All ducks are equal but some are more equal than others

I made the worst decision of my life the other day and think the guilt will linger for at least another decade. You know those little parks you can go to which are liberally scattered with ducks? Ducks on all the ponds, ducks mingling with the sheep and random alpacas, ducks pestering visitors for food in the picnic areas? Everywhere.

So we visited one of these parks and happened upon a lost duck who’d managed to get itself separated from its flock. On one side of a small fence were ducks floating on a tranquil little pond; on the other side, quacking forlornly and pacing back and forth, was the duck in question.

“Ha ha, why doesn’t it just fly back over?” I said.

“Because it’s a duck and it’s stupid,” the boyfriend said.

Well I’d grown up with pet ducks and chickens (not literally with them. I was raised by actual humans. In a house). But, yes, I did have to agree with the boyfriend that ducks really are very stupid. Once, a fox got into our open-roofed pen and, instead of flying away, the vast majority of our ducks let themselves get eaten. See, not the cleverest members of the avian race.

So we hit on what, in retrospect, is clearly a hideously bad idea. I picked up the stupid duck and gently threw it back into the enclosure. Now, normally when you throw a duck, they flap to the ground. This one didn’t. It kind of crash-landed in the mud.

Hmmmm, I thought, its wings are clipped. Maybe it wasn’t actually meant to be in that particular enclosure…

We watched on with mounting horror as the duck metamorphosed from a cute little creature into Duckzilla the dictator duck from hell. It stormed onto the water and set about trying to KILL one of the innocent residents of the enclosure, swinging it around by the neck and basically trying to force it beneath the concentric circles of a watery doom.

“Oh no,” said the boyfriend. “What have we done?”

Before you get too upset, nothing actually died. Although I think the brutalised Mallard did look a little depressed once it had been released and had recovered from its ordeal enough to return to paddling around dibbling its beak in the (feather-strewn) water. Dictator duck then proceeded to chase the female ducks around, doing an impression of a drunk dude in a cheesy nightclub. And I have been left with the lingering guilt of knowing I have sentenced that whole flock to live under the rule of the avian reincarnation of Josef Stalin.

As I should have remembered from the childhood trauma of witnessing what tended to happen when a new duck is introduced to a flock, birds have what is cleverly termed a ‘pecking order’. This ultimately allows peaceful coexistence of everyone in the flock but, at first, there can be a bit of a power struggle while all the ducks work out who is the toughest, meanest duck that gets to boss all the others around.

See, ducks and chickens, while not being particularly intelligent as species go, do have their own little personalities. We had this one pet chicken that, over its ridiculously optimistic 15 year life, resolutely remained the grumpiest inhabitant of the hen house. It hated everything and everyone and, while all the other chickens would let me pick them up and carry them around, this one would peck anything that came close to touching it. Nothing messed with this chicken. Not even Death, it would seem, considering the fact that it managed to live nearly as long as the world’s oldest hen. This chicken was born mean and it died mean, maintaining a remarkably stable personality for all those years.

But other chickens are more pathetic. My parents had this thing for rescuing battery chickens and every year, they would introduce a few featherless, twitchy birds into the pen and we’d watch with crossed fingers to see how they’d fit in with the rest of the flock. Occasionally, there’d be one that, to heap more trauma on top of its already miserable existence, would get pecked so horribly that it would have to be separated from the others until they’d all got used to each other through a chicken-wire barrier. But, in the end, everyone would learn to get on with everyone else, and the battery chickens would grow back their patchy feathers and be less disturbing to look at.

All this has got me thinking about what kind of chicken I am. Do others size me up upon first meeting me and work out that I am very unlikely to peck them back if they try to pinch my choicest vegetable peelings? Am I destined to live out my own life being pushed around by others or can a chicken better its position in the social hierarchy? More importantly, why am I attempting to analyse my own personality based on chickens?

Giving me some hope that we don’t always need to accept our lot in life is an ambitious experiment currently being performed by my slightly mad parents. Chickens can’t exactly fly, providing a good example of how evolution can work in both directions, removing a previously successful adaptation from a species that no longer needs to use it. But my parents are attempting to teach their ex-battery hens to take to the skies using the motivation of grapes dangled from a great height. So far they’ve had moderate success although the chickens’ eyes weirdly roll over white whenever they jump, which is both strange and slightly terrifying to witness.

I think it is close to a metre off the ground. Chickens really like grapes.

Why I will always hate aphids

 

A 500-word news article on a research paper and two days to write it. You'd think it would be simple. Yeah, right. One week into my first foray into the world of science journalism and I feel like my soul has been severely paper-cut with my own poorly phrased copy.

To be fair, the majority of the responsibility for this probably lies with me. Today's Important Journalistic Lesson was how much writers have to rely on talking to the author of a paper and other experts in the field. Understanding a paper is one thing, but there's no way a normal human-being could absorb enough of the nuances of a subject area in an hour to see where it fits into the bigger picture. What might appear to be a paper about the mating dance of the Irish Pink-spotted squid could be key to the evolution of language to a squid-expert. Or the missing link! Or it could just be a paper about oddly-behaved calamari. Sometimes, the press release gives you a clue to the important take-home message of a paper. Other times, the press release is not entirely accurate. 

This is why science writers call up the author and ask them lots of questions before writing anything. Unfortunately, through a combination of French public holidays and the only author on the paper capable of answering my questions off hiking in the wilderness, I had to make do with a slight language barrier and a giant understanding barrier. And when it came to talking to other experts in the field, my two days of expert-hunting experience failed me utterly and the only person I managed to snare was fairly luke-warm about the paper, which wasn't much help.

Then the deadline caught up with me and it was all 'get it submitted', 'check the facts', 'find related articles for the website', 'work out how to use the complicated submission system', 'panic, panic, panic.' Then it was gone and I was left with a vague feeling of disquiet.

Fast forward a few days and I can see that I could have done a few things better. Such as checking that the copy-editors hadn't removed an integral "-like" from the title. Unfortunately, a few scientists who commented on the post also spotted the flaws. So we had to issue a correction. Then then someone else pointed  out a paper from April that I missed, and we had to correct something else. And I've been in a science-based sulk ever since.

What this did make me realise is that journalists sometimes get an unfairly hard time when science reporting goes a bit wrong. But it's impossible to know everything about a subject and you put a certain degree of trust in the peer review process, the authors accurately representing their work, and the press release not over-selling the importance of the results.

Where do science writers get their ideas?

I’m a week into a month-long placement in a science journalism office made up of real journalists and me – a research scientist who is rapidly learning a new respect for those who write about science in a professional capacity. In the past, I know I’ve Googled ‘where do science journalists get their ideas’ and ‘how to write about science’ and ‘what does it mean when your tongue goes green’, and this post touches on at least two of the above. Only from the point of view of someone who isn’t a professional journalist and doesn’t fully know what they are talking about. Tomorrow I will be giving advice on how to do brain surgery.

But first on to the results of my knowledge-leech/journalist-stalking behaviour...

So where do science writers get their ideas?

• Embargoed papers from the big journals which are available a few days before the papers are published. Science, Nature and PNAS are the only ones I've seen so far and a huge majority of the covered papers seem to originate in these journals. Even then, maybe only one per issue will be interesting enough to cover.
• Daily press releases from Eurekalert and other sources, which are again journalist only resources (I couldn't even register with Eurekalert because I am a working scientist and therefore deemed unworthy/untrustworthy to access embargoed papers). These lists include press releases for papers and important reports and, from what I've seen, contain a lot of dreck as well as the interesting stuff.
• Keeping an eye on the news for disease outbreaks, natural disasters, pharma company share prices, takeovers, policy info, funding announcements, politicians saying silly things about science, and many other things I am yet to fully grasp. Everyone seems to have their own area of particular interest.
• Blogs written by scientists or industry insiders can often turn up mentions of new developments in the field, or point out areas that would be worth thinking about. 
• Conferences can be a good source of soon to be published work and ideas, although some aren't open to journalists. 
• Then there are the connections journalists build up with scientists or companies, or pet subjects they've been watching for years writing for the right paper to come along. A few times, I've heard someone mention a scientist emailing them in quite a non-scientisty bout of self-promotion.
• Finally, there's trawling through next tier down journals for recently released papers that didn't send out press releases and have slipped under the radar. This is harder as generally the really world-changing stuff goes into the super-journals but I did manage to find one really interesting paper and was allowed to write a 120-word summary of it, which was cool.

British Science Association media fellowship

For the next month, I am taking a teeny break from science to pretend to be a journalist at Nature News. It's a scheme aimed at teaching working scientists about how the media works by dragging them out of the lab, bleary eyed with the residual smell of growth media lingering upon their person, into the wonderful world of 10am starts and actual, real deadlines.

Three days in, and I have learnt:

1) Science journalists know much more about science than I do. Sure, they couldn't tell you all the three hundred ways there are to accidentally kill a culture, or the gene number of the TB glycerol kinase. But I'm beginning to wonder why, exactly, I've spent so many years filling my own brain up with all this esoteric trivia while neglecting some of the important stuff. Like science policies that directly impact on my work. Or Exciting Stuff happening in fields that are unrelated to my own.

2) Journalists are not the anti-Christ. From how some people in science talk about the media, you'd think everyone who writes about the news sacrifices babies in their spare time and has no regard for things such as factual correctness or the truth. Yeah, Nature is about as sciencey as science journalism can get - its aimed at actual scientists for starters, not those other bipedal furless mammals I am occasionally forced to interact with. But I was still surprised by how much effort goes into fact checking and writing a balanced story. I will, in fact, write an entire post about the creation of an article at some point.

3) Some scientists don't half moan. Getting a quick peak into another industry makes me realise how small and insignificant I am to the world of science as a whole. I think maybe it's easy for scientists to forget how lucky we are when we are constantly surrounded by others who share our worries and fears. Yeah, there are plenty of things in science that could do with being fixed. But whining doesn't help anyone. Fixing them fixes them. Being in a different work place makes it painfully clear that those bitter, complaining scientists who you can find lurking in every lab are not what I want to become </end bitching>

4) So much science is not news. No one wants to read about the latest advance in understanding membrane signalling proteins in Th96 CD61+ T cells, even if the scientist who wrote it is Very Clever and Important. August isn't the greatest month to work in science journalism as there isn't very much going on. I keep trying to find things to write about but very few papers come out that would work as news. 'Surprise, sensationalism and significance' are all required. Makes me realise how insular my own scientific niche is -  even the biggest, most self-important scientists in my field have rarely done anything newsworthy when it comes to their millions of Nature/Science/Cell publications.

5) Phone interviews can be painful. If an author is busy, do you wait patiently for them? Noooo, you phone them again and again, and their co-authors, and anyone else you can think of and PESTER! And, if they don't give you a good enough answer, you keep asking until they tell you to go away. It's like working in a call centre, only without bonuses. This is the part of the placement that I don't think I will quite get used to. That cringing, 'I can't believe I made a stranger hate me in the name of science'-feeling. Urrrgh, scarred for life. But, looking at the positives, I think is will cure me of any residual shyness still lingering from childhood.

6) The novelty of a free canteen runs out very quickly.

Finishing Things

So last week I ‘finished’ my latest book. It’s a young adult novel about a girl who can find lost things and the search for a mythical forgotten city with a beating stone heart said to hold the key to immortality. Also, man-eating gargoyles.

I’m not very good at finishing things, so getting to the point when I can bear to stop messing around with a book is a cause for celebration. Oscar Wilde once said: “I was working on the proof of one of my poems all the morning, and took out a comma. In the afternoon I put it back again.”

That’s me—staring at the same page for hours, trying to think up a more evocative way of saying ‘she walked to the door’. And then the dawning realisation that this is the most boring sentence known to mankind (no matter whether she walks, stumbles, or minces) and it needs to die.

At the other end of the spectrum, I see loads of writers who type ‘the end’ and think they’re done. But on top of the four months I spend writing a first draft, I need another three to get my manuscript into a state suitable for inflicting upon others. Sometimes longer (and sometimes an eternity would not be enough. Zombie poodles? What was I thinking?).

One of the most stressful periods of my life was writing up my PhD thesis ridiculously quickly so that I could start a new job (and get paid!). I still cringe when I think of how much better (and shorter) it could have been if I'd been able to go through it a few more times and make some changes. But when my examiners failed to mention what I thought was a declaration of war against the English language, I realised that sometimes my endless faffing actually acheives very little. I suppose there's a balance between getting something right and attempting to polish it to such a high shine that you scrub so hard its bones start to poke through the skin.

So here is how I know when to stop:

Do I have enough distance from the project to see all its faults?
When you’re looking at the same thing day in, day out, it is hard to be objective. But take a break and let the project simmer in its own juices and suddenly all the flaws become all too apparent. Hitting send on that submission the moment you write the last word is not a good idea.

Am I too attached to my precious words to do what’s necessary?
If a character or scene or sentence isn’t adding anything to the plot it needs to go. Yeah, I might think the idea is awesome but others won't be so impressed with my self-indulgence.

Have I read it and re-read it and removed the majority of the errors?
My Achilles heel is typing ‘that’ instead of ‘than’. And how ever many times I read something, I will always manage to find one that I’ve missed. The odd mistake is one thing. But it annoys me no end when I hear fiction writers say something along the lines of ‘I’m rubbish at grammar and can’t be bothered to learn, but that’s an editor’s job anyway’. Great way to make a professional first impression.

Am I happy with it?
Chances are, if an agent or publisher takes it on they are going to request tonnes of revisions but that's not a good excuse for not making something the best you can. Competition to be published is huge and submitting something with obvious flaws or plot holes is a terrible idea (and I say this from past experience. Oh the shame).

Once I am satisfied with these questions, it is time to let go and move on to something new! Hopefully that something new will include finding time to post science-related articles on this blog...

Murder Your Darlings

It makes me laugh when I hear people say that they don’t like fantasy or science fiction novels because ‘it’s not real’. All fiction, by definition, is made up. Yet, when it comes to imaginary monsters or aliens or magicians with pointy hats and white beards, many people don’t want to read something so removed from reality. The reason I have a problem with this isn’t that some people don’t want to read the sort of book that I happen to write. These differences in taste are what make the world interesting. But their reasoning does bother me. And this is because all book are about people. In 1984, Orwell made his people into pigs to show the dangers of totalitarianism; Philip K. Dick used androids to make us think about what makes us human in Do Androids Dream of Electric Sheep?; Tolkien had hobbits and elves and wizards, but The Lord of the Rings was about the power of temptation, and humanity’s relationship with death. 

There are very few new ideas in the world, but there are a million ways of saying them. The eternal question of what makes us human doesn’t change if you happen to dress it up with the odd dragon. Love still conquers all if it is up against fairies and talking trees. I personally read books in the hope that they will teach me something new, or make me think about something in a different way. And all  it takes is someone to package those ideas up in a way that resonates with me. The plot might be a post-apocalyptic fight for survival, but the message is on the futility of war, or the strength of the human spirit, or maybe even the meaning of life.

One of the hardest things to learn as a writer is your ‘voice’. It can be a richness of prose like Dickens, or the inclusion of certain recognisable elements like Roald Dahl or quirks of language like Shakespeare. Or it can be a unique approach to the rules of grammar reminiscent of Cormac McCarthy. While few think about it, your real-life voice is just as unique and just as capable of boring or intriguing or exciting those who listen to us. There are people who we enjoy talking to, and there are those who change us—they find a way to say something that gets under our skin and makes us rethink our opinions. The same goes for books. On his literary inspirations, Martin Amis said: “I find another thing about getting older is that your library gets not bigger but smaller, that you return to the key writers who seem to speak to you with a special intimacy. Others you admire or are bored by, but these writers seem to awaken something in you.”

There’s a form of magic to finding a way to say something in a way that sneaks into the head and heart of a reader, and plants the seed that will grow into a new way of thinking about something. But that’s the important part—to only sow the seed instead of trying to ram a fully grown tree down someone’s throat. It’s a sneaky kind of persuasion—tricking someone into coming up with the very idea that you wanted them to have without even noticing you, the writer, quietly whispering in their ear. However, try too hard and a writer’s voice becomes a boastful five-year-old screaming ‘look at me, look at me.’ And it’s something many novice writers struggle with. The fine line between cultivating a unique voice and ensuring that this voice is unobtrusive enough that the reader doesn’t feel clubbed into submission.

There’s a saying among writers: ‘Murder your darlings.’ British writer Arthur Quiller-Couch is quoted as saying, "Whenever you feel an impulse to perpetrate a piece of exceptionally fine writing, obey it—wholeheartedly—and delete it before sending your manuscript to press." It all comes back to the need to control that writer’s voice to a point where it flows over a reader instead of drowning them in a sea of flowery language and esoteric wit. But it’s a paradox for beginning writers who, at the same time as needing to develop their unique voice, also need to know when to rein it in.

My stomach always lurches when I hear writers utter the words, ‘my book is my baby’. It’s a commonly known fact that people tend to lose their objectivity when it comes to their own kids. Revising a novel from first draft terribleness to something others might actually want to read involves listening to criticism, and then ripping all your precious words apart and sticking them back together again. Few people are willing to dismember their ‘babies’ to create Frankenstein’s monster. But the words on the page are not the story, they are merely a vessel to sneak your ideas into someone else’s mind. Words are the tools, but the art is the ideas they conjure in the reader’s head.

The same goes for any career other than writing, science included. Presenting a graph of your data isn’t enough if you can’t find a way to package it as something others want to read. I’m not talking about clever turns of phrase or poetic descriptions, which have no place in scientific writing. The words don’t need to be beautiful to do their job, but it’s a mistake to think they don’t matter. They need to gently prod the reader in the right direction by highlighting the important parts, allowing fellow scientists to reach the same conclusions that the author did, only in the space of thirty minutes rather than ten years. You can’t shout your side of the argument and expect others to give in—a fault I do sometimes see with scientists’ attempts to deal with certain controversial subjects such as cloning. You have to say it in a way that makes someone listen, and then makes them think.

That’s the secret behind any good writing—whether it’s designed to entertain or educate, whether it’s about bacteria or dragons. In the end, everything is about people and how we fit into the world around us.

Getting our heads around African sleeping sickness

African sleeping sickness is one of those scary diseases that seems kind of alien to anyone living in the Western world but which is a real threat to those living in sub-Sahara Africa, causing around 50,000 cases each year. The disease gets its name from the most recognisable symptom—a disruption of sleeping patterns after the parasite infects the brain. A recent paper published in PLoS One shed some light on how the parasite makes the treacherous journey from the blood to the brain. But why does a parasite spread by infected blood want to get into our head to start with?

The three forms of trypansomes - slender, intermediate and stumpy.

Any infectious agent needs to have a plan of attack for dealing with the host’s immune system. Some microorganisms go along the route of actively switching off the immune response. Others hide from the immune cells that would otherwise kill them. The trypanosomes responsible for sleeping sickness use a less subtle but highly effective method to stay one step ahead of the immune system while circulating in the blood. The parasites are coated with ten million copies of the same protein which is recognised by the host, allowing the immune system to start clearing the infection. But, just as the host starts to get the upper hand, the parasite subtly changes this protein disguise so that they are no longer recognised by the immune system.


Without drugs, it is impossible for an infected person to deal with the infection and the disease is always fatal. But sleeping sickness has a fairly high rate of relapse even after treatment. One of the reasons for this could be that, at some point the parasite decides to make the trip from the blood and into the brain. Here, it is effectively protected from drug treatment, and can pass back into the blood system to continue the infection. An evolutionary explanation for this could be that some hosts are better at dealing with the infection than humans, and the brain represents a hiding place from the immune system.

Tsetse fly. Yuk.
Image from Wikipedia

This late stage of the disease—the brain stage—is not well understood. It takes weeks and months for the late symptoms including confusion, reduced coordination, daytime sleepiness, and insomnia at nigh to emerge, and the reasons for this remain elusive. One of the most interesting of these symptoms—the change in sleeping patterns—has an interesting explanation. Sleeping sickness is spread by the tsetse fly. The tsetse fly is one of the less pleasant creatures in the world and it has fairly disgusting table manners. It bites a hole in the skin, vomits up some of its last meal complete with any parasites along with agents to prevent the blood from clotting, and then feasts on the resulting blood pool. This isn’t particularly pleasant for the unfortunate owner of the blood. Therefore it helps if the meal happens to be asleep at the time of being fed on.  

But how does the trypanosome succeed in altering a person’s sleeping patterns? It appears that this is a side effect of a signalling molecule used by trypanosomes to control cell density. When the parasite gets into the brain, it doesn’t want to cause extensive inflammation and get itself noticed. So it secretes a messaging molecule called PGD2 that tells neighbouring parasites to commit parasite-suicide for the good of the overall population. But PGD2 has also been shown to cause non-REM sleep when injected into the nervous system. So secreting PGD2 directly into the brain is useful to the parasite when a person is far more likely to be bitten by the tsetse fly if they fall asleep during the day.

The sleeping sickness parasite makes
its way to reside between the Pia mater
 and Glia limitans at the edge of the blood.
Image from: Wikipedia

So how does the parasite get into the brain in the first place? Our brains are cut off from our blood supply by the blood brain barrier—a barrier which actively prevents such things as parasites from making the trip out of our veins and into our central nervous system. In addition to the blood brain barrier, we also have a barrier between our blood and the colourless liquid in which our brains float, and it is across this barrier that the parasites make the journey into the brain. Hartwig Wolburg and coworkers demonstrated that this journey takes the parasite through hostile territory until it reaches it’s a position at the edge of the brain where it is protected from the immune system but can still reinvade the blood if it so chooses.

But the group responsible for this work also addressed the question of why the brain stage takes so long to emerge. Something interesting about their attempts to reproduce the brain infection in rats was that it proved impossible to simply inject parasites into the nervous system. Instead, the infection needed to take its usual course, beginning with the blood stage and progressed to the brain stage after some time. It appears that there are three forms of the parasite (shown in the figure at the top of the post)—a stumpy form which does not undergo the variation in its coat proteins and is killed by the immune system, an intermediate form which is responsible for the blood infection, and a slender form which can cross into the brain. How this slender form emerges and whether it really is required for brain infection remains to be determined, however.

Research such as this has the potential to help the development of future vaccines and drugs by teaching us more about how the infection progresses. The current treatment for the later brain stage of the disease involves an arsenic-derivative which kills one in twenty people and has been described as ‘fire in the veins’ by those unlucky enough to need to take it. Over the past few years, sleeping sickness has slowly been decreasing in numbers and it is hoped that in a decade this disease may finally be eliminated.