31 January 2010

Comments for second half of January, 2010

Janet Stemwedel, a.k.a. Dr. Free-Ride, asks at Adventures in Ethics and Science about leniency for students caught cheating. I advocate consistency.

Professor in Training continues talking about what potential tenure-track faculty should look for after getting a job offer. I add three points.

Blue Lab Coats picks up from Professor in Training and on my post about lab personnel; I stress the variation across institutions.

At On the Market, Doctor Becca asks why other postdocs are not writing about their job search experiences. Perhaps because a couple of apparently pseudonymous descriptions were not as discreet as the author hoped?

Doctor Becca also asks for some input on some popular science writing she did. Remember, she asked, and I’m just trying to help.

At The Tree of Life, Jonathan Eisen doesn’t like “connectome.” What else you got?

Biochem Belle ponders what makes an undergrad institution create a doctoral program. Tough to say, but it seems ill-timed, to say the least.

30 January 2010

Journal Club vs. Ethics Bowl

Study in contrasts yesterday.

We had the first meeting of Journal Club yesterday. A paper had been sent by email earlier in the week, and we moved the time forward a bit to try to make it a bit more friendly to students.

Start time rolls around, and there are six faculty and one student – the one who picked the paper for discussion.

Another student shows up about 10-15 minutes late.

Last semester, when we had a few more students showing up, it was often like trying to pull teeth to get student to venture an opinion.

After Journal Club, I drove down to a coffee shop where there was a meeting of the Ethics Bowl team. Our university placed in the regional competition, and will be competing in the national competition in March.

By the time I got there, there was the team’s coach and about five students involved in animated discussion of the cases. A few more students showed up a later. People occasionally have to be reminded to let the other person talk.

And the score at half-time:

Ethics Bowl, several hundred; Journal Club, nil.

It’s damned depressing. I crave that intellectual back and forth in our department. I’ve tried to encourage it and foster it. And apparently I have earned a great big fail on that count.

Single use clothing

Mitch at Chemistry Blog describes his postdoc interview. He writes:

Lesson #3
You need to wear a suit.

I never get why academics insist on wearing clothes to an interview that they’ll never wear again if they get the job.

Image from here.

29 January 2010

More journals that smell like spam

A while ago, I shared a loopy email from an Indian scientific publisher asking me to publish in their journal. I got another one, and it’s an interesting study in convergence. For entirely different reasons, this one also convinces me not to take it seriously.

This is a group called Science Publications. The email they sent is actually simple, clean, and correctly spelled. Although that it’s signed only by “Editor,” not a person with, you know, a name is a bit of a worry.
Since I do neurobiology, I had a look at the American Journal of Neuroscience. And almost every page on that website makes my bullshit detector ping.

  • The current issue has exactly one article. For a journal that is supposed to be published every six months, one article is a pretty slim haul.
  • Claims to be at volume 6, but clicking the “back issues” page shows nothing of volumes 1 through 5.
  • The editorial board contains three people. No institutional affiliations are given. Compare this to the journal Neuroscience, which lists an editor-in-chief, an associate editor, seventeen section editors, and seventy-three members of the editorial board, and each one has an institution listed by the name.
  • The authors’ instructions refuse to accept references that are not on the internet.
  • The critical page is, naturally, “Method of payment.” So, there will be a fee for publishing or processing or something. But they don’t tell you how much it is. If it’s on the site, it’s hidden pretty deep.

That’s one journal. Another annoys me by spelling “online” as “OnLine” in its title: a weird compound neologism that nobody uses.

It’s be great that the publishing revolution creates the potential for new journals. But from a research author’s point of view, it’s the wild, wild west out there. And it’s not clear yet who are the honest settlers and who are the cattle barons and con men.

Credit convergence

Bora Zivkovic, he of A Blog Around the Clock, Open Laboratory and Science Online unconferences, beat my Science letter to the punch by about two years.

Maybe more indication that this is an idea whose time has come?

28 January 2010

Food fit for a king

You know what one of the good things about being a boss / mentor / educator / professor / teacher / supervisor is?

Sometimes, you get students who are more excited over something than you are.

And they remind you that maybe you’ve done something kind of cool.


Thanks, Sakshi.

I got this in celebration of my letter in Science and in tribute to this post.

Letter in Science!

The kind of research I do very rarely gets in the so-called “glamour magazines” of science, so this is likely to be the only time I get anything in a major weekly scientific journal.

My letter is in response to an editorial by Science’s editor-in-chief Bruce Alberts earlier this month (Alberts B. 2010. Promoting scientific standards. Science 327: 12. http://dx.doi.org/10.1126/science.1185983). I propose that credit in scientific papers might be better served by using credits for something like cinema instead of literature.

The PDF is behind a paywall, but you can listen to it on the podcast! It is dead last, but if you want to use the wonders of fast-forwarding, you’ll find it at 29:48 from the start.

I’m pretty pleased that I submitted it as a letter instead of just blogging about it.

Faulkes Z. 2010. Taking a Cue from the Silver Screen. Science 327: 523. http://dx.doi.org/10.1126/science.327.5965.523-a

Follow-up posts

Credit converegence

Chittin’ and chattin’ with Open Lab 2009 editor, Scicurious

The Open Lab 2009 anthology of science blogging will soon be upon us, and in the throes of making revisions and such for my entry, I asked if the editor, Scicurious, would take a few minutes to answer a few questions. She graciously agreed!

How did you get the job of editing this year's Open Lab anthology? Did you seek it out, or were you approached?

Bora (Zivcovic) actually asked me to edit this year’s edition, and I was really flattered that he asked. It’s been a big job to live up to, and it’s definitely been a learning experience, but I’m very glad I said yes.

How do you and the judges sift through the hundreds of entries to come down to 50?

The judging process varies from year to year. This year I parceled out posts (no one got their own, obviously) to the judges and had them score for the first round, and then took the top scores to narrow it down for the second round. It was a very difficult process, and the final 50 were very hard to pick!

How important is the mix of selections for the anthology? Do you consciously try to balance out, say, “life as a scientist” posts with pure “research analysis” posts?

We do try to achieve some balance, because I’m sure if you wanted to, you could have an entire anthology on the evolution/creation debates. We wanted a good balance with representation of what went on during the year, but we also just looked for some great examples of writing. But of course, we can't consider a post for inclusion unless its submitted. So if we had low numbers of, say, neuroscience posts submitted one year, it might be harder to get a balance. All the more reason to submit lots of posts for next year! Make sure your stuff gets good representation!

I’ve already started a list of posts made in December and January that I plan to nominate for next year!

What changes get made to posts in the transition from blog to book?


Well, the biggest change is obviously the links, and of course any photos that the writers don’t have the rights to. We also need to look carefully at context, we don’t want all the posts to begin with “so last week there was this blow up in the media/blogosphere/the scientific world.” Other than that, I have been working very hard to make the transition easy, and to stay relatively hands off with editing. What makes so many of these bloggers so incredible is the unique voices that they bring to the table, and so I try to make sure that that unique voice and point of view comes through in the final piece.

Has being the editor for this project been easier or harder than you expected?

I’d say it was about as much work as I thought it would be, thought it has entailed a little more cat-herding than I expected! But I’ve learned a lot that I think will be useful.

Even an editor is allowed to have favourites. Is there any particular entry that you have a soft spot for? (Your own post and mine are exempted from this discussion!)

I might have a favorite or two, but I won't say until it’s out!!

Thanks Sci! Scicurious blogs at Neurotopia.

27 January 2010

Dinosaur colours – more exciting than an Apple tablet!

Called it!

Here’s the story in Nature. Really surprised it’s not the cover story, frankly.

Ed Yong breaks the news on Not Exactly Rocket Science.

Movie rentals and journals

There is an online DVD rental business that bothers me. First, this business stinks up the net with pop-under ads. Argh! Haven’t businesses learned how irritating those are? Why can’t you just buy banner ads, you maroons?!

I also dislike that it forces me into paying for a recurring monthly subscription. Why won’t you let me just rent one movie?!

And yet... I have a subscription and do business with this company. Despite my annoyances (and the ads do annoy me – a lot), they are pretty much the only business that does what they do. They provide a service that is useful to me. So I hold my nose and pay their subscription fee.

This parallels my attitude towards many research journals, particularly regarding open access. I would like it if journals were open access, just as I would like it online DVD rental business wouldn’t buy those damned pop-under ads. But a lot of those journals do provide useful services. They do good jobs on the editorial side, good production values, and good distribution, even if not open access.

There are some researchers who advocate never publishing in any journal that isn’t open access. But how much perfection do you demand in any product?

26 January 2010

Tuesday Crustie: Oh yes it is



Since last week I put up a picture of something claiming to be Blepharipoda occidentalis, but wasn’t, I thought it was only fair to put up something to show what the spiny sand crab really looks like.

I know the image isn’t great, but converting photos to digital when I was a grad student wasn’t as easy or as good as now.

Academic reproduction

Continuing with yesterday’s theme about expectation rifts and institutional diversity, Mike the Mad Biologist inadvertently provides another example of how the situation at Major Research Universities dominates discussions. He writes a piece about how funding generates excess numbers of scientists.

As long as the economic incentives are for academic researchers to produce far more PhDs than are needed to replace themselves**, we will continue to have this problem. ...

** Even a modest training regime – let’s say, one student for a six year period with no overlap between students – will result in five students during a faculty member’s career.

What is missing from this analysis, though, is a population view. The size of a population depends on birth, death, immigration, and emigration. The quote above focuses on just one aspect of that: academic “birth,” and even that is incomplete.

To continue using the reproductive metaphor, not every academic “parent” will have offspring. Indeed, many academics, because of the institution they are at, will never train a Ph.D. student in their life. We have a situation much like that of highly competitive animals like bull elephant seals: you have super winners who have many offspring, and super losers, who have none.

Photo from Flikr, used under a Creative Cpmmons license.

25 January 2010

The brown bear... of communism! Texas Board of Education's case of mistaken identity

I have not commented much on the Texas State Board of Educations review of standards other than science, because I claim no expertise in things besides science. But this story is too interesting not to pass on.

In its haste to sort out the state's social studies curriculum standards this month, the State Board of Education tossed children's author (Bill) Martin, who died in 2004, from a proposal for the third-grade section. Board member Pat Hardy, R-Weatherford, who made the motion, cited books he had written for adults that contain "very strong critiques of capitalism and the American system."

Trouble is, the Bill Martin Jr. who wrote the Brown Bear series never wrote anything political, unless you count a book that taught kids how to say the Pledge of Allegiance, his friends said. The book on Marxism was written by Bill Martin, a philosophy professor at DePaul University in Chicago.

A bad defense of two-sided science journalism

CBC journalist Stephen Strauss writes about a common complain from scientists: that when covering a science related story, journalists feel compelled to present “two sides” to an argument, even if one is crap, from a scientific point of view. Strauss writes:

I have a somewhat different take on the "other side" controversy. Part of the reason the media went looking for an opposite view on climate change was because two-sidedness was easy to convey.

On one side are most of the world's atmospheric scientists, who say that human-initiated emissions of greenhouse gases have started to seriously change the world's climate. On the other is a much smaller number of scientists who are saying that there is no evidence yet that humans are responsible for any of the slight warming we seem to have seen, and that future effects might not be so dire.

Participants in the debate can bring forward different amounts and examples of evidence, but there are definitely two sides to the issue.

Instead of defending this thread, though, Strauss then goes into a discussion of “wicked problems,” using cattle as an example. His example boils down to, “We know cattle produce greenhouse gasses, and there’s a lot of disagreement over how to manage that.”

And thus, Strauss misses the point entirely.

He confuses the small scale where the science is in progress with the large scale where the science is much more... emphatic, shall we say. (For I know I’ll get dog-piled, rightfully, if I say anything like “settled” or “certain.” Science doesn’t deal in certainties, and we must always admit when we could be wrong. Bring your evidence.)

The whole cattle story is something where I think it’s fair to say, the science is not settled. There are real difficulties in knowing what to do. I don’t think you’ll find scientists who are going to call such reporting “two sides” on a small scale issue a problem.

What irritates scientists so profoundly is the insistence on “two sides” on the big picture issues. In the case of climate change, the big picture are that climate is warming due to burning fossil fuels. Strauss does not appear to contend this point.

But it’s on reporting of this big picture where scientists get mad – where the expertise of people actually doing real science (collecting and analyzing data) is always sharing space with flat-out denialists: people from “think tanks” who either deny climate change is happening, or deny that fossil fuel burning is causing it, or deny that it’s a problem. Strauss need look no further than the comments to his article, where commenters have tossed around accusations of fraud and conspiracy by scientists.

By way of analogy, scientists contending that the earth is round get annoyed when the media brings in a flat-earther to show there are “two sides” to the story. Strauss would seem to justify the flat-earther presence by pointing out the difficulty in measuring exactly how much wider the Earth is around the equator than the poles.

The expectation rift and institutional diversity

There’s been some good posts at Professor in Training and Blue Lab Coats that I’ve been commenting on. I also riffed on this a bit last week. What stands out to me is just how divergent people’s expectations and experiences in starting a lab are.

What some people take for granted as things new faculty must have to survive as scientists are pipe dreams for other people. And it seems to be difficult to convince some people that such variation even exists out there in the university ecosystem.

Many students starting in doctoral programs expect that they are going to go down the same track as their boss: running an externally funded lab. But, according to the recent National Science Foundation Science and Engineering Indicators 2010 report:

Academic institutions employed about 42% of individuals with S&E doctorates, including those in postdocs or other temporary positions.

That’s all academic institutions, not just the major research universities. There are a lot of questions that data set doesn’t answer, but the point remains that staying in academia is not the most common thing people do with doctorates. Supervisors do bit of a disservice to their doctoral and postdoctoral fellows if they don’t convey the other options that are out there. (In some ways, I can’t blame the supervisors: they often don’t have experiences at other kinds of institutions besides big research intensive ones.)

The more I thought about it, the more I wondered if the science blogosphere is tilted towards discussing research at particular kinds of institutions. I read a lot of blogs that are set at euphemistically set at MRU (Major Research University), where the complexities of how to get R01s are dissected in detail, and papers seem to be headed for Science or Nature.

This got me thinking about diversity. The much praised Science Online 2010 conference contained a panel on diversity in STEM, which is mainly concerned with racial, ethnic, and gender issues. Something that comes up as a virtue about blogging is that it can help people, particularly those who are in a minority of some sort, “normalize” their experiences. “Wow, it’s not just me, other people run into the same problems.”

I want to put forward a case for the importance of institutional diversity. (Bad term for it, but can’t think of something better yet.) My impression is that there’s not a lot of science bloggers writing about the experience of doing research at institutions that are not massive research players at the national or international level. It’s important for researchers at such places to do so, because researchers at such places are already marginalized, career wise. I am not saying that the level is anywhere near like the sort of marginalization that can be experienced by, say, a racial minority; just there are similar underlying patterns of behaviour.

A researcher could be looked down upon for not aspiring to become a R01 funded PI at an MRU. Those who did aim for such a job, and didn’t get it, might feel that they are a failure. Ideas or advice from someone at a research extensive university may not be taken as seriously as that of someone from an ostensibly more prestigious, or older, or bigger, or better-funded institution.

Just as a seemingly innocent question like, “When are you two having kids?” can bring along with it all sort of soft-pressure social expectations, so too can “How many postdocs do you have?” emphasize expected norms.

23 January 2010

Histology hazards

On Twitter, I commented, “When I do histology and see what the chemicals do, I am amazed that more people in the field didn't manage to kill themselves.” Here’s the kind of stuff I’m talking about.


Those were originally two separate pieces. Culprit: Propylene oxide.


The one on the right started off looking like the one on the left. Culprit: Osmium tetroxide.

22 January 2010

How I lost and what I’ve learned

P.Z. Myers wrote recently that he started the Pharyngula blog in 2003. Considering that this is one of the best known and widely read science blogs, I thought to myself...

“How did I screw up?”

I’ve been blogging since 2002. That puts me on the “online science” map early, and I missed some opportunities. It took me a long time to figure out what I’m doing. I really only got serious about it in the last two years, and it took more than a year before I started to feel the work pay off. Here’s some of the things I’ve learned.

1. I’m not interesting. A lot of earlier posts were of the “Here’s what’s going on with me for the last week” variety. Meh – who cares? Increasingly, I think that while I am not interesting, I can use my knowledge to tell interesting stories. Participating more in Researchblogging.org has been very helpful in this regard.

2. A blog should be an offer to help, not a cry for help. Corollary to the above. When I started writing more outward looking posts, I started getting more feedback.

3. Blogs are a waste of time... but not a complete waste of time. Blogging is inefficient. There are lots of other things out there to look at, so it takes time and hard work to build an audience.

4. Community. Posting on other people’s blogs and being on Twitter have helped me slowly find some like-minded souls, who are often kind enough to spread the word when I get something right. I’m not a chatty guy, and networking is not something I do easily or naturally, but it’s been very rewarding.

Speaking of community, BioChem Belle also had a nice post on social networking. If you're a scientist, go take her poll!

I’'ll also take this moment to point to Chad Orzel, who’s also been blogging since 2002, talking a bit in Inside Higher Education article about why he blogs, and how it led to his writing a book.

21 January 2010

No postdoc? No problem!

Professor in Training tries to warn people starting tenure-track what they’re in for (second installment here). Unsurprisingly, the first two points both revolve around money, and a big chunk of that concerns postdocs.

For those of you who one day hope to be tenure-track, have you thought about what you can do if you can’t have postdocs?

Your first response might be, “I wouldn’t take a job where I couldn’t have a postdoc.” Are you sure you want to limit your opportunities that much? Especially in the current economy?

You can survive and conduct research without postdocs, but you have to think about it. It’s very helpful to have ideas for $5 projects in your pocket as well as $50,000 projects. There’s a lot of research that can be done with time and elbow grease instead of big bucks.

Undergraduates can be awesome in the lab. The trick is to recruit them early, in their first year. That way, you have the potential to work with someone for three or four years. Still, you can get a lot of good work with people who are around for a year.

There are programs a-plenty to support undergraduate researchers, both financially and intellectually. Beta Beta Beta publishes a journal of undergraduate research. If the work with an undergrad student goes well, some might stay for graduate work.

Institutions that don’t have postdocs are also unlikely to have doctoral programs, but there are often master’s programs. Master’s students have more experience, but the turnover rate is often faster than for undergraduates. There are also far fewer funding opportunities than for undergraduates or doctoral students.

Big labs in big universities train so many people that they get to think that those are the one and only model for scientific success. That does not need to be the only way to do research.

20 January 2010

Dinosaur colours next week?

Back in grad school, I remember reading a comment by paleo artist David Paul, who said something to the effect of, “In reconstructing dinosaurs, what colour they were is the most asked, the least important, and the least knowable.”

Fast forward to September, 2009. Carl Zimmer posts on his blog, The Loom, “Old Colors: First Birds, Then Dinosaurs?”, which ended with a great big tease:

There are now lots of dinosaur fossils that have what just about all scientists agree now are feathers. If they’re preserved well enough, you should be able to put them under a microscope and see melanosomes. And if you can make out their patterns…

Stay tuned.

And I thought, “Does the good Mr. Zimmer know something about this that I don’t?”

And then, today’s Nature podcast ended with:

Next time, tune in for news on coloured dinosaur feathers...

Ack!

I cannot tell you how much I am awaiting next week’s issue of Nature.

Epidexipteryx hui

Mulling over certainty and uncertainty in teaching

I start teaching general biology today, one of the largest introductory classes on campus. This class focuses on biochemistry, cell biology and molecular biology.

And I so badly want to tear it down and start again from scratch.

One of the traditional marks of an education is having facts internalized, at your fingertips. But this article hits on some of my frustrations:

Too many college students are introduced to science through survey courses that consist of facts “often taught as a laundry list and from a historical perspective without much effort to explain their relevance to modern problems.” Only science students with “the persistence of Sisyphus and the patience of Job” will reach the point where they can engage in the kind of science that excited them in the first place, she said.

And I’m as guilty of that as the next guy. I tell students, “This is how it is.” It’s a simple, straightforward thing to do: be a tour guide of information. “And over on your left, you’ll see the valence electrons...” And I’m grateful to this post on Usable Learning that has computers in the title, but is really about pushing the notion that there must always be right answer.

That’s another, increasingly important mark of an educated person: being able to cope with situations where there is no right answer.

I think one way to get comfortable with uncertainty is to really get at the way evidence is gathered and analyzed. By looking at process. I want to figure out how to show students evidence. I want to be able to say, “Okay, here’s how we know that there are these steps in glycoloysis,” or, “This is how we know there are three binding sites in ribosomes.”

Many textbooks say they showing process, but it’s usually splashed in here and there, in teensy pieces. And I can see why. If I were to try to figure out those original experiments that worked out the pathways in photosynthesis, I probably couldn’t do it. And I’m not sure if it’s worth it in a lot of cases.

On the one hand, I do want students to have a certain amount of material internalized, because I think you need that intellectual infrastructure. But I think they’re not getting anywhere near enough practice with dealing with analysis to prepare them for tackling new problems. I’m completely conflicted.

19 January 2010

Tuesday Crustie: Oh no it isn't

Occasionally, as an academic, you have these moments of shock, when you recognize something that you have personally worked on and that you know about. These moments are often followed by disappointment, when you realize that it is completely wrong.

I was walking along the walkway on the South Padre Island World Birding Center, and come across this on a sign.



I was so pleased to see the name of the species I spent about six years working with for my Ph.D., and published four papers about: Blepharipoda occidentalis. And Blepharipoda are sometimes called mole crabs, though they more typically called sand crabs.

Then, the disappointments start.

First, that picture is not Blepharipoda occidentalis. That picture is probably some species of Hippa, which is not even in the same family as Blepharipoda.

Second, Blepharipoda occidentalis is a species that lives in California, not the Gulf of Mexico.

Third, there are no species of Hippa on South Padre Island, either. There are mole crabs on South Padre Island, but they’re Lepidopa and Emerita.

So this sign is wrong at least three different ways. The sign had the logo for NOAA on it. It’s surprising, because agencies like this usually have access to experts and the scientific literature.

And in among realizing all this, you also realize that you’re one of maybe a half dozen people in the world who would know or care.

Photo by Kevin Faulkes. Thanks, Dad.

18 January 2010

Chittin’ and chattin’ on South Padre Island next month

If you happen to be around South Padre Island in a month or so, please come see my talk about things that live in the beach. It will be Saturday, 20 February 2010, 11:00 am at the South Padre Island Birding and Nature Center.

There are several other presentations by my colleagues in January through March; a list is here.

They’re free and non-technical.

The journal article... of the future!

ResearchBlogging.orgElsevier is trying a new format for research articles here and they are, somewhat pretentiously, calling it the “article of the future.” It’s always risky to attach “future” to these sorts of things, as it tends to get people bitching that they don’t have their flying cars and personal jet packs yet.

As far as I can tell, Elsevier’s experiment seems to be confined to one of its big flagship journals, Cell, for now. An example is here, which I like because it has brains (click to enlarge).



What problems of the traditional research paper are they trying to solve? An editorial says:

(W)e have worked to develop an online format that breaks free from the restraints of paper and allows each reader to create a personalized path through the article's content based on his or her own interests and needs.

That’s supposed to be a problem? Of all the various media that I use, print is one of the easiest to create a personalized path. It’s called, “turning the page.” I guess the editors at Cell never read murder mysteries, so never experienced that thrill of knowing that you can go right to the end of the book find out who the killer is, without all that tedious investigative mucking about in the middle.

Let’s say I want to create a “personalized path” and read the introduction and discussion – very common thing for researchers to do. Notice the number of tabs at the top? I have to click, scroll through the introduction, scroll back up to the top of the page, locate the tab, click again, and start scrolling down again. Clicking through all the tabs feels like a lot of pointless work. Further, click one of the main tabs, and you are often presented with two more sub-tabs, one for the text, and one for the references.

The constant breaking down of the article into little pieces reminds me of David Pogue’s jab at wizards in his talk here (fast forward to 7 minutes and 50 seconds).



I much prefer the single page approach. I start at the top, and can just keep scrolling down. HighWire Press journals even provide a little shortcut menu at the top of each section, making it easier for me to jump to the next section I want to read.

Tabbed and hyperlinked navigation through the Introduction, Results, Figures, Experimental Procedures, and Discussion allows subject-area experts to quickly access in-depth information on a particular experiment while providing more general readers an opportunity to absorb the conceptual insights without being overwhelmed by additional details.

Let the skimmers be lazy while still providing details that experts demand? A good abstract does that. Again, this feels like a solution being offered to a non-existent problem.

(A) film strip of thumbnails for all of the figures... allows a reader to rapidly scan through the data and then connect from an individual figure to the related textual discussion of the findings.

This is under a tab called “Data,” rather than “Figures,” since it can include spreadsheets and the like. I’m neutral to this. It neither seems to add value or to be annoying.

The Results tab lets the reader view a zoomable figure, the legend, and associated Results text easily on a single screen.

Keeping the text and relevant figure visible side by side at the same time is a excellent idea, but it’s hamstrung here with a horribly clunky execution. The results break down into three skinny columns: one for text, one for the figure legend, and on for the figure caption. The text column is so skinny, it forces me to do more near-constant scrolling. I want to read, not scroll. Reading is made even harder because paragraphs aren’t separated by either spaces or indents.

Highlights and a Graphical Abstract on the landing page of each article complement the traditional Summary text and promote article browsing by creating a visual summary and bullet points that easily convey the main take-home message of the paper.

Cell may be able to get good mileage out of the “graphic abstract,” because so many of their papers are all about cellular and biochemical pathways, so it’s easy to make a flowchart summarizing results. I’m not sure that this is something that could be used by other journals. Perhaps a better way to think about it is to think in terms of general “entry points”: images that can provide a way in for the reader. They may not have to be summaries, but something relevant like a picture of an organism, a field site, or a juicy pull quote.

(T)he online display fully integrates supplemental information including multimedia content within the context of the main article and facilitates more fluid navigation between the two.

Then why is it called “supplemental” at all? If it’s incorporated into the paper in the same way, present the data democratically. I suppose that it needs to be labeled as such because it’s material that won’t go into the print edition.

The treatment of references is one of the nicest additions. You can reorder them alphabetically or chronologically, and there’s a little sparkline at the top of the main reference section showing how the references are distributed by year of publication. You can also click to see how the article is cited in the text, which could be very useful in identifying interpretation problems, and so on. Very well done, and really does point a way forward in using references that I haven’t seen before.

Not showing the digital object identifiers (DOI) for articles in the references is nearly inexcusable, though. I don’t want to have to go through PubMed to get to an article, I want to go directly to the article.

There are audio and video clips, given the cutesy names of “Paper Flicks” and “Paper Clips.” One example of video I’ve looked at is a basically a mundane PowerPoint talk dumped to video. This does not interest me, personally. Video could be helpful if the actual material is highly visual, like movies of cells dividing or something.

They’ve also added a comment section. If the experience at other journals is anything to go by, they will sit and gather dust, for the most part. No rating system, though.

Finally, I like that they are offering a single PDF file that rolls in all the supplemental material. Very logical and sensible. I’ve often had to go digging for supplemental material, only to be confronted with multiple PDF files for me to keep track of.

My current analysis is much like my first impression: I’m unconvinced. The approach feels like someone with a hammer looking for a nail to hit: “We have these tools, so are there any problems we can solve with them?”

Apart from the ability to do a little impromptu data mining in the reference sections, and a convenient PDF, this “article of the future” feels needlessly complicated. It’s a little too early to tell, but I wonder if the “article of the future” might end up looking like predictions from old popular science and mechanics magazines.

“In the future, we’ll play polo... on motorboats!”

Hat tip to Dr. Doyenne.

Reference

Marcus E. 2010. 2010: A Publishing Odyssey Cell 140(1): 9. DOI: 10.1016/j.cell.2009.12.048

17 January 2010

I’m not saying you have to nominate me...*

Researchblogging.org is hosting a competition for, well, research blogging. And this is no “your prize is the recognition of your excellence” stuff, this is cold hard cash dollars up for grabs. Admittedly, most of prizes are just enough to pay a fine in Night Court, but the big prize for research blog of the year is a cool grand.

The nomination form is here.

Not sure how the category “Research Twitterer of the Year” got into a blogging competition, though.

* Though if you did, I would certainly appreciate it.

Hat tip to Dave Munger.

15 January 2010

It’s time for a new (rank) order

In the sciences, journal articles are probably the most important factor determining your career success. Much has been written about how to compare publications in different journals in different fields.

Currently, in our department’s evaluations, publications are weighted differently depending on what journal you publish in. We don’t use anything like impact factors, though. Journals are ranked as:
  1. International
  2. National
  3. Regional
In some disciplines, the idea of a “regional” journal may sound a bit strange. After all, chemistry is chemistry regardless of where you are. But in biology (and maybe geology?), there is often a niche for research that is tied to particular locations. So you have the Canadian Journal of Zoology or the Texas Journal of Science (where a lot of faculty in my department have published – including me).

But there’s always been these niggling difficulties. An international journal may actually have a smaller readership and reach fewer people than a national journal (at least in the United States).

Given how much distribution networks for journals have changed, a better rating of journals would be:
  1. Online and open access
  2. Online and behind a paywall
  3. Print only

Comments for first half of January 2010

Biochem Belle looks at post-doc salaries and asks, “Are departments so hard up?” Yeah, they are. She also does some thinking about social networking for scientists, and I put up a fairly long comment about why you can’t convince a skeptic that social networking is worth it.

Doctor Becca asked for a glance into what an email from a search committee chair might mean.

Endless Possibilities does not like conferences. I increasingly have a love hate relationship with them.

SciCurious at Neurotopia is annoyed that media outlets don’t provide citations when they’re covering new research. I point out that sometimes, researchers are the problem...

Professor in Training asks what people want to see on faculty websites and why anyone wants grant proposals on paper.

Zuska at Thus Spake Zuska really got me thinking with this post about Hispanics in higher education.

Dave Munger asks what makes a good blog or a failing blog. I suggest that a clear purpose makes for good blogging. The Better Posters blog exists to stop people putting up ugly posters at conferences. The Marmorkrebs blog exists to promote a research organism.

Susan Steinhardt on the BioData blog wonders if lab notebooks are obsolete; I extol paper’s track record.

Climate Progress looks at the recent article on Don McLeroy and company in The Washington Monthly with an eye towards climate science. A couple of commenters imply that the Texas State Board of Education influences university decisions; I point out they don’t.

14 January 2010

Gloating

Back in December, I publicly stated that I wanted to get three papers into the hands of editors before classes started again. I made it with a week to spare. I used that time to get a fourth paper off my desk and submitted to an editor. Add in a paper I submitted back in November, and that’s five articles on editor’s desks – a personal best, by a longshot.

Of course, that doesn’t mean that they’re all going to be accepted. But one of those five papers has already been accepted and is in press.

I also found out that one of my posts will be coming out in the Open Laboratory 2009 anthology, which I mentioned earlier.

And, just to put the cherry on top, I should have a letter coming out in a prominent weekly science glamour magazine. I’m glad I submitted it to the journal instead of blogging about it.

All of which leads me to think that this week, I have perhaps earned to right to say:

“KING OF THE LAB!”

13 January 2010

Boredom: bug or feature?

Playing some video games I got for Christmas reminded me how much of a game can be boring. I’m not talking about bad games, but games I enjoy and put in many hours to complete.

I’ve played many games where you spend large chunks of time doing nothing but trudging from one location to another. Not fighting enemies, not solving puzzles, not making strategic decisions, just... walking.

And heaven help you if you miss a room in the dungeon. Back you go, tromp, tromp, tromp... Couldn’t you give me a shortcut back to places, guys?

It got me wondering if the “down-time” of boredom is actually deliberately put into the games to make the high energy moments seem more exciting.

This thought wandered out and connected with a section in Randy Olson’s Don’t Be Such a Scientist, where he argues that it’s not reasonable to expect getting an education without a certain amount of pain – including the boredom of studying.

As an instructor, I am often pursuing engagement relentlessly. I am keenly aware of the need to compete for students’ limited attention. But I wonder if students might be a more tolerant to a little bit of boredom than they’re given credit for. Can a little boredom enhance engagement? Is there some optimal level?

12 January 2010

Tuesday Crustie: “The flavour of the day is...”

“...strawberry.”

It’s always great to see inverts in the news, particularly crustaceans, but I have some misgivings about the stories that made this pretty wee beastie news-worthy...



They’re calling it the “strawberry crab.” This goes to show that something as mundane as finding a new invertebrate (which happens all the time) can make world news if you can give it something that copy-writers can sink their teeth into. Don’t get me wrong – this is a very pretty beast, but so are many other crusties, as the regular “Tuesday Crustie” feature has tried to show.

This AFP wire story has been picked up by many news services, Stories about it can be found in the Times, the LA Times, the Telegraph, the Daily Mail and elsewhere.

But this is a bad example of how to proceed in science. The Times article says (emphasis added):

“We will formally announce the discovery in a thesis to be published in the quarterly Crustaceana published in the Netherlands,” chief researcher Ho Ping-ho said.

“Scholars at the National University of Singapore have also found a male Strawberry Crab on a Pacific island and made it into a specimen. We plan to jointly write the paper to announce the discovery,” he added.

If I was on the Crustaceana editorial board, I’d be mightily pissed.

It sounds very much like the technical paper hasn’t been written, or even started! It’s bad form to say, “This is where it’s going to be published,” before you have:

  • Completed the manuscript to journal specifications
  • Submitted for initial editorial review
  • Have had the manuscript peer reviewed
  • Receive the comments of the reviewers and make any requested changes from them and the editor
  • Get official acceptance from the editor; this is the absolute point you should get to, but there is still more...
  • Receive page proofs and check for errors
  • Submit proofing corrections

Journals reject papers all the frickin’ time. You can’t presume that your work is just automatically going to be accepted and published in general, much less in a specific journal. It implies that the journal lacks rigor, and that they’ll publish any old slop.

The Daily Mail article says:

Taiwanese crab specialist Wang Chia-hsiang confirmed Professor Ho’s finding.

No! Peer review is not asking one other person what he thinks. Wang might be close to Ho. There may be a conflict of interest there. I don’t know how closely Wang has scrutinized the material, or if others in the field will agree.

Several stories specifically mention how closely this animal resembles an already described species, Neoliomera pubescens. When you’ve got a putative “new” species – particularly in one of the more speciose animal groups in the world, with around 6,559 living species (De Grave et al. 2009) – that looks very much like an already described species, you have to:

  • Comb the literature thoroughly to make sure you’re not re-describing something that has already been described
  • Provide evidence that this falls outside the range of variation of Neoliomera pubescens

There will no doubt be rare cases where you want to get news out before the technical paper is published. But this is not one of them. It would not have killed anyone, or hurt anyone’s career, to do a proper job of the species description, have the paper accepted, and only then put out a press release.

Reference

De Grave, S., N.D. Pentcheff, S.T. Ahyong, T.-Y. Chan, K.A. Crandall, P.C. Dworschak, D.L. Felder, R.M. Feldmann, C.H.J.M. Fransen, L.Y.D. Goulding, R. Lemaitre, M.E.Y. Low, J.W. Martin, P.K.L. Ng, C.E. Schweitzer, S.H. Tan, D. Tshudy and R. Wetzer. 2009. A classification of living and fossil genera of decapod crustaceans. Raffles Bulletin of Zoology Supplement 21:1-109.

Open Lab 2009: Made it!

My post, “I want to be Carl Sagan, but can’t,” has been selected for Open Lab 2009, the annual best of science blogging anthology. Competition is fierce (final list of 760 nominations here), and I’m more than a bit surprised to have managed to get something included for a second year in a row. I am, as they say in Australia, chuffed.

Additional: And here’s the final list of those fortunate fifty that made the cut. Two posts my bio writing students short-listed made it in (You aren’t what your mother eats and Sleep paralysis). Plus, I see a few things I nominated also made it in. (No, I’m not saying which ones, because they may well have been nominated by other people.)

11 January 2010

eTextbooks

My quickie post about textbooks 50 years from now prompted this very good question from Philosopher's Mess:

Why isn't their a push in Academics to get of textbooks?

Indeed. It seems everyone else is thinking hard about ebooks and ebook readers (or “smartbooks”), as this article, and this blog post, and this radio interview (scroll down to part three) show. You thought the music industry freaked out about mp3s? You ain’t seen nothin’ yet.

That academics haven’t moved to ditch textbooks is a classic example of how universities are simultaneously the greatest engine for innovation in the world, and the slowest, least agile, most conservative institutions you’ll find anywhere.

Academics are like kids in dysfunctional families, in some ways: they repeat the patterns they they themselves went through. Because they had textbooks when they went through their undergrad training in the 80s (or earlier), they think it’s normal for their students to have textbooks.

Academics also obsess about standards. They like textbooks because they go through a fairly rigorous vetting process. Wikipedia? Barely a month goes by where I don’t hear a colleague ranting about Wikipedia. “It’s plagiarized.” “It’s unreliable.” “They (students) don’t understand that’s not a valid source...” So their response is to tell students, “Don’t use it at all,” rather than, “Here’s the ways to use evaluate what you find on Wikipedia critically, and use it as a way into literature.”

And in the back of people’s minds, there might be worries about obsolescence. They don’t want to be the person who bought Betamax and has a stack of 8-tracks in the closet.*

Books are one of the “most perfect objects ever invented,” so it is no surprise that people are reluctant to let go. People who love books as physical objects and mementos. Fine. Film didn’t kill theatre, television didn’t kill movies, and mp3s still haven’t managed to exterminate vinyl. But the old technologies have become occasional, premium experiences, not mass market.

Few people have such attachment to their introductory general biology textbooks, though.

I’ll try to explore this some more in a later post.

* And speaking of Wikipedia, I bet I’ve just sent a couple of people there by referencing Betamax and 8-tracks.

09 January 2010

It’s an election year

Another article about quarreling, divided Texas State Board of Education came out in the Dallas News. Eight of the Board’s 15 seats are up for election this year, so the entire fabric of the Board could change dramatically.

McLeroy and most political observers see the election as pivotal for the social conservatives – particularly with the board scheduled to adopt new science textbooks in 2011, new social studies books in 2012 and new health curriculum standards beginning that year as well.

And I have to hand it to Texas State Board of Education member Don McLeroy:

He is always quotable.

“If you're going to be in a political office, you have to promote your views, and I’m confident and proud of the stands I've taken and my votes on the major issues,” McLeroy said.

Emphasis added.

I was under the impression that in democracies, elected officials were generally tasked with promoting the views of their constituents, and that promoting your own views was the prerogative of dictators and tyrants.

08 January 2010

Shameless cross-promotion

I normally don’t cross-promote my other blogs. But I was pretty pleased with how the Better Posters checklist came out, and thought it might be worth mentioning here, in case a few of you missed it over the new year. There’s a PDF version here.



I was also pleasantly surprised to get a very positive response to yesterday’s post on the “arm’s length” test. So you might want to check that out, too.

07 January 2010

Misplaced confidence



The 7 January 2010 Nature podcast has an interview with Per Ahlberg, one of the authors describing some wonderful new old tracks – new to science, but dating from 397 million years ago. They’re fossil tracks of early tetrapods – which is the lineage including amphibians, reptiles, mammals, and bird.

About four and a half minutes in, Ahlberg says:

This is going to be in the textbooks fifty years from now.

And I thought, “Wow. He’s confident.

“I wouldn’t be so sure that textbooks are going to exist in fifty years.”

It will be a shame if we are still relying on “dead tree” compilations of old research to teach students fifty years from now.

A good summary of the tracks and their importance can be found here.

Cuttlefish camouflage split decision

ResearchBlogging.orgCephalopods are the masters of camouflage, as I've written about before. But what happens if they have to try to match two different backgrounds? Allen and colleague (containing several members who worked on the paper I wrote about earlier) tackle this problem with cuttlefish (Sepia officinalis).

There's a couple of possibilities. Because octopus and squid and such can control colour on each half of their body independently, they'll try to match both sides. Another possibility is that they will opt to match only one pattern, and the third option is that they'll opt for something half-way between both.

Cuttlefish match their colour patterns using vision, so the authors created a tank where each half had a different pattern on the bottom. The cuttlefish chose the compromise solution. When against a large checkered pattern and a uniform background, the animals picked something that could be described as a small checkered pattern.

This paper does some other experiments with substrate choices. When they tested more than one substrate at a time, the animals didn't have strong preferences. When given just two choices, cuttlefish like gray bottoms over white ones. But the key finding in substrate choices was that cuttlefish strongly prefer anything that lets them bury themselves.

Why bother trying to look inconspicuous out in the open if you can just hide?

Reference

Allen, J., Mathger, L., Barbosa, A., Buresch, K., Sogin, E., Schwartz, J., Chubb, C., & Hanlon, R. (2009). Cuttlefish dynamic camouflage: responses to substrate choice and integration of multiple visual cues Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2009.1694

06 January 2010

As Nigeria is to banking, India is to science publishing

I recently received this in my inbox. And I was all, like, “Whoa.” It was like I’d traveled back in time to the early 1990s and landed on an old GeoCities page. The explosion of typefaces and random colours, the spelling mistakes, the random religious element... slap on a page counter and some blinking text, and it would be indistinguishable.

But no, this is supposed to be from a serious scientific journal. Excuse me, “Joournal” (see third paragraph). I was definitely reminded of Bentham Publishers spam emails, but I think this surpasses Bentham’s standards.


Let’s start with the completely random assertion, first line, that “God is.” Is... is what? Even if you don’t make me reach for the delete key by mistaking this for some attempt at religious conversion, you’re just pissing me off with a sentence fragment! And how is a statement about God relevant to a scientific journal on biotechnology?

Putting titles in quotation marks can be okay, but here, it makes it look like a nominee for the “Blog” of “Unnecessary” Quotation Marks.

Then we get into the random typography. Text turns from black to blue, goes smaller, then normal, then larger, in crazed attempts at emphasis.

Then, the attempt to boost my ego. “As you are well known expert in these fields...” Please. I have some knowledge of my own science, and my own standing in the field. I’m not a biotechnology researcher, I’m not well known, and I’m not falling for it.

Then, a few paragraphs down, we get to the chase. They want me to be a fellow, for the low, low price of $1,000 (presumably U.S. dollars). OoooOOOoooh, and I get to use the “FISBT” acronym after my name! That will impress exactly... nobody. I can get the same effect by making any old random acronym. “Associate Professor Doctor Zen Faulkes, B.Sc., Ph.D., NSFREUPI, UTPABMSGPC.”

“You can also be prestigious and Hon'ble member of our editorial board.” Now how much would you pay?

Pretty much everything about this email screams at me not to submit, not to join, and not to take seriously. These guys may well be doing good science, but this isn’t helping.

05 January 2010

Tuesday Crustie: Celebrate diversity


First, you may be thinking that’s not a crustacean. It is... from a certain point of view. There’s a reasonable amount of evidence that insects are the direct descendants of crustaceans. This idea, which was deemed “goofy” on some crustacean email lists when I was a grad student, has been gaining more ground, in part due to studies of the similarities in the nervous systems.

Thus, insects are crustaceans – in the same sort of way that birds are dinosaurs.

Second, I wanted to remind everyone that this is the start of the International Year of Biodiversity. And insects are the most speciose group of animals on the planet, and beetles have the greatest number of species of insects. Insects are among the little things rule the world, as E.O. Wilson put it.

Photo by user Steve_C on Flickr. Used under a Creative Commons license.

04 January 2010

Not necessarily new, but important

Washington Monthly has a profile of Don McLeroy and colleagues that looks at his efforts to change Texas public education. Nothing new for anyone who’s followed this story, but it’s still important. Plus, it will be new to many people at the national level.

(N)o matter what happens at the ballot box, the next generation of textbooks will likely bear the fingerprints of the board’s ultraconservatives—which is just fine with McLeroy.

Carnivals for January 2010

Two blog carnivals to which I regularly contribute have their latest entries up.

Hiding in plain sight: The caterpillar masquerade

ResearchBlogging.orgA short paper in Science offers a new take on camouflage. Usually, we think of camouflage as making an animal hard to detect in the first place. Another possibility, though, is that you can be perfectly visible, but not recognized as the thing you actually are.

Skelhorn and company tested this by taking a couple of different species of caterpillars that seem to mimic twigs (Opisthograptis luteolata is pictured). They exposed chicks (caterpillar predators) to hawthorn branches, which caterpillars live on and might be mimicking. Although they don’t say it, hawthorn is apparently very spiny, and I’m assuming that the chicks don’t like it very much. Some chicks got a “raw” hawthorn branch, some got a hawthorn branch wrapped in purple thread, and some got no branch.

The prediction is that chicks that have learned hawthorn is prickly and ouchy will avoid anything that looks like hawthorn – say, a twig-like caterpillar. But because caterpillars don’t have purple stripes, chicks that were exposed to the modified hawthorn, or no hawthorn, will go straight for the caterpillars.

As expected, when they gave the chicks caterpillars right out in the open, with nothing to conceal them, those that had previous experience with the unmodified hawthorn were slower to peck at the caterpillars and handled them for a longer duration.

Chicks with experience with the hawthorn wrapped in purple went for the caterpillars, presumably because the caterpillars didn’t look like the nasty branches. It all suggests that even if you’re readily visible, looking like something unpleasant might be able to give you a survival advantage.

A fun manipulation would have been to wrap the caterpillars in purple string, like the modified branches. You would predict that you should be able to get the effect to change so that the chicks that had seen the branches in purple string would avoid the coloured caterpillars, and go straight for the “raw” caterpillars.

There is one important qualifier buried in the supplementary material for this paper, though:

Caterpillars were refrigerated before use to reduce movement.

The authors are minimizing a very important cue that the chicks might use to distinguish between ouchy branch and tasty meal: movement. This makes it more difficult to extrapolate their results from the lab to what might be occurring in the field.

Even with that price they’ve paid, I’m sure they’ll come and join the masquerade...



Reference

Skelhorn, J., Rowland, H., Speed, M., & Ruxton, G. (2009). Masquerade: Camouflage Without Crypsis Science, 327 (5961), 51-51 DOI: 10.1126/science.1181931

Photo from here.

01 January 2010

The mountain does not move

Not only has the mountain not moved, neither has my review paper, staying firm at the #2 position in the journal for the third consecutive month.


Goal for the year

Be more dangerous.