
(1)

A study by Chung's co-author Kasper showed that mice that were raised germ-free could have their immune systems "rescued" by certain microbes up to the first several weeks of age.
http://www.scientificamerican.com/article.cfm?id=species-specific-microbes-immune

(2) http://www.economist.com/node/21560523

A lot of the medical conditions the microbiome is being implicated in are puzzling. They seem to run in families, but no one can track down the genes involved. This may be because the effects are subtly spread between many different genes. But it may also be that some—maybe a fair few—of those genes are not to be found in the human genome at all.

(3) http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032118

(4) Even traditional ideas about what constitutes pathogens may require some revision.
http://www.nytimes.com/2012/06/14/health/human-microbiome-project-decodes-our-100-trillion-good-bacteria.html?_r=3&smid=pl-share&

COMMENTS

"This all presents a nice concise package, (ie, the gene-centric interpretation of evolution) except that it isn't the full story and it may not even be fully true."
Gerhard, you are far too kind and gentlemanly! :)
I think the realistic version of the contribution of gene-centrism to evolution is that it is of no value at all.
After all, what can it predict?
One thing only, that the genes of fitter organisms will tend to spread in a population.
And that was put first by Fisher, who did not link it directly to evolution, but to natural selection.
Those two concepts are not the same despite the misunderstanding of gene-centrics.
And the prediction is essentially a truism - it is not an explantion of evolution.
Interestingly, Fisher was smart enough to not throw selfishness into his account - he was a numbers man.
Apart from that, a great article! :)

Steve Davis | 04/22/13 | 21:09 PM

Thanks ... I'm glad you finally got to make a comment :)

Gerhard Adam | 04/22/13 | 21:46 PM

If I ever hear another libertarian tell me the "common good" is purely a human moral construct they can go dip their eye in hot cocky's cack ...

Genetic Circuit Allows Both Individual Freedom, Collective Good

John Hasenkam | 04/23/13 | 01:40 AM

John, that's an interesting article.It brings to mind the view of the greatly under-appreciated Robert Ardrey, that the fittest groups are those that cater for both individual diversity and the stability that comes from social conformity.
Gerhard, you've raised subjects here that are covered in detail in Tom Wakeford's Liaisons of Life, a great read.

Steve Davis | 04/23/13 | 20:52 PM

Sounds like a good book.

What I find fascinating is examining natural selection's "blind spots". In other words, if a particular function is provided by a microbe, then there is no selection pressure on the genome and consequently the entire organism is being selected for a trait that it can't even provide by itself [i.e. the microbe does it].

This raises all kinds of interesting questions about how often this type of thing might occur and how deep some of these ramifications may run.

Gerhard Adam | 04/23/13 | 21:44 PM

"...if a particular function is provided by a microbe, then there is no selection pressure on the genome and consequently the entire organism is being selected for a trait that it can't even provide by itself."
Ah, but Gerhard, that was explained by RD in The Extended Phenotype - the function is carried out by the microbe on instructions from the host genes!! Were you not paying attention? :)
The power of delusion is great.

Steve Davis | 04/23/13 | 23:20 PM

Ahh, but that's the interesting part, because it really appears to be the other way around.

Gerhard Adam | 04/24/13 | 07:21 AM

My talk at the University of Indiana at Bloomington

2013-04-21T20:12:00.001-05:00

I had the pleasure of visiting The University of Indiana at Bloomington in early April. With nearly 80 biologists sprinkled across the integrative department including many good friends and tweeters, Bloomington is an intellectual hub of life sciences research.

Here's my seminar "Mainlining the Hologenome into Biology". The term hologenome is rather new to biology and some may consider it controversial, even jargon. Part of me concedes that it could be, but a rising number of biologists think that we do need a term like it, i.e., holobiont or metaorganism. For an intro to the origin of the concept, the New Scientist recently featured the hologenome theory on their cover. The future of biology continues to be integrative where the lines between disparate disciplines are increasingly blurry. The term hologenome is useful because it encompasses the rather simple idea that the total microbiome of a host plus its nuclear and cytoplasmic genomes comprise a unit of selection from which nature picks the fittest organism / hologenome. This concept melds the diverse vantage points of evolutionary geneticists and microbiologists; hence, it will not be accepted immediately, nor should it. Big ideas demand big evidence. Further, terms will not change knowledge, but they help to fashion the framework of experimentation that will.

Disclaimer: exuberant editing on the quote slide done in iMovie.

Related blog posts:
1. The story behind Speciation by Symbiosis? (April 26, 2012)
2. Is the microbiome part of the organism or the environment? (May 11, 2012)
3. Is the microbiota species specific? (June 23, 2012)

4. ASM's "Small Things Considered" spotlights the Speciation by Symbiosis article (August 16, 2012)

Microbiome: Can A Fecal Transplant Cure Autism?

2013-04-18T08:43:00.001-05:00

Bar chart showing autism diagnosis increase in the U.S. from 1996 through 2005.CC-BY-SA-3.0 (http://creativecommons.org/licenses/bysa/3.0/)],
via Wikimedia Commons

Studies of the microbes and their genes, which we collectively term the Microbiome, have been performed for many chronic illnesses including Autism. There is considerable and recent attention on this issue, but thus far, scientists have shown potential correlations between autistic patients and shifts in their microbiome. Nothing conclusive and other studies do not find the same correlations. There's even a documentary on the topic called the Autism Enigma that perhaps oversells the idea that the microbiome is the cause of autism.

News links:

Open Access Papers:

A microbial association with Autism (mBio 2012)
The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease (Gastroenterology 2009)
Differences between the gut micrflora of children with autistic spectrum disorders and that of healthy children (Journal of Medical Microbiology 2005)

While I'd like to hope that something as enigmatic as Austism has a microbial, and therefore potentially, curable basis, I was disappointed to find a chat on line where a fecal transplant had been performed to transplant healthy poop/microbes into the gut of an Autistic child. Unfortunately, weeks of monitoring after the fecal transplant did not appear to significantly affect the symptoms of that child. Its a sample size of 1, so take it with a grain of salt. But in this case, the fecal transplant did not cure Autism behaviors.

However, minor OCD with fans and holding/twiddling 2 of the same item remains.

The transplant did seem to stabilize gut symptoms:

At the 3 1/2 week mark, still no bacteria flares or yeast flares, all with no antimicrobials and just 1 culturelle a day. Bowel movements are still really good with no diarrhea or blow outs. Appetite is nice too. Weight is steady with maybe a slow increase.

I've previously written about the powerful affects that fecal transplants have on IBD, IBS, C. diff, Colitis and perhaps Multiple Sclerosis.

If anyone has any other information on how probiotics, prebiotics, or stool transplants work for Autism, do share them here to spread the word around.

As always, thanks for reading and sharing your opinions.

Seth

Museum of Science in Boston Brings Together Microbiome Luminaries

2013-03-29T22:38:00.001-05:00

This video below, entitled Friends with Benefits: The Human Microbiome, is one worth watching. It was recorded Feburary 6, 2013 and hosted by the Museum of Science in Boston with funding from the Lowell Institute (original ad). It features four brilliant microbiome researchers - each of them arguably have transformed the life sciences in just the past few years. They each speak for 15 minutes and then have a Q&A with the audience. I've noted the times at which each speaker appears in case you want to skip ahead. They appear in the following order:

Introductions - 0 to 2:00
Prof. Rob Knight (U. Colorado) - 2:00 to 26:10, Development of the Human Microbiome
Prof. Eric Alm (MIT) - 26:10 to 41:00, A Year in My Microbiome
Prof. Marty Blaser (NYU School of Medicine) - 41:00 to 1:01, Long Term Pertubations of the Microbiome
Prof. John Cryan (University College Cork, Ireland) - 1:01 to 1:23, Microbiota-Gut-Brain Axis
Roundtable Q&A - 1:23 to 1:30 - Between speakers
Roundtable Q&A - 1:30 to end - Between speakers and audience (perhaps the best part!)

NIH issues press release on Wolbachia and our bacteriophage work

2013-03-27T10:48:00.001-05:00

I do not often mention our bacteriophage work on this blog, but a large arm of the lab studies the evolution, mechanisms, and relevance of bacteriophage. Bacteriophages are the "smart bombs" of the microbial world - viruses that specifically target and often kill bacteria. The NIH Evolution of Infectious Disease Program, which funds this work, kindly put out a press release today on it. (This work is perhaps most well known for the discovery of rampant horizontal gene transfer of bacteriophage between obligate intracellular bacteria that were once presumed impervious to bacteriophages and large-scale gene transfers). For all those young scientists struggling to get their first grant, its humbling to reflect that this work almost never saw the light of day some years ago. Two reviews on this research are:

Phage WO of Wolbachia: lambda of the endosymbiont world (Trends in Microbiology, 2010)
The complexity of virus systems: the case of endosymbionts (Current Opinion in Micro, 2012)

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Inside Life Science

View All Articles | Inside Life Science Home Page

Taking the 'Bite' Out of Vector-Borne Diseases

Emily Carlson
Posted March 27, 2013

Mosquitos, ticks, worms—these all are "middle men" when it comes to disease spread. They can carry and transmit bacteria, viruses and other pathogens to us that cause dengue fever, Lyme disease and other vector-borne infections. As one approach to help reduce and even eliminate these diseases in people, researchers funded by the National Institutes of Health are studying the basic mechanisms that let the infection-causing organisms flourish inside their hosts.

The mosquito is just one of the many organisms that Wolbachia infects. Credit: James Gathany, CDC.

A "Mind-Blowing" Bacterium

One such bacterium that scientists are interested in is called Wolbachia.

"It's probably the coolest bacterium in the world," says NIH's Irene Eckstrand.

Wolbachia infects more than a million species, including insects, shrimp, spiders, mite and tiny worms. It lives and reproduces in its host's cells, primarily reproductive ones. The bacterium can manipulate these cells in ways that boost its own survival and reproductive success.

Seth Bordenstein, a Vanderbilt University scientist who studies Wolbachia, says the bacterium alters the reproductive life of its insect and other hosts in four "mind-blowing ways":

It kills infected males.
It turns genetic males into females by shutting down certain hormones.
It allows infected females to reproduce asexually.
It promotes the survival of embryos from infected females only.

Ecology and Evolution

"Aside from stimulating the imagination, Wolbachia serves as a tool for studying the evolution and ecology of infectious diseases," notes Eckstrand, who co-manages an NIH-National Science Foundation program that's dedicated to this topic.

A Wolbachia cell infected with bacteriophages. Credit: Seth Bordenstein, Vanderbilt University.

When Bordenstein, whose research is supported through the program, started studying Wolbachia about a decade ago, scientists thought that the bacterium and ones like it didn't frequently acquire new genetic machinery. The theory was that living inside other cells isolated the bacterial genomes, inhibiting the exchange of genetic elements with other bacteria that enables evolution.

Since that time, the theory—and Wolbachia itself—have evolved. Bordenstein discovered that Wolbachia can move to different cells and to new hosts, some of which are infected with other types of bacteria as well as different Wolbachia strains. This co-infection allows the bacterium to acquire new genetic elements.

Scientists also have learned that Wolbachia harbors a bacteria-infecting virus, called a bacteriophage, that can introduce other genetic elements. Bordenstein found that Wolbachia's interaction with the bacteriophage and its exchange of genetic elements through co-infections creates a cycle of evolution with implications for how diseases spread.

Disease Control

Elephantiasis caused by parasitic worms (top) affects more than 120 million people, primarily in Africa and Southeast Asia. Credit: CDC.

While Wolbachia doesn't directly infect mammals, it is the root cause of several serious mammalian diseases. It infects parasitic worms that, by way of mosquitos, can cause heartworm in our pets. Other types of Wolbachia-infected worms hitch rides to ultimately reach human hosts, where they can trigger severe inflammatory responses that lead to river blindness and elephantiasis. In an ironic twist, researchers are actually using Wolbachia to help fight these infections.

One strategy that Bordenstein is beginning to explore focuses on bacteriophage enzymes that can wipe out Wolbachia. Some organisms, including the parasitic worms, actually need the bacterium to reproduce. By eliminating the Wolbachia infection, the enzymes could render the worms sterile and unable to further spread disease.

Scientists also are harnessing Wolbachia's wanton ways to control the spread of dengue virus, which is transmitted to humans by mosquitoes. Researchers have discovered that Wolbachia-infected mosquitoes can't replicate the dengue virus. Releasing more Wolbachia into the mosquito population or finding and introducing the Wolbachia genes that interfere with replication are promising new avenues for reducing the spread of dengue. The approach could potentially apply to other vector-borne diseases like sleeping sickness, which is transmitted by the tsetse fly.

According to Bordenstein, studying Wolbachia has yielded some surprising new insights on microbial evolution that could help us understand, treat and prevent certain infectious diseases. "It's what gets me up every day and keeps me excited about doing this work," he says.

Learn more:

Also in this series:

This Inside Life Science article also appears on LiveScience .

New TED talk on the teeming microbes in buildings

2013-03-25T22:27:00.003-05:00

Is science getting cooler by the day or what? Check out this TED talk (with a very high tech/3D animation by Autodesk) on why we need to think about what microbes are in our buildings, from the air we breath when the windows are closed to what's in the bathroom. This is an idea whose time has come. I am thrilled to be meeting her and other faculty/students at the University of Oregon in the very near future when I visit the NIH Center for Systems Biology called The Microbial Ecology and Theory of Animals (META) Center. Graduate student Ashley Bateman, @MicrobesRock, invited me to speak on our work on the hologenome theory.

"Our bodies and homes are covered in microbes -- some good for us, some bad for us. As we learn more about the germs and microbes who share our living spaces, TED Fellow Jessica Green asks: Can we design buildings that encourage happy, healthy microbial environments?

Jessica Green wants people to understand the important role microbes play in every facet of our lives: climate change, building ecosystems, human health, even roller derby -- using nontraditional tools like art, animation and film to help people visualize the invisible world." Source

Have you used a MOOC? Crowdsourcing feedback.

2013-03-24T20:44:00.002-05:00

In December, I wrote an introductory blog on MOOCs entitled The Digitization of Education: What is all the fuss about MOOC? It is very basic and almost outdated, but it does have a great Ted talk video by Cousera's founder Daphne Koller that I recommend. Vanderbilt is on board with Cousera.

Still in their infancy, MOOCs are popping up around the country's universities and I imagine some readers of this blog have first hand experience or at least more insight on what its like to start or use a MOOC. Any answers to these questions wouldl be of help to myself and readers.

1. How has the experience been with setting up or using a MOOC?
2. What is fundamentally different or unexpected in using a MOOC?
3. What has worked well? What would you do differently in MOOCs?
4. Do you receive a break or compensation from your normal teaching load?

Are there bacteria in the brain?

2013-02-19T20:47:00.004-06:00

BREAKING: I am posting this without much commentary because I have not had time yet to read the paper in full. A new report in PLOS ONE collates evidence that bacteria regularly inhabit the brain of immunocompromised brains. On the surface, the evidence seems pretty strong. mRNA detection and sequencing, in situ hybridizations, and brain tissue transplants from humans to mice....For those that would rather skip the science jargon, there is one press release from Boston.com. Is the brain microbiome a new frontier? As a related point, we published a paper in 2011 in Genetics on immunocompromised wasps that have remarkable bacterial infections in their brains (Figure 2D), resulting in altered mate preference behavior (Figure 8).

Citation: Branton WG, Ellestad KK, Maingat F, Wheatley BM, Rud E, et al. (2013) Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status. PLoS ONE 8(1): e54673. doi:10.1371/journal.pone.0054673

Abstract

The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1^−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1^−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain’s microbiome regardless of underlying immune status, which could be transferred into naïve hosts leading to microbial persistence in the brain.

Figure 1. Deep sequencing detection of bacterial and bacteriophage RNA sequences in human brain.

(A) Total sequence tags that were unambiguously identified as belonging to a bacterial phylum were grouped for each patient from which the percentages for each phylum were displayed. All patients showed a predominance of Proteobacteria-associated sequences. (B) Despite inter-individual variability the mean percentage of Proteobacteria sequences among the HIV, ODC and SURG groups was similar. (C) The majority of bacterial sequences identified in all patient samples belonged to the Proteobacteria phylum, which showed the greatest similarity to the α-proteobacteria class. (D) The majority of bacteriophage sequences identified matched Proteobacteria-tropic phage sequences although bacteriophage sequences were not detected in the SURG samples. doi:10.1371/journal.pone.0054673.g001

My talk at the University of Illinois at Urbana-Champaign

2013-02-15T14:51:00.001-06:00

Earlier this week I had the pleasure of visiting The House that microbiologist Carl Woese Built - The University of Illinois at Urbana-Champaign. With nearly a 100 evolutionary biologists and ecologists along with National Academy Members sprinkled across the integrative departments, its a wonder world of life sciences research. Indeed, famed virus hunter Nathan Wolfe happened to be visiting the campus the same day.

Here's my seminar on The Hologenome / Speciation by Symbiosis (Part I: 0 to 31:20) and Microbial Genome Evolution (Part II: 31:20 to Q&A). I usually am hypercritical of my own talks and find all sorts of things wrong with them. This seminar is perhaps the one time that the talk went off without a hitch. I even landed a few laughs with a joke on hybrid lethality (phew).

4. ASM's "Small Things Considered" spotlights the Speciation by Symbiosis article (August 16, 2012)

Darwin Day

2013-02-13T09:25:00.002-06:00

Yesterday was a mild victory for promoting science, reason, and the future in the United States. Congressman Rush Holt (D-NJ) introduced a resolution to declare February 12th, DARWIN DAY, in honor of the 1809 birthday of one of the greatest scientists. Sadly, this resolution will not make it far, I fear, but change in government happens by small steps. This motion, coupled with the enacted Golden Goose Award introduced by Nashville's own Jim Cooper to honor federally funded research (my blog post on its origin), are steps that should give us hope.

Here's a very short video of Rep. Holt's introduction of the Darwin Day resolution. It may just energize you a little bit more today. It did for me.

Part IV: Thoughts on Survival/Success in the New Era of Academia

2013-02-08T10:17:00.000-06:00

Here is the last installment of tweets on this theme folks. Hope they've been of some help. Id like to pivot you to Josh Drew's blog post this week on the same theme. He has some things that just need be said more often. Here's an excerpt.

However, it occurs to me that the majority of the tasks I do ever day I have had very little to no formal training in. In a given week I 1) teach, 2) advise students, 3) apply for funding, 4) do research, 5) manage a graduate program and 6) write. Now here’s the crux getting a Ph.D. is actually fairly poor preparation for the majority of these activities.

In my case, I recall explicitly asking for a course on grantsmanship in graduate school. The idea was generally scoffed at, for reasons that I can only speculate as a cultural one. What is noteworthy is that in this new era of academia with limited federal funding, we are all getting more serious about what we do, who we train, and how we train them. This shift is part of the good in what can seem to be a troubling pattern in science funding.

1/27/13: If Life is the greatest show on earth, then biologists get to be at the circus for their entire career #tosrb #hallelujah

1/29/13: Scientists almost never get career breaks; They work hard & persevere in the face of doubt. Recognition comes retroactively #tosrb #Woese

1/29/13: Excellent training of students requires honesty to them, even when its hard. Excellent learning requires being honest w yourself #tosrb

1/30/13: When giving a seminar/lecture of excellence, remember to inspire regularly. Engagement is the button that turns on self-illumination #tosrb

2//13: EXPLORE not where your field is now, but where it is going to be in 3 years. It will transform and transcend you in your endeavors. #tosrb

Part III - Thoughts on Success/Survival in the New Era of Academia

2013-02-06T10:52:00.002-06:00

Third installment...for background see previous two blog posts.

Thoughts on Success/Survival in the New Era of Academia Part I
Thoughts on Success/Survival in the New Era of Academia Part II

1/25/13: Biology PIs run small businesses too. Our labs must be well managed and produce a product that is sold to the granting agencies #tosrb

1/25/13: So much of attaining excellence is the confidence and courage to simply try. Anything less is a prescription for status quo #tosrb

1/25/13: Imagine a future in which you better engage your students or solve bigger questions - now pull that future forward to right now #tosrb

1/26/13: 6 NIH grants or 10 NSF grants is a career's worth of research. You dont got many chances to spur a paradigm. Choose wisely #torsb

1/26/13: PIs must give equal time to broadcasting and receiving info with students. I do this because my students are smarter than me #tosrb

Part II - Thoughts on Survival/Success in the New Era of Academia

2013-02-05T09:18:00.002-06:00

Yesterday, I started Part I of a blog post series on survival/success tips for the new era in Academia. My hope is that I can pass on some insight to those that are just beginning their careers - from students to new PIs. By doing so, by coaching through accrued wisdom, together we can speed up the pace of excellence in science for future trail blazers, rather than wait for people to learn these things themselves over a long career.

As noted, 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!

1/24/13: Students must recognize that they will be pushed to the brink, because their PIs know better than them how far they can go #tosrb

1/24/13: Letting go of limitations is part of the journey to excellence, for students and colleagues alike. Academics should heed this. #tosrb

1/24/13: I can't or I don't or I'm not are words that we should never ever use. We hide the gift of new knowledge for humanity if we do #tosrb

1/24/13: Science is the noblest of occupations for it discovers new truths. And that discovery is driven by 20-something's. Remarkable #tosrb

1/24/13: Education is the sibling of science for without it we can not build a family of humanity that sustains itself #torsb

Thoughts on Success/Survival in the New Era of Academia Part I

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

2013-02-04T12:00:00.001-06:00

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!

1/23/13: 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
1/23/13: Most grad students transform in grad school. Fewer transcend. 14% ultimately get academic jobs. We need to talk about why. #tosrb
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
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
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

2013-01-31T15:19:00.005-06:00

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

2013-01-20T23:12:00.001-06:00

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]

2013-01-08T20:09:00.001-06:00

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