How to write a paper in 12 easy steps—Part 1

How to write a paper 1

By Nik Papageorgiou.

What’s it all about?

Research Grants comic

By Nik Papageorgiou.

Waste not, want not

My intrepid benchmate had a bit of a rough time today. Nothing, she lamented, seemed to be working. She came in to an incubator full of agar plates with nothing growing on them, which apparently set the tone for the rest of the day, unfolding as it did with various minor disasters and pesky obstacles. Nothing devastating — just enough to annoy.

But she was most concerned about her blank plates: seven entirely different supercoiled plasmids, all zapped into expensive competent bugs from a reputable company starting with S. What, she speculated, might have gone wrong? We talked through her protocol: the bugs were working fine, because I’d used them myself only a few days ago. Her transformation manipulations were text-book, and the DNA itself was above reproach. We were both stumped.

But then she slowly reached for her lab notebook and muttered, “Hang on a minute.” A few moments of page shuffling and plate examination ensued. And then:

“Oh, damn.”

Somehow, she’d plated the two kanamycin-resistant bugs on ampicillin plates, and the five ampicillin-resistant bugs on kanamycin.

Ouch.

But fortunately, there was a happy ending. She realized that the tubes full of bugs were still somewhere in the bin underneath our bench. Scrabbling through the trash, gloves and pipettes flying every which way, she finally managed to find all seven tubes and was able to restreak all of her transformed cultures onto fresh plates. (I told her if she really wanted to go for it, she should re-use the plates that nothing had grown on. But she wasn’t too impressed with that idea.)

The purists may frown, but I’ll bet they grow. Stay tuned.

No news is good news

So I’ve just submitted my paper – the culmination of 4 years of hard scientific work – to a very good journal.

It’s Thursday afternoon, nearly Friday. I feel like I’ve been run over by a tank. And I find myself thinking, I don’t care if it gets sent out for review and ultimately gets rejected:  I’m just happy that don’t have to think about it for a while.

So go ahead, referees: take as long as you like.

Really.

Industrial dis-ease

Guest post from Nik Papageorgiou:

Every culture has taboos. There’s a dark side to the Force. And for every mythology, there’s always some kind of power, dominion or netherworld whose name must never be uttered—or only with solemn care. And I’d like to think that by now, scientists have realized that they are not exempt from such cultural dynamics—after all, we have all the identifying marks of separate culture: traditions, rites-of-passage, ceremonies, unspoken rules, spoken rules, succession, sensitivity to stereotyping, hierarchical structures and, of course, taboos.

So today, we fiddle with the hex.

It’s true that, given scientific economics are in the bust phase of their cycle, industry does and will continue to attract scientists from academia. There are other, many and varied, incentives, but in many cases, industry is simply the only way to go.

I currently work in industry. It’s not the first time—I also did an MSc industrial placement, which I remember as the best-funded research I’ve ever carried out (“Only £2,000? Buy two”). And I’ve yet to meet the scientist whose childhood dream was to work in a pharmaceutical or biotech company. But I’ve met many who dreamt they were falling and had to wake up before they hit the ground.

For a long time, industry has a stigma in academic circles. It is regarded as either a last refuge for those who couldn’t “hack it” or an end of innocence—a less-than-happy finale to the academic fairy tale. Back in my PhD days, I remember discussing a student who’d accepted an industrial position. It was a virtual memorial service: staff members shook their heads sadly and sighed deeply: “Such a waste. He’d make a good scientist.”

So what I wanted to do is try to address some misconceptions about working in industry. First, some caveats:

  1. In no way am I trying to diminish academia. I’ve spent many exciting and formative years in the academic scene and my debt is respectfully and sincerely acknowledged.
  2. This mostly applies to pharma/biotech; but I suspect the same arguments could be raised for other commercialized fields too.
  3. It’ll end up sounding like it, but I’m not trying to paint a rosy picture of industry. But I do think it offers many advantages that many in the academic route have never considered or are mostly unaware of. My last university certainly made a commendable effort to inform postdocs that there lies more beyond just another grant.
  4. This comes from my own experience, peppered with what others have imparted to me over the years. Your experience might be entirely different and you may disagree. We’d love to hear about it in the comments.

So here we go:

Industry is all about money

And what isn’t? Okay, charities. But we’re scientists, and we ought to look at facts. Take a cross-section of any science news-feed/blog/sticky note in the past year and see how much has been devoted in the discussion of science funding. Main argument: how can we value science? It’s invaluable! cry scientists. Of course, say the money people, but we’ll need some receipts.

Fact is, we live in economies driven by profit. Science, in its spectral purity, has to figure out a way to keep going. It might offend our sensibilities, but money has become the fuel that drives—not ignites—science. Ask yourself: how well would you work in research without a salary? How much science is limited by lack of a grant? Or why is there a drive to create/improve commercial relationships between academic research and companies?

I’m not cynical—please. But I am realistic. Industry has the ability to drive science faster and more efficiently than the current academic condition. It’s sad, but true nonetheless.

Industry will restrict my scientific freedom

That’s a common fear. And not unfounded, depending on how you define “freedom”. If you mean “I won’t get to work on whatever I want”, then you’re right. Industry works with pipelines, which are simply VERY big Gantt charts. There is no other way. Yours will be a crucial, yet relatively small, piece in a project of mind-boggling proportions; whether early on identifying potential targets or towards the end, carrying out quality control or characterization work on developed products, you are inevitably part of a larger and pretty well-defined team that extends both ways into the distance. There is no “my project” in industry, and that’s mostly what academics find unpalatable. Teamwork is crucial. Interaction is crucial. Communication of both success and failure is crucial. Transparency is crucial. Seeking help and advice is crucial. The measures of success are diametrically different. Individualism will only hamper you. You watch your corner, pass on the baton, and prepare for the next thing coming at you.

That won’t appeal to everyone, and that’s fine. But it’s a work process that constantly challenges technical and mental skills, develops adaptability and is more often than not far more scientifically exciting than the isolation that often marks academic research (for my postdoc, I spent two years working alone in a cell culture lab. I’m thankful for mp3 players). If anything, you develop a vastly wider technical knowledge.

If on the other hand, you mean “I’ll be a robot and no-one will care for my ideas,” I can flat-out tell you that’s not true. In my industrial experience, ideas and contributions are asked for, welcomed and appreciated—I’d say more than in academia, where money and “that’s the way we’ve always done it” dominate most labs. In industry, it’s fair to say that employees are actively encouraged to make things more efficient, for obvious reasons.

Industry is obsessed with going by the book

And rightly so—unless you want the next paracetamol you pop to kill you. The pharmaceutical industry makes stuff that goes in your bodies to make you better. That means that everything it does prior to that must be held up to independent and very high standards—especially in the development phase of the pipeline where consistency and robustness are of critical importance (and in which lab aren’t they?). Lab books are not creative art projects. Data can’t be fudged. Work cannot be communicated in an arcane unintelligible language understood only by me, myself and mine. Protocols have to be clear, precise, detailed and comprehensive. No margin-scrawling of mysterious calculations. There must be a standard of work that, in my experience, often does not correspond to academic work (and a lot of it really should). Myself included, there are many who come into industry from an academic setting only to be shocked by the prospect of doing science “properly” (I was trying to avoid that, but we were all thinking it). There’s no room for dashing rogue scientists with a charming smiles and cowboy attitudes—and I’m finding that the same is starting to go for academia too. In the end, whether it’s a paper or a drug, you want your yea to be yea and your nay to be nay.

Don’t you?

I’ll stop there. I’m sure there will be many who disagree and think that I’m trying to discourage academic scientists from being all they can be. I’m not. But I think that industry is not the terrible out for losers that certain ivory towers make it out be. Real and often next-level science happens there—and there’s nothing wrong with being part of it.

Quite the contrary.

—Nik

What?

At a conference

By Nik Papageorgiou.

This isn’t what I signed up for

Scientists get a lot of junk mail. Even though I carefully avoid putting my email or postal addresses on anything, not least the mailing lists at marketing booths in conference expos (no amount of cool swag is worth that sort of pain), I somehow get inundated with crap nonetheless. Of course there’s nothing I can do about what comes through the post, aside from chuck it straight into the recycle bin. One day I’m sure they’ll make unsolicited post illegal, but for now we’re stuck with it.

On the other hand, I take great pleasure in unsubscribing from the daily crop of marketing emails that clutter my email inbox. I enjoy the ones that allow you to give a reason:

The very best unsubscribe websites, though, are the ones whose final parting dialogue box says “Thank you for your interest in our products”.

“Interest”: I don’t think that word means what you think it means.

Is there life after science?

Guest post by Nik Papageorgiou

Having read some recent pieces on the age-related disorders and pass-the-pie funding patterns that punctuate the modern scientific landscape, it struck me that the biggest challenge to Science today isn’t cloning, stem cells, climate change, invisible particles or perfect tea-making. No, friends, what whitecoats should be preoccupied with at the moment is solving the inscrutable puzzle of Science Money: whither, to whom and for what.

I have no pretensions that anyone’s having an epiphany here. In the whole Science Funding bandwagon (and I’m using that term only positively), I’m the guy who’s running behind, shouting ‘HEY! WAIT UP!’ I can hardly believe that I’m writing something for LabLit that isn’t a short story or a PowerPoint cartoon with delusions of subtlety. Last time I did that – well, let’s just say it made some people cry. Myself included.

But as funding stands, we are faced with a sad reality: most of those who venture into the straits of research will not get far. The bottleneck squeezes and the sails hang limp for lack of wind. I know; like most scientists, I’ve been there and back. More than once.

Which raises the question, one I have asked myself many times and for many different reasons: at what point do you call it quits? At what point do you say, ‘Wow, I actually can’t do this anymore – not because of science, but because of the business of science’?

Scientists are a peculiar breed, and we ought to be glad for it. No matter how heroically we try to communicate our arcane trade to the public – and rightly so – we will always stand a bit apart from popular embrace. Why? Just add up the hours you’ve spent in some cold, lonely, white room and it’ll tell you something. Obsessing over some fluorescent colours at 3 AM on a weekend is not normal for the rest of the world. Blu-tacking pictures of cells over your family desk photo does not fall in the middle of the world’s bell-shape curve. I doubt it even falls at the edges. Oh – you know what a bell-shaped curve is? Guess who doesn’t.

We do it ‘cos we love it. But the numbers say that most of us simply won’t be able to do it. What then? I’m all for fighting it. But as an old soldier, I know that there comes a critical point in every fight when the fight isn’t worth it anymore; it’s not, as they say, cost-effective. Too few papers. Too few – ahem – good papers. Not enough postdoc experience. Too much postdoc experience. Too few places. Too young. Too old. And of course, that never-abetting curse: no money.

So, at the risk of demoralizing everyone (again), I just wanted to ask: when the music ends, how do scientists go out? With a bang or a whimper? Do they bow out or something less graceful? And, of course, what can they do when they have shuffled off the mortal coat?

Little things mean a lot

If you’re like me, you might sometimes wonder what would happen if you were to omit particular steps in an experimental protocol. I’m the sort who religiously follows instructions, even when I suspect they’re not that important, so I don’t often have the chance to find out.

Not so our poor rotating graduate student. This afternoon, he discovered  exactly what transpires when you don’t wet your membrane in methanol prior to equilibrating in buffer and performing a Western blot.

Utter carnage.

Don't try this at home, kids

Make my day


By Nik Papageorgiou.