28 September 2012

You do not know the end of your story

This post by Naomi at IttyBiz is something that many academics can benefit from, regardless of whether you’re a stressed undergrad, unappreciated grad student, disgruntled post-doc, freaking out tenure-tracker, or grumpy tenured professor.

You do not know the end of your story.

That won’t make sense until you’ve read Naomi’s piece.

In 1897, Churchill watched one of his fellow army dudes get slashed to death by a Sikh bad guy during the Greco-Turkish war.

You think he was like, “It’s cool, ’cause one day I’ll beat the Nazis”?

No, he was not.

A good visual metaphor for how academics view careers is tightly pulled chain: a straight line, with each link leading to the next. If one breaks, the whole thing goes. If you’re ambitious and forward thinking, this means that you are worried about the ramifications about every decision.

“If I don’t get in the top tenth percentile on the GRE, I won’t get into Dr. Fancypants lab, and he can’t set me up for a postdoc in Big State University, so I can’t get the tenure-track position in the Major Research University, and I’ll never get the Nobel prize!”

Academics tend to gloss over career struggles. Let’s face it, nobody likes to boast about how they got Cs on their undergraduate transcript (I did), were wobbly on their comprehensive exams in the Ph.D. (I was), how they struggled to get tenure (I did), or cannot seem to crack the shell on external grants (I am). Jacquelyn Gill has suggested a way to try to make these more visible, by creating a shadow CV.

If we acknowledge problems of successful scientists, they’re usually cast as mere speed bumps that are overcome with genius, courage, and determination (but usually genius).

You do not know when you will have an opportunity to contribute and do something valuable. That you failed does not mean that you are a failure.

Related posts

The genius myth
The downsides of meritocracy
The sports psychology of academia

External links

Is this the end of the story? 

Building a shadow CV

Picture by Max Klingensmith on Flickr; used under a Creative Commons license.

26 September 2012

Why not retract the rat cancer / GM corn paper?

Those who have looked at mMy mini-crusade to get the conflict of interest statement changed on the forthcoming paper by Séralini and colleagues might well ask: “Why change the conflict of interest statement alone? Why not just retract the paper?”

Henry Miller makes the case for retraction in Forbes this morning. In short, he argues that Séralini and colleagues are con men:

There is no question that the publication of Séralini’s latest attack on genetically engineered foods was a well-planned and cleverly orchestrated media event. The study was designed to produce exactly the false result that was observed and was deliberately allowed to continue until large, grotesque tumors developed.

I think retraction is a bad idea. First,those opposed to genetically modified (GM) foods seem to be prone to conspiracy theories (the trailer for Tous Cobayes? makes this clear). The anti-GM would revel in the retraction, and see it as proof of a cover-up by the establishment. I don’t see any way for the retraction to come out as a win for scientific integrity.

I think updating the conflict of interest statement is a win, because it invokes something that the anti-GM people in Tous Cobayes? bring up as something they want:

Transparency.

The anti-GM crowd say there is a cover-up and information being suppressed? Fine. Now be held to that standard. There should be no objection to disclosing funding sources. There should be no objection to noting that the lead author has a book. There should be no objection to pointing out that documentary film crews were in the lab filming the results of this project.

There is also a broader issue of when a journal should retract a paper, and what retraction indicates. The editors of PLOS Pathogens have recently announced they will retract papers unilaterally if a paper’s main conclusions are shown to be wrong. I weighed in on this in the comments about this on Retraction Watch, and my comments there are relevant here. If I may be allowed to quote myself:

The situation now is that “retraction” is a cryptic, inconsistently applied marker for “a bad problem.” Why not just make it explicit and descriptive?

“Contains fabricated data.”

“Experiment not supported by replication.”

“Incorrect statistical analyses.”

“Correct data sharing agreements not signed as required by law.”

People sometimes talk about “the scientific record” as though is should be some sort of pristine, distilled essence of very important knowledge. (For instance, you hear people talking about results they don’t think are important “cluttering up the record”.) It isn’t, and never has been, so trying to purify the “scientific record” is a fool’s errand. Leave it all it, but work on better follow-up, tracking, and commentary.

Retracting the paper by Séralini now would be a classic case of shutting the barn door after the horses have gone. It’s too late.

25 September 2012

Tuesday Crustie: Din-dins!


This little porcelain crab is trying to snag some food. It is using those fan-like setae on its mouth parts to filter feed.

From here. Hat tip to Miriam Goldstein.

24 September 2012

What did you think those film crews were doing in the lab?

I often tell my students, “When you’re evaluating a claim, don’t ask whether the source is trustworthy; ask what the evidence is instead.”

Last Wednesday, a paper came out by Séralini and colleagues purporting to show a link between eating genetically modified corn and cancer formation in rats. This was quickly picked apart as unconvincing by multiple sources. The authors don’t show all the data. Phrases that should worry you whenever you see it in a research paper: “All data cannot be shown in one report.” In particular, they don’t show the data from the controls; look at their Figure 1 and 2. Look at the pictures of the rats with tumors in Figure 3. The implication is that, “Oooh, look these rats are incredibly sick,” which implies that the controls are totally fine. But unless they show us, we can’t know that. I say, “Case not proven.”

The paper blew it on presenting evidence. The authors then blew it on the trust, too.

What I want to know is how these authors can put this in their paper with a straight face:

Conflict of Interest
The authors declare that there are no conflicts of interest.

No conflicts of interest? You mean other than a book (first noted in BoingBoing comments) and a movie (both titled Tous cobayes with different end punctuation; roughly translated, “All of Us are Guinea Pigs”) coming out exactly one week after the paper? (I recall reading in Retraction Watch somewhere that the authors requested the journal release the paper on a specific day, though I can’t find that post now.)


You have a movie about your research. And a book. Coming out exactly one week after your paper. This means it was in the pipeline while doing the research. This is a conflict of interest.

Furthermore, the movie seems to be advocating one big conspiracy theory. It’s hard to read anything else into their claim that there is a straight line from the development of the atomic bomb in World War II to the creation of genetically modified organisms. I suppose I can see how to someone outside of science, this might seem plausible, but as someone working in one of those fields (biology), the background knowledge and skills needed to work as a physicist and a geneticist are rather different. Sort of like asking the photocopy repair guy to fix your broken toilet.

Before I learned about these media projects, I thought they might have just done a poor experiment. The movie blows any chance the authors had of convincing me that this is an honest test of a scientific hypothesis.

I call upon the editors of Food and Chemical Toxicology to require Séralini and colleagues to change the conflict of interest statement before the final version of record is published, to record and reflect that this project is featured in a book, and was extensively recorded for a film documentary.

Additional: You can email the journal’s editor-in-chief here. Here’s the letter I sent:

The paper by Séralini and colleagues that is in press in your journal contains the following conflict of interest statement: "The authors declare that there are no conflicts of interest."

In the few days since this paper has been published, we've learned that the lead author has a book, "Tous cobayes!" being published this Wednesday, which appears to be GM foods:
http://www.amazon.fr/Tous-cobayes-Gilles-%C3%89ric-S%C3%A9ralini/dp/2081262363

The lead author also appears in a movie, also being released this Wednesday, with an almost identical name, “Tous cobayes?” A preview of this film, with English subtitles, can be found here: http://www.youtube.com/watch?v=Wyubtjh3H5w

The online preview of the film makes it quite clear that the scientists were extensively interviewed for this documentary, and that film crews were actively filming the project and its results.

Both of these activities are conflicts of interest for at least one of the authors, if not more. Lead author Gilles-Eric Séralini stands to make money from the sale of his book, and his appearance in the movie may also mean that he stands to benefit from publicity for that movie.

I strongly suggest that the paper’s conflict of interest statement be revised before the final version of the paper is published to disclose the projects ties with these two projects.

More additional, 25 September: Some funding sources also appear to be missing from the paper (Google translated English version). Hat tip to GMOpundit on Twitter.

Additional, 28 September 2012: A new article in the Guardian provides Séralini’s responses to the criticisms. Note that it misses the biggest one:

Where are data from the freakin’ controls?

Reference

Séralini G-E, Clair E, Mesnage R, Gress S, Nicolas N, Malatesta M, Hennequin D, Spiroux de Vendômois J. 2012. Long term toxicity of a Roundup herbicide and a Roundup-tolerant genetically modified maize. Food and Chemical Toxicology: in press. http://dx.doi.org/10.1016/j.fct.2012.08.005

External links

Under controlled: why the new GMO panic is more sensational than sense by Scicurious
Bad science about GMOs: It reminds me of the antivaccine movement by Orac
Stenographers, anyone? GMO rat study authors engineered embargo to prevent scrutiny by Ivan Oransky
From Darwinius to GMOs: journalists should not let themselves be played by Carl Zimmer
Authors of study linking GM corn with rat tumors manipulated media to prevent criticism of their work by Maggie Koerth-Baker

Frankenstein and Galileo

They often say there are only a few basic stories, and everything is just a variation on those. Hero’s journey. Small band of heroes against an evil empire. Revenge. Boy meets girl.

I was thinking about what makes a story “anti-science” (prompted by some online discussion with Karen James about The Lizard in this summer’s The Amazing Spider-Man - I may have more to say about this later). I was trying to think about the deep archetypes in stories about science, and I’ve identified two so far. Pehraps not surprisingly, they are the opposite numbers of each other, tragedy and triumph.

Frankenstein

Mary Shelley’s Frankenstein is a modern myth about science. But it is a deeply pessimistic one. It is a story of overreaching, failure, and in the end, a morality tale with the message, “There are things humanity was not meant to know.”

It is a phenomenally popular story archetype. It’s Wells’s Doctor Moreau and Crighton’s Jurassic Park and I don’t even want to guess how many others. It’s easy to see why: it has a flawed lead character with a (scientist with great pride), and a failed experiment that immediately creates conflict.

Weirdly, I don’t think the anti-science theme in such stories always discourage people from science. Jurassic Park is a classic cautionary “It’s not nice to mess with nature” tale, yet it got a lot of people interested in paleontology anyway.

Galileo

Galileo is arguably one of, if not the first, scientist in the modern sense. His famous “disagreement” with the Church is an optimistic take on science. It is a story of a lone genius taking on the establishment, and in the end, it tells us, “Truth will out.”

The story of Galileo is a real story, of course, but it has become larger than life. Berthold Brecht turned it into a play, but you can find variations of Galileo’s story in all kinds of art. The old movie Dr. Ehrlich's Magic Bullet tells the story of Paul Ehrlich much like Galileo: lone genius fighting ignorance. Robert J. Sawyer turned Galileo into a dinosaur in his novel Far-Seer. Ellie in the book and movie Contact face Galilean types of challenges.

While the “lone genius” story has roots in reality, it can be almost as unrealistic as Shelley’s ghost story. Most successes in science are recognized as such pretty readily, and many people who like to pain themselves as put down by the establishment are just wrong.

Are there other science story archetypes that I’ve missed?

21 September 2012

Academic astrology

ResearchBlogging.orgLast week, I published a little post about my predicted h-index scores over the next 10 years. There has been more discussion that I think warrants follow-up.

First, I put no more faith in this predictor than I would in astrology. The h-index predictor ought to come with the sort of disclaimer that skeptics asked newspapers to add to horoscopes: “purely for entertainment purposes.”

Justin Kiggins made the best critique of the h-index predictor:

according to the H-Index predictor, my cat will have an H-Index of 9 in 2022


So in ten years, Justin’s cat will have a higher h-index than I do after 20 years of publishing science. In fairness, though, this is Justin’s cat:


More seriously, I was a little surprised by some of the discussions I saw around the Nature paper (Acuna et al. 2012). For instance, this news article botches the basic idea of the article.

But the new formula is more than twice as accurate as the h index for predicting future success for researchers in the life sciences.

It’s not “more accurate” than the h-index, it is the h-index. It’s just a way to predict h-index out into the future, when h-index is a calculation based on what you’ve done in the past.

There’s a few other things that are worth pointing out about h-index.

First, the whole point of h-index is that it is supposed to give some indication of scientific quality or reputation, and not reward people for publishing rubbish papers. Someone who publishes a lot of papers that nobody cares about or cites should have a low h-index. The theory is sound, but a recent paper found that the number of papers you’ve written explains 87% of the variation in h-index (Gaster and Gaster 2012).

In a way, this is reassuring. This suggests that most scientists are competent, and most papers are worth citing. But it suggests that paper quality is not very important to this measure.

Another issue is reproducibility. For instance, my h-index according to Google Scholar is 8. According to Web of Science, it’s 6. There is no way that h-indices are going to be calculated by hand by human beings; they must be done by computers running algorithms. And if different datasets give the different results, it’s limited in its usefulness.

Measures like h-index this are entertaining, and as I’ve said before, they are expedient. But the moment you hear any administrator seriously suggesting using these alone, in isolation, to make important decisions like tenure and promotion, run. Or fight. But don’t just accept it.

References

Gaster N, Gaster M. 2012. A critical assessment of the h-index. BioEssays 34(10): 832. DOI: 10.1002/bies.201200036

Acuna DE, Allesina S, Kording KP. 2012. Future impact: Predicting scientific success, Nature 489(7415): 202. DOI: 10.1038/489201a

Related posts

Expedience
Gazing into the crystal ball of h-index

External links

The Genius Index: One Scientist's Crusade to Rewrite Reputation Rules

19 September 2012

The sports psychology of academia

At about the one minute mark in this clip...


The world ain’t all sunshine and rainbows. It’s a very mean and nasty place and I don’t care how tough you are, it will beat you to your knees and keep you there permanently if you let it. You, me, or nobody is gonna hit as hard as life. But it ain’t about how hard you hit, it’s about how hard you can get hit and keep moving forward, how much can you take and keep moving forward.

Rocky Balboa, Rocky Balboa (2006), written and directed by Sylvester Stallone

Every academic gets hit. And hit. And hit again. Bam. Whap. Smack.

Your grant proposals and papers are going to be rejected. A paper you slaved over won’t be cited as much as you want. Your students will think you’re boring sometimes.

Persistence and grit are key to being an academic. Playing sports or games is a good way to remind ourselves that success is never final and failure is never fatal.

Inspired by Kate Clancey (here, here) and Scicurious (here).

18 September 2012

Tuesday Crustie: Dig in

One of the good things about deciding to self-publish some of my slipper lobster research was that I found this video again.


I did this about six years ago, when I was getting ready for a presentation at the Society for Integrative and Comparative Biology (Faulkes 2005). I did a quiet, calm version that I showed during the talk. The silent version was the first thing I posted to YouTube six years ago this month.

I’d thought I’d lost the music video version.

Now, if I could find just the video where I showed sand crabs moving to the tune of Peter Gabriel’s “Digging in the Dirt”...

Reference

Faulkes Z. 2005. Do shovel-nosed lobsters shovel with their noses? Integrative and Comparative Biology 45(6): 994. http://dx.doi.org/10.1093/icb/45.6.955

17 September 2012

How tenure is like YOLO

Too often, it’s used as an excuse to do something lazy or stupid...

Instead of a reason to do something bold and great.

(YOLO = You only live once.)

16 September 2012

Comments for first half of September 2012

Dr. Isis asks how many first author papers someone needs to get in the game for a faculty gig.

Biochem Belle asks what you wish you’d learned more about in your coursework.

The most maddening ads about scientific research I’ve seen in a long time. “Cancelled 18 theater nights. Did not celebrate 2 wedding anniversaries. Developed 1 new method to diagnose cancer.” Yeah, because the gratitude of anonymous strangers totes makes up for ignoring the people we supposedly love. Why not throw in, “5 estranged children. 3 broken marriages.” while you’re at it? It’s stupidity for the ages, and earns a classic facepalm:


Athene Donald was asked, “Did someone ever inspire you to be a scientist?” She asks the readers of Athene Donald's Blog the same question.

Drugmonkey looks at limiting the number of citations in journals.

Labrigger has a set of guidelines for fixing electrical equipment.

Classic facepalm by Alex E. Proimos on Flickr; used under a Creative Commons license.

14 September 2012

Finding self-published papers

It does no good  to publish a paper if nobody knows about it. When I published an original research paper on my blog, one of the concerns that even supportive onlookers raised was, “Will people be able to find this paper?”

The answer is, “Yes.”

If someone is looking for distal leg motor neurons of slipper lobsters in Google Scholar, they should see something like this in their results:


My self-published paper is second from the top.

Google Scholar latched on to the PDF of the paper I created and uploaded on my university website. This also answers another question I was asked, “Why bother making a PDF at all, if you’re posting it on your blog?” Because the blog post isn’t showing up in this search engine, but the PDF is. And that only took about a week, tops. It might have been even less time.

Some will no doubt see this as a flaw in Google Scholar. I sympathize. I’m ambivalent about this paper showing up so readily in the search results. Good for me, obviously, but definitely reminds people that you always have to keep your wits about you with any resource. It may well be that Google Scholar will end up changing its algorithms to exclude papers like mine that explicitly advertise themselves as “not peer reviewed.”

Update, 9 December 2013: Found a “How to” for getting your self-published papers indexed in Google Scholar.

Related posts

The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae)

Why I published a paper on my blog instead of a journal

DIY typesetting and science publishing

External links

I thought Google was trying not to be evil
How to game Google Scholar
Inclusion guidelines for webmasters

Itsy bitsy neurons

Encarsia formosa is a wasp that has been well researched as a biocontrol agent. But there’s something else about it you can’t miss, which is how easy it would be to miss:


It is one tiny little insect. For those of you who are practising biologists, maybe this will provide an even better sense of how small this wasp is:


The whole beast pretty much fits inside the eye of a fruit fly.

ResearchBlogging.orgExtremes never fail to be fascinating in biology, because they often challenge your notions of what is possible. What do you have to sacrifice to be able to make an animal that small? In a new paper, Hustert argues that this wasp hasn’t given up too much behaviour: it is still able to do the things that other wasps do, like fly, respond to stimuli, groom themselves, walk, and jump.

Has this wasp sacrificed neurons at the cellular level? Are the neurons just smaller, or are there fewer of them? The shape of the nervous system is different than larger insects: everything is clumped together into fewer masses of cells. And there are probably a smaller number of sensory hairs than in other species.

The neurons themselves are also tiny. The cell bodies about 2-3 µm, though they seem to have a fairly normal structure otherwise. Most axons have diameters 0.2 µm across or less. No, that is not a typo. One micrometer is one millionth of a metre, so these are one fifth of one millionth of a metre. The smallest axons are about one twentieth of a millionth of a metre (~0.05 µm).

These tiny neurons raise interesting physiological questions that are asked, but not answered, by this paper. Small neurons conduct action potentials more slowly, so how does the animal cope with having slow communication withing the nervous system?

For that matter, do these neurons conduct action potentials at all? An axon can only get so small before it cannot transmit action potentials: you just can’t fit enough voltage gated sodium channels (needed to start an action potential) on the cell.

Hustert quotes earlier theoretical work predicting that you could not make an axon smaller than 0.1 µm in diameter, because enough sodium channels would be opening spontaneously that you would get random action potentials, and noise is not good in a signalling system. Hustert suggests it’s possible this wasp might be using non-spiking neurons, but this seems unlikely, because in other invertebrates, non-spiking neurons tend to be fat. Alternately, maybe the wasp neurons’ physiology is different in some other way. Hustert says that maybe the neurons fire in bursts, which could increase the reliability of the signalling.

One of the things I like about this paper is not just that it documents the tiny, but asks the reverse question: what has this animal kept relatively large? After all, space is at a premium here, so if you’re going to have an axon with a diameter of over a whole micrometer, where most are 0.2 µm or less, that’s got to be a pretty special cell. Hustert does find a few of these relatively large cells, and suggests that they are responsible for detecting puffs of air, and could trigger escape.

A decent number of neurobiologists record the electrical activity from fruit flies. I have always referred to these people as “masochists.” But we may need a new breed of masoch— er, physiologists willing to try to get into these even smaller insects, because there are some great questions that will never be answered by looking at their anatomy: we’ll need to see the neurons in action.

Reference

Hustert R. 2012. Giant and dwarf axons in a miniature insect, Encarsia formosa (Hymenoptera, Calcididae). Arthropod Structure and Development: in press. DOI: 10.1016/j.asd.2012.08.002

Photo from here.

Related posts

Non-nuclear nano neurons
“Oh, what a tangled web we weave”... because of small brains?

13 September 2012

Gazing into the crystal ball of h-index

According to a new article in Nature, this is my academic future for citations, Specifically, my h-index:


It is entertaining to “twiddle the knobs” and see what it does to the trendline. That I have published in many different journals seemed to cause my stock to continue rising, rather than tapering out.

I’m going to schedule a post with this graph for 2017. We’ll see how close it is.

External links

H-index predictor

Hat tip to Bradley Voytek on G+.


12 September 2012

There is no ceiling

At a meeting about tenure and promotion today, our Provost made a comment about changing expectations for tenure and promotion. He said, “If I were to try to get tenure today at the university where I originally got tenure, I don’t think I would get tenure.”

His point was that it expectations were getting higher and higher across the board. As far as I could tell, he either welcomed it, or at the very least did no seem to think this was a problem. I should have counted the number of times he said some variation of “moving forward.” He seemed to think it was logical to ask our new hires to do more than the last people hired, so that the university could “move forward.”

This worried me. Because I look around at what it took for myself and my colleagues to get tenure, and you want the new people to do even more?

Human beings can only work so hard and do so much. There is going to be a breaking point. There is going to be a point where there is no more blood to be squeezed from the stone. There is going to be a point where you drive everyone out of academia except single workaholics. And even a lot of them won’t get tenure.

Mistaking the bottle for the wine

Latest insight gained from listening to advanced undergraduate students about how they see scientific publishing.

I gave students an original journal article and Ed Yong’s write up about it: same story, but told different ways. Then, I asked them to write out what distinguished the writing style of the two pieces.

One of the things a few of the groups wrote down for the journal article was, “scientific method.” This puzzled me a bit, since they were both reporting the same information. When I asked them to elaborate, they said, “It has an introduction, methods, results, and discussion section.”

They took the format of the paper to be “scientific method.” Not generating hypotheses, designing controlled tests, or analyzing evidence. I’m not sure yet if this is just confusion over terminology or a deeper misunderstanding. It’s not good either way.

Related posts

Science writing as seen by students

11 September 2012

Tuesday Crustie: That’s a whole lot of crustacean


Hermit Crab Migration from Steve Simonsen on Vimeo.

What amazes me is not only the mass of hermit crabs, but that there are enough snail shells for all of them.

More about the science of the migration here.

Hat tip to Jerry Coyne.

10 September 2012

DIY typesetting and science publishing

Last week, I decided to post one of my original research papers on my blog. As expected, the post about why I blogged the paper has received far more hits than the paper itself. What I could not expect (but hoped for) was the excellent comments and discussion I received in response. Thank you, all.

I spent a few hours Friday afternoon and Saturday morning turning the paper that I self-published as a blog post into a PDF, deliberately trying to emulate what a final typeset article in a professional journal might look like.

Have a look. How close did I get?

I did all that in Microsoft Word 2010. Some writing and typographic purists who will groan at this, then tell me I should have used this or that and I would have gotten better results. Yes, I know. But the point is, this is consumer software that most people have, and the PDF is... not bad. (If there is enough interest in how I did this, let me know, and I'll write a detailed “how to” post.)

This is relevant to the matter of publishing a paper on my blog, because one of the arguments that goes around about academic publishing is whether publishers provide useful services to authors. (I contend that they do.) One of the ways that publishers provide “added value” is with professional typesetting. I still prefer reading typeset PDFs of journal articles to manuscripts.

I spent a few hours with Word and got something that is maybe 90% the quality of what professional typesetters working for academic publishers do. And that’s without much practice, although a lot of experience with Word. I could probably speed up the process considerably.

Meanwhile, I’ve been waiting for over two months for my most recent paper to move from “provisional PDF” to the final typeset form. That is not an isolated incident.

That does not make me a happy partner in scientific communication. It makes me want to say, “Pick up your game, publishers, or these first self-published papers on blogs won’t be the last.”

Additional: I received an email from Bryan Vickery at BioMed Central, indicating that there have been changes in their production process that have caused delays. They know about the problem, and are working on it. Sensibly, they focused on getting the HTML version out first, so there was something that could be read and cited. See more here.

Related posts

Good thing I’m not in a hurry

External links

The Typography of Authority — Do Fonts Affect How People Accept Information?
Analysis: When will your BMC paper be typeset?
The Glacial Pace of Scientific Publishing: Why It Hurts Everyone and What We Can Do To Fix It
The Glacial Pace of Change in Scientific Publishing

07 September 2012

Why I published a paper on my blog instead of a journal

TL;DR: I had a research project that has been sitting for more than a decade without finding a home in a scientific journal, so I decided to post it on my blog instead as an experiment.

Yesterday, I posted an original scientific paper here on my blog. The obvious question is, “Why is it on the blog instead of in a peer-reviewed journal?”

This project goes way back to the last century. I was doing my first post-doc, and I applied for an NSERC post-doctoral fellowship. I proposed a project that came out of my Ph.D. research. I had been studying leg motor neurons in crustaceans (published in Faulkes and Paul 1997). There was this one paper about spiny lobsters that just did not jive with everything else I had found. In my fellowship application, I proposed to try to resolve those questions by re-examining spiny lobsters’ neurons – in other words, the project that I posted yesterday.

To my surprise, I got the fellowship. I used it to move to Australia and do a post-doc with David Macmillan. It was a wonderful experience. But what happened to the proposed project was... normal research happened.

David Macmillan asked me to pick up another project in addition to the leg motor neuron one (Faulkes and Macmillan 2002), and help mentor an Honors student (Patullo et al. 2001).

I had setbacks in getting animals. Spiny lobsters were too hard to work with. Suppliers for slipper lobsters didn’t come through, and I thought I was sunk until I finally stumbled on seafood place down the road that had live slipper lobsters. All hail the Queen Victoria Market!

Then, once I had the slipper lobsters, I made serendipitous discoveries that I just had to pursue. Discoveries like that slipper lobsters didn’t have giant neurons needed for escape behaviour (Faulkes 2004) and that they were diggers (Faulkes 2006a). And the seafood supplier came through again, with live spanner crabs, which I’d been dying to look at since my thesis on sand crabs (Faulkes 2006b).

I did the leg motor neuron project around all of those others during that post-doc. Clearly, I had lots to show for my time in Australia regardless. But that was a post-doc project, and I’m a tenured associate professor now, so... you can do the math. This has been sitting around, waiting, for over a decade, to see the light of day.

I haven’t even presented this research at a conference. I should have.

All that time, it’s been gnawing at me.

It’s been gnawing at me that I had this project done, but that it wasn’t out yet. Especially because this was the project that I had gone to Australia to do in the first place.

And it’s not been for lack of trying. I’ve submitted this paper, in one form or anther, to about three different journals over the years. It was rejected every time. I may post the reviews later in a separate post. In a nutshell, one of the major issue that the reviewers had was that the data just weren’t conclusive enough. And honestly, I think they’re right. It drives me nuts that I wasn’t able to pin down what was happening with those two medial cell bodies. Reviewers of a different paper that used the same techniques called the methods, “old fashioned.” If they were old fashioned before, they’d probably be criticized as ancient or obsolete today (even though they let me answer the questions).

What could I do? I’m not in Australia, so I couldn’t get more Ibacus. There are no slipper lobsters around the South Texas coastline that I know of. There was no way that I can get any more slipper lobster data.

For a long time, I thought I would try to do the anatomy of the leg motor neurons from another unstudied crustaceans, like a shrimp. It would turn it into a broader comparative paper with more data. But... that wouldn’t shore up the weaknesses in the slipper lobster data. Plus, even if I did get more data from another species, that would take even more time – time spent when I have enough other irons in the fire. How long would it take before this project would be out? Another decade?

I still considered submitting the manuscript, more or less in the form I posted, to yet another journal and trying my luck. But I couldn’t figure out what was an appropriate one. Journals that used to publish crustacean locomotion stuff don’t do much of that now, mainly because the number of researchers in the field has contracted. I was considering submitting it to the forthcoming PeerJ when it opened, for instance. Even then, that I agreed with the limitations that the reviewers pointed out to me meant that I didn’t fancy my odds. Nevertheless, I’m confident enough in what I wrote that I bet that if I keep at it, sooner or later I could find a home for the paper. But do I want to put it out in the Chinese Journal of Irreproducible Crap? Is that any better than burying it in my back yard (if I had a back yard)?

Those, if you like, are the negative reasons to publish the slipper lobster paper on my blog: because it sucks so much that it couldn’t get past the gate at a real journal.

But there are positive reasons to publish it on my blog, too.

Because I am tenured, I have the good fortune to be free to experiment a little. I’ve been productive enough the last few years that whether this slipper lobster paper gets out or not is not going to affect my promotion prospects, any grant applications, my career advancement, etc. Having tenure is supposed to be a way for people to try risky things.

I thought, “Let’s try something new.”

Regular readers will notice that over the last year or so, I’ve been experimenting with different ways of doing my science. I’ve written about independent science. I’ve participated in #SciFund in addition to writing regular grant proposals. I self-published my Presentation Tips ebook on Amazon. Publish some original science on my blog? Well, why not?

As I wrote back at the start of the second round of #SciFund (new emphasis):

(S)o many scientists are still in the place artists were. We’re waiting to be chosen. Waiting to be given permission. Working and working and working in the hope of being given a shot at the big time by someone else with more money, power, and influence. ...

It doesn’t always have to be that way now.

After all, in the last year we’ve seen Rosie Redfield live-blogging her research on arsenic life, even before depositing a complete pre-print in arXiv. And all of that was okay with Science magazine, who published the final version. The rules for biological publishing are not as rigid as they were. Putting manuscripts out on the Internet for people to see is not the absolute kiss of death for publication in a journal that it used to be. I’m thinking my blog post is functionally equivalent to a pre-print on arXiv. Maybe at some point, I can still get this into a real journal. (Hope springs eternal.)

I’ve also been paying attention to the people who say that scientific publishing is broken, and we should blow it up and start over. Lot of those people are basically advocating what I just did yesterday: “just blog the paper.” (The list of influences here is long and varied, and I can’t pull up all the relevant names, posts, ideas and such right at this moment.)

Could blogging research work? We won’t know until there are a few people crazy enough to try. It’s not without precedent. Bora Zivcovic had a blog post of original research that eventually was cited in a paper in a peer-reviewed journal. (Also crustaceans, coincidentally!) [Correction: I got this exactly wrong. Bora was making the point that his post was not cited. Redfaced that I didn’t re-read his post entirely.]

This paper was a good one to try for the experiment. As a scientist, you have to develop a gut instinct for evaluating your own work. Is this publishable? If I was reviewing this, what would I want to see? My instincts told me this paper was stuck in an uncomfortable zone between “publishable” and “shouldn’t see the light of day.” There’s enough good about it that I want to share it, but there’s enough shortcomings with it that I know it would be a continuing struggle to go through traditional scientific publishing.

I do not plan on doing this routinely. It was this very particular set of circumstances with this particular project that led me to try blogging it.

The problems I’ve had getting my slipper lobster paper published are far from unique. People talk about the “file drawer” problem: projects that were never published because they were negative results, or weren’t significantly novel, weren’t published fast enough to avoid getting scooped, or any number of other reasons. There might be a single experiment that that the reviewers think is inconclusive, so you take that out of the final manuscript, even though it might be a clue to other researchers. What do you do with all that data?

Figshare is partly a reaction to, and solution for, problems like this. It allows people to put up datasets and figures and such that wouldn’t going to make it into a paper on their own. (The two key data figures in yesterday’s post are on Figshare and have DOIs, making them citable on their own.)

But I wanted to do more than share the figures. I wanted to tell the scientific story. I wanted to give context to those figures. So, I’m trying this with a blog post.

Do I have concerns? Hell, yes. Another thing I’ve written routinely about on this blog are problems of archiving.

While I was converting the manuscript to blog format yesterday (almost as intense as if I were getting ready to submit it to a journal), I was updating the references. I was pleasantly surprised; almost amazed, honestly. Almost every paper was online, with a DOI, and a PDF. The exceptions were book chapters and a couple of now defunct journals. A lot of them did not used to be online; I know, because I’d checked. The commercial publishers have done a fine job in digitizing those back issues, and making a lot of that old literature more readily available than ever before.

I am worried about that blog post being ephemeral. I do plan to put up a PDF on my home page, and will probably deposit copies to my university library, too. Any other suggestions would be welcome.

Ultimately, I published the paper on my blog because it wasn’t doing anyone any good sitting on my hard drive. It may still not do anyone any good (it is pretty darned specialized, and there are not as many crustacean neurobiologists as there once were), but at least now the chance is more than zero.

Okay, everyone. Fire away. I know people are going to have opinions on this. Indeed, I bet that this will be like the situation where the DVD bonus features are more interesting than the actual movie: more people will care that I posted a paper on my blog than about crustacean motor neurons. And that is just one more positive reason to do it: publishing a paper on a blog is still unusual enough to be worth talking about. Another paper in a niche journal isn’t. Conversation starter, publicity stunt, call it what you will: I plead guilty.

Did I give up on trying for a peer-reviewed journal too easily? Am I showing the way for how science publishing will be done in the future? Am I crazy, or just completely crazy?

Related posts

The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae)

Abandonment issues by Al Dove (the homeless paper I mention in the postscipt was the one I posted yesterday)

External links

Why or why not cite blog posts in scientific papers?


Circadian Rhythm of Aggression in Crayfish

References

Faulkes Z. 2004. Loss of escape responses and giant neurons in the tailflipping circuits of slipper lobsters, Ibacus spp. (Decapoda, Palinura, Scyllaridae). Arthropod Structure & Development 33(2): 113-123. http://dx.doi.org/10.1016/j.asd.2003.12.003

Faulkes Z. 2006a. Digging mechanisms and substrate preferences of shovel nosed lobsters, Ibacus peronii (Decapoda: Scyllaridae). Journal of Crustacean Biology 26(1): 69-72. http://dx.doi.org/10.1651/C-2628.1

Faulkes Z. 2006b. The locomotor toolbox of spanner crabs, Ranina ranina (brachyura, Raninidae). Crustaceana 79(2): 143-155. http://dx.doi.org/10.1163/156854006776952874

Faulkes Z, Macmillan DL. 2002. Effects of removal of muscle receptor organ input on the temporal structure of non-giant swimming cycles in the crayfish, Cherax destructor. Marine and Freshwater Behaviour and Physiology 35(3): 149-155. http://dx.doi.org/10.1080/1023624021000014734

Faulkes Z, Paul DH. 1997. A map of the distal leg motor neurons in the thoracic ganglia of four decapod crustacean species. Brain, Behavior and Evolution 49(3): 162-178. http://dx.doi.org/10.1159/000112990 [Note: Yesterday’s post will make a lot more sense if you look at this paper.]

Patullo BP, Faulkes Z, Macmillan DL. 2001. Muscle receptor organs do not mediate load compensation during body roll and defense response extensions in the crayfish Cherax destructor. The Journal of Experimental Zoology 290(7): 783-790. http://dx.doi.org/10.1002/jez.1129

Photographs by David Paul.

06 September 2012

The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae)

Zen Faulkes
Department of Zoology, University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia

Current address: Department of Biology, The University of Texas-Pan American, 1201 W. University Drive, Edinburg, Texas, 78539, U.S.A. Email: zfaulkes@utpa.edu

Ibacus peronii (left) and Ibacus alticrenatus (right). Photographs by David Paul.

Abstract. To test whether palinurans share a common ground plan of distal leg motor neurons with other decapod crustaceans, I examined the distal leg motor neurons in the scyllarid species Ibacus peronii and Ibacus alticrenatus. By backfilling the distal leg nerves individually, a total of about sixteen cells fill are seen, distributed in three clusters in the ganglia: an anterior cluster of about twelve, a posterior cluster of three, and a single medial cell. Although one medial cell fills when distal leg nerves are filled separately, two cells that are similar to two medial inhibitory cells in non-palinurans are visible in more proximal fills. The neural map is similar to those described for other species, suggesting that the distal leg motor neuron grand plan is conserved across reptantian decapod taxa.

Key words: decapod crustaceans, evolution, neuroanatomy, pereopods, walking legs

04 September 2012

Tuesday Crustie: Baby pictures

If you look at someone’s baby pictures, you might have a hard time matching them to photos of that person as an adult. Recognize this person?


Or this one?


And you have it easy with humans. Humans don’t undergo metamorphosis or anything. Unlike this wee beastie:


ResearchBlogging.orgThis crustacean baby was described from the stomach of a dolphin way back in 1828. Just for perspective, Charles Darwin was still in university at the time, and his voyage on the H.M.S. Beagle was still a few years in the future. Because this species had these big horns and elaborately armoured exoskeleton, it was named Cerataspis monstrosa. You can probably recognize the second half of its name means “monster.”

At the time, it wasn’t clear that this was a larva, which obviously hindered a more definitive identification. But there was a bigger problem: it was just rare. So even as new genetic techniques were developed, Cerataspis monstrosa was not found in usable condition. Bracken-Grissom and colleagues, in a forthcoming paper, seem to have had just one Cerataspis monstrosa from to take DNA from. They used that DNA try figure out if it was a larval form of a better known crustacean.

The DNA work was tricky. They tried several times to use a sequence of DNA often used for barcoding, and failed repeatedly. Fortunately, other regions of the genome worked.

Thanks to Bracken-Grissom and colleagues, we now know that that turns into this:


This is Plesiopenaeus armatus, which is a very deep water living shrimp. Bracken-Grissom and colleagues give records of it living in waters of more than 1,000 m deep.

So what of Cerataspis monstrosa? Bracken-Grissom and colleagues recommend that the larva be given the adult name – Plesiopenaeus armatus. This is not a done deal, however. The larvae got their name first, and that would mean that it would normally take precedent. The authors note that they are applying for an exception to the rule on the grounds that the adult for the genus is much more often used, so renaming the genus from Plesiopenaeus to Cerataspis would cause unnecessary confusion.

Oh, and as for the human baby pictures above? They are, in order:


Harrison Ford, and...


Tobey Maguire.

Reference

Bracken-Grissom HD, Felder DL, Vollmer NL, Martin JW, Crandall KA. 2012. Phylogenetics links monster larva to deep-sea shrimp. Ecology and Evolution: in press. DOI: 10.1002/ece3.347

Larval photo from here; adult picture from here.

Harrison Ford pictures from here.

03 September 2012

Save Siccar Point


This is Siccar Point. This is where we first learned that the Earth is ancient. Not just old, not just thousands of years, but so old that it seemed almost to have been around forever. It is arguably the birthplace of modern geology. The concept of an ancient Earth was important to Darwin’s thinking about evolution, too.

Now, there is a proposal that could damage this incredibly important location by digging a trench across is and filling them with concrete. Learn more here, including ways you can lodge objections.

Here’s the email I sent:

I'm an biologist and educator. I tell my students about the importance of Siccar Point in the development of science, and how geologists used Siccar Point to demonstrate the great age of the earth. That Siccar Point taught us something so fundamental about the history of the planet makes it a scientific landmark. As such, it should be preserved as best as possible.

Consequently, I object to the plan put forward by Drysdales Limited, because I am concerned about the potential damage done to this historic geological formation.

I think Siccar Point should be something like a World Heritage Site.

Photo by arvidbr on Flickr; used under a Creative Commons license.

How students see scientific publishing, part 2

It’s fascinating to see how outsiders think a process works compared to how it actually works.

Like last year, I asked my biological writing students, “What happens to a manuscript between the author finishing writing and it being final form that an audience can read?” I asked them to make a little flowchart. This year, there seemed to be greater understanding that there was some sort of review, though only about half specifically mentioned peer review.

Like last year, students were uncertain about who was doing the reviewing. Some people said publisher, some said editor, and some said reviewers.

One of the more interesting points in discussion, though, was when I asked them, “Who makes the decision about whether a paper goes into a journal or not?”

The students were unanimous in their opinion: the publisher decided if an article was accepted for a scientific journal. They thought the role of the editor was to check for grammatical errors, consistency, and things like proper comma usage. And students considered the reviewers to be more like fact-checkers, rather than people evaluating things like the significance of the work, experimental design, and other bigger picture stuff.

I tried to explain that in scientific publishing, a “publisher” usually refers to a large entity, like a large multi-national for profit corporation or a non-profit organization. Individuals are rarely publishers, and publishers don’t have much say in day-to-day decisions. I don’t interact with publishers directly when I submit a manuscript; I’m getting emails from editors.

The names of the titles are no doubt contributing to the confusion here. It’s so logical to think that a decision to publish would be made by a publisher. Students hear us talking about editing manuscripts, and think that the language crafting is all the job entails.

I wonder at what point a student working in the sciences figures out how the publishing system works. At the undergrad stage? Early graduate career? Late career? Whenever that first manuscript goes out?

When did you figure out how a manuscript turns into a paper? And did you get someone explicitly telling you, or did you figure it out by example?

Related posts

How students see scientific publishing

01 September 2012

Comments for second half of August, 2012

A post on Impact Factors at Reciprocal Science has a big ol’ comment thread, and I’m part of it!

How academics can create an online presence. Was surprised that someone’s first recommendation was... LinkedIn? Haven’t met anyone who’s gotten much out of that (and I say that as someone with a profile.)

The Tracing Knowledge blog talks about evidence of insect photosynthesis.

Life After Thesis wonders why more academics aren’t online in a significant way.

Hot button topics in science are tricky issues, as Unofficial Prognosis discusses.

Mike the Mad Biologist asks who we need to persuade to make changes to scientific publishing. (Hint: Follow the money.)

Neuropolarbear ponders whether to discuss the old science or the new science in his presentations.

Pondering Blather looks at the ever decreasing security afforded by tenure.

Neuroskeptic says that replicating experiments is not the critical thing to worry about in making a science credible.

Steve Caplan at No Comment tries to defend the idea that journal names are a good proxy for the quality of individual papers within, on average. I remain unconvinced.

Scott Berkun be hatin’ Prezi. I zoomin’.