List of links/phone #s for people in need of help (or offering help) #BostonHelp #bostonmarathon

Not going to report, since the facts will probably change before I hit publish, but these links should remain useful: Google people finder - for folks that can't get in touch with friends/relatives

Boston Globe-run form for people looking for or offering places in the city

Lots of folks offering help on twitter via #BostonHelp

Mayor's hotline for people looking for friends/family 617-635-4500 (via the globe)

Anyone with videos/pictures of the route (could be evidence) call 800-494-TIPS (also via Boston Globe)

Red Cross is not looking for blood donations now, but would love you to schedule for later (site was down when I checked, probably heavy traffic right now)

I've been following this almost since the news broke, and I'm beat. Gonna disconnect from social media for a bit... I'm OK, and everyone closest to me is OK, but a lot of people are not. Even setting aside the injured, there are a lot of runners stranded (many area hotels are shut down) and could probably use help. Pitch in if you can.

Friday Link Dump

Science - There's a new flu strain running around in China. As is often the case, Maryn McKenna over at Wired has the most important piece to read.

- Allie Wilkinson's piece in Ars Technica about a climate change's irreversibility, but not inevitability... it's a weird distinction, but it makes sense.

- Another good post from Keith Kloor on GMOs, but I'm not a fan of equating Monsanto with GMOs. One is a company, the other is a technology. Just because the technology is used by the company, that does not imply that the two are related.

Not Science

- The most important video I've seen in a while. Normally, I dislike TED - but this is important. Lawrence Lessig on money and politics

- Google bought up Nik Software (tools for editing photographs), and recently released them all for cheap. I've been using them for less than 24 hours and I am in love... absolutely amazing. You can try them for 14 days for free. Only downside is you can't use them for non-destructive editing, but still.


Haven't been listening to much music lately, but this song is amazing:

Allergies, Asthma and Eczema - New SITN Flash

The latest issue of the Science in the News "Flash" is out now about the connections between atopic disorders - namely allergies, asthma and eczema.

Itchy, watery eyes, and a drippy nose. Constricted, swollen airways secreting thick mucus. Itchy, red, dry, cracked skin. These symptoms describe three conditions -- allergies, asthma, and eczema, respectively -- that are commonly found together in the same people. Yet, what causes these symptoms and why they are so closely associated with each other is still poorly understood.

The Flash is written and edited by graduate students, an all-volunteer effort to explain complex science to the general public. Last month, I wrote about the link between obesity, inflammation and type 2 diabetes. This month, graduate student Elizabeth Brown from the Human Evolutionary Biology department writes about another problem involving an overzealous immune system.

Despite progress in fighting infectious diseases in developed countries with increased sanitation, antibiotics, and antiviral medications, allergies have become increasingly common in these regions. A few hypotheses have been put forth to explain this trend.

Check it out!

subunits of DNA found in meteors

Dear Readers, I have been more absent than usual from this blog, which is something I regret. However, the time constraints of preparing for my upcoming qualifying exam necessitate this. I decided to break my strict "no distractions" policy to bring you this bit of info that was emailed to me by a lab mate.

Scientists have discovered DNA components in a meteorite, and they seem to be fairly certain it was made there! You can read the actual NASA press release here, and check out a cool video of one of the scientists explaining the discovery here. The cliff notes version is that, while claims of meteorites containing DNA components have been made before, they may very well have been terrestrial contamination. This seems to be different, because the meteorite also contains similar molecules that are never found in biological matter, which is what would be expected if the DNA molecules (technically nucleobases) were created chemically on the meteorite. This has implications for the evolution of life on earth, and all those big exciting questions about how the search for alien life.

The actual paper (which I admit, I have not had time to read yet) can be found, freely accessible here, in the most recent issue of PNAS.

I know, this might remind you of another fairly recent NASA press release that seemed to tease us with hints of alien life, but I, personally, am much more optimistic about this one.

Thats all for now, wish me luck studying. I promise all sorts of exciting new microbial knowledge to share after I (hopefully) emerge "Docrotral Candidate" from the other side of this exam.


What can climbers teach us about #elevatorgate?

I've refrained from commenting on #elevatorgate snafu, mostly because I feel like I can't add anything original and neither side is making any sense any more. Or at least, the extremests on both sides are drowning out the people who are making sense. For my part, it seems to me like everyone did some things wrong. Elevator dude acted a bit creepy, he probably shouldn't have done that. Watson called out a student who dared contradict her and lumped that student in with misogynists when she couldn't defend herself, Watson probably shouldn't have done that. I'm not sure why people couldn't just walk away with some lessons learned, but there it is.* But all of this was on my mind when I saw this thread on Reddit last week:

Jessa Younker bouldering. Phew! I think I'm in love

Which linked to this picture:

Jessa Younker bouldering (Source for all the photos in this post)

I clicked the link, and my first thought was, I admit, "wow, hot." The first few comments were predictable affirmations of her actractiveness, and then I saw this exchange:

Screen Shot 2011-08-09 at 12.57.08 PM.png

... and other responses ranging from the asinine to the thoughtful. For those of you unfamiliar with reddit, users can vote up or down on posts and comments, and that comment about the locker-room atmosphere currently has the second highest rating (right behind someone who posted a larger-resolution image for people to use as their desktop image). And at this point, a lot of the comments that just say "wow, hot" were down-voted. So that's at least progress right?

The major criticism was that this photo is just a glamour shot showing off cleavage - not really showing her skill. By all accounts, Younker is a fantastic climber, so why not show off her climbing ability, especially in a forum about climbing? Like this one:

Jessa Younker works the Corkscrew (V6).jpg

My impression has been that climbers in general are the coolest community of people ever, and I think this was reaffirmed here. A bunch of people made great points about wanting women to feel comfortable in the community (climbing in general or that subreddit), and there was some good debate about whether or not the reaction was appropriate. Hopefully some consciousness was raised, and of course there are going to be guys who won't get it, but most of the discussion was thoughtful and civil. Why can't people bahave this way everywhere on the internet?

PS - Some pictures of awesome female climbers doing retardedlyincredibly hard stuff (also from that thread on reddit) after the jump.

Plus, a video.

Emily Stifler: Emily Stifler and The Corkscrew (V6).jpg

Jen Vennon: Jen Vennon on the Big Easy boulder.jpg

Dumpster Barbecue, 5.13c from Rock & Ice on Vimeo.

"artificial, engineerable, animal chloroplasts": coming soon to a laboratory near you!

ResearchBlogging.orgAs many of you are no doubt aware, both mitochondria and chloroplasts are thought to have come to us via microbial endosymbiosis (that is one cell living within another) with prokaryokes. Some photosynthetic bacteria eons ago found itself nestled inside another cell, realized it was a pretty sweet place to call home, and viola - a new cell organelle was born. OK fine, that is a bit of an oversimplification. The endosymbiotic theory is a bit more complicated, but that's the general idea. The details of how a symbiont over time could lose its unique identity and became a part of the host itself are keys that would unlock many evolutionary mysteries... mysteries that if we could understand them could allow us to better understand evolution, and possibly to engineer symbioses of interest.

I came across this article recently in a university-wide email newsletter. The article was a bite sized appetizer with hints of science fiction, green energy, history of life, not to mention a pretty picture with green sparkles. I needed more, so I found the paper where the study was formally written up.

I am a sucker for short, elegant, intriguing titles - ones that pull you in rather than make you re-read 3 times before you have any idea what the paper is about. "Towards a Synthetic Chloroplast" (open access: was just such a title. By the end of the abstract I was still engaged and wanting more.

Our results show that it is possible to engineer photosynthetic bacteria to invade the cytoplasm of mammalian cells for further engineering and applications in synthetic biology. Engineered invasive but non-pathogenic or immunogenic photosynthetic bacteria have great potential as synthetic biological devices.

The paper made me think of one of my favorite books, "Oryx and Crake" by Margaret Atwood, which describes a world in which bioengineering has created a group of people with photosynthetic pigments in their skin. Hungry? No problem, just go sit in the sun for a while. So, what did these Harvard Medical School scientists do that seems to poise them somewhere along the path towards futuristic biological engineering?

First they injected individual Zebrafish embryos with up to 10 million Synechococcus elongatus cells before the embryos underwent their first cellular division. The researchers compared this to injections of E. coli (both living and dead) cells, and found that while both types of E. coli cells killed the developing embryos very rapidly, the S. elongatus cells seemed to have no impacts on the embryo's development. These embryos are clear, so light could penetrate to the photosynthetic bacteria injected into the cell. The bacteria were easy to track because of their red autofluoresence. Scientists saw the bacteria throughout the embryo (even in the brain and eye), but did not see any abnormal morphological changes in the embryos. The bacteria survived for 12 days within the embryos, and at that point the experiment was stopped because the fish began to become opaque, which would block the light that the bacteria would need to survive.

In a second experiment the scientists wanted to see if S. elongatus could invade mammalian cells if they were provided with the genetic machinery to do so. They identified genes in a different bacteria (invasin from Yersinia pestis Yersinia pseudotuberculosis (see comment below) and listeriolysin O from Listeria monocytogenes) that are known to cause invasion of mammalian cells. They then inserted these genes into S. elongatus. After this, 4.8% of the mammalian cells that they exposed these S. elongatus were positively fluoresent, showing that they had been successfully invaded by the engineered version of S. elongatus.

A third experiment involving macrophages showed that, unlike E. coli, the engineered S. elongatus was able to increase its fluoresence within the host cell (for a few days at least). This means that the bacteria were growing and dividing successfully within the cell.

The work described in this paper demonstrates, in a controlled laboratory setting, the first few steps that would be required to establish an intracellular symbiosis such as the one believed to have been responsible for the first chloroplasts (which therefore enabled the evolution of plants, an oxygen atmosphere, animals, and eventually you and I. There are no known mammalian endosymbioses, and work such as this is one way to understand why. The demonstration that it is possible to engineer a bacteria to be able to invade a mammalian cell has implications for synthetic biology in addition to allowing us insight into the evolutionary history of symbioses in general and even photosynthesis specifically.

Agapakis CM, Niederholtmeyer H, Noche RR, Lieberman TD, Megason SG, Way JC, & Silver PA (2011). Towards a synthetic chloroplast. PloS one, 6 (4) PMID: 21533097

P.S. (5/9/11) I just learned the first author of this paper also blogs here, and wrote her own post about this work. Check it out here!

Why I Love Science by the Pint

... because I love science and I love beer, obviously. I had a great time moderating Science by The Pint last night! It is always awesome to be reminded how enthusiastic non-scientists often are about science. I find events like this incredibly refreshing when I have been stuck in a science rut or simply less enthusiastic about my work than usual.

I had participated in one of these events last year, when an upper level grad student was speaking. I wandered from table to table talking about how cool hydrothermal vents are, and why we think its important to study them. People asked interesting, important, tough questions, and I was really impressed with the quality of the dialogue. You don't need a strong, or even any, science background to have a great conversation about science. This time around I saw it from a different perspective. Being the moderator, I saw it from a few steps back. I tried to make sure every table had a scientist to talk to, and that things were going well with the restaurant (insert plug here for the awesome folks at Tavern by the Square, Porter Square who made sure last night ran smoothly and have been very supportive of Science by the Pint this year). My favorite part of my new role last night was hearing from the speaker and his colleagues afterwards how much they got out of the event. Like me last year, they were pleasantly surprised with the quality of the science discussion, and seemed to enjoy it more than expected.

This type of venue is different from what most scientists are used to. We are used to giving prepared talks and fielding tough nitty gritty questions afterwards that may or may not be trying to poke holes in the research (aka our blood, sweat, tears) that we have just presented. We are not accustomed to (unless we spend a good deal of time teaching) informally discussing our research with a large group of non-scientists who are genuinely curious. It is good practice for us to make sure we can explain our research and why we do it without discipline-specific jargon or over-complicated explanations. It is also good to get very different types of questions than what we are used to answering from our colleagues.

I had a thought last night... that this format would be a great way to talk to students. Not the beer part, obviously - although that certainly would get kids thinking science is cool, but I generally try to stay away from the dark side. Anyhow, I think that rather than a scientist going to a classroom, presenting their research, and answering questions from the students who ask them, I think a scientist going to a classroom with a few colleagues, and breaking into groups and having discussions with the students in smaller groups one on one might be a very effective way to reach these students and get them thinking about the possibility of becoming a scientist themselves.

So, in conclusion, I really like the science café format. I am now re-enthused to go into lab and get my science on!

Science by the Pint - Tonight

Those of you living in Bosto-Camber-ville* might be interested in attending tonight's Science by the Pint. Our featured speaker is Alex Bradley - the author of the guest post critiquing the Arsenic paper a while back. Come to Tavern in the Square - Porter Square tonight, March 8 at 7pm to chat with Alex and his colleagues about microbially-catalyzed biogeochemical cycles and the coevolution of life and Earth. Yours truly will be hosting, and it will be awesome. Cheers!

* Boston, Cambridge, or Somerville, MA

Speaking Truth in Violent Times

It might seem strange at first to use reflection on the recent shooting in Arizona to make a point about progressive politics, but it's absolutely compelling. Go read this, seriously:

Instead our shadow in this country is economic greed, and there is a constant pull to unfetter business, to disallow regulation, and to let business do the business of business no matter the social cost. I have no brief against business and economic activity. It is a human thing. It can be glorious. And, it has deep shadows, including the inclination for the rich to simply continue getting richer while the poor get poorer. The growing gap between the fabulously rich and the rest of us, and the increasing uncertainties needs to be noticed, needs to be challenged. And challenged from a pulpit informed by a deep knowing of our intimate connections, all of us. The average American is being taken for a ride, hearing the false witness of conservative and libertarian economists and other apologists for the rich, pretending we all might get there, too. For the sake of the many, for those who have never benefited from the business of business, as well as those who have succeed in this enterprise but remain of good heart for all, who show us how it can be done, I will not be silenced.

Speaking for the poor who have broken one law to cross our borders, to become a part of the dream of possibility, who provide the hardest labor upon which this country's comforts are built, but who live in shadow and fear and become the scapegoat for those who would rather we not look into the dark hearts of those who are making most of the money, I will not be silenced.

Speaking for a fair and equitable access to healthcare for every one of us, I will not be silenced. Speaking for access to a good education for all, I will not be silenced.

Speaking for those who are given second class tickets to the feast of life because of their color, and who continue to struggle, having to be twice as good to get to the first rung of our society's economic ladder, I will not be silenced.

Speaking for women who have finally, in this country, at least, and some others, achieved most of the rights we assume are human rights, but whose positions are still fragile, who need men to stand with them, I will not be silenced.

Speaking for lesbians and gays and bisexuals and the transgendered, people who have been for too long the easy scapegoat for imagined ills, whose love has been denied for vastly too long, and who now stand at the edge of genuine freedom and an authentic place within our culture, I will not be silenced.

Speaking for our precious planet, beautiful and fragile, ravaged by our human hands, and in need of healing, I will not be silenced.

Speaking for this wondrous country of possibility, acknowledging its long shadows, and its astonishing potentials, a republic of dreams, a home for the birds of paradise, celebrating it for its good and chastising it for its crimes, I will not be silenced.

And, neither should you.

Really, you should read the whole thing.

Dr. Strangebacteria or: How I Learned to Stop Worrying and Love Using my Gut Instinct

A male fly walks into a bar and orders cornmeal-molasses- yeast. A pretty female fly comes and sits next to him. They look at each other, he starts to say hello, but then she orders some starch. He turns away. She looks at his glass of cornmeal- molasses -yeast and gets up to leave.

A recent study, published in the Proceedings of the National Academy of Sciences, shows that mating preference of fruit flies (the ones you see swarming near a piece of rotten fruit) is dependent on their diet because it changes the composition of bacteria that live in their gut (gut microbiota). This intriguing study stems from previous experiments in which fruit flies bred under different environmental conditions preferentially mated with other fruit flies from the environment in which they have been reared.

Gil Sharon and his colleagues at Tel Aviv University in Israel and University of Maine in the United States decided to experiment with food sources and see if they induce preferential mating in fruit flies. They reared one population of fruit flies on a diet of cornmeal, molasses and yeast for 37 generations and another population on starch for the same amount of time. After eleven generations, the flies showed preferential mating when the populations were mixed in equal proportions. Of the 38 recorded matings observed 29 were homogamic (i.e. "starch males" and "starch females" or "CMY males" and "CMY females").

However, this trend was abolished if the fruit flies were fed antibiotics before the two populations were mixed. Of the 38 recorded matings in this experiment only 18 were homogamic whilst the other 20 were heterogamic. Antibiotics are chemicals that target bacteria, and this experiment suggests that the bacteria living in the gut of the fruit fly might have some role to play in who they chose as a mate.

After fingerprinting the gut microbiota, the authors noticed that eating starch led to enrichment of a particular type of bacteria in the "starch flies". This increase in number corresponded to a change in cutaneous hydrocarbons (CH) secreted by the "starch flies". CH are components of sex pheromones (sex pheromones are chemicals that animals secrete to convey their species and type and attract similar mates) in fruit flies and play an important role in mate selection. Hence, an altered composition of CH would mean that the "starch flies" would smell very different compared to the "CMY flies". How the "starch flies" respond to their own altered sex pheromones is a question that is yet unaddressed....

The role of commensal gut bacteria in influencing behavioral patterns is an intriguing aspect of evolution. Think about it when you walk into a bar....

The immune system has trade-offs

Most biological systems have trade-offs, so this really shouldn't come as a surprise. A recent paper published in Science shows that in sheep, some females have a stronger immune system and tend to live longer, but also tend to reproduce less often. This seemed to translate to roughly equal reproductive fitness over the course of their lives. It's a cool study, clearly involving a lot of work (they took samples over the course of a decade). The New York Times comes soooo close to having a great science article - they just forgot one thing.

They found that the average life span of the 410 ewes surveyed was 6 years. But there was a wide variation, with some living 15 years, and many others dying at age 3 or 4. The short-lived ewes had lower concentrations of antibodies than the longer-lived ones, which suggested why their lives were so short. But why was natural selection not weeding them out?

Dr. Graham said the researchers found this to be a puzzle: "What are all these sheep doing with low antibody concentrations?"

The answer, she said, was that the short-lived ewes were more likely to produce lambs. Those that died young reproduced almost every year, often having twins. Sheep that lived longer did not reproduce every year.

The researchers make the point that it could be an energy expenditure issue, and that's certainly plausible. The immune system requires a great deal of energy to fight infections, and babies require a great deal of energy. Resources are limited, yada yada yada...

All of this is true. There's no wild misinterpretation of the data, no far reaching conclusions (I can just imagine the headline: "Having trouble conceiving? New study suggests taking immunosuppressives will increase your chances of having a baby" - ugh), and they even give you an interesting bit of history about why these sheep were good experimental subjects - something you couldn't have gotten just reading the paper.

The only major qualm I have with the report is the credulousness that starts with the title. There's absolutely no data to suggest that the Ewes with weak immune systems have more offspring because they have weaker immune systems. The two are correlated, but no causal relation was demonstrated. Not that I blame the reporter - the fact that the explanation for a causal link makes such intuitive sense makes it easier to fall prey the fallacy

population genetics, evolution, and ocean ecosystems (repost)

[This post was originally published at] I was trained as an Environmental Scientist long before I was at all interested in Microbes. So, I get excited when I come across microbial studies that are environmentally relevant. I get particularly nerd-cited when these studies take place in the ocean. A paper published in PNAS last month describes identifies what may be the key environmental factor distinguishing the evolution of microbial populations in the North Atlantic and North Pacific sub-tropical gyres.

The finding that populations of the abundant, widespread, and relatively well studied marine microbes Prochlorococcus and Pelagibacter (both) in an Atlantic study site had much higher frequencies of genes related to phosphorus (P) acquisition and metabolism than similar organisms in a Pacific study site was no surprise to the researchers. What was shocking was that virtually all of the genes with significantly different frequencies in the two sites were related to P use or uptake. This implies that reduced P concentrations in the Atlantic (relative to the Pacific) is the primary, and possibly sole, environmental factor driving the evolution of the P limited population. Environmental complexity generally prevents such complete correlations in studies comparing distant environments.

The methods in this study involved sampling water at three different depths at the two sites, isolating and culturing microbes of the two types and they sequencing the genomic DNA each population. Then they analyzed the variety in the sequences, and compared them to previously sequenced lab strains of each type, looking for genes that were present in some, but not all of microbes in the population. Most of these differences were due to random variation and neutral (not evolutionarily advantageous) evolutionary processes. The genes of interest were those that were more abundant (statistically speaking) in one site or the other, because that indicates that that gene is conferring some evolutionary advantage in that environment, but not in the other. In Prochlorococcus, there were 29 such genes, and nearly all of them were more abundant in the Atlantic site, and were phosphorus-related. This pattern was confirmed with Pelagibacter. The conclusion is strengthened by the fact that these two types organisms are very different. Prochlorococcus is a photosynthetic cyanobacteria, where as Pelagibacter is a heterotroph

Microbial ecology is a relatively young science, and very little ecological theory has been tested with microbial populations. Studies like this one allow scientists to make predictions (that future work can support or contradict) about how evolution is working in microbial populations in natural environments. These types of studies on marine microbes are especially important because we know so little about these communities, and many of them are beginning to deal with changing environmental conditions. The paper concludes with the following statement.

In this way, population genomics of ocean microbes not only is a powerful tool for diagnosing environmental change, but also can illuminate the fundamental evolutionary processes underlying biological organization.

Reference: Coleman ML, & Chisholm SW (2010). Ecosystem-specific selection pressures revealed through comparative population genomics. Proceedings of the National Academy of Sciences of the United States of America PMID: 20937887

mantle to microbe: a grad student's first conference

Hi ScienceBlogs... it is GREAT to be here! I just spent the weekend with many of the scientists whose research has comprised the bulk of my reading material (ie brain-biggering) over the last 1.5 years... yikes! I also got to meet many other young scientists hoping to make a career out of this crazy science game. It was totally awesome, and quite a whirlwind.

I was at the 2010 Ridge2000 community meeting in Portland, OR. It was a meeting of about 140 people united by their shared interested in better understanding what goes on at mid-ocean ridges. We represented disciplines ranging from geophysics, to macrofaunal ecology, to geochemistry, to microbiology. There were thematic sessions dedicated to sensors and technology, volcanic "event" response, biogeochemical processes, biogeography, modeling, mantle and crustal processes, and education and outreach. There were also location specific sessions bringing together all the researchers who work in one particular area.

The uniting theme of the Ridge 2000 program, and what makes it relevant to this blog, is "from mantle to microbe". The program's goals are explained on the website as follows:

"to work toward a comprehensive, integrated understanding of the relationships among the geological and geophysical processes of planetary renewal on oceanic spreading centers and the seafloor and subseafloor ecosystems that they support. Studies under the Ridge 2000 program are defined by an integrated, whole-system approach encompassing a wide range of disciplines and a progressive focus within scientifically defined, limited geographic areas."

I enjoy the idea of thinking in terms of mantle to microbe. I like the telescoping concepts of scale, the implication of inextricable linkages, and of course the clever alliteration. While "integrated" and "whole-system approach" can seem like buzz words, the cross-discipline collaborations evident at this meeting assured me that they are terms that actually describe what this group, as a whole, is doing.

I spent a lot of time over the last few days listening to the experts in my (and other) field(s) talk about the state of our knowledge, the accomplishments of the past couple of decades and their vision for the figure of vent research. In addition to being inspired and reaffirmed that I study the coolest environment out there (if Sir Attenborough can't sell it, no one can!), I was genuinely surprised and impressed by the dedication the community showed to sharing their work with scientists outside the "vent" community as well as with the broader public.

It is easy, especially as a grad student, to get caught up in the minutiae (pun intended) of what we study and lose sight of the fact that each scientist is part of a community of people dedicated to growing our understanding of this planet. My contribution is insignificant on its own (so far at least!), but after this weekend I feel a part of something much bigger, and much more significant.

... less sap next time, I promise.

Science in the News: Microbes of the Gut!

We beasties came together through our love of microbes, but also through a graduate student group called Science in the News. SITN is completely run by graduate students, and our mission (much like the mission of this blog) is to share our love of science with the general public. We have a lot of events to this end, from school out-reach to a monthly newsletter to Science Cafes (called "Science by the pint" - we basically get drunk and talk science with whoever happens to be in the bar). But our main event is a lecture series every fall. And it just so happens that this week, I'll be presenting on a topic near and dear to our hearts here at We Beasties, "Our Microbial Organ: The Good and Bad Bugs of the Human Gut."

If you're in the Boston area, you should come check it out. It'll be Wednesday from 7-9 in the Armenise amphitheater at the Harvard Medical School. And if you can't make it, we're also posting video (we're trying to do it in a timely fashion, but I'm in charge of video).

Rally to Restore... Something

I was there! Not that it was easy. We decided to park in VA (in the parking garage of the National Science foundation - totally by accident) and take the metro in, but evidently the entire world had the same idea; the metro was about a 2 hour wait, and the bus stop had like 3 buses worth of people, and only two buses scheduled in the next hour. So we decided to walk the 6 miles to the National Mall, with less than an hour before the thing started. I was at Obama's inauguration two years ago, and there were screens and speakers all the way to the Lincoln Memorial, but apparently Comedy Central only had a permit to set stuff up until 7th street. In any case, it was hard to really hear anything, and I actually saw more of the rally yesterday online than I did while AT the Rally. Still, I was glad to be able to go and support the message, but what exactly WAS the message? Whatever it was, PZ didn't think much of it:

I was left cold by the fuzziness of the event. It could have been great; instead of embracing an apolitical perspective and saying nothing at all about values, it could have been a rally for moderation that emphasized the actual values that moderates hold: we believe in tolerance for people of different ethnicities and religious views and sexual preferences, we believe in building an egalitarian social and economic infrastructure, we believe in privacy and personal freedoms, etc., etc., etc., and they could have held to the theme of the rally by advocating rational argument and unified, organized activism within the system to advance those goals...but they didn't. There was no purpose given other than a generic insistence that we all get along nicely. And to what end, I ask?

It seems a bit presumptuous to disagree with him on my very first day here at ScienceBlogs, but I'm going to go ahead and do it anyway. I'm going to do it by agreeing with him first though - all of those values are important. The thing is, I think that those values PZ speaks of were expressed. Tolerance was arguably the largest organizing principal, and a repeated theme in many of the musical choices and skits. "Unified, organized activism within the system" is exactly what was happening. It's true, they didn't exactly use rational argument, they used comedy - but that's because they're comedians.

I can understand why PZ is wary of arguments that are about tone, and I'm sympathetic to his position. I find myself agreeing with him most of the time. But I also think there's a difference between the sort of religious "tone" arguments that he addresses most of the time, and the call for sanity and rationality in politics that I think Jon Stewart was advocating on Saturday. In the religion debate, as an atheist, the only way to not offend is to not make your argument. I can understand why PZ rails against others trying to disqualify any argument he makes as failing on tone. But we can have debates on what makes good policy without labeling our opponents as marxists or bigots. The point of the rally, in my opinion, was precisely to say we need to have rational arguments, not ceaseless ad hominem. The money line, in my opinion:

We can have animus, and not be enemies.


One final point: as an immunologist, I would be remiss if I failed to point out this line:

The press is our immune system. If it overreacts to everything, we actually get sicker--and, perhaps, eczema.

Rally to Restore Sanity and/or Fear
Jon Stewart - Moment of Sincerity
Rally to Restore Sainty and/or Fear The Daily Show The Colbert Report

Edited for egregious typos.

We, Beasties

It is an honor and a privilege to be joining ScienceBlogs. Many of the first blogs that I ever read were on this network, and the efforts of PZ, ERV and Orac (among others) to communicate science directly from the lab to readers was in large part what motivated me to start blogging myself. I love the process of discovery that is made possible by science, but I also think that any discovery is useless if it's not communicated to others. We welcome your comments, questions and criticisms, and hope that you enjoy reading. But first, let me tell you a bit about who we are and what we do.

In 1674, Antonie van Leeuwenhoek pointed a microscope at pond water and saw what he called "wee beasties" flitting about, kicking off the field of microbiology. Since then, scientists have discovered microorganisms living just about everywhere, in every kind of environment, from the crushing depths of the ocean in hydrothermal vents to the crypts of our own intestines. WE beasties are graduate students at Harvard, studying some of the many ways that microbes make their impact on the world.

As my PI once said, "We don't live in a perfect world; We live in a microbial world." Indeed, there are ten times more bacteria cells in your gut than there are human cells in your entire body (another reason I think "We, Beasites" is so apt). In just about every ecosystem on earth, microorganisms bracket the food chain as producers at the base and decomposers at the peak.

I (Kevin Bonham) am in the immunology program at Harvard, and study the interactions between microorganisms and the mammalian immune system. My work revolves around the signaling networks downstream of Toll-like receptors, which recognize conserved molecular patterns on bacteria, viruses and fungi and kick-start the earliest immune responses.

Heather Olins, Emily Gardel and Dipti Nayak will be occasional contributers. Heather studies the microbes at the base of the food chain in hydrothermal vents that use chemical and heat energy rather than solar energy to fuel their habitat. Emily studies the way that microbes produce energy with the goal of harnessing their efficiency to produce electricity. Dipti studies the evolution of metabolic pathways in bacteria that eat single carbon compounds.

We've already put up some of our favorite posts from the last year to give you a sense of what we're about, but feel free to kick around our old location on your own.

Thanks for having us, we hope you enjoy!

Walking bacteria - and some weighty researcher cajones (repost)

[This post was originally published at] Most papers I read these days are long. Nature and Science papers tend to have 3-4 figures (Cell and Immunity papers can be twice that), tons of supplementary data and are at least a couple pages of dense, science-speak prose. I think I once read a paper (from like 20 years ago) that had a gene sequence as figure 1, a hand-drawn model for figure 2 and one figure of functional data, and I thought that was sparse.

So imagine my surprise when I stumbled on this new paper. One figure. Less than 500 words. And it's about bacteria that seem to get up on their legs (wait, bacteria have legs?!?!). Published in Science - one of the most prestigious science journals in the world. Anyone that is willing to submit a 1 figure paper (not to mention get it accepted) in Science with a sentence like

Bacteria stood upright and "walked" [...]

in the abstract is either extremely clever, or extremely ballsy (or a healthy combination of both). Here's what they did: they took pictures of huge numbers of Pseudomonas aeruginosa at the surface of biofilms and then used computer software to analyze how individual bacteria were behaving. They noticed that a large number of bacteria near the surface appeared to lift up into a vertical orientation, then walk along the surface of the biofilm on little appendages called type-IV pilli (TFP). I've mentioned biofilms before, but the easiest way to think of them is as a bacterial community. Mostly we think of bacteria as single-celled individuals, but biofilm-forming bugs can achieve a measure of cooperation, and the formation of biofilms is a requirement for a lot of bacterial pathogens (like Pseudomonas) to actually cause disease.

The TFP's were always known to be used for locomotion, like the propellers of a boat. Indeed, when these bugs were in a horizontal orientation, they could crawl in straight lines for long distances. But in the standing orientation, the pilli seemed to act like legs for the bacteria to scuttle along at a faster rate, though they seemed less directional:

Each mechanism confers advantages for surface exploration[...] Crawling enabled directional motion; walking enabled rapid local exploration.

Picture 2.png

In part A of this figure, red represents the "walking" orientation, and is a pictorial representation of the motion of individual bacteria - each line represents a single cell's motion over time. Comparing those lines to the blue ones, you can see that the crawling orientation tends to be much longer and much straighter.

Part B is just quantifying (putting into numbers) what is represented in A. They actually analyzed about 70,000 individual bugs, and if you look at the axis labeled "L," it shows the distance that each individual traveled, and you can pretty clearly see that the red guys all cluster in the much shorter distances.

They also mention some observations about the cell division behaviors - the TFP seem to be important for daughter cells to move away from each other after they divide - but this seems like more of an appeal to increase the relevancy of the paper. As I said before, it was known for a while that TFP were required for movement, and none of the data presented demonstrates that this walking movement is necessary. In fact, they say

daughters left the division site by detaching, walking, or crawling

It's just that TFP are required for all of these events.

Understanding he way that biofilms affect the life cycle of bacteria is crucial to understand the role of biofilms in disease, but the data presented here is really just observation. It doesn't provide any mechanistic insight, though it will hopefully lead the way to more detailed understanding of how and why this is important. On the other hand, it clearly impressed the editors of Science enough to get included.

UPDATE: After I originally posted this, one of the authors dropped by and left a comment linking to one of the actual videos. It's pretty awesome - and he promised a full-length paper is in the works and almost ready for submission.