Culturing Science – biology as relevant to us earthly beings

Archive for February 2011

Transitioning into “real” science journalism

In which Hannah treats her blog like her livejournal circa 2003.  Livejournalism — reflections on being a blogger-turned-journalist.

Two-and-a-half weeks ago, I started interning at The Scientist magazine.  One day I was a scientist, and then decided to leave it all to try my hand at writing about science for a living.  I really didn’t know what to expect, but as the start of the internship crept toward me, I started to become afraid.

My only writing has been on the web, with unlimited space and freedom of form.  I knew that, writing professionally, I would no longer have the freedom to wax philosophical and provide pages of background, as I am wont to do.  Would I be forced to play into hype?  Bend or even break my principles?  Would I leave completely jaded, turned off from science writing altogether?

None of my fears have been confirmed thus far; in fact, the past weeks have been both amazing fun and full of learning.  In each story I’ve covered, I have been able to see the hype point but have always pushed it far, far away from me.  (And I even laugh a little when I see the story distorted elsewhere — that is, before I start crying for humanity.)

I’ve spent the last couple days researching a news story about a PLoS ONE paper about human contamination in databases of genomic sequences that went up tonight.  I was absolutely fascinated by the topic.  The second I spotted the paper, I contacted the scientist, Rachel O’Neill, to hear from her the story behind her research.

Let me tell you — once you start talking to scientists about their work, you can never go back.  There’s really nothing better than to hear what they care about, why they did the work, and, of course, to get the details of the methods explained without having to read wikipedia articles on various genetics tools just to get a sense of it.  It is the most fun part of the job (and also the part I was most afraid of).

After I talked to Rachel, I needed to get a second and even third source to read the paper and let me know what they think.  A scientist can’t help but give a biased account of her own work, after all.  I tried to contact a number of people who work in large-scale genomic sequencing, but no one was willing to give me an interview.  Maybe I picked people who were too big name and above puny me; or maybe the story seemed a bit too controversial and researchers didn’t want their names tied to it.  Either way, I was struggling, and I needed help.

“I have tons of scientist friends on the internet!” popped into my head.  It seemed strange, like I was crossing an illegal boundary between my life as a “real journalist” and a blogger.  This effect is particularly strong for me considering that I’m a huge idealist and can’t escape my view that the world is a meritocracy.  I need to make it as a journalist on my own, without my bloggy friends!  Right?

Nope.  I needed help so I contacted Jonathan Eisen of the Tree of Life, a big-shot genomicist, open access advocate, and evolutionary biologist.  (Did I mention that I might be his #1 fan in a creepy internet way?  Hi, Jonathan! What’s up?)  I learned a ton from him during our talk and it was such a joy to speak to him as he biked across campus (in the wind – what a champ!).  I felt a little strange about it, again like I was breaking some rule because he, like, retweeted me one time or something.  Was I being biased by talking to him? was the thought running through my mind.

When reading the news later it struck me that Monday’s news on a lateral gene transfer between humans and gonorrhea could just be an instance of contamination – an idea that was confirmed by Eisen.  I frantically emailed my boss (Literal: “This could be REAL SCIENCE JOURNALISM, gritty like in the movies!” to which she responded, “I’m confused.”  A little over-excitable, perhaps?)  I emailed Rachel O’Neill about it, but didn’t know how to proceed further.

So, with a sigh, I settled down to read my Research Blogging RSS feeds in the morning.  And what did I come across?  A blog post with the title: “Human DNA in bacterial genomes? Yes? No? Maybe?”  Could this be a dream come true?  I went to the blog and, sure enough, it was written by a genomicist, Mark Pallen.  I emailed him immediately, and later called him up to discuss whether the data in the gonorrhea paper definitively proved that there was no contamination in the database.

I wrote up the story, had a blast doing so, and now it’s on the front page of the website.

For all the fighting I’ve done with myself to avoid being biased in choosing my sources, maybe Jonathan and Mark deserve to be chosen.  They are active communicators, expressing their desire and ability to explain science on the web.  Is that really a bias?  Isn’t that really just.. a logical choice?

In which case… shouldn’t the science blogging community, and Research Blogs in particular, be a goldmine for journalists?  It’s basically a list of scientists (and others.. but many scientists) who want to talk about what they’re doing, make a point to keep in touch with what’s happening in their field (and others), and whose work you can evaluate before even speaking with them.  Is this biased reporting?  I don’t think so – unless they’re your friends, that is.


The second I posted my story, I looked at twitter and saw that Ed Yong had posted a similar story, gonorrhea and all.  But it wasn’t the same story – and that’s because, in the end, blogs do have a win over more mainstream journalism.  I mentioned word count on twitter, but really it’s the story format.

If you’re trying to directly communicate basic information about a new science article, you’ve gotta do it at the beginning — or at least that’s the current practice.  And I do understand the reasoning behind it: if people don’t have time to read the whole article, at least the kernel is provided up front so they can leave learning something.  It also is a good way to get the news out fast; the beginning is the hardest part to write, and by having a formula, most of the thinking is already one: summary of research, implications, outside source quote.  Then you can zoom out and back up.

But because of that, I can’t write the science like a story, or not with the same flow.  I can’t start out with an anecdote about how the scientists started studying the topic, a funny quote, a philosophical anecdote, or anything else.  Scientific research IS a story – as I’ve written elsewhere – a story of how the research progressed, the interests of a person who happens to be a scientist.  The best science writing plants curiosity and leads the reader to ask the same questions the scientists did.

But the news model persists because it’s modelled off of other fields, or sets an easy demarcation of what is worth covering.  “It’s new so we’d better write about it.”

I do believe that journalism and the media are changing for the better, and that a lot of it has to do with blogs and writing online.  Freedom of space and form lead to more interesting stories, better stories.  Right now science journalism tries to frame science to make it a story — let’s reveal this bias, or let’s talk about how xyz new finding has changed the world.

But science doesn’t need framing; it already is a story.

Even if right now I’m constrained by format, I’m not shaken – I still want to continue in science journalism more than anything.  Not only for the joy of it – but if you want to make change, you have to play the game for a little, as I learned from SLC Punk.  (Has this film guided anyone else’s worldview? Please say I’m not alone!)  Maybe one day I’ll edit a magazine and I’ll throw away the formula and get to test whether it’s successful.  But I need to get there first.

…in my dreams right?  Didn’t I say I’m an idealist?

Anyway, enough for tonight.  Here are the articles I’ve written for The Scientist so far if you want to check them out.

  • 3rd Feb 2011 – New mosquito identified: on a group of mosquitoes that hasn’t been targeted – or even identified – in the fight again malaria in sub-saharan africa
  • 10th Feb 2011 – Cellular chaos fights infection:  why disrupting RNA degradation could create antibiotics
  • 14th Feb 2011 –  The mouse is not enough: early development differs between mice, the standard model organism, and cows, further encouraging scientists to study multiple model organisms
  • 16th Feb 2011 – Contaminated genomes: human sequences have been found in over 20% of sequenced non-primate genomes in databases

(I know – I still can’t write a title for my life.  Sue me!)

Written by Hanner

February 16, 2011 at 11:57 pm

Posted in My life, Reflection

Tagged with

The many relationships of leaf-cutter ants

Are those little leaf scraps on the ground? Or is it a line of leaf cutter ants (Atta cephalotes)? Photo taken at La Selva Biological Station, December 2008 by Hannah Waters

Trying to capture the movement of a colony of leaf-cutter ants in a single photo is nearly impossible in my (amateur) experience.  The queues of ants follow a worn-down trail in the ground that they themselves made with the impact of their little ant feet.  There are ants moving in both directions, between the food source and their nest, but you rarely see them run into each other.  (Though small ants, minima, will hitch rides on another ant’s leaf.)  It’s an organized flow of ants and materials – but a photo can only capture the single frame, as if it’s just bits of leaf littering the ground.  The sense of movement is lost.

But that’s only the the frustration if this is the aspect of ant symbiosis you’re trying to capture: the leaf cutter ants collecting foliage to feed to their cultivated fungus. What if it’s a different symbiotic relationship you’re interested in?

BOOM! Image by mass spectrometer to measure the amount of an antibiotic, valinomycin, on a leaf cutter ant, Acromyrmex. by Schoenian et al. 2011.

Leaf cutter ants, of the genera Atta and Acromyrmex, live in huge colonies and can form nests more than 30 meters in diameter.  They’re most noted for their agricultural behavior: they harvest leaves (and can defoliate entire trees in the process) which they bring back to their nests to feed their mutualistic fungus (of the family Lepiotaceae), which acts as a food source for the ants in exchange for the food.

Imagine being in that nest, inside a cavern full of warm, wet fungus.  Most organisms would be looking forward to gorging on this food source, or to growing there themselves.  The ants meticulously clean their fungus gardens and even secrete an antimicrobial acid to keep themselves from bringing in outside visitors, but is that enough to fend off the various microbial and fungal intruders?

In 1999, Cameron Currie (whose ant colony has a twitter account) identified a microbe (Streptomyces) living on the ants’ bodies that produces an antibiotic chemical.  He found this same microbe living not just on one, but many leaf-cutter ant species, including two genera of fungus-growing ants that evolved earlier than the leaf-cutters Atta and Acromyrmex we know and love.  This microbe produced an antibiotic that was very potent against a common garden-invading fungus, Escovopsis.  So it seemed that this was a 3 way mutualism: the ant, the fungus it feeds on, and the microbe that helps protect the garden.

Is anything in biology ever so simple?  The hunt began to find more bacterial antibiotic-producing symbionts.  Scientists have found many more symbionts and garden parasites, revealing the complexity of this ecosystem.  But the microbial symbionts aren’t always masked superheroes protecting the fungal garden: their antibiotics can also do harm to the farmed fungus itself.  Additionally, if there are many species of microbes around, an evolutionary arms race can emerge in which the microbes try to outcompete one another, creating stronger and stronger antibiotics which could be harmful.

Instead of simply listing off the species of microbes they discover on ants, Dieter Spiteller and his lab have been working to identify the antibiotics they produce.  This approach allows them to more easily identify what antibiotic types work on what pathogens and parasites and see what combinations of antibiotics show up together.  After all, the ants don’t care much about what species of microbe lives on them: only the benefit of the antibiotics.

Many of these microbial symbionts are not well-studied, if at all, so figuring out what type of antibiotic they are producing is a bit of a trick.  In their recent paper, the researchers used the evolutionary relationships of the symbionts – constructed using 16S rDNA sequences, which are commonly used to measure the “closeness” of two species – to find their closest relative that had already had its antibiotic identified by scientists.  This allowed them to narrow down their screen to look for the antibiotics that were most likely being produced by each bacterial species instead of having to screen for ALL of them.

They identified many types of antibiotics that fell into three main categories:  antimycins, valinomycins, and actinomycins, the latter so toxic that they aren’t used as antibiotics in humans due to damage to surrounding cells.  Then they tested the effectiveness of each antibiotic against a variety of pathogens and parasites that could endanger the nest: fungal pathogens of the gardens and insects, the common soil bateria Bactillus subtilis, microbial isolates taken from the ants and garden, and even the mutualistic fungus itself, Leucoagaricus gongylophorus.

The antibiotics varied in their strength and specificity.  Unsurprisingly, the most potent was the combination of the three – thus biochemical and microbial diversity is quite important to the success of these ants.  However, the antibiotics can have detrimental effects on other microbes living on the same ant (in particular actinomycin).  But this competition encourages the selection of stronger antibiotics in other species, which is beneficial to the ant and thus the symbiosis overall.

And that brings us back to that second image above: a visualization of the valinomycin distribution on a single ant.  As you can see, it’s pretty widespread – and is found more regularly in a high concentration than in the fungus gardens.  This makes logical sense: an ant would want to kill as many pathogens as possible BEFORE it brought the leaf into the nest.  But it also keeps the antibiotics from killing off too much of the ants’ fungus food.

To sum up: I just wrote a post about antibiotics produced by bacteria, which are competing for space on the back of an ant.  This ant climbs trees, cuts down leaf pieces, and carries them back to its nest to feed to a fungus which it then eats.  The antibiotics produced by the bacteria on its back keep pathogens at bay – protecting the fungus garden, thus the ant, and thus the bacteria. Phew! Currie, C., Scott, J., Summerbell, R., & Malloch, D. (1999). Fungus-growing ants use antibiotic-producing bacteria to control garden parasites Nature, 398 (6729), 701-704 DOI: 10.1038/19519

Schoenian, I., Spiteller, M., Ghaste, M., Wirth, R., Herz, H., & Spiteller, D. (2011). Chemical basis of the synergism and antagonism in microbial communities in the nests of leaf-cutting ants Proceedings of the National Academy of Sciences, 108 (5), 1955-1960 DOI: 10.1073/pnas.1008441108

Written by Hanner

February 8, 2011 at 10:20 pm