Here are the best things I’ve read all week. The pieces are not necessarily news and could be decades old, and they’re probably longform writing but not always. Maybe there is one link, maybe there are forty. But they all were thought-provoking enough that they hopped around in my brain long past the read. Enjoy.

1) A rare interview with John McPhee (‘John McPhee, The Art of Nonfiction No. 3′) from the Spring 2010 issue of the Paris Review is about so much more than how he writes, though it is about that — from getting ideas to structuring to getting words on paper. It also gives a fine sense of the man who is an inspiration to many of us nonfiction (or, as he prefers, ‘factual writing’) writers.

The thing about writers is that, with very few exceptions, they grow slowly—very slowly. A John Updike comes along, he’s an anomaly. That’s no model, that’s a phenomenon. I sent stuff to The New Yorker when I was in college and then for ten years thereafter before they accepted something. I used to paper my wall with their rejection slips. And they were not making a mistake. Writers develop slowly. That’s what I want to say to you: don’t look at my career through the wrong end of a telescope. This is terribly important to me as a teacher of writers, of kids who want to write.

2) How do you want to live the final months, weeks, days, hours of your life? Many of us, healthy, would say, “with my friends and family,” but this rarely happens in practice: too many of us will die fighting for even one more second of life. But, as physician Ken Murray points out in an article at Zócalo Public Square, doctors themselves, who should be best informed to choose how they will die, rarely go out fighting. And in ‘How Doctors Die,’ Murray tries to answers the question: “How has it come to this—that doctors administer so much care that they wouldn’t want for themselves?”

It’s not a frequent topic of discussion, but doctors die, too. And they don’t die like the rest of us. What’s unusual about them is not how much treatment they get compared to most Americans, but how little. For all the time they spend fending off the deaths of others, they tend to be fairly serene when faced with death themselves. They know exactly what is going to happen, they know the choices, and they generally have access to any sort of medical care they could want. But they go gently.

If you enjoy this article and find it thought-provoking, definitely check out ‘Letting Go’ from the August 2010 issue of the New Yorker by Atul Gawande, which is one of the best things I’ve ever read.

3) For 14 years now, the scientists behind the All Taxa Biodiversity Inventory have been working to catalogue all the species in the Great Smoky Mountains National Park, which is contained within North Carolina and Tennessee. And an article published in November in Knoxville, Tennessee’s Metropulse by Jesse Fox Mayshark (’17,000 Species in the Great Smoky Mountains. And Counting.’) recounts the project and whether it has a future.

The old-fashioned ambition of the project presents some serious challenges, though. There are, first of all, the unforgiving terms of the mission: Count everything. The name says All, not Some or Most. There is the problem that the natural world does not stand still. Every count is a snapshot of this year, this organism, this place. One of the hopes for the ATBI is that it will make it easier to understand the effects of forces like climate change, air pollution, and invasive species. But those forces are already at work, which means that things already counted have to be monitored and revisited even as the search for new species goes on.

The project has come a long way, as Mayshark explains, but it faces the same problem as much of taxonomy and species collecting: funding.

The funding that got the ATBI started has largely fallen off, and people to do the hands-on research are increasingly difficult to come by. It turns out that for all its scope, the kind of work the project demands is not, in a lot of ways, the kind of work that modern science most values and rewards.

“What happens when the hopeful, impossible task runs up against pragmatic reality?” Bartels says. “That’s the question.”

While Mayshark doesn’t address them head-on, the article raises all sorts of questions about what scientists, the public, and funding institutions value about science. And the sort of nitty-gritty work that should be — and perhaps must be — done.

Check back next week for more gems.

Image: via Mo Riza on Flickr under Creative Commons licensing

That is until New Years Day 2012, when new rules passed at the International Botanical Congress in Melbourne, Australia this July, take effect: the botanists voted on a measure to leave the lengthy and time-consuming descriptions behind. Additionally, the group released their concerns about the impermanence of electronic publication, and will now allow official descriptions to be set in online-only journals.

“Probably in 1935 [when the Latin requirement was instated], most people who got serious university degrees were required to take Latin,” says botanist Jim Miller from the New York Botanical Garden, who published an accompanying paper in the journal PhytoKeys in July. “But it has become less true that Latin is universally accessible.”

The botanists’ abandonment of Latin is yet another opportunity for this amateur Classicist to bemoan the passing of Classical study — but when I spoke with Jim, he really did have me convinced that it was time. This isn’t just a simple Latin name we’re talking about, or even a sentence; for example, when Jim discovered a new species of tree in Suriname, he had to pen the following in order to officially name it Cordia koemarae:

Arbor ad 8 alta, raminculis sparse pilosis, trichomatis 2-2.5 mm longis. Folia persistentia; laminae anisophyllae, foliis majoribus ellipticus, 12-23.5 cm longis, 6-13 cm latis, minoribus orbicularis, ca 8.5 cm longis,  7.5 cm latis, apice acuminato et caudato, acuminibus 1.5-2 cm longis, basi rotundata ad obtusam, margine integra, supra sericea, trichomatis 2.5-4 mm longis, appressis, pagina inferiore sericea ad pilosam, trichomatis 2-3 mm longis; petioli 4-7 mm longi. Inflorescentia terminalis vel axillaris, cymosa, 8-10 cm latis. Flores bisexuales; calyx tubularis, ca. 6 mm longus, 10-costatus; corolla alba, tubularis, 5-lobata; stamina 5, filis 8-10 mm longis, pubescentia ad insertionem.

Okay, so it’s not exactly a prime example of Golden Age Latin poetry. But, nonetheless, the Latin requirement presented a hindrance to botanists who are busy trying to name nearly 2,000 new species of plants, algae and fungi each year to disseminate the findings to other scientists and naturalists. “If we can increase the efficiency by which biologists can do their work and name species that we are racing against the clock to describe before they are lost or go extinct because of galloping deforestation, that’s a good thing,” says Miller.

And in another unanimous vote at the conference, which is held every six years and includes 8-10 hours of discussion nomenclature each day, the botanists decided to allow publication in electronic journals. The group had a similar discussion six years ago, Miller told me, but at the time the web still felt very impermanent — I’m thinking geocities or angelfire impermanent. And if you’re a botanist consulting a lengthy record of described plant species, you don’t want to lose some of those descriptions into the black hole of cyberspace. But this year, the botanists decided the web was less spooky and now can describe species in any electronic journal that has an ISSN, for the purpose of archiving.

“I think the importance of what happened at the Melbourne conference — whether elimination of Latin or allowing electronic publication — is that there was a real feeling among the people who attended the nomenclature session that we face a daunting task trying to catalogue, make sense out of, describe and name all of the species that are on this planet,” says Miller. “And we need to facilitate that, not encumber it.”

So on this New Years day, don’t just make resolutions and seek a kiss — also do your part in welcoming the botanists to the 21st century, a century in which we no longer speak in Latin and the web feels like a somewhat permanent destination… at least for now.

Images: from the Aztec herbal Libellus de Medicinalibus Indorum Herbis, first translated into Latin in 1552. Images in the public domain and found on Wikimedia Commons.

Even with such enlightenment, it’s nice to be reminded of why people once thought the opposite — that the universe revolves around the earth — to briefly knock us off our ivory tower of knowledge and be reminded of just how far we’ve come.

This feeling struck me as I watched ’Finding Oregon,’ a stunning time-lapse video from the Portland-based Uncage the Soul video production company. The four-minute video highlights the sky, in night and day, from different viewpoints around the state. Intended to be a tourism promotional film, it really does much more. It’s breathtaking, literally, and hair-raising in an inspiring, not horrifying, way. And watching the stars careen through the sky gave me pause. Because a person born in a vacuum would conclude that the heavens, in fact, revolve around the earth after watching the video.

So sit back, full screen the video, turn up the volume and enjoy. And click through to the vimeo page to learn more about how the team put the video together.

If your heart doesn’t stop, I declare you inhuman.

Image: Screenshot from ‘Finding Oregon‘

A group of college students studying at the Marine Biological Laboratory in Woods Hole, Massachusetts caught ahold of the trend, and have put together an audio piece featuring scientists, the tattoos hiding under their lab coats, and the underlying scientific passion that inspires them. They got the idea because one of the group members, my sister Emily Waters, had recently joined the ranks of tattooed scientists.

“I just got my first tattoo: a big plant stem cross section above my knee,” she says. “I was on the lookout for a cool topic for the radio piece, and it was then that I stumbled across Carl Zimmer’s blog and got the idea for the radio project.”

Science writer Carl Zimmer has been collecting science tattoos for years at his Science Tattoo Emporium on his blog, and last month published a book, Science Ink, featuring the extensive collection. The radio piece, embedded below, includes an interview with Zimmer who espouses his thoughts on why scientists get tattoos about their science.

Also featured are testimonies from four tattooed scientists: SciCurious, a biomedical postdoc and fellow Scientific American blogger; Josh Drew, a marine biology postdoc; Amanda Gallinat, a full-time bird bander and researcher (and my college roommate); and Nathaniel Comfort, a science historian at John Hopkins School of Medicine.

Listen to their fabulous radio piece below.

The video features a song from the fabulous Philadelphia band The Tough Shits, which you can hear in-full on muxtape.

I read his obituary and my body stopped functioning. I froze on the spot, limbs tense but trembling. My mouth went dry, my vision blurred. As I waited for my train in the packed station, I could barely stand as my muscles turned to jelly and legs folded beneath my body. I tried to maintain composure in the public space, but my contorted face betrayed my sorrow.

It was shocking to me: I felt real physical pain — a biological response brought about by stress hormones — in response to death. Not only was the feeling new to me, but it also didn’t make sense. Mourning left me depressed, unable to work, even unable to eat at times (the real shocker). And everyone mourns; as long as we are mortal, death and grief happen. So why would such a negative reaction to death be passed on through the generations? We’re certainly less able to reproduce when we’re grieving. Why didn’t natural selection help me out and ensure that I felt less awful?

Evolutionary biologists think that grief is passed on not because it provides benefit in itself, but rather it is a side effect of having relationships. As anyone who every had separation anxiety as a kid — or who lost track of their parents at the beach — knows, our bodies produce stress hormones when we’re separated from our parents, and the only way for those bad feelings to go away is to come together again. This biological reaction to separation keeps us together because staying together provides an evolutionary benefit. Kids and their parents — the core relationship evolutionarily — rely on one another for protection and genetic proliferation respectively, and so being drawn together and kept together is advantageous.

In more social animals, such as humans, those reciprocal relationships extend beyond parent-child. Our siblings help us survive, as do our aunts, uncles and friends. And, when we are separated, our bodies send out alarm cries to bring us back together. But, after death, the two cannot be rejoined. I stressed out while my hormones pushed me to find Pat. But he isn’t coming back, compounding the stress. “Grief – in its most basic form – represents an alarm reaction set off by a deficit signal in the behavioural system underlying attachment,” writes psychology professor John Archer of the University of Central Lancashire in his book The Nature of Grief.

This idea was endlessly comforting in my mourning. In an 1843 letter to his second cousin, Reverend William Darwin Fox, Charles Darwin wrote, “Strong affections have always appeared to me, the most noble part of a man’s character and the absence of them an irreparable failure; you ought to console yourself with thinking that your grief is the necessary price for having been born with (for I am convinced they are not to be acquired) such feelings.”

Grief is the price we pay for friendship.

Digital love

But these clear ideas became muddled when Steve Jobs died last month. The massive public displays of mourning confused me, as did the outcries from so many friends. When I heard the news, I let out my obligatory, “oh my god,” but didn’t even feel butterflies. My sadness was abstract, not substantial: I could recognize the loss and empathize with those who actually knew the man, but I myself was not in any kind of mourning.

The onslaught of mourning continued, nonetheless. First with disbelief, then meditations on what we lost, leading into the less savory game of casting blame. Twitter and Facebook were flooded with updates and links for weeks. At first I wondered whether the outpouring would have occurred in a world without social media. But many people in my parents’ generation can pinpoint the spot they were when they heard that Martin Luther King, Jr., JFK, or Elvis died. Mass public mourning is not new — but why does it occur?

Here culture seems to play in more than strict biology. We know that death is sad, and that inspirational people are worth grieving over, even if they did not directly touch our lives. Oftentimes their deaths are symbolic: the loss of a freedom fighter, a rock ‘n roll pioneer, or, yes, a technological genius.

Yet there is something performative about mourning for public figures, which is evident on social media. To let others know that you are in the know, and that your heart is big enough to recognize the role of relative foreigners in your life. And this isn’t just true of public figures. Since (and certainly before) Martial in Ancient Rome, writers have documented false acts of mourning for personal gain, whether material or just for attention.

After I heard about Pat’s death, those who did not know him all asked me the same question: “Well, were you close with him?” The answer is no. We shared many experiences that shaped me in my adolescence, but I hadn’t seen him in half a decade. And even so, his death paralyzed me. I even berated myself for just seeking attention and using his death to showcase my own humanity.

In the Iliad, Apollo rants about Achilles’s revengeful slaying of Hector for the death of his friend Patroclus. “Man may lose one far dearer than Achilles has lost,” he told the other gods. I could lose friends far dearer than Pat, people could lose ones far dearer than Steve Jobs. But grief strikes us just the same. Maybe they remind us of our own mortality. Maybe they are symbols of just how much we have to lose. Or maybe we’re just sad.

The mark of a technophile

Some of the grief over Steve Jobs was focused less on the man and more on the products he gave to us. “Can you imagine a world without the iPod? What if we all carried Zunes?” was a common refrain. Eulogies focused on his design aesthetic and his understanding of what customers value. More than Jobs himself, did we mourn for the brain behind our beloved objects and the loss of his potential innovations?

Even as a luddite, I must admit that I love my tech. I once spent hours on a frigid Minnesota winter night hunting for my lost silver iPod with a flashlight on a field of icy snow — an act that could be chalked up to cost rather than love. But we feel so strongly about our technology that we desperately seek proof to demonstrate that we have real relationships with these devices. The NYTimes even published a terribly erroneous op-ed on the topic, so great is the public desire for such biological evidence.

I’ve recently experienced the death of my favorite technology: Google Reader sharing features. I won’t go into the details of why I’ll miss it, as they’ve been meticulously documented elsewhere. But this experience, shared by other ‘sharebros,’ or google reader sharers, is quite akin to mourning. I kept a tab with the old version of reader open for days, even though its features were no longer functioning. I’m angry, sad, and scold myself for becoming so dependent upon it. And my brain has not yet adjusted to its demise: I still try to share items with my friends, despite my knowledge of the broken link — an experience Greg Hunter described as “Internet phantom pains.”

Whether these feelings are mourning for the end of a relationship or simply withdrawal to an addiction is unclear — and some scientists think that they are similar processes. In which case mourning for the tech and mourning for the man behind the tech may not be unlike. The public figure Jobs is a symbol for the technology with which we have a relationship, making his death meaningful to all who love his brainchildren.

Images:

Candle: ‘I’m with you‘ by Flickr user rosmary under Creative Commons licensing

Post-it: ‘Thai Apple Fans React to the Death of Steve Jobs‘ by Flickr user Nopphan Bunnag under Creative Commons licensing

How many untrue 'facts' have I unconsciously picked up from reading collections like this one?

Stories have the power to take us to other worlds, and no genre more so than science fiction and fantasy. But even the wildest fantasy novel has to have some basis in reality; otherwise, most readers become discouraged. (I mean, have you read the Silmarillion?)

Science fiction constantly toes the line between fact and fiction to create worlds that are plausible yet twisted. Readers easily accept premises that are obviously false, as long as they follow some set of predictable rules. But stories set in a more realistic time and place demand more of the reader: to decide for herself what makes sense and whether her disbelief can stay suspended.

My last repost about the wonders of science fiction was republished at Geekosystem last year and a commenter blew off the entire genre for being unresearched and inaccurate and, thus, unworthy of his time. My friend, one Erinrose, retorted:

Instead of finding fault in science fiction, I encourage you to reevaluate what it means to be entertained while intellectually engaged. If entertainment — to you — means reading a wholly accurate, meticulously researched text that asks of its reader to suspend her disbelief but not so much as to forget whether the heart produces blood, then you must think little of the imagination.

I agree with this sentiment. Writers should expect a certain intelligence in their audience, and readers need to be willing to meet the challenges presented by the writer. But I’m not going to lie to you: when I find scientific inaccuracies in movies and books, I react viscerally: a cringe, a wince, and, frequently, a vocalized correction. I can’t help it! I’m a very fact-oriented person, although it rarely results in an inability to reimmerse myself in astory.

But, until recently, I hadn’t really thought seriously about a different angle: what if I didn’t know enough to pinpoint these errors, and instead carried them with me throughout my life as fact?

This thought came to me as I picked through writer Salman Rushdie’s essay collection Imaginary Homelands last week. One of his essays, a mere four pages, deals with the very problem of errata in fiction. He begins by recounting several stories told by the narrator of his novel Midnight’s Children, which won the Booker Prize in 1981. The narrator, Saleem Sinai, explains Hindu mythology to the reader, details of the Bangladesh War, architectural detail in Bombay, and train lines through India.

The clincher: all of these facts are incorrect. But not by the mistake of the author. Rushdie intentionally introduced these inaccuracies after the fact.

I went through some trouble to get things wrong. Originally error-free passages had the taint of inaccuracy introduced. Unintentional mistakes were, on being discovered, not expunged from the text but, rather, emphasized, given more prominence in the story.

My audible gasp as I reread this passage drew looks from sittersby during my lunch break. Rage welled up within me, even as I tried to quell my discomfort. Rushdie is a writer, I consoled myself: he’s free to do what he wants and I have no right to tell him what to do.

The real reason for my discomfort was that these are exactly the kinds of facts that I would ponder over, or retell at parties without remembering the source. I can see it: “I can’t remember where I read it, but I definitely read it somewhere,” I would say. How much of what I think I know is actually tainted by errors introduced by writers, on purpose or otherwise?

I’m not alone. Rushdie addresses those like me in the essay: “Many readers wanted it to be the history, even the guidebook, which it was never meant to be… These variously disappointed readers were judging the book, not as a novel, but as some sort of inadequate reference book or encyclopaedia.” I get it, okay? I should confirm all my facts (which I try to do) and should certainly not believe everything I read. But then whom do I trust? Even non-fiction introduces elements of fiction and storytelling; how can I differentiate between truth and artistic flourish?

The point of Rushdie’s essay is to explain why exactly he got things wrong intentionally. His desire was to make his character as human as possible and, thus, he did his best to reproduce the frailty of human memory and experience.

He [Saleem] is also remembering, of course, and one of the simplest truths about any set of memories is that many of them will be false. I myself have a clear memory of having been in India during the China War… I also know that I could not possibly have been in India at that time. I was interested to find that even after I found out that my memory was playing tricks my brain simply refused to unscramble itself. It clung to the false memory, preferring it to more literal happenstance. I thought that was an important lesson to learn.

Reading it explained, I love Rushdie’s sentiment. I personally have many memories that I know I fabricated unintentionally. Greg Boustead, science writer and editorial producer of the World Science Festival, wrote about the distortion of September 11th memories just last month. And this is the process Rushdie emulated. To tell the real truth about people, he had to distort the facts of history and tradition — and we read fiction, not for fact, but for those human truths.

But my frustration continues; the two sides of my brain continue in their battle. But it’s only because it points out my own failures. If I read Midnight’s Children, I know I’m the type to retell those errata as fact. And I would remember them incorrectly as coming from an accurate source.

I guess, for writers of fiction, the question is not whether it’s permissible to fudge facts, but when it’s appropriate. Misrepresenting fact because the research seems too hefty is not acceptable to me; but purposefully altering fact for the sake of character development, or to bring the reader to another world, feels acceptable. Because there are different kinds of truth, and not all are based in fact.

Nonetheless, I will continue to cringe, if I know enough to cringe. But, if the writing is worth it, I will reshape my face to normalcy and read on.

Image: via Flicker use Chris Drumm under Creative Commons

Planet Comics #4 (1940), in the public domain

I didn’t really grow up reading science fiction.  Sure, I was (and am) completely obsessed with some fantasy novels (e.g. Lord of the Rings), but never made the leap to becoming a true sci-fi enthusiast.  It wasn’t until I started studying science more fully that I developed an interest in speculative science fiction.  Many of the stories deal with technology taking over civilization – but embedded within this framework is a great deal of excitement, along with some deserved anxiety.

My favorite stories are those that feel as though their coming true is just beyond the horizon.  For example, we are slowly inching closer to developing lab-produced organs, which would be incredibly beneficial for a lot of obvious reasons.  Just this month [as of July 2010] there have been developments toward mass-produced red blood cells, as well as bioartificial lungs.  Eerily, I read about these discoveries as I was tearing my way through Margaret Atwood’s Oryx and Crake, a speculative fiction novel about a bio-engineered future, including “pigoons” (pig/balloon) that have grown to massive sizes in order to grow 6 kidneys at a time for organ harvest, and “ChickieNobs,” a fast food product made from transgenic chickens that have no brains or beaks and grow 8 chicken breasts at once.  While reading, I simultaneously was in wonderment about how we could be reaching the ability to actually engineer these creatures, but obviously nervous about the implications described in the novel.  (No spoilers here!)

Some scientists might write this kind of anxious thinking off as trash.  “We’re trying to develop organs to save lives – we don’t need a bunch of crazies trying to stop us in order to avoid a hypothetical bioengineering apocalypse!”  But scientists are born and raised to be skeptical – and that’s all that much of this writing is.  Being skeptical about the pure goodness of scientific advance.

EC Comic's "Weird Science" #6 (1951)

Sci-fi also provides a venue for discerning how our ways of thinking about science have developed historically.  One of my favorite time periods for sci-fi is the 1950s: it was a time when just enough was known to speculate wildly, but not enough to fully disregard these speculations.  After all, Watson and Crick did not discover the DNA structure until 1953!   Thus you have the birth of many of our superheroes, variously mutated by ‘cosmic rays’ or radiation, altering their molecular structures and giving them superpowers.  We had just enough pieces to wonder, but not enough to know the full picture.

And sometimes the stories told ended up being truths nowadays.  Reading stories that feature scientific dreams of these writers, and now knowing that they’ve come true, can be heart-wrenching.  In one of my favorite short stories, “The End of the Beginning” in R is for Rocket, Ray Bradbury describes a couple gripping their seats with excitement and nervousness as their son boards a shuttle – the first shuttle to land on the moon.  This collection was written in 1965, 4 years before Apollo 11 landed on the moon.  Bradbury’s description is incredible:

All I know is it’s really the end of the beginning.  The Stone Age, Bronze Age, Iron Age; from now on we’ll lump all those together under one big name for when we walked on Earth… Millions of years we fought gravity.  When we were amoebas and fish we struggled to get out of the sea without gravity crushing us.  Once safe on the shore we fought to stand upright without gravity breaking our new invention, the spine, tried to walk without stumbling, run without falling.  A billion years Gravity kept us home… That’s what’s so really big about tonight … it’s the end of old man Gravity and the age we’ll remember him by, once and for all.

Gives you shivers, eh?  Of course, this day has come and gone in real time.  We are still constrained by gravity, we haven’t set foot on a planet beyond the moon.  But these science fiction stories can bring us back to that time of wonderment, help us to experience a feeling we missed: the great excitement of space potentially conquered.  And although it didn’t happen quite the way Bradbury described it, we can pretend for at least a little while.

Science is about that excitement.  About that drive to discovery, about idealism and hope.  It’s easy to forget that, working away at my lab bench, pipetting DNA into tubes.  Now we know a little more about science – enough that we no longer dream of mutated superheroes.  But we still dream about the day when we’ll make our big discovery, solve our own scientific problem.

Science fiction can remind us of this wonderment and hope.  But it also sends us a warning – to think about the potential implications of our findings, beyond our idealistic dreams.  While those implications might not be as exciting as a science fiction novel, they exist, and scientists should be aware of them.

With that, I’ll leave you this quote from David Brin from Nature‘s series of interviews with science writers this past winter.

Science fiction is badly named — it should have been called speculative history… Whether you are in a parallel reality or exploring the future, it is all about the implications of change on human lives. The fundamental premise of sci-fi is not spaceships and lasers — it’s that children can learn from the mistakes of their parents.

From "Weird Science" #6 (1951)

Picture of an autistic teenage girl. (I felt weird putting a picture of my lil bro on the internet without his knowledge.)

When I unwrapped my New York Times on Sunday, I was met with a surprise: A front-page, above-the-fold story about a young adult with autism. The story — a must-read, which you can do here — follows Justin Canha, a 20-year old with autism as he stretches towards adulthood and aspires to an independent life. The feature, written by Amy Harmon, who won a National Academies communication award last week for her “Target: Cancer” series, is beautifully wrought and a joy to read. It’s already been praised as a brilliant and insightful piece of medical journalism on blogs and twitter.

But I want to praise it for something else. Many articles about autism focus on the highest-functioning people on the spectrum, who certainly struggle socially, but who are brilliant beyond average academically or in some other quirky way. (Often they have Asperger’s syndrome, which will no longer be a diagnosis with the publication of the fifth edition of the psychiatric handbook, the DSM-5, in May 2013, merging into the broader autistic spectrum.) Instead, Harmon celebrates Justin, a young man with a knack for cartooning, but whose autism is more familiar to me than in any profile I’ve read thus far.

And I am quite familiar with autism, as my youngest brother, Jonah, is on the autistic spectrum. There was a point in my life when I had to explain what autism was nearly every time I spoke about him. But I rarely have to do that anymore. As soon as I mention his diagnosis, acquaintances sigh with recognition, as if they know what that means. And, no doubt, they know more than they once did: autism awareness has never been higher, with one in 110 children born now diagnosed. But I wish I were still given the chance to explain. Too frequently, they follow-up with statements about his intellectual gifts — “Oh, he must be really smart then.” — a sign of the influence of the stories about those with high-functioning autism.

I usually laugh, and respond, “ah, yes, he is smart.” But I don’t mean ‘smart’ in any way that society currently values. At nearly 16-years old, Jonah can’t count change or multiply. He has favorite books, but he flips through them too frantically to actually absorb the text. I swell with triumph whenever we have a conversation that lasts longer than 30 seconds, an actual exchange rather than repetitions of his favorite topics, which include pasta shapes, wheeled vehicles, and what we’re having for dinner that night. What I see as his ‘smartness’ is his view of the world, little influenced by the social and societal pressures that feed my own insecurities.

In her article, Harmon gets at that smartness in her descriptions of Justin. It’s very difficult to articulate but, given the expanse of a feature, she was able to do it through dialogue and his interactions with others. And my eyes teared up as I recognized Jonah, the kind of autism that I know and love so dearly, in an autistic character portrayed elsewhere.

I’m not trying to denigrate those profiles of high-functioning autistic people. Those people and those stories are important in their own right, for one. But additionally, from a journalism and awareness standpoint, it’s also so much easier for NTs — neurotypicals, as autistic people call us — to understand those who are high-functioning. After all, who hasn’t felt that they themselves had a useful skill that went unrecognized? Who hasn’t felt socially insecure, held back by their own (in)abilities?

Many stories are also told about the parents of autistic children. As Wired writer Tim Carmody explains on his blog, Snarkmarket:

Most readers of newspapers and consumers of serious media are typical, healthy, middle-class adults. They sympathize best with fates that are either totally fantastic or resemble their own. Most people find it easier to imagine being the parent of an autistic child. They find it harder to imagine being autistic and struggling with the problems of autistic adults themselves.

In her piece, Harmon invites NTs to sympathize and understand an autistic adult in his own right. Autistic adults are in our society, and as the children now diagnosed with autism grow up, there will be even more. It is thus critical that assimilated folk learn to understand them and no longer ignore them, push them aside, or worse. Journalism can do that. Journalism can help people understand other people. And, as I toddle around in my baby-journalist shoes, that is truly inspiring.

So, thank you, Amy Harmon, for taking this step of bringing those non-genius autistic people, generally ignored after puberty, into public attention. Thank you for highlighting Justin’s trials and spilling light onto people undergoing similar ones.

But it means more than that for me. When I talk about Jonah, everyone asks, “What is he going to do when he grows up?” And, honestly, I don’t know. He still has five more years of school — he started public high school this year! — and I will not let anyone decide for him what he is capable of, and certainly not when he’s still a teenager. But I dream of a world where people see him on the street and don’t edge away, where society is more accepting of those whose brains are, well, atypical. I don’t know if society will ever find a productive role for lower functioning autistic people. But a society whose citizens put in the bit of effort required to understand the individual autistic people they encounter? That is something we can work toward.

Image: an autistic teenage girl, via Wikimedia Commons

The report was commissioned by the National Vaccine Injury Compensation Program, whose employees bear the task of sorting through a few hundred claims every year made by people who think they have suffered injury from vaccination. But because there had never been a thorough analysis of what vaccines can actually cause what complications under what circumstances, evaluating each claim is slow-going. With the report now released, the office should be able to sort through them more quickly — a benefit for everybody.

When I got the press release for the report in my email, I was nervous: oh great, I thought, here is an opportunity for the press to incorrectly play up the supposed dangers of vaccines (which, I repeat, are limited to a few people with immune problems, as I wrote about in my Nature Medicine blogpost on the subject.) But overall, they didn’t. The press release was entitled “Few health problems are associated with vaccines,” and all news outlets I saw followed this line, even highlighting that they don’t cause autism. (If you did find coverage otherwise in the mainstream media, let me know in the comments.)

So overall I was content and let it pass. But yesterday I read a blog post by science journalist Erika Check-Hayden about how the report missed an opportunity to communicate with the public:

But only someone who is completely out of touch with today’s society would fail to realize that such a report needed to be thought out and presented much more carefully than it was to avoid fueling the anti-vaccine panic that is raging across the country.

I do understand this idea. The 600+ page report is a horrendous read, drenched in jargon and pretty poorly organized, for what it is. If you just glance at the thing, it wouldn’t be hard to get caught up in the length and incomprehensible text and just throw your hands up — “there must be many terrible things in here!”

But, in the end, this is a report about the adverse effects of vaccines. It wasn’t about judging the safety of vaccines. I guess you could say that therein lies the core problem: that refusing to make a statement about their safety is a cop-out. But I don’t know how the panel could have said more and stayed accurate. Adverse reactions do happen, albeit very rarely. The summary for the report says, “overall, the committee concludes that few health problems are caused by or clearly associated with vaccines,” and members noted that these events are very rare, both within the report (“we do want to emphasize [that] many of the adverse events we examined are exceedingly rare in the population overall”) and to the media.

More important than what is actually contained in the report is how it will be used. Yeah, the media reports on it, we can blog about it, but in the end it will be used by those who actually matter: doctors. Yes, the people who do the most to inform patients about their health and health risks, and who, most of the time, have the strongest sway.

The doctors I spoke with about the report were all quite excited about it. The vaccine compensation office doesn’t have a reference guide to vaccine adverse effects; but neither do doctors! When parents and patients come in with questions about vaccines, doctors have to generalize about the safety and risks. They are relieved to now have a resource they can point to — to say “this report came out and there are so few adverse effects, that vaccines are exceedingly safe. But if you want to talk more, here is what we know, and here is what we can do to plan.”

And if doctors are more confident in their statements, the report can only help soothe those on-the-fence about vaccines.

But what upset me more was the suggestion that the report should not have been released in the first place if it wasn’t going to suitably assuage the general public. Check-Hayden finishes her post with:

The Institute of Medicine committee gathered 16 eminent doctors and public health specialists who truly care about protecting the nation’s children against vaccine-preventable diseases. Didn’t any of them realize that it probably wasn’t a good idea to release a report that focuses so myopically on the drawbacks of vaccines in today’s increasingly anti-vaccine climate?

Scientists can’t stop doing their work, including commissioned government reports, so that people won’t freak out. Sure, the committee could have written a better summary in nice language. But if people are going to ignore rationality, and listen to their friends before they listen to their doctors, the problem is deeper than one that can be solved by clearer writing in an Institute of Medicine report.

The sad truth is that the people who are going to freak out about this report probably wouldn’t listen to scientists saying that vaccines are safe anyway. If they were going to listen to scientific evidence, they already would have.

I squealed on the spot. But as I got down to planning out the lesson with my brother, I began to doubt myself. I wanted to take my 45 minutes and inspire all the students to embrace science — but how? How could I be concrete enough to teach them something real, as necessitated by the public school standards, while also abstracting enough to open the door to wonder? I wanted them to know that they could get out of their crummy neighborhood and be scientists themselves, that it wasn’t just for crazy-haired white dudes. I wanted them to wake up the next morning and ask a question about their world that they wouldn’t have asked before.

It turns out that all my fretting was for naught. Because my showing up, period, has more of an impact that anything I could say.

My brother is a teacher! Awww

That’s the message that I took away from last week’s Science Online NYC panel. Science Online NYC (known as #SONYC on twitter and pronounced like the blue Sega character) is a monthly panel on a different aspect of science and science communication (facebook group). On Wednesday, the topic was reaching niche underrepresented groups with science — but, in practice, it was about education.

After the two-hour discussion, one fact alone stood out to me, told to the audience by Bernice Rumala of Rockefeller University. She said that it only takes a single classroom visit — one day of students interacting with a scientist or visiting a lab — to change their mindsets, making science less scary and more attainable. And the question quickly became: how do we get more scientists into the classroom?

There are some initiatives set up to connect teachers to scientists. Scientific American has its very own 1,000 Scientists in 1,000 Days program, which they announced in May. SONYC organizer Lou Woodley tweeted a GoogleDoc collecting links to similar programs or websites, including the US’s National Lab Network.

But I don’t think these go far enough. These programs, while a good start, place the burden upon the teacher to either suggest a project or reach out to the scientists themselves. But imagine being a teacher and getting an email from a scientist offering to help, no effort involved. That would speed up the process, and make it far more likely to actually happen. Despite time away from the lab, I imagine that many scientists would be more than willing to take a day off to hang out with fun kids and talk about themselves. In fact, it should be a requirement.

Maybe talking to a class of kids seems scary. But there is nothing easier. When I spoke to Jacob’s classes, all I did was tell them about what I did. I presented the basic landscape of what I researched, asked the students for any questions about the topic, and we talked about how you could go about answering them. I showed them pictures from field sites and they oohed and ahhed over my flask collection. And, in the process, we covered some serious ground: talked about the scientific method, why we use model organisms, experimental design, and — of course — did a general science Q&A.

When I left the SONYC panel on Wednesday night, that day came back full force. The fun of teaching, hanging out with the students during lunch, illustrating the questions we wanted answered about the world. And that fun was only compounded by learning that showing up actually can change the lives of these students.

So as soon as the school year starts, I’m going to look up the schools in my neighborhood and email the teachers, principles, and counselors to force myself upon them. Because it’s far easier to accept help than to reach out for it.

And, all you scientists, I recommend you do the same. Arrange a phone call with local science teachers and try to get in there! That single day is more meaningful to the students than it is to you.

It’s a lot of ground to cover and it’s so well done. Get ready for 12 straight minutes of butterflies and chills. I haven’t failed to get them each time I watch it, an unquantifiable number of times at this point.

In this video and his others, the artist seems to truly grasp the magnificence of the universe. At its heart, this video is about natural disasters, embracing extinction and death as key to how we got here – and true awe at the fact that we exist at all.

[Edited and reposted from the previous incarnation of Culturing Science.]

Maybe you imagine a dark wood with sunlight reaching a mottled floor of foliage, thrushes singing and chipmunks hopping. Maybe you peer through grassy dunes at sanderlings running back and forth in the surf , occasionally halting to frantically peck at the sand. Or maybe you see an expanse of cedars bearing a snowfall, deer perusing the bark, and nuthatches hanging from a limb.

In any of these visions, is there a human in sight?

Our species largely views nature as a separate entity from the world we inhabit. We can traverse it on a camping trip, and even bring along our binoculars to better analyze this space so foreign to our own. In heavily populated areas, we visit parks to escape from the city, although we recognize that these spaces are not true “nature,” but manicured to our specifications for our greatest enjoyment.

This divide between the two worlds is a fallacy. Its premise is that, before our invasion, ecosystems were static environments that we have, over time, displaced with our buildings and soot and trash. But, while our cities certainly displace the former environment, they also create new ecosystems. And we are intimately involved in these systems, whether we recognize it or not.

By flickr user rasdourian under Creative Commons

The rise of the study of urban ecology and evolution tips a hat to this idea: that, despite our delusions of dominance, other organisms fill and influence our lives as much as we influence theirs. But it doesn’t go far enough. Humans still play the role of sculptor in our current versions of urban ecosystems. This rehashes the anthropocentric idea that we stand apart from the rest of the organisms, as laid out in the Bible.

In some ways, this mindset is understandable. The advent of medicine has mostly allowed humans to elude the grasp of natural selection. Society and population overload lift the biological need to pass on our genes and increase our abundance. After all, we now have other ways to extend our individual reaches beyond our deaths, the consciousness to overcome our biological drive, and various exploits to fill our time.

The final nail on the coffin encasing human involvement in ecosystems is our removal from the local food chain, particularly in Western culture. Humans are no longer physically bound to our environments for our daily requirements, instead linked by invisible paths globally. But this still presents a rather limited idea of how ecosystems function. They are based in more than just the food chain, but rather in an endless number of interactions between species and organisms. If we could find a way to highlight, not only how humans influence other organisms, but also how they influence us, we could at least begin to reintegrate our species into a larger ecosystem.

Environmentalism is probably the closest we get to reintegration. Tracing the sources of our food, or considering the impacts of carbon dioxide emissions, overfishing or clearcutting requires thinking about humans as a player in a broader system of species interactions. But, in the end, we still return to the old trope. While environmentalism, at its core, is about preserving resources for our own use, most subscribers articulate it as a desire to take care of nature for its own sake, because we care about nature. And, there it is: that anthropogenic separation rears its head once more.

So how do we do it? How do we reintegrate ourselves into the ecosystems that surround us? It’s not easy. I’ve been working on it for years. I mostly try to think about how the organisms that surround me affect my life, however indirectly, and how my decisions, in turn, affect those organisms — ad infinitum. Some of these thoughts are rather basic. We provide food for pigeons and, by eating our trash, they clean our streets. (Seriously: imagine how filthy a city would be without its columbine denizens.) White-footed mice, highlighted in a recent article about urban evolution by Carl Zimmer, disperse seeds, and, without plants, my life would be less fresh and far hotter.

These may seem like meager steps in the day-to-day; I’m willing to admit that this idea is a work in progress. Because, in the end, usually my only influence upon these organisms that I can think of is… that I (with my fellow humans) allow their continued existence.

The key may be thinking on a larger scale. An article in New York Magazine from last September highlights the diversity of organisms in the areas we consider the most desolate, and hints at the city as a more integrated ecosystem. (Hat tip to Eric Heydenberk)

Urban ecologists are now taken by the idea of a feedback loop, in which the sullied, mixed-up nature of the city begins to affect the nature of the entire Northeast region. This is what happens when herring planted in the Bronx become food for bluefish in the Gulf of Maine, or when the uncommon trees grown in the NRG’s seed bank in Staten Island are planted in Pennsylvania. But it occurs in less premeditated ways, too. We see the feedback loop in the avian flyway that runs from Alley Pond Park to the little wetland on the brook that runs through the Wykagyl Country Club in New Rochelle and then up through the Hudson Valley into Vermont. Or in the wildlife corridors that connect the Lenoir Preserve in Yonkers through Bear Mountain State Park to the Catskill Forest Preserve. Or in the growing number of green roofs that connect insects across boroughs and counties, slowly turning Google’s satellite view of the city from gray and black to dusty green.

Zooming out puts the smaller decisions made in the city into a larger context, connecting urban ecology to larger ecosystem dynamics. The shellfish in the river that filter contaminants from the water make my bike rides along the Hudson path more pleasant, sure. But they also improve the quality of water entering the ocean, boosting fish abundance for the sake of marine ecosystems, as well as the seafood that I consume.

And, to take it a step further, we can consider the geology of the city. Where did the rock that composes these Brooklyn homes come from? What does that area look like now and how has it changed? How many millions of years ago was the rock formed? What minerals compose it, and when were they formed out there in space? The non-profit research organization Friends of the Pleistocene, whose publication Geologic City I anxiously await, has some answers:

On the way to Prospect Park we passed massive stacked rows of Triassic sandstone.  These solid blocks (literally) of geology are installed on the streets as the City’s iconic “brownstones.” This rock is 250 to 200 million years old–that’s pre-dinosaur. Brownstones are one of the most common buildings in Park Slope, but we typically forget that while inhabiting such spaces, we’re living inside the materiality of deep time.

A larger geologic context — stretching back to the formation of the universe — helps me to place myself in the context of life’s history and larger scale ecology. While our species built these cities, stone by stone, we are still bound by the larger scale workings of the planet and the ecosystems it harbors.

But I’m still not satisfied. The one thing that still irks me is that, despite all my lecturing about anthropocentrism, it’s inescapable. I try my best to rearticulate the world to myself holistically, without our species at the central point. And I will continue to fight those battles each day as I walk to the subway, take a nap in a grassy knoll, or sit on my stoop hammering my laptop keyboard. But, in the end, humans are the movers and shakers on this planet, literally. As civilization changes, the ecosystems change as well, and, at this point in time, the power to change them lies primarily with people. So maybe I’m the delusional one after all. Maybe, for now, the greatest influence we have on the white-footed mice or trees that line my street is their continued perseverence.

Dimethylsulfide.  Does that word mean anything to you?  “Why yes,” you organic chemistry nerds may say, “It clearly is a molecule of sulfur with two methyl groups attached.”  That’s as far as I could have gotten – until this past week (July 19, 2010), when I inundated myself with information on dimethylsulfide (DMS), inspired by a paper published in Science.  Now I’m enlightened – what a wonderful molecule!  Let me spoil it for you: it is a chemical cue pervasive throughout the marine food web that also affects the earth’s climate.  (See illustration at bottom of post for summary.)  That’s right.  Just a sulfur molecule with two methyl groups attached.  Now let’s back up a bit.

DMS is a sulfur compound that accounts for around 60% of the total natural reduced sulfur flux to the atmosphere (even more than either volcanoes or vegetation). (Data last updated January 2011.) We tend to think of atmospheric sulfur as detrimental because it can cause acid rain. But it is also plays an important role, as it helps form clouds. In order for water to transition from gas to a liquid cloud in the atmosphere, it needs to cling onto another particle: a cloud condensation nucleus. Sulfur oxide, which can be derived from DMS, is one of these particles. Clouds not only carry precipitation, but help to reflect sunlight and heat back into space, cooling our planet.

Illustration by me, under creative commons for use with attribution. (I know, you all want to frame this drawing and get it tattooed onto your calves, I understand. JUST CREDIT ME.)

Once scientists realized its importance as a cloud condensation nucleus, they began to search for DMS’s planetary source. They found that 95% of the atmospheric DMS originates in the oceans – but from where?  As illustrated in my drawing over there on the right, it is formed in certain species of phytoplankton. Phytoplankton convert their cellular stores of sulfur into a molecule called DMSP.  When the cell wall breaks down, often by consumption by herbivores, the phytoplankton releases DMSP and an enzyme, DMSP-lyase, into the surrounding water.  This DMSP-lyase removes the phosphate group, leaving us with our favorite molecule of the day, DMS.

Notorious biochemist James Lovelock and a handful of his lackeys integrated DMS into large-scale atmospheric theory in 1987 in the CLAW hypothesis (named for its authors) to support his Gaia hypothesis. The Gaia hypothesis suggests that microorganisms regulate the Earth’s climate to maintain conditions suitable for life.  CLAW hypothesized that a too-warm climate causes phytoplankton to produce greater amounts of DMSP in order to release DMS into the atmosphere, deflecting sunlight and causing global cooling. However, like most support for the Gaia hypothesis, CLAW requires that phytoplankton act altruistically, upregulating DMS for the good of the planet — a concept that does not make much sense in light of natural selection.  (A good review of this and the above sections can be found in this paper by Rafel Simo.)

Instead of considering why phytoplankton release DMSP, a paper published in Science this week (July 16 2010) by Justin Seymour, Rafel Simo, and others looks into the effects of DMSP on the smallest grazers: microbes.  The researchers used a microfluid device to control the diffusion of DMSP in seawater and tried to imitate its motion in the open ocean to the best of their ability. They measured the strength of attraction of 4 different types of microbes (7 species) to varying concentrations of DMSP.

The tested organisms interacted with the molecule in different ways. One algal species and two bacteria absorbed it, presumably for its carbon and sulfur. One algae did not react, and the other cleaved the DMSP into DMS and assimilated that. The final two plankton species moved towards the DMSP, not because they wanted to consume the molecule, but because they wanted to feed upon those that drew near. One herbivorous plankter Oxyrrhis marina gobbled up the baited algae, and a predatory plankter ate the bacteria consuming the DMSP.

This last part is the most interesting: the DMSP is a chemical signal that drew these last two species to their planktonic food.  Out of all the molecules that could leak from the burst cell and indicate prey, it is this very molecule, DMSP, that does the trick.

The story does not end here, as DMSP works as a prey indicator at higher trophic levels as well.  A 2008 Science paper out of UC-Davis and UNC found that planktivorous fish aggregate near DMSP hotspots. Furthermore, in 2008 Gabrielle Nevitt reviewed the literature on how seabirds (Order: Procellariiformes) track fish and squid by smelling out DMSP — which the prey themselves honed in on to locate their own prey, in turn. A similar pattern has also been observed in seals and whale sharks.

Don't you love my handdrawn illustrations? under creative commons for use with attribution

All of these diverse species evolved the ability to sense DMSP, of all molecules, to draw them towards food.  Why DMSP? It has something special to offer that other molecules don’t: sulfur.  We all know that smell, and perhaps it is this stinkiness that has allowed it to become such a pervasive indicator throughout the marine food web.  In her review, Nevitt discusses the evolution of DMS-sensitivity in seabirds. Using evolutionary trees, she points out that only those species which rely on smell alone to identify food in dark burrows have DMS-sensitivity as adults.

It’s tempting to jump even further and consider how these predator-prey relationships affect DMS-influenced climate.  I doubt that we can enumerate any direct consequences. The authors of the Science paper note that “microbial behaviors, played out over microscale chemical landscapes, shape planktonic food webs while potentially influencing climate at global scales.”  DMS could generate a positive feedback loop: its initial release draws herbivores to open more cells and leak increasing DMSP, which in turn draws more herbivores, ad infinitum.

Some studies suggest that climatic variables such as light, temperature, and salinity determine what species thrive and thus how much DMSP is produced (review by Stefels et al. here). But it seems to me that the DMS-as-prey-cue and DMS-as-climate-regulator processes are unlinked, so would not work together in any predictable way. As all biogeochemists know, the stuff of the air frequently comes from the stuff we live on and in: soil and water.  This is simply another example of how microbes and abiotic stuffs tie to climate-regulating molecules.

(Sidenote: should I give up strict science and become a science illustrator?)

DeBose, J., Lema, S., & Nevitt, G. (2008). Dimethylsulfoniopropionate as a Foraging Cue for Reef Fishes Science, 319 (5868), 1356-1356 DOI: 10.1126/science.1151109

Nevitt, G. (2008). Sensory ecology on the high seas: the odor world of the procellariiform seabirds Journal of Experimental Biology, 211 (11), 1706-1713 DOI: 10.1242/jeb.015412

Seymour, J., Simo, R., Ahmed, T., & Stocker, R. (2010). Chemoattraction to Dimethylsulfoniopropionate Throughout the Marine Microbial Food Web Science, 329 (5989), 342-345 DOI: 10.1126/science.1188418

Simó, R. (2001). Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links Trends in Ecology & Evolution, 16 (6), 287-294 DOI: 10.1016/S0169-5347(01)02152-8

Stefels, J., Steinke, M., Turner, S., Malin, G., & Belviso, S. (2007). Environmental constraints on the production and removal of the climatically active gas dimethylsulphide (DMS) and implications for ecosystem modellingBiogeochemistry, 83 (1-3), 245-275 DOI: 10.1007/s10533-007-9091-5

Van Alstyne, K., Wolfe, G., Freidenburg, T., Neill, A., & Hicken, C. (2001). Activated defense systems in marine macroalgae: evidence for an ecological role for DMSP cleavage Marine Ecology Progress Series, 213, 53-65 DOI:10.3354/meps213053

G. V. Wolfe, M. Steinke, & G. O. Kirst (1997). Grazing-activated chemical defence in a unicellular marine algaNature, 387, 894-897

Cod fishery in Newfoundland. Image by Derek Keats on flickr under Creative Commons.

Perhaps our species’s greatest misconception about the sea was that it is inexhaustible. The idea seems rather silly now, in a world where most people are familiar with the word “overfishing.” But men once gazed into the deep and imagined that it teemed with life so plentiful that we could take and take without ever running out.

Now we know that you can take too much. Unfortunately, it’s only because we’ve run our own real-life experiments and have to live with their results.

One of these experiments truly ran out of control: the cod fishery off of Nova Scotia, Canada in the northwest Atlantic. Cod catches increased through the 1950s and 60s, peaking at 800,000 tons in 1968. From there, catches dropped significantly — a warning that the population wasn’t doing so hot — with fishermen only able to catch less than 150,000 tons of cod in 1978. (That seems like a lot, but compared to 800,000 tons, it’s nothing!) From there, catches continued to drop but it took nearly two decades for the Canadian government to take control, closing the fishery in 1993.

The cod’s own prey, forage fishes, thrived following the fishery collapse. As the cod reached their record lows in the mid-1990s, forage fish numbers climbed, peaking at a whopping 900% of their pre-collapse abundance. The forage fish, in turn, greatly reduced their own prey, the zooplankton, allowing the photosynthetic phytoplankton to thrive.

This pattern of alternating gains and losses down the food chain caused by the loss of a top predator is called a trophic cascade, and has been seen in other systems. Scientists hypothesized that this type of trophic shake-up would lead to a new stable ecosystem, with any imbalances eventually reaching equilibrium and forage fish ruling the seas.

And for a several decades, this seemed to explain what happened off the Scotian shelf. As forage fish decimated the zooplankton, they also consumed cod eggs and larvae, suppressing their return to dominance. Forage fish reigned and the cod couldn’t recover, despite the abundance of their own prey. Maybe this was the new stable ecosystem.

But the past decade has finally seen some changes. Forage fish peaked at 10 million tons, more than double what scientists estimated the ecosystem could support. They subsequently decreased in abundance, as there wasn’t enough zooplankton food to support so many organisms. The forage fishes’ bodies were smaller and of lower quality, with less fat and protein — a reflection of how little food was out there.

Caught cod aboard a ship in Newfoundland. Image by Derek Keats on flickr under Creative Commons.

This depression has given the cod and other predatory fish their chance, and researchers from Dalhousie University in Nova Scotia reported last week that they seem to be coming back. Cod, redfish (Sebastes spp.) and haddock (Melanogrammus aeglefinus) populations are higher than they’ve been since the early-1990s and the weights of individual fish are on the rise.

Although  the ecosystem is still far from stable, this suggests that the ecosystem may be reverting away from a forage fish-dominated system back to its original predator-dominated ecosystem. The authors note that haddock seem to be more prevalent than cod currently, so it doesn’t mean that the ecosystem will necessarily return to normal. Haddock could reign instead of cod, which would effect the species composition of the entire system.

If the trends continue, the message here is hopeful: That these systems can return to their original stable state if given enough time to recover. The fishery has been shut down for nearly two decades, giving the community a rare amount of space and time to reorganize and work itself out. This Nova Scotian community indicates that simply leaving a system alone for a while can help significantly.

The other factor necessary for recovery here was that there were still enough cod, haddock and redfish around to generate the eggs and larvae to recover. Not all systems have been so lucky. A a literature review published a few weeks ago summarized how the eradication of top predators — from jaguars to seastars —  affects communities, examining many types of ecosystems around the globe. Overall they found that ecosystems entered a new stable state with widespread changes including nutrient flow, plant abundance, and species diversity. If you have no top predator babies to replenish the lost species, you obviously can have no recovery. (For picures of ecosystems before and after top predator removal, see this Wired slideshow.)

But removing top predators isn’t the only way to damage an ecosystem. A second study out last week modelled how harvesting forage fish at maximum sustainable yield — the most that can be fished sustainably — affected the trophic structure in five different regions around the world. They found that forage fish removal rippled throughout the ecosystem, altering the abundances of seabirds, marine mammals, and zooplankton alike. Halving exploitation rates would result in much lower impacts, the authors argue, while still retaining 80% of current catches.

I hope that people don’t read the story of the Nova Scotian shelf the wrong way: that we can exploit to our heart’s content as long as we stop fishing in time. For two decades the industry has been shut down affecting peoples’ livelihood  – and the patterns of exploitation seen there are clearly not healthy. Other similar fishery collapses have not recovered because invasive species, such as jellies, have rolled in to take advantage of the mess. The cod’s recovery is hopeful but it’s safest to treat it as an outlier.

Estes, J., Terborgh, J., Brashares, J., Power, M., Berger, J., Bond, W., Carpenter, S., Essington, T., Holt, R., Jackson, J., Marquis, R., Oksanen, L., Oksanen, T., Paine, R., Pikitch, E., Ripple, W., Sandin, S., Scheffer, M., Schoener, T., Shurin, J., Sinclair, A., Soule, M., Virtanen, R., & Wardle, D. (2011). Trophic Downgrading of Planet Earth Science, 333 (6040), 301-306 DOI: 10.1126/science.1205106

Smith, A. D. M., Brown, C. J., Bulman, C. M., Fulton, E. A., Johnson, P., Kaplan, I. C., Lozano-Montes, H., Mackinson, S., Marzloff, M., Shannon, L. J., Shin, Y., & Tam, J. (2011). Impacts of Fishing Low–Trophic Level Species on Marine Ecosystems Science DOI: 10.1126/science.1209395

Frank, K., Petrie, B., Fisher, J., & Leggett, W. (2011). Transient dynamics of an altered large marine ecosystem Nature DOI: 10.1038/nature10285

A pyramid of numbers by W. E. Pequegnat from the January 1958 issue of Scientific American

The first known pyramidal of numbers was drawn by Charles Elton in 1927 to explain the flow of energy through ecosystems. Plants convert carbon in the air into sugars, and this bulk carbon forms the base of his pyramid. (The phytoplanktonic base in the image above.) When herbivores consume these plants, because of waste and digestive inefficiencies, the starting carbon pool shrinks, with the herbivores absorbing less carbon than they eat. And then when the herbivores are, in turn, eaten, the resulting pool of available carbon shrinks even more.

Thus, the pyramid illustrates the change in absorbed carbon with each step up from the starting pool. But they are also used to explain other patterns of energy distribution in ecosystems. Typically there are more plants than rabbits than foxes than hawks — or there are fewer individual organisms representing higher trophic levels. Similarly, there is typically more available biomass total in lower trophic levels than higher ones.

The metabolic theory of ecology combines these pyramids of numbers with temperature to describe the fundamental biological growth rate. I’ve never been good with formulas, but essentially the idea is that small animals are more abundant and grow more quickly, while larger animals are less common and grow more slowly.

And this rule is pretty widely followed — but only if we leave out those grand blood suckers and freeriders, the parasites. Parasites make up at least half of species diversity, but we tend to forget them when devising grand theories branching across life on earth.

Think about it: where would you stick a parasite in a pyramid of numbers? Feather lice, for example, live in the feathers of birds. If they are sucking the blood of a hawk, does that make them higher on the food chain than the hawk? Are they at a greater trophic level, despite being as small as they are? Does parasitism count as predation?

Basically: They mess up our theories. They don’t fit in neatly. And they’re so small that it’s easy to forget about them.

A group of researchers published a paper in the journal Science last week trying to integrate parasites into trophic ecological theory. They collected data about organisms living in three Californian estuaries, and plugged them into equations representing the metabolic theory. Unsurprisingly, the parasite data — those quickly-reproducing, infrequent and small buggers — did not fit with the accepted generalizations of the theory. But when the researchers reformulated the equations slightly to incorporate the trophic level of the organisms, the data followed a consistent pattern, suggesting a broader ecological theory.

Trophic level and primary production with body size, redrawn from the paper for clarity.

Of all the figures in the paper, one pair stood out, which I’ve redrawn below: those showing the relationships between body size with trophic level and population production. The top graph overturns a standard “pyramid of numbers” trope that trophic level increases with body size. As you can see here, the little bitty parasites at a high trophic level flip the line up into a U shape, rejected the linearity of non-parasite models.

The bottom figure goes after the “lower trophic levels produce more biomass” trope. Keep in mind that population production measures the biomass produced for the average size of an organism, not total biomass, and the entire figure is normalized for trophic level. What that straight line means is that, at each trophic level, organisms of a particular size will produce the same amount of biomass regardless of whether they’re free-living or parasitic.

The paper is titled “A Common Scaling Rule for Abundance, Energetics and Production of Parasitic and Free-living Species,” and this is the rule the authors speak of.

What does it mean? If the rule holds up, it could help those who measure land to figure out how much biomass is available in the system, based on the size of the organisms alone. They wouldn’t need to think about trophic level, period; just size. And that would simplify things a lot.

Hechinger, R., Lafferty, K., Dobson, A., Brown, J., & Kuris, A. (2011). A Common Scaling Rule for Abundance, Energetics, and Production of Parasitic and Free-Living Species Science, 333 (6041), 445-448 DOI: 10.1126/science.1204337

Rachel Carson National Wildlife Refuge. Image by Hannah Waters (Creative Commons reuse with attribution)

Hardly four years ago, I started my first job in science. After an 8-hour drive up the east coast, my brother escorted me into a small, single-floored building facing a woody patch above a salt marsh, the headquarters of Rachel Carson National Wildlife Refuge. My heart swelled with anticipation: Here I was, finally living the dream. I envisioned a summer working along the idyllic Maine coastline, rescuing endangered birds and punching invasive species in the face, while basking in the beauty of nature and my many successes as a conservation biology intern.

Boy, was I wrong. (Well, except for the idyllic part.) The summer was to be trying, one that would challenge everything I thought I knew about conservation — but also one that would redefine the way I thought about the same.

I dove eagerly into my work, pacing the beaches to scan for the rare piping plover eggs camouflaged into the sand. A shout indicated a found nest, which we encircled with a chicken-wire fence and roof to keep predators out. I sat on the beach at dusk to count least terns while greenhead flies and mosquitoes took advantage of every inch of my exposed skin. I wandered through (what felt like) miles of marsh searching for saltmarsh sharp-tailed sparrow nests, slipping into ditches and toiling to extract my wader-bound legs from the mud.

But all for naught. In a single night, an unidentified predator ate every least tern egg in the colony. Few of the cottonball piping plover chicks survived to adulthood, and I wept to see one carried off by a hawk early one morning. We had failed, I thought. We had wasted our time.

That's me holding an endangered saltmarsh sharp-tailed sparrow. Image by Ward Feurt, but it's on my camera so it's MINE. Hannah Waters, creative commons for reuse with attribution.

After a few weeks of hard thinking, I sauntered into my boss’s office one evening. The boss, Ward, spoke gruffly unless he spoke of his refuge, which he described in a tone that oozed love, betraying his tough exterior. We had hit it off from the moment we compared bird tattoos early in the summer. That day, I plopped myself down across from his desk and, as an overconfident youth, declared, “I want to talk about conservation.”

Ward chuckled and, with a smile, encouraged me to tell him more. “All this work that we do: Does it actually have a point?” I asked. Without our efforts to protect the vulnerable nests, raccoons would have decimated those plover eggs within a week — and the work we had put in had largely failed. How did those little birds even stand a chance? Wasn’t the real problem that beach-goers didn’t watch their step, homeowners couldn’t bear to keep their cats inside, and that civilization allows trash-dependent predators to thrive and threaten the birds?

In other words: Is the fight against human stubbornness hopeless?

Dusky seaside sparrow, Ammodramus maritimus nigrescens. Image by P. W. Sykes of the US Fish and Wildlife Service, Wikimedia Commons

Ward sighed before he spoke. Prior to joining the refuge in Maine, he told me, he worked down in Florida. People first flooded the wetlands to drown out mosquitoes, then drained them for development.  The efficient work quickly swallowed up the nesting grounds of the dusky seaside sparrow, an endangered bird with an already narrow range. During his tenure at that refuge, Ward watched the sparrow population dwindle until there were six known birds left in the wild. Six birds that had no chance of survival as their habitat was destroyed and predators encroached.

It was then that Ward watched his boss make what was, undoubtedly, one of his life’s is hardest decisions: to capture the remaining birds and place them in captivity at Disney World. The biologists hoped to breed the birds and release them once their population was large enough — but instead, seven years later in 1987, Ward saw the last one die in captivity.

“The last one, the last dusky seaside sparrow that will ever exist,” he said. The birds he had loved and worked so hard to save were gone, never to return. Maybe our efforts seemed hopeless, he said. He looked me straight in the eye with a sure sadness and added, “but I have to do something.”

Just like that, Ward transformed before my eyes. Conservation biologists aren’t just happy-go-lucky folk who like to play outside and hang out with animals. Their every day is an uphill battle, holding out for the day when society sees things the way they do, while trying to change that mindset however incrementally.

Now I realize that I acted childishly. As childishly as those who grew angry when I asked them not to swim in protected habitat on the fourth of July, or as childishly as those who wouldn’t let us protect plovers on their property because the exclosures were eyesores. Like them, I couldn’t think in the long-term and demanded instant gratification: that if conservation was going to work, it was going to work now, goddamnit. But conservation work requires long-term hope, and double hope, at that. Conservation biologists have to believe, not only that their efforts will pay off in the future, but that society is capable of change and will grow to support those efforts.

Rachel Carson National Wildlife Refuge wildlife biologist, Kate O'Brien, during a tern count. Image by Hannah Waters (Creative Commons for reuse with attribution)

I thought of this story when I read a series of correspondences published in Bioscience over the past few months. The authors bicker about the specifics, but they seem to agree on the main point: that pessimism has stained the hope that all conservation biologists must hold dear. It’s pessimism on the part of the scientists charged with training the next generation, who have yet to see their labor bear fruit. And it’s pessimism in the media, which constantly reports on conservation issues as if we have already lost the polar bear, or as though there is no point in changing our behavior if we can’t save the polar bear.

I don’t support naive hope, but I also don’t support the mindset that preserving biodiversity is a false hope. There is certainly real work ahead of all who care about conservation. But, as David Shiffman and Andrew Thaler so elegantly described on their blog Southern Fried Science, there have been victories. Animals near extinction have been resurrected through conservation efforts and education.

And education is necessary because a few scientists can’t do it on their own. Conservation biologists focus on the short term fixes — breeding programs, monitoring and, yes, constructing fences around bird nests. But the long haul will take education about the challenges of conservation and the steps non-scientists can take that will have a real impact. It will come down to everyone learning to respect the land and water, more than anything.

So now I really understand why I stood on the beach in Saco, Maine on the fourth of July that summer, sweltering in full Fish and Wildlife uniform. Because the work I did that day, talking to beer-clasping beach-goers about the weird circular fence around those birds and its purpose, is the most important work. The long-term plan requires a change in how people see and interact with wildlife, and how their actions extend beyond the immediate time and place.

We must have hope. Because Ward’s tale of his dusky seaside sparrow could be read two ways: that there is nothing we can do, or that next time we have to do better. We must hold tight to this latter optimism. Am I idealistic? Perhaps. But so is anyone whose wishes cannot bear fruit in the status quo.

Cannot end without thanking everyone who made that summer what it was: Mike, Mike, Amelia, Carrie, Kate, Shonee, Angie, David, Zeb, Bob and, of course, Ward. You are all mine forever.

Patten, M., & Smith-Patten, B. (2011). “As If” Philosophy: Conservation Biology’s Real Hope BioScience, 61 (6), 425-426 DOI: 10.1525/bio.2011.61.6.2

Swaisgood, R., & Sheppard, J. (2010). The Culture of Conservation Biologists: Show Me the Hope! BioScience, 60 (8), 626-630 DOI: 10.1525/bio.2010.60.8.8

Swaisgood, R., & Sheppard, J. (2011). Hope Springs Eternal: Biodiversity Conservation Requires That We See the Glass as Half Full BioScience, 61 (6), 427-428 DOI: 10.1525/bio.2011.61.6.3

So what is Culturing Science? I always struggle to answer this question. “Erm, it’s about ecology and evolution and science education and natural history and stuff” is my standard response. But that’s not really the complete answer. While there are topics I write about more than others, the purpose isn’t to provide expertise on any one alone.

I aim to look down at the scientific world from the view of a soaring bird, focusing on the “big picture.” What I do here is put recent research into context, describe scientific ideas throughout recorded history, and reflect upon the importance and meaning of science in the modern day and age. It’s about placing isolated snips of science back into culture — scientific culture and beyond.

Though, I must admit, this blog is even more personal that that. Culturing Science is also a very public documentation of a girl growing up in love with science, constantly confronted by all she doesn’t know. I write to make sense of it all and to continue learning all the time.

Enough babbling. To get a sense of what this is all about, here are some example posts from Culturing Science’s former home.

• I’m fascinated by what I see as the false dichotomy between human civilization and nature, a topic I’m currently researching in my spare time. (Let’s not talk about that “spare time,” shall we?) In a post published in 2010’s issue of Open Lab, I considered overfishing carried out, not by humans, but by a waterbird, the great cormorant.
• When my pet turtle poops, it just gets sucked into the filter in his tank. But fish poop in the ocean has a more noble function: providing food for ocean creatures at depth. Read more about this marine snow here.
• Developing a scientific worldview: why it is hard and what we can do
• As a science-type and Latinist, clearly I have a penchant for ancient science. Here’s the first post of my ancient science series which I will continue here at Culturing Science’s new home.
• How natural history collections have been used recently in ecological research.
• And to get a little personal… a reflection on the year of 2010 primarily about my youngest brother, Jonah.

About the banner image

This is another clip from the same image that I also considered for my blog banner.

See that little picture up there next to the blog title? It’s a clip of a drawing from an 18th century alchemy text, currently in the holdings of Yale University’s Beinecke Rare Book and Manuscript library.

Why that picture? Well, animals are cute, and animals doing science are even cuter.

More importantly, it’s a glimpse at a former scientific world. Alchemy, the transformation of lead into gold, is surely not science, but it is the basis of much of modern chemistry. We always need to remember that popular scientific ideas be wrong and that we can still learn from them.

About me

I’m Hannah Waters, dabbler and aspiring dilettante. I studied Biology and Latin at a liberal arts college in Minnesota a few years back and now live in Brooklyn, NY. I’ve done research on marine food webs, wetland conservation, tropical ecology and grassland ecosystems. I worked as a lab technician in Philadelphia studying molecular biology and the epigenetics of aging. I studied in Italy for a semester, imagining ancient Roman society in the modern city. I even worked on a tour boat off the coast of Maine, spouting wildlife facts over a loudspeaker while serving drinks.

I’m currently earning my wage writing news for an academic medical journal — though I am, admittedly, a career nomad at the present. But I don’t define myself by my job and you shouldn’t either. I’m just a girl who loves science, music, books, and living things of all kinds, from barnacles to aspens to bacteria to people.

Comments

Comments are great. I want to learn from you and hear your thoughts on anything written here. But if you’ve got an attitude that I deem unworthy, I will delete your comment. This is a place for discourse and unwarranted vitriol will not be tolerated.

I’m very excited to be here and hope you’ll stick around! Subscribe to my RSS feed, follow me on twitter and let’s be friends on the internet forever.

I highly recommend you go to the blog network landing page and dig around. Also check out SciAm Editor-in-Chief Mariette DiChristina’s welcome post.

Edited 7/6/2011 1:12 AM to correct RSS feed link.