29 November 2013

Editors retract paper claiming GM food caused cancer in rats

The wheels grind slowly, but they do grind.

Last year, a paper by Séralini and colleagues came out that claimed eating genetically modified (GM) food caused cancer in rats. The online reaction was swift and sharp: the samples were too small, too many data were not shown, the statistics were odd or missing. The reaction that made it to the journal’s printed pages was almost equally critical.

The journal editors have now unilaterally retracted the paper, Nature reports.

The journal editor went back, got the raw data, and had the paper reviewed again. The press release claims the small sample size was seen as a shortcoming of the paper in the first round of reviews from peer-review... unfortunately, given that the journal follows the normal editorial process of keeping all reviews secret, there is no way to verify this claim. We have no idea how many reviewers saw the paper, who they were, or what they said.

The press release says:

The peer review process is not perfect, but it does work.

What I would have liked to read following that statement was something to indicate that peer-review could be improved. This is a good example of how peer-review could be improved easily by making peer review more transparent. Publishing the reviews with the paper, for instance.

The press release goes on:

Ultimately, the results presented (while not incorrect) are inconclusive, and therefore do not reach the threshold of publication for Food and Chemical Toxicology.

Interesting. I am not sure whether “conclusive” results should be the threshold for publication. I have never seen “conclusive” listed in the requirements for publication in any journal. Indeed, Food and Chemical Toxicology’s own guidelines don’t include such words:

Papers submitted will be judged on the basis of scientific originality and contribution to the field, quality and subject matter.

If “conclusive” is truly a criterion for publication, we should probably have much more stringent criteria. We should probably demand larger sample sizes or insist on power analyses, lower p values from 0.05 to 0.005, and demand independent replication from another lab before publishing.

The press release doesn’t talk about of the important role that the online community played in drawing attention to this paper. No, it was only the published letters in the journal that were valuable:

Likewise, the Letters to the Editor, both pro and con, serve as a post-publication peer-review. The back and forth between the readers and the author has a useful and valuable place in our scientific dialog.

I get the distinct notion that Elsevier would rather not acknowledge the online community. I wonder if the editors would have gone back and re-reviewed the paper were it not for the Internet shitstorm that erupted?

I’m interested that the press release, in the quote above, specifically points out that there were “pro” letters. But this is classic case of “false balance,” a rhetorical trick to make a one-sided situation look less like a rout; the vast majority of the letters they themselves published were highly critical.

When the paper came out, I argued against retracting it:

The anti-GM would revel in the retraction, and see it as proof of a cover-up by the establishment.

The initial reaction from the authors suggest my prediction was correct:

Séralini and his team... allege that the retraction derives from the journal’s editorial appointment of biologist Richard Goodman, who previously worked for biotechnology giant Monsanto for seven years.

I will be following the reaction to see if my take on this was correct. For a certain kind of conspiracy-minded individuals, I suspect this will be the sort of move that constitutes “proof” of nefarious efforts to hide evidence, rather than clumsy moves to “correct” the “scientific record.”

Additional: In Forbes, a surprisingly comprehensive article for appearing so soon after the news broke. Also shows anti-GM food advocates are not saying, “This is normal science”:

Claire Robinson, editor of the anti-GMO activist site GM Watch and a separate website set up to promote the Séralini study, GMO Seralini, blasted the move as “illicit, unscientific, and unethical,” the first salvo in what will no doubt be a vigorous defense of the study in the weeks ahead.

However, in fairness to Robinson, she raises an excellent point, which echoes mine above:

Robinson also claimed that the retraction violated scientific guidelines laid out by the Committee on Publication Ethics (COPE). COPE guidelines state that the grounds for a journal to retract a paper are: (1) clear evidence that the findings are unreliable due to misconduct (e.g. data fabrication) or honest error; (2) Plagiarism or redundant publication; or (3) Unethical research.

Note that “inconclusive” is not a reason to retract a paper.

More additional: Retraction Watch covers this, and the comment thread is lively.

Additional, 1 December 2013: P.Z. Myers characterizes the retraction as “belated”. This raises a question: what is the right speed for a retraction? Retracting the paper as soon as criticisms appeared (which was was the journal posted the manuscript as “in press”) would have been rash. While I might fault the editorial board for many things, they did due diligence on investigating the paper before deciding whether to retract it or not.

When you visit the article on Science Direct today, however, there is no indication of the retraction. Why put out a press release about the retraction without immediately putting the retraction into effect and marking the paper accordingly?

Update, 6 December 2013: The Ecologist blog reports on a group letter to the Food and Chemical Toxicology editor, which contains this high-handed passage:

This arbitrary, groundless retraction of a published, thoroughly peer-reviewed paper is without precedent in the history of scientific publishing, and raises grave concerns over the integrity and impartiality of science.

“Arbitrary”? When many people call for a paper to be retracted, I don’t think you can call it entirely arbitrary.

“Groundless”? The letter itself describes the paper as “published, thoroughly peer-reviewed paper”, but it doesn’t go out of its way to say the paper is any good. As far as I can tell, and in the opinions of many, the paper is deeply flawed. Also, given that the authors did not specify conflicts of interest, there is a case for it to be retracted for being unethical, although the editor did not take that position.

“Without precedent”? That’s overkill. One of the first times I wrote about retraction was for a paper for which there were no concerns about the quality of the science. There was also this controversial statement statement from PLOS ONE:

If a paper’s major conclusions are shown to be wrong we will retract the paper.

That’s close to what the Food and Chemical Toxicology editor is doing, it seems to me. There are probably many other examples.

Update, 11 December 2013: The editor has a response to the decision to retract the paper. It is an interesting peek “behind the curtains” of the editorial process. In particular, the editor says the guidelines for retraction were followed, answering Claire Robinson’s concern in Forbes. Hat tip to Nathanael Johnson.

Related posts

Why not retract the rat cancer / GM corn paper?
What did you think those film crews were doing in the lab?
Fallout from “GM food causes cancers in rats” paper

External links

Elsevier Announces Article Retraction from Journal Food and Chemical Toxicology
Study linking GM maize to rat tumours is retracted
Notorious Séralini GMO Cancer Rat Study Retracted, Ugly Legal Battle Looms
Controversial Seralini GMO-rats paper to be retracted
Belated retraction of Seralini’s bad anti-GMO paper
Scientists pledge to boycott Elsevier
Food and Chemical Toxicology Editor-in-Chief, A. Wallace Hayes, Publishes Response to Letters to the Editors

25 November 2013

Identifying a mentor

Recently, I spoke at a “Mentoring matters” panel here at my institution, and I was asked to speak about “identifying a mentor.” (Picture at right; apparently I was saying something so ironic that it needed scare quotes.)

I realized before I started talking that I was a good example of what not to do. I didn’t see out a mentor in research; I was shanghaied. I was only rarely proactive. I was god’s fool, and made it through unscathed.

Sure, it worked for me, but I can’t recommend to students, “blunder through the minefield, it’ll all work out.” That’s not a plan, that’s just hoping.

In my own defence, it is much easier today to be proactive about identifying a mentor than it used to be. Because Google exists.

Students know that when applying to grad school, or research programs, or scholarships, they will be scrutinized by faculty before being allowed to join. Students should scrutinize their prospective faculty mentors first, before they will allow themselves to be recruited.

(Yes, I’m advocating you Google stalk potential mentors.)

When you look up a prospective mentor, look for someone productive. Grad degrees are research degrees, and you want to look at faculty’s recent track record in their research. You want someone active in their research field.

I emphasize “recent” because it’s easy to confuse “fame” with “productivity.” Some researchers may be famous for work they did years ago. It’s only when you look at their publication record that you realize they haven’t done much for ten years.

Similarly, you should look at their publications and see how many of a faculty’s papers have student authors. Try to work out how many papers their students get out, how quickly they get those papers out..

I hope that it goes without saying that any student should talk to potential mentors. In person is great, but even a phone call or Skype call can go a long way in establishing a dialogue.

If at all possible, talk to other students who have that person as their mentor. You can learn how that person works, what their expectations are. And you might get some early heads up on potential pitfalls, like any unpleasant personality traits. (Sadly, many faculty have these. Remember, research culture is not a utopia.)

Another online resource I wish I had when I was blundering through grad school was peers and faculty on social media. There are blogs written by students and faculty at each and every career stage, and they contain so many honest insights into the process of working through academic training. There are scientists on Twitter in every research field.

A good tactic might be to try to find some people who are in your peer group, and some people who are in just ahead of you. If you're an undergrad, find some grad student blogs; if you're a post-doc, read some blogs by people who have just started their tenure-track positions.

The amount of expertise, and mentoring going on through social media, is nothing short of staggering. Why wouldn't you take advantage of that?

23 November 2013

Would you like a jelly baby?

I’ve done a “What Doctor are you?” quiz before, but since today is a special day for Doctor Who, I am sucker enough to try another version of the quiz...

Your result: Congratulations! You’re the Fourth Doctor

Do people refer to everyday events in your daily life as "mad schemes"? Do they sometimes call you "impossible," but happily accept the sweets you are quick to offer round as soon as you meet new people?

Do you have clothes in your closet that other people simply would not wear, but somehow you make them look pretty good?

And are they always on the alert, in case you are seized by an alarming impulse and suddenly have to dash off out of the room?


Related posts

Great balls of fire!

External links

‘Doctor Who’ Personality Quiz: Which Doctor Are You?

Save the Day essays #7: How the Doctor made me better

The man who makes people better. How sanctimonious is that?

– The Master, “The Sound of Drums,” Doctor Who, 2007

Doctor Who helped make me become a scientist.

True, I might have been a scientist if I never watched Doctor Who. I had a lot of personality traits that helped pushed me towards being some sort of technical career. I was always inclined to science as a kid (dinosaurs and spaceships littered my rooms), I consumed a lot of science fiction, and I was a “smart kid” who got good grades in school.

But there’s a big difference between things that you do when you’re playing as a kid, and sticking out a long haul in graduate school to make science your life’s work. Grad school is tough. It has a high attrition rate. Lots of people do not make it. To make it, you need something to look forward to that can keep you going.

When I introduce myself to students, I joke that, “I went to grad school so I could be called Doctor Zen, and sound like the villain from a bad kung fu movie.” That gets a laugh, but it’s not true. (Though I am prouder than you know that “Doctor Zen” is a role-playing game villain; see here and here.)

The truth is that one of the things that kept me going in grad school was that if I made it, I could be called, “Doctor.” Just a little bit like one of my heroes.

Doctor Who made the title conferred by a Ph.D. important to me in a way that nothing else ever did.

For most people, “doctor” means “physician.” I never, ever, had any interest in going into the health professions. Of all the other scientific characters that I loved from science fiction, none of them really brought the title to the fore. Spock from Star Trek was always, “Mr. Spock” (I guess Spock only ever finished his master’s). Buckaroo Banzai was just, well, Buckaroo Banzai.

Doctor Who made me want to be a doctor. So I could be called “Doctor Zen.”

I didn’t have direct inspiration from the TV series when I was in grad school.

“Survival,” the last episode of the classic series (above) aired the year I started grad school. A series of books (“The New Doctor Who Adventures”) rarely satisfied me. The TV movie (right) aired after I defended my dissertation. I became a doctor when the Doctor was missing.

I wrote back in 2003 when the show’s rebirth was announced:

The Doctor represented so much of what I thought a scientist should be. Adept in solving problems of all sorts, whether it be preventing a Dalek invasion or patching a piece of broken equipment. That “Renaissance man” aspect in particular is one I love... . Not taking the word of authority ... Traveling the universe. Good companions. .. And it’s one reason why I sometimes suggest people call me “Doctor Zen” – it has the sort of same slightly cool ring as “Doctor Who.” At least it does to my vain ears.

It’s not just me:

I see so many children in schools who, because of their love of this silly old show, want to act, write, record music, sing or become scientists.

And it’s not just Doctor Who. Jacquelyn Gill wrote:

Watching The X-Files again reminds me of how big of an inspiration Scully was to me. Bigger role model than any living scientist.

I mentioned Spock before. The actor who created the character, Leonard Nimoy, has met lots of scientists that trace their lineage back to him.

(B)ecause Mr. Spock and Star Trek have inspired so many young viewers to become scientists, researchers who meet him are always desperate to give him lab tours and explain the projects they’re pursuing in peer-to-peer terms. Mr. Nimoy nods sagely and intones to each one, “Well, it certainly looks like you’re headed in the right direction.”

There is a lot of concern in the scientific community to provide scientists with role models and mentors. Those are important. But let’s never forget how many people are inspired by heroes from fiction. Dare I say, those made up characters might matter more in making decisions about what kind of person we want to become.

We tell the tale of heroes to remind ourselves that we also can be great.
- Tao of Shinsei

The Doctor is one of my heroes. I have yet to fight monsters or save the day, but I do love that in my job, I get to imagine and discover new things. The Doctor taught me that there’s a whole universe out there to explore.

Come on. We’ve got work to do!

Save the Day essays

Save the Day essays #1: Restoration
Save the Day essays #2: Recovery
Save the Day essays #3: Family
Save the Day essays #4: Rewatching the rebirth
Save the Day essays #5: Playing favourites
Save the Day essays #6: Anarchy in the U.K.

Related posts

A role model returns

External links

Carrying the torch – Doctor Who at 50

22 November 2013

Save the Day essays #6: Anarchy in the U.K.

A lot of fictional heroes are either police, or very thinly disguised police. And this was probably more true in the 1960s than now. Go back to that time, and you won’t see Batman as a vigilante, but a hero often working closely with Commissioner Gordon and the police.

When you strip away all the glamour – the cars and booze and women – James Bond is a civil servant. He’s an authority figure who’s working for “the man.”

The Doctor is an unusual hero because he doesn’t fit that mold.

In story terms, Doctor Who starts with a rapid succession of crimes by the show’s ostensible hero. Off screen, before the first episode starts, the Doctor steal his TARDIS (not “the” TARDIS, because there was originally more than one in the story) and goes on the run with his granddaughter Susan from his own people. This is promptly followed by kidnapping his granddaughter’s teachers, Ian and Barbara. Then, he’s hefting up a rock in an (unsuccessful) attempt to kill a caveman.

While the fugitive aspect of the Doctor was toned down even during Hartnell’s era, the Doctor remained, perhaps not a criminal or an anarchist, but certainly an anti-establishment character. In some of the classic series, it seemed that “toppling oppressive regimes” was a very close second to “stopping alien invasions” on the Doctor’s to do list.

The Troughton and Pertwee stories often played with the Doctor as a defiant figure. The Doctor was in conflict with the Time Lords, the established authorities on his planet. And how the Doctor resented the times he was yanked around like a dog on a chain to carry out missions from the Time Lords.

On top of that, the Doctor was forced to work with the authoritarian military (U.N.I.T.). This conflict led to some of the show’s most interesting relationships, the Doctor and Brigadier Lethbridge-Stewart. There were frequently sharp words between the pacifist Doctor and the military man. That conflict never really died away even, as the characters became close. The Doctor respected the Brigadier personally, but never what he did professionally.

That slightly anarchic side of the Doctor continued through the classic series, whether in large strokes (the season-long battle when the White Guardian yanked the fourth Doctor’s chain, much like the Time Lords had before) or tiny details (the eighth Doctor pulling an alarm, being asked why, and responding, “To liven things up!”; the second Doctor being told, “You”re not allowed in there!” and saying, “Me? Not allowed? I’m allowed everywhere!”). The Doctor’s suspicion of Time Lord authority had been proved to be well-founded, as later stories showed an a system rife with political corruption and backstabbing.

I don’t think it’s any accident that many of the show’s biggest, best, most popular, most effective villains are authoritarian military regimes (the Daleks, the Cyberman, the Sontarans) and a despot, who name is authority incarnate (the Master).

When the show returned, the Doctor couldn’t be the tamed agent working for the Time Lords any more. They’re gone. The Doctor couldn’t rebel against that authority. The series played with the Doctor becoming the voice of power. In “New Earth,” he says:

I am the Doctor. If you don't like it, if you want to take it to a higher authority, there isn't one. It stops with me.

That theme goes even further in “The Runaway Bride” and “The Waters of Mars.”

Adelaide: Little people? What, like Mia and Yuri? Who decides they're so unimportant? You?

The Doctor: For a long time now, I thought I was just a survivor, but I'm not. I'm the winner. That's who I am. A Time Lord victorious.

Adelaide: And there's no one to stop you?

The Doctor: No.

Adelaide: [Noticeably angry] This is wrong, Doctor! I don't care who you are! The Time Lord victorious is wrong!

It might have been easier for the Doctor to be a rebel in the 1960s when he was young (so to speak; the show was young, in any case). It got more complicated the Doctor for the Doctor to fight powers when returned in the twenty-first century, middle-aged (the show as in its 40s).

But... But! The point of those stories is to show that the Doctor rejects having that much authority. The point of those stories is that he realizes he needs to be stopped from doing whatever he wants. He doesn’t become the thing he hates.

After you’ve watched your hero for a long time, you can lose track if some of the elements that resonate with you are because you have those character traits to begin with, or whether you picked them up from watching your hero.

That deep uneasiness with authority is something I share with the Doctor. I don’t automatically respect people in the military. I enjoy (sometimes more than I should) rattling cages and pushing back against overly rigid system. I like to rebel just a little bit. To liven things up.

But, like the Doctor, as you go, you tend to accrue more authority. You’re given responsibility, and the chance to make decisions that genuinely affect other people’s lives. The question becomes what you do with it: embrace it completely and wield it like a club to suit your own ends? Or do you try to use it sparingly, to genuinely improve the lot of others?

In the end, the Doctor is never part of “the system.” He’s powerful, but never “the power.” He’s one person in a box.

Related posts

Save the Day essays #1: Restoration
Save the Day essays #2: Recovery
Save the Day essays #3: Family
Save the Day essays #4: Rewatching the rebirth
Save the Day essays #5: Playing favourites

21 November 2013

Save the Day essays #5: Playing favourites

When the matter of a favourite Doctor comes up, for fans of the classic series, Tom Baker is usually mentioned. For fans of the new series, it’s David Tennant who is usually mentioned as a favourite.

My favourites from the old series and the new?

In theory, Tom Baker should be “my” Doctor, because he was the first one I saw, in Episode Three of “The Seeds of Doom.” And yes, I did have a very long scarf. But now, when I watch his stories, there is something that is just a little too self-indulgent about the performance.

For a while, I thought of Colin Baker as a favourite. I liked the uncompromising nature of his Doctor... and I liked him partly because others didn’t. It was a shame he never got a chance for some of the long-term plans he had for the character to be played out.

Classic series favourite: Jon Pertwee

As time has gone on, though, I think I have settled on Jon Pertwee’s portrayal of the Doctor as my favourite from the original series. His performance, with its elegance and charm and slightly over-the-top-costume, solidified the character of the Doctor, and the Doctor’s been that way more or less ever since.

Some of the moments I remember most strongly about Pertwee were the moments of moral outrage. His Doctor had a strong sense of right and wrong. Given that much of the third Doctor’s tenure was spent in the company of the military, the Doctor, a pacifist action hero, often had a lot to be angry about, railing against the blunt methods the soldiers around him favoured.

But Pertwee’s Doctor was also kind and generous, even to those who often exasperated him, like Brigadier Lethbridge-Stewart. And he would turn from exasperated to warm in second... and you believed those two emotions were both just there under the surface.

The third Doctor was a bit more of a straight scientist than most of the other portrayals, and as a working scientist today, that’s another element that appeals to me. Maybe it’s one reason why a personality quiz said this was the Doctor I most resembled.

Third Doctor video playlist

New series favourite: Christopher Eccleston

He saved the show.

If Christopher Eccleston’s Doctor hadn’t worked, Doctor Who would have had one season in 2005, died, given classic series fans one more DVD boxed set for their collection, and that would be that. I am absolutely convinced of that.

I’m also convinced that the show wouldn’t have been as successful if it had launched with David Tennant’s Doctor. It’s a worldwide hit now, but I remember when even within science fiction fandom and the the geek community, Doctor Who was a tiny specialized fan niche. The show was viewed as something of an embarrassment by a lot of people: too convoluted, obsessed with its long history, and too eccentric.

The ninth Doctor was the most grounded Doctor. Eccleston’s was probably the first interpretation of the character that wouldn’t look out of place walking down a street. The Doctor’s trademark leather jacket was not such an obvious costume as previous incarnations, but it was a great symbol of a traveler. The Doctor’s eccentricities were toned down a little. Doctor Who needed that kind of performance right then for new audiences to get into the show.

Like Pertwee, when I think about Eccleston, some of his angry scenes sometimes come to mind. Like Pertwee, Eccleston’s Doctor had that sense of moral outrage, and sometimes he wasn’t kind. My favourite ninth Doctor moment is where he is maddest, in “Bad Wolf”: “It means, ‘no.’”

But it’s also when he’s his strongest and most resolute.

And when I rewatched his stories earlier this year, I was struck by how often he was grinning. Madly. With complete exuberance. While he was described sometimes as the “gunslinger” Doctor, a man who was wounded and lonelier and more vulnerable than ever (watch him meet the last Dalek), there was always that joy of exploring the universe, and being excited to see what was around the next corner.

Finally, when talking about favourite Doctors, there is always a hint of, “Which version would you most like to be, or feels closest to you?” Let’s just say I own a leather jacket and leave it at that. And that personality quiz I mentioned above? Ninth Doctor was second choice.

Chris Eccleston saved Doctor Who. He saved a show I loved and help make it into a worldwide success and ensure that I got many, many more stories from the TARDIS. And I will always be grateful for that.

Ninth Doctor video playlist


Once, when I met actor Nicholas Courtney (Brigidier Lethbridge-Stewart) at a convention, he was asked which was his favourite Doctor. He replied with a line from “The Five Doctors” that sums up my feelings, and those of a lot of fans, near perfectly:

Splendid chaps. All of them.

Related posts

Save the Day essays #1: Restoration
Save the Day essays #2: Recovery
Save the Day essays #3: Family
Save the Day essays #4: Rewatching the rebirth
Great balls of fire!

20 November 2013

Save the Day essays #4: Rewatching the rebirth

Earlier this year, I started rewatching Doctor Who from its rebirth in 2005 with someone who had never seen it before, or even knew anything about the show. I was a fan of the classic series, and had seen pretty much everything there was to see, and it was fascinating to watch the reaction of someone seeing the series cold.

I knew she was hooked when she gasped when the store dummies moved in “Rose.”

It was shocking to her when the Doctor regenerated. “I thought this series was about those specific two characters!” But even more interesting was how exactly her reaction mirrored that of Rose. In “The Christmas Invasion,” Rose says something like, “This wouldn’t happen if the proper Doctor was here,” which prompted an emphatic “YES!” from the woman sitting next to me.

Ultimately, like Rose, she not only accepted David Tennant’s tenth Doctor, but now he’s her favourite Doctor (so far).

Then we hit “Doomsday.”

My god, I had almost forgotten how completely and utterly devastating that episode is.

We kept watching though the next season with Martha Jones. She didn’t like Martha very much, and said more than once, “Why couldn’t he have Donna as a companion?” (It took so much willpower for me not to even hint, “Just wait...”.)

On re-watching the show, it was the seasons after “Doomsday” that cemented in my mind how brilliant the new Doctor Who was, and how different than before. If it had been the old series, Rose would be all but forgotten after the next story. There might be a line or two, but then a new companion would be introduced, and on we go. (Watch how Liza Shaw is written out, or how long the Doctor refers to Sarah Jane Smith, in the old series.)

This time, the Doctor mourned. And he kept mourning for a long time.

That the Doctor didn’t just “get over it” was a testament to the show’s commitment to honesty in its emotions (even as it engaged in hand-waving and frippery over the details like what the sonic screwdriver could do). That honesty was part of the reason the new series was so successful in reviving the show.

I can’t help but wonder if it was being so committed to making sure those relationships in the show mattered was why, so often, Russell T Davies would hurt his characters so deeply. He said in an interview before the new series launched, “There will be times when it’ll just break your heart.” There aren’t many happy endings when companions leave in the new series.

Maybe it’s because when we cry, Davies know he created something that is meaningful to us watching.

Related posts

Save the Day essays #1: Restoration
Save the Day essays #2: Recovery
Save the Day essays #3: Family

19 November 2013

Tuesday Crustie: Manicure Monday

It’s a ghost crab; unsure of species. But I do note that the lovely manicured fingernails in the background you see are those of Alexis Rudd.

She posted this photo yesterday as part of a coordinated effort by Hope Jahren to photobomb Seventeen magazine’s regular “Manicure Monday” hashtag game on Twitter with images of science! Hope wrote:

I have small dream: that @seventeenmag will acknowledge #Science hands to its 700+k followers. But tonight it feels like a pretty big dream.

Here’s a quick video of the results:

External links

What I learned from #ManicureMonday

Tuesday Crustie: Think you’ve seen it all?

From I Can Haz Cheezburger, of course.

Feel my power!

Cartoon Action Hour is a role-playing game of vintage cartoons. And I really want the latest one...

The series focuses on an interdimensional madman known as Doctor Zen who brings his armies to our reality to transform our world into his world. The heroes of the series are special men and women who have been chosen by the “spirit” of each of their people and given a sacred weapon to fend off the threat with. In Britain, Merlin gives a young woman Excalibur. In Africa, Anansi gives a young man his “story web.” The spirit of Baba Yaga gives a young woman her mortar and pestle. And in the United States, the spirit of Coyote gives a young man his magical cloak that allows him to transform into any animal or person.

By the inimitable John Wick. Blurb from here; cover from here.

Related posts

The empire of Zen 
Master of Ancient and Forgotten Science: 2

External links

Spectrum Games

18 November 2013

Research culture shock

A couple of years ago, when the Ecological Society of America meeting was in Austin, a few students from my institution went to give posters. One of the women showed up in a dress and four or five inch heels, and one of the men showed up in a jacket and tie. This at a meeting where sandals are typical footgear.

The students did not understand the culture of the ecology meeting.

It might come as a surprise to beginning students that there is a distinct culture around academic research. And just like someone moving to a new country, there can be culture shock, and new students can have a hard time adjusting to the culture of research.

Here is my attempt to identify some of the key elements of research culture.

1. Science is not utopia.

I can’t say it any better than Dr. Rubidium did here.

There are people that believe science is above all the bullshit. Because science is facts and reason and shit, so scientists are totally above bullshit of any kind. Scientists have achieved a Utopian State Of Bliss which non-scientists can only dream of.

To those science-as-utopia people, I say this:

Come join us in the real world.

When I asked on Twitter about what surprised them about research, a very common answer was that people were surprised by how big the egos are, and how much that drove science.

Students, this means that some of the crap you hope might not be an issue any more... can still be an issue.

2. There are hierarchies.

One example of hierarchy was in titles. It grates someone with a doctorate to be called “Mister” or “Miss.” Someone with a Ph.D. is referred to as “Doctor” if you’re using titles.

There are hierarchies of all sorts in academia. Some of them are formalized (academic rank: undergrad, grad, post-doc...), some are about individuals (tenured over non-tenured faculty), some are about institutions (university “tiers”), and many are informal. It pays to understand what the ladder is is and what rung you are on, even if your particular lab or institution doesn’t play the game of trying to climb the ladder.

3. Work ethic

Researchers have a strong work ethic. Being in the lab on the evening or the weekend is not seen as unusual in the slightest. Some labs essentially demand it. Personally, I don’t think such labs are healthy, but they do exemplify the attitude that anyone who wants to do research should not hesitate to come in at hours outside of 9 am to 5 pm, Mondays to Fridays, at least occasionally.

If you think being asked to come in on an evening or weekend is an unreasonable demand, always, you’re not going to be happy in research.

4. Reading the literature

Part of that work ethic that I just mentioned is an expectation of reading original journal articles. I think many beginning students expect that research is only about getting, and maybe analyzing, the data. It isn’t. Reading is part of the job. And not just the research in your field; there’s an expectation that you’ll be somewhat aware of what’s coming out in the glamour magazines, and that you will keep pace with science news generally.

Subscribe to the table of content alerts for the journals in your field.

5. Criticism is the norm

A lot of beginning students have a very hard time getting criticism. Sometimes, the reaction is that professors are just mean. It takes a while to realize that the criticism can be coming out a very pure desire for the work to be good, not just to tear down students.

Related to point #4 above, you’re not only expected to read papers, you’re expected not only to read, but to dissect papers. Pull them apart. What makes them tick. And what are the weaknesses? You not only have to be ready to take criticism, you have to be willing to give it, too.

6. Labs work in many ways, but many are tight knit

For many (but by no means all), being part of a lab is almost like being part of your own small tribe, or even a second family. It can be a very intense working environment, and it can, at its best, draw people together in a good, powerful way.

Maybe it’s no accident that academics trace lineages much like people trace their family trees.

7. Financial considerations

Beginning students have only the haziest ideas of the cash flow in academia. A very common question when I talk about publication and I show one of my papers is, “How much of that $30 for the paper do you get?’ Well, none.

Researchers fret about money. A lot. I think some researchers try to keep those issues away from students, but it bleeds out. I sometimes think students might be aware of money, but don’t learn how to manage money in research in any practical fashion.

Corrosive culture?

If there is something that is common to all of these elements of research culture, it is that all of them have to potential to be malicious when taken to their extremes. When I was giving a talk about this, I worried that I was being too negative. But the important thing to realize is that a culture need not lead to its worst behaviours.

A culture of a strong work ethic does not necessarily mean overwork.

A culture of criticism does not automatically lead to nastiness.

Being aware of the culture gives people a chance to recognize what might be places where to guard against falling victim to the more negative parts of that culture.

External links

Science Online Oceans science geek fashion show

Photos from here and by niznoz on Flickr; used under a Creative Commons license.

16 November 2013

Comments for first half of November 2013

Deevy Bishop talks about psychology’s self-publishing, including going it alone on Kindle.

Erin Podolak writes about the irrelevance of Carl Sagan, a familiar topic to me.

15 November 2013

Texas may be nearing the end of textbook battles over evolution

The Dallas Observer has an excellent, lengthy feature about the ongoing tussle about the teaching of evolution (and a few other subjects besides) in Texas. There are useful profiles of several players that I hadn’t seen before, such Ray Bohlin. Bohlin, a creationist, has published proper scientific papers on biology, but stopped.

Faith in a theory for which there is no experiment turned out to be a dead end.

And therein lies the problem with all efforts to tie evolutionary biology to creationism.

Recommended reading.

External links

Creationists' Last Stand at the State Board of Education

Naming a new university

Five names for the new university that mine will morph into have gotten enough suggestions to warrant serious consideration from the University of Texas system. Here’s my take on them.

The acronym kills this idea. “UTI” already has an unpleasant meaning: “urinary tract infection.” Eeeewwwww. No, no, no, no.

Even if you go “UTIN,” it makes you think of a cheap, malleable metal that you can food in.

How did this suggestion make it onto a list of suggested names? Not enough people with any sort of biological background, and probably not many women.

“University of Texas International” also has problems shared by our next two candidates.

“...of the Americas” was featured in the background of the original announcement for the formation of the new university. I suspect that there is someone in the University of Texas System, maybe the chancellor, who is very fond of this idea and just won’t let it go.

“Las Americas” is the same idea, just running further with the notion that we are somehow going to be a bilingual university.

All three of these suffer from the same problem: it is disconnected from the community that the university serves.

The University of Texas System wants the new university to be big and ambitious. Hence, we have three names that try to suggest that this is an international institution. But 93% of the students enrolled at UTPA come from the four counties of the Rio Grande Valley (page 11 here). That’s where our students come from.

I suspect the stats for University of Texas Brownsville are similar, and that this will probably also be true of the new university.

We’re not an international university. We’re not even a state university. We’re a regional university. That is not going to shift anytime soon, grandiose plans notwithstanding.

A new university has to connect with the supporting, surrounding community. “International,” “of the Americas,” and “Las Americas" send a signal to the local community: “This is not for you.”

“University of Texas South” sounds a little grammatically dodgy, but that is not my main problem with it. I’ve introduced people to my university for over a decade. I know what the reaction of people is when I tell them “Southern Texas.”

“San Antonio?”

“No, near the coast and further south.”

“Corpus Christi?”

People who hear “University of Texas South” will think of the wrong place. I guarantee you that.

To make matters worse, like the three names above, it doesn’t connect with the community. People here don’t refer to this region as “South Texas.” This is what people from outside the region call it.

To make matters still worse, this name would be confused with South Texas College, a completely separate institution.

Several people have suggested “The University of Southern Texas.” This sounds smoother, but the University of Texas System won’t allow it. The name has to begin with “University of Texas.”And people would still confuse it with South Texas College.

I wish I had blogged about this so I could prove what I am about to write: I have been saying for years that my university, The University of Texas-Pan American, should be renamed “University of Texas – Rio Grande Valley.”

People living in this area call it “The Valley” all the time. The name is more specific than “South.” And the acronym, UTRGV, has assonance: the repeated long “E” vowel sound in “T,” “G,” and “V.”

A poll on a local newspaper site suggests this name is the most popular among residents by a long, long ways.

I hope that the the UT System will catch up with what I’ve said all along!

Meanwhile, in other good news, $196 million has been approved for infrastructure on the new university. This including $70 for a science building. That’s great, because we are full here.

External links

What’s in a name?
Regents approve PUF funding for new university, medical school in South Texas

14 November 2013

Save the Day essays #3: Family

For a show about a lone wanderer through space and time, ironically, Doctor Who has been at its most successful when it’s been about family.

It’s easy to forget that the very first companion in the TARDIS was Susan, the Doctor’s granddaughter.

Since then, there have been a lot of crews in the TARDIS, and the most memorable ones have been the ones that felt most like a family.

The second Doctor, Jamie, and Victoria had the sort of close-knit feel of a family, which was, somewhat amazingly, retained with Zoe joined. (This was no doubt due partly to the good working relationship between actors Frazier Hines and Pat Troughton.)

During the third Doctor’s exile on Earth, the U.N.I.T. team – Jo, the Brigadier, Benton, and Yates – was often described as a family. Even the villain, the impeccable Roger Delgado’s Master, became part of the family.

That sense of family weakened for a long while. The fifth Doctor had a little TARDIS crew for a while, but it always felt more thrown together and lacked a certain closeness in the scripts.

When the series returned in 2005, it was a family drama in more ways that one. “Nine hundred years of time and space, and I've never been slapped by someone’s mother.” Mothers and daughters and boyfriends and fathers and all those relationships were there in full force.

It may have been a dysfunctional family, but Rose and Jackie and Mickey and Captain Jack and Sarah Jane – how wonderful, Sarah Jane again, better than ever! – gave the Doctor an odd new family. I think that one one of the elements that contributed to the huge success of the series’ return.

Amy and Rory? Family again. And didn’t the dynamic get even more interesting when Rory’s dad got added to the mix?

While the Doctor and companion as pals and partners-in-crime can work (the seventh Doctor and Ace, the eleventh Doctor and Clara), the times the show has had the tight-knit, frequently recurring cast have been some of my favourites.

Related posts

Save The Day essays #1: Restoration

Save the Day essays #2: Recovery

13 November 2013

Watch how “might” vanishes

Hey, I Fucking Love Science, let me fix this photo you posted on Facebook:

To their credit, there was a link next to the photo. But when you click the link, it goes not to the primary article, but to another I Fucking Love Science site, which claims:

Earlier this year, it was discovered that Jupiter can form diamonds in its atmosphere.

If you click that link, you get a secondary news article from Nature with a sub-heading that reads (my emphasis):

Lightning storms create carbon soot that might be compressed into diamonds as it falls through the atmosphere.

“Might.” As in “maybe.” As in a possibility. Not definite. Not that you would get that from I Fucking Love Science, which presents it as a fact.

The photo includes Neptune as a diamond weather spot, but the Nature article doesn’t (my emphasis again):

Forget diamonds in the sky — it may actually be raining diamonds on Saturn and Jupiter, according to two planetary scientists.

The Nature news article provides reasons to rule out Neptune for diamonds:

Luca Ghiringhelli, a physicist at the Fritz Haber Institute in Berlin, Germany, is also sceptical of the pair's conclusions. His own previous research showed that the concentration of carbon is not high enough in Uranus and Neptune — which are several times richer in carbon than Jupiter and Saturn — to grow diamond from the 'ground up', building the crystals atom by atom.

IFLS, you’re increasingly becoming part of the problem, not the solution. It takes as much time to make a picture that’s right as one that’s wrong. Why not make it right?

07 November 2013

Academic search team-up

This is big news for academics.

It’s no secret that I’m a big fan of Google Scholar. It has transformed how I do research. After Google Reader shut down (I still mourn it) a lot of academics were worried that Scholar might be next on the chopping block.

That fear seems to be over with a major, major announcement that Scholar is partnering with one of, if not the, other heavy hitter in the academic search market, Web of Knowledge. And, as the article notes, this could be just the beginning. Other scientific databases might start to play nice.

Not long ago, David SHotten wrote:

In this open-access age, it is a scandal that reference lists from journal articles — core elements of scholarly communication that permit the attribution of credit and integrate our independent research endeavours — are not readily and freely available for use by all scholars.

This announcement by two private companies could either mark the start of greater availability to scientific literature than ever before, or it could mark the start of greater efforts to make citations into a product to be controlled and sold. I am hoping it will be the former, since you can’t this sort of complex data integrated in a way that is useful to users without considerable effort. Making the citation data open might be a logical step for the companies, and maybe their product would move more towards thinks like analysis tools.

Related posts

Research Google
PubMed vs. Google Scholar
Google Scholar profiles
Finding self-published papers
The terrifying death of Google Reader

External links

Thomson Reuters-Google Scholar Linkage Offers Big Win for STM Users and Publishers
Publishing: Open citations

Picture from here.

06 November 2013

SfN 2013 bingo!

I’ve done these before, but this one was easy. Thank you, Twitter hashtag game.

Additional, 11 November 2013: Here’s the story behind row 1, column 4, as told by the inimitable Doctor Becca.

Related posts

Neuroethology bingo

05 November 2013

Tuesday Crustie: Rub-a-dub-dub

Patrick Stewart in a tub. He tweeted this for Hallowe’en, but appropriate for any occasion, I reckon.

Breaking Bio design chat

Earlier this year, I chatted with Morgan from Breaking Bio during Science Online 2013. That interview never made it to air, because it was a little too short.

I contacted Morgan and pleaded with them to let me have another shot at it. They were good enough to indulge me, so I sat down with the Breaking Bio boys again to do a little chitting and chatting (plus a substantial rant in the middle) about poster design.

I need to work on avoiding that slow blink.

The Captain Canuck post I mention in the beginning will be up this week!

External links

Episode 48: Let anarchy reign with Zen Faulkes!

Breaking Bio YouTube channel

Captain Canuck
Captain Canuck YouTube channel

01 November 2013

Comments for second half of October 2013

Reaction Norm has a surprising figure about the age of directors at the NIH. They’re old.

If you ever want to go to Science Online, you should try to figure out what you want to get out of the experience, as Kelly Hillis suggests. Then tell Karyn Traphagen (karyn AT scienceonline DOT com) what your answer is.

Ethan Perlstein does some analysis on science crowdfunding across four crowdfunding platforms.

DrugMonkey asks who has busy posters, and who’s neglected, in the poster sessions at conferences.

Small Pond Science has a series of observations from his travels around universities that are interesting.

Down with Time think nobody reads his blog. Prove him wrong!

This blog makes a cameo on a post about self-publishing science. at the Neuroconscience blog.