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

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

Coda

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!

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

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

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.

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.

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

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

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?

Tuesday Crustie: It’s a fact!

From Fake Science.

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.

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

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

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.

Save the Day essays #2: Recovery

I went to a Doctor Who convention in 1986. John Nathan-Turner, then producer of the show, was asked about efforts to recover the old missing stories. He said something like, “They may have dried up, and there may be no more to find.”

He was wrong.

We got back most of “The Ice Warriors” in 1988. We got back all of the epic “Tomb of the Cybermen” in 1991. We got back an episode of “Galaxy 4” in 2011, to name a few. But there is always this fear that the next recovered episode from the 1960s could be the last to be recovered.

If, not too long ago, you had told me that during the fiftieth anniversary year of Doctor Who, that there would be nine episodes recovered (completing one story and almost completing another)...

And that one set of those (“The Web of Fear”) would be a story featuring the Great Intelligence, a villain that had been brought back to the current show just months before (“The Snowmen” Christmas special from 2012, “The Bells of St. John,” “The Name of the Doctor”)...

And that I’d be be able to download them online and watch them mere days after their discovery had been announced...

I would have brushed that off as the most wishful of wishful thinking. It sounds too improbable, too good to be true, to have so many coincidences align.

The moral of the story is that sometimes, the improbable happens. And it can be wonderful.

Tuesday Crustie: Nibbles

Yes, there are crustaceans in this picture. Enlarge and look closely at the second and third toes from the left...

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

Save The Day essays #1: Restoration

My “Save the Day” essays will be a series celebrating the fiftieth anniversary of Doctor Who, which is less than a month away.

I didn’t start watching Doctor Who at the beginning. I was part of the early wave of Doctor Who fandom in North America. Like a fair number of people, I’d started watching Doctor Who in the late 1970s and early 1980s, when the fourth Doctor series were syndicated to public television in the United States.

I learned many of the old Doctor Who stories were lost. Many original tapes had been wiped, because the BBC considered television ephemeral. Most of the old black and white stories from the 1960s existed because someone had pointed a 16 mm camera at a TV screen and filmed episodes for overseas sales.

I was excited when I learned that our nearby American public television station would be showing all the existing stories from the show’s beginning. But at first, I was disappointed. So many of these stories felt so bad to me.

It wasn’t until years later when I started seeing some of the DVDs that I realized my judgment had bee compromised. I wasn’t just reacting to the show; I was reacting to the low quality of the images. What I saw on public television were unrestored 16 mm prints, with scratches on the frames and hiss on the audio.

Seeing the restored versions on DVD were a revelation. This comparison of an original and restored frame (from Seeds of Death, a second Doctor story) shows how huge the difference could be. Here’s the sort of image I saw broadcast:

And here’s the DVD.

The difference is stunning. Episodes that looked cheap and tired suddenly looked professional and even ambitious.

I realized that I was responding to the scratches on the film far more than I’d even thought. I hadn’t been judging the old stories on their own merit, but I’d been heavily influenced by the presentation of them.

I had a similar reaction when I started to watch DVDs of old Godzilla movies. Like Doctor Who, I’d seen the movies on low quality prints that had scratches and crummy reproduction. I love them, but they seemed cheap. Seeing them remastered on DVD from original negatives, and with subtitles instead of dubbing, completely changed my thinking about the movies. They looked glorious. What I thought was a bad production was actually bad reproduction.

It makes me wonder how many things I rate lower than they deserve because of incidental flaws in how they are presented.

External links

Doctor Who Restoration Team

How common is “co-first” authorship?

Deciphering authorship of scientific papers is an esoteric task. Something that raises red flags for those in the tribe of science (like 300 publications with 40 as last author) means little to anyone on the outside. “Why do you mention last author? Does it matter?”

In many fields, it is viewed as good to be the first author. But only one person can be first author, which leads to the practice of some labs having “co-first” authorship. This is usually designated by a footnote to the effect that “authors Smith and Jones contributed equally to this work.”

In one of my classes, I was discussing the practice of co-authorship, and I commented that this was rare. As it happened, later that day I had occasion to review a couple of sets of CVs, from different fields of biology. One set of CVs fell on the “basic organismal biology” side, and the other set tilted much more heavily towards the “biomedical” side.

Only 5% of the organismal biologist listed papers with “equal contributions,” compared to 45% of the biomedical scientists. Note that this isn’t percent of publications, but the percent of scientists with one or more papers with “co-first” papers. This surprised me; I didn’t think it would be that high.

I wonder if this reflects a real difference in the two fields. I think it might be. Biomedical research, I suspect, is a field where there is more money, more competition, and more team members. I think this creates an incentive for people to try to scrape together any additional credit, no matter how tiny. I have yet to meet anyone who cares about “equal contribution” footnotes when reviewing publication records.

I dislike co-first authorship, but it’s just a symptom of another antiquated part of scientific publishing that dates back to the days of small numbers of scientists. Trying to figure out who did what under current authorship practices is like trying to slice bread with a club: messy.

Related posts

Letter in Science!

External links

Co-first Authorship is a lie and a sham and an embarrassment to our profession (DrugMonkey has written extensively on co-first authorship; search his blog for much more.)

That’s the best evidence for a STEM shorage?

The National Math and Science Initiative blog claims there is a STEM crisis. We just aren’t producing enough skilled STEM graduates, it claims. The article advances three pieces of evidence for a "STEM shortage." All are problematic.

Less than 40% of students who start out as STEM majors in college receive a STEM degree.

The number of students who leave does not address whether the number of students who remain are adequate to meet employment needs. A lot of students start off university wanting to be physicians and health professionals. Not all of them make it. That doesn’t automatically mean we’re failing in education or that there is a shortfall of qualified individuals. It might mean it is a stringent, selective, difficult profession.

Nearly half of the Army Corps of Engineers are eligible for retirement.

First, it is risky to extrapolate from a single subset of one STEM discipline to all disciplines, with all degrees. Second, "eligible" to retire is not the same as "planning" to retire. Shortfalls due to retirement were routinely predicted for academia in the late 1980s, which never materialized.

More than half of the fastest growing jobs in the nation are in STEM fields.

That demand is growing fast does not in and of itself tell you about whether there is adequate supply. Also, those “growing jobs” are likely a widely varied mix, with different skill sets and qualifications. As Biochem Belle noted, it doesn’t make much sense when talking about a STEM shortfall to lump jobs that need a bachelor’s in computing with those that need a doctorate in chemistry, and call them all “STEM jobs.” And probably most of those fast growing jobs are computing and a little engineering.

External links

Once more, with feeling: computer science job growth dwarfs all others

Tuesday Crustie: Venom

Bonus Tuesday Crustie! Because breaking crustacean news!

I’ve featured remipedes before, because they are cool in many ways. They are cave-dwellers, and probably the closest relative to insects.

This remipede, Speleonectes tulumensis, is in the news today because it has become the first crustacean discovered to have venom. Check the links below for great summaries!

Related posts

Tuesday Crustie: Insect cousin

External links

First venomous crustacean discovered – Nature News
Of 70,000 Crustacean Species, Here’s The First Venomous One – Not Exactly Rocket Science
The first venomous crustacean is found – Why Evolution is True

Picture from here.

Tuesday Crustie: Better than Darjeeling or Earl Grey

From here. Hat tip to Craig McLain and Andrew Thaler

Do you know what your professor does?

Last week, I gave a talk on research culture, about which I shall write more later. I wanted was feedback from people who work with or hire starting research students, especially at the undergraduate stage. I took to Twitter, and was grateful for the feedback on this question (and several others). I asked, “What do students do right, or wrong, when they first contact you about research opportunities?”

The most common answer, by a long, long, looooooong ways was, “I want students to have some idea of the research I do.” To give few examples:

Wrong = have no idea what my lab does.

– OdysseyBlog

I want someone who knows why they want to work in my lab.

– Elena Bennett

Read some lab pubs before talking to PI.

– Laura Williams

Wrong: they don't know that my lab is computational. Right: they have checked some of my publications.

– Gabo MH

Do show up in my office having read a few of my publication abstracts (on my web site) with a specific possible interest.

– Christopher J. Cramer

Show that you have actually looked at my website and read some papers, and explain what skills you have that are aligned.

– Lorena Barba

Prospective student claimed interest in my lab, then asked what I study & if I have pubs. Informed her about Pubmed.

– Emilie Reas

This reflects a larger aspect of research culture: the expectation that people who want to join in research will read the literature. Of course, new people may not know what “the literature is,” thinking we mean Dickens, Chaucer, Homer, and the like. But we can explain that to them.

That said, back at a mentoring workshop I was participating in a while ago, when I told students that they should have an idea of what professors do, one student spoke up. “Isn’t it egotistical for you to say you’ll only work with students who will work on projects interesting to you?” I can’t remember my answer. I’m still struggling with this question. Research opportunities on any given campus are finite, and I do wonder how many people get turned away who might be able to make good contributions.

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

Today in “What the hell is wrong with people?”: Me

Science blogger Danielle Lee was on the receiving end of bad behaviour. On the other hand, science blogger Bora Zivcovic engaged in bad behaviour. Priya Shetty ask the science blogosphere to explain the difference in reaction, saying of the latter:

But what about his fellow science writers who are normally a highly articulate and outspoken bunch? What explains either the deafening silence or the bizarre closing of ranks?

Insults are simple. Insults documented in pixels might even enter the realm of clear cut, or straightforward. In this case, I thought I could do something positive. I re-posted Dr. Lee’s (now restored) post about getting an insulting question.

Harassment is complicated. Harassment with only personal accounts, even when both participants agree in broad strokes about what happened, even more so. It’s hard to know what to make of the situation, what should be done, and what is appropriate restitution. In this case, I don’t know if there is something positive that I can do – yet.

Layer on top of that the tribal issues – who’s in, who’s out, who’s being attacked and who is doing the attacking – and you part of the explanation Shetty is asking about.

Update: Knowing what to make of the situation is getting less complicated.

More additional: Actions have consequences (part 1, I expect). Bora Zivcovic has quit the Science Online board.

Update, 18 October 2013: Yet another hard to read but important account of Bora Zivcovic’s bad behaviour has appeared. As is so often the case, just one tug starts to unravel more. And I still don’t know what I can say or do that would genuinely be positive.

More updates, 18 October 2013: Actions have consequences (part 2). Bora Zivcovic has resigned from Scientific American. This was the only possible outcome, I think. Where do we go from here? I don’t know.

Related posts

Today in “What the hell is wrong with people?”: Danielle Lee’s story

External links

Another Sexual Harassment Case in Science: The Deafening Silence That Surrounds It Condones It
This happened
The insidious power of not-quite-harassment
Two stories: One man got away with it — will the other, too?
Confronting Sexism in Science Communications – Link round-up, added 21 October 2013

Using “journal sting” papers for teaching

Say what you will about John Bohannon’s Science article about dodgy peer review, he’s done a service by getting people talking about problems of journal credibility and peer review. My link list is over 50 pieces now, and still growing.

Bohannon may have done those of us teaching technical writing another service. When I teach students how to read through original research papers, I want to show them bad examples as well as good examples. Bad examples force you to confront and articulate the details about why the paper doesn’t make its case.

Jeffrey Beall found at least four websites that published one of Bohannon’s hoax papers, and has archived them on his blog:

• Arthogalin inhibits the growth of murine malignant prostate sarcoma cells in vitro
• Nephrosterinic acid inhibits the growth of murine malignant pleural sarcoma cells in vitro
• 7-chloronorlichexanthone inhibits the growth of murine SV40 transformed lymphoid sarcoma Cells in vitro
• Schizopeltic acid inhibits the growth of murine polyploid pulmonary blastoma cells in vitro

The sites that put the hoax paper up have done a passable job of typesetting them. They have included on the hoax papers all the usual paraphernalia that you see in regular journals: page numbers, banners, DOI numbers, ISSN numbers, and so on. Thus, to an untrained eye, there are no obvious giveaways in the presentation that these are anything other than a short paper published in in the usual way. Bohannon has created papers that, to a student, look like the real deal.

The paper is short enough (3-5 typeset pages) that students can do a read through and start picking it apart in a single class period.

Even better for teaching purposes, Bohannon provides a “key” to the paper’s major problems in his Science article. The problems do not require a specialist’s knowledge in cell biology, or cancer, or probably even biology, to pick them out. For instance, one of the key graphs claims it shows a “dose dependent” effect. Most people can grasp the idea of a “dose dependent” curve, if you present it right. “If something is anti-cancer, what do you expect to happen to cancer cells if you give them more of it?”

When they first start to read the scientific literature, students can be a both a bit too deferential and bit too trusting. You need the bad examples to convince yourself that you need to read critically and not take things at face value

Related posts

Open access or vanity press, the Science “sting” edition

Comments for first half of October 2013

Christina’s LIS rant looks at the journal sting conducted by Science magazine.

The journal sting is also the subject of Brian Wood’s Human Ecology blog.

The Lab and Field asks us to stop using the #ICanHazPDF hashtag on Twitter. Sure, as soon a Interlibrary Loans makes getting a paper somewhat close to as fast and as convenient as sending a tweet.

Neuroecology asks why there isn’t a coherent neuroscience blogosphere.

Tuesday Crustie: Ice blue

This lovely little caldoceran Moina macrocopus has a frosty colour.

Photo by PROYECTO AGUA** /** WATER PROJECT on Flickr; used under a Creative Commons license.

Initial reactions: can we hide the sex of authors? And should we?

Maliniak and colleagues (2013) have found an important fact: if a paper in international relations has only female authors, it will be cited about 70% as often as a paper with only male authors.

In a guest blog post, co-author on that study, Barbara Walter, says there is a “relatively easy” solution to fix this. I was reminded of the saying, “For every complex problem there is a simple solution, and it’s wrong.”

(There’s a) potentially easy solution: anonymity. What if we set up evaluations in academia so that we never knew the gender of the person being evaluated (or at the very least downplayed it as much as possible)?

Under this suggestion, I should be “Z. Faulkes,” always, in my academic writing.

I am sympathetic to the idea of removing identifiers. After all, if something is supposed to be judged on its content, then let’s focus on the content. But what bugs me is that the authors say this is “relatively easy.” Indeed, the example they use makes it sound easy:

Prior to adopting anonymous auditions in which candidates sat behind screens when they played, less than 5 percent of all musicians in these orchestras were women. Once blind auditions were instituted women were 50 percent more likely to make it out of the preliminary rounds and significantly more likely to ultimately win the job. Today, 25 percent of all musicians in these elite orchestras are women.

The more I thought about it, the more the analogy with a musical audition unraveled.

A musical audition asks different performers to perform a set, predetermined piece of music. In academic evaluation, researchers are submitting original works, and no two are alike.

A musical audition is a solo endeavor, where you can judge the performance of the individual. In academics, particularly in science, you are often working with many authors, and it’s very difficult to disentangle the contributions of the authors.

Evaluating academics isn’t like auditioning a single soloist in an orchestra. It’s more like digging through demo tapes of rock bands. And you may have heard the band before at a bar or showcase gig.

For academics, their manuscripts and their CVs are extensively reviewed.

Double blind reviews of single manuscripts has been tested occasionally. For instance. Budden and colleagues (2008) claimed this increased the number of papers with women as the first author. Those results were contested, however (Webb et al 2008; Whittaker 2008). But even the authors of the original study admitted it was incredibly difficult to get data on the effects of different peer-review practices, since so few journals are willing to tinker with it, or share data about it.

As a practical matter, I don’t think there is any way to make a CV even close to anonymous. Manuscripts are perhaps a more promising target for being reviewed anonymously. The nature of peer review, trying to find the most qualified people to review papers with the most expertise, makes it highly likely that reviews will be done by people who have met the authors and know what their research is.

For instance, early in my career, I got wind that my name had come up in an Animal Behavior Society meeting. Someone (I think it was Zuleyma Tang-Martinez) was making the point that the society should know the sex of all of its members, “For instance, is this ‘Zen Faulkes’ male or female?”

As it happened, not one, but two of my professors from my university were in the room. They laughed, and said, “Male... You should have asked!”

For that matter, making a work anonymous will most likely change the “females cited 70% as often as males” if the problem is bias at the reviewing stage. It is unlikely to address the citation problem that is coming post review, like males being more active in self-promotion and networking.

A few years ago at Science Online, Ed Yong mentioned that he often had scientists emailing him, asking if Ed could mention their newest work. These were invariably men. The women in the room reacted with surprise. None of them had thought that this was something that they could or should do. Whether you think such requests are out of line or not, you could see how that kind of difference in promotion could lead to men being better known in their field, and getting some more citations as a result.

That the scientific community is a community means that anonymity will be difficult to come by except in very early careers. Double blind review might be much more practical in situations like applications to grad school.

Let’s fight biases whenever we come across them. but let’s not pretend it’s going to be easy. It’s going to be a tough, hard slog.

Hat tip to Miriam Goldstein for bringing this to my attention.

Update, 16 May 2015: Any discussion of making peer review blinded or not is probably incomplete without referencing this post by Hilda Bastian, which systematically reviews a big chunk of the literature on effects of anonymity in peer review. She concludes:

I think institutionalizing anonymity in publication peer review is probably going out on a limb. It’s only partially successful at hiding authors’ identities, and mostly only when people in their field don’t know what authors have been working on. If blinding authors was a powerful mechanism, that would be evident by now.

Update, 21 September 2022: Another paper claiming to show bias in peer review made the rounds recently on Twitter, which again prompted many people to argue, “Blinding manuscripts is the answer, obviously.” Hilda Bastian once more enters the fray with another deep read and analysis of the paper. A few choice points from her post.

An effect on peer reviewers’ opinions isn’t the same thing as an effect on publication bias.

Good editors matter.

Could this manuscript be an inherently divisive one? We can’t know, because no evaluation of the manuscript by methodological and content experts was reported, and the expertise of the peer reviewers for the particular subject matter wasn’t reported either.

We are being asked to take a lot on trust here.

Hilda concludes that this paper is still relatively unconvincing in making a case for blinded peer review. She notes that a big study is in the works and should be out soon. But I recommend reading her whole post.

References

Maliniaka D, Powers R, Walter BF. 2013. The gender citation gap in international relations. International Organization 67(04): 889-922. DOI: http://dx.doi.org/10.1017/S0020818313000209

Budden AE, Tregenza T, Aarssen LW, Koricheva J, Leimu R, Lortie CJ. 2008. Double-blind review favours increased representation of female authors. Trends in Ecology & Evolution 23(1): 4-6. http://dx.doi.org/10.1016/j.tree.2007.07.008

Webb TJ, O’Hara B, Freckleton RP. 2008. Does double-blind review benefit female authors? Trends in Ecology & Evolution 23(7): 351-353. http://dx.doi.org/10.1016/j.tree.2008.03.003

Whittaker RJ. 2008. Journal review and gender equality: a critical comment on Budden et al. Trends in Ecology & Evolution 23(9) 478-479. http://dx.doi.org/10.1016/j.tree.2008.06.003

Budden AE, Aarssen LW, Koricheva J, Leimu R, Lortie CJ, Tregenza T. 2008. Response to Whittaker: challenges in testing for gender bias. Trends in Ecology & Evolution 23(9): 480-481. http://dx.doi.org/10.1016/j.tree.2008.06.004

External links

How to reduce the gender gap in one (relatively) easy step
The problem is that scientists are human
Weighing up anonymity and openness in publication peer review
Photo by Penn Provenance Project on Flickr; used under a Creative Commons license.

Today in “What the hell is wrong with people?”: Danielle Lee’s story

Danielle Lee is someone the blogosphere, and science, and science writing, needs a lot more of: smart, passionate, articulate. Can never have too much of that.

She doesn’t deserve the treatment she got in the story she described below.

She also doesn’t deserve this post being taken down by Scientific American, on which blog network this was originally posted. I am grateful to Dr. Isis for archiving it, and giving us a chance to spread this story far and wide.

Because the treatment that she got deserves to be called out and condemned. I almost hope I get asked to blog by this site so I can say in no uncertain terms, “No. I haven’t forgotten how you treated Danielle Lee.”

Update, 14 October 2013: I posted this before I realized how much of an Internet shitstorm was raging about this. Since then...

The person who asked Dr. Lee the insulting question was fired by Biology-Online. Both Biology-Online and Scientific American have issued apologies (varying in their explanations, and which are not satisfactory to many readers).

Despite Scientific American’s editor-in-chief apologizing, Dr. Lee’s post still cannot be found at  her Scientific American blog, The Urban Scientist.

Have I mentioned I’m not a big fan of words without deeds?

More update, 14 October  2013: And within less than an hour of writing the text above, Dr. Lee’s post is back up, with an explanation of why it vanished. Do I consider this particular matter settled? I’m not sure. Regardless, the issues raised by it are a long way from being resolved.

---

Wachemshe hao hao kwangu mtapoa

I got this wrap cloth from Tanzania. It’s a khanga. It was the first khanga I purchased while I was in Africa for my nearly 3 month stay for field research last year. Everyone giggled when they saw me wear it and then gave a nod to suggest, “Well, okay”. I later learned that it translates to “Give trouble to others, but not me”. I laughed, thinking how appropriate it was. I was never a trouble-starter as a kid and I’m no fan of drama, but I always took this 21st century ghetto proverb most seriously:

Don’t start none. Won’t be none.

For those not familiar with inner city anthropology – it is simply a variation of the Golden Rule. Be nice and respectful to me and I will do the same. Everyone doesn’t live by the Golden Rule it seems. (Click to embiggen.)

The Blog editor of Biology-Online dot org asked me if I would like to blog for them. I asked the conditions. He explained. I said no. He then called me out of my name.

My initial reaction was not civil, I can assure you. I’m far from rah-rah, but the inner South Memphis in me was spoiling for a fight after this unprovoked insult. I felt like Hollywood Cole, pulling my A-line T-shirt off over my head, walking wide leg from corner to corner yelling, “Aww hell nawl!” In my gut I felt so passionately: “Ofek, don’t let me catch you on these streets, homie!”

This is my official response:



It wasn’t just that he called me a whore – he juxtaposed it against my professional being: Are you urban scientist or an urban whore? Completely dismissing me as a scientist, a science communicator (whom he sought for my particular expertise), and someone who could offer something meaningful to his brand.What? Now, I’m so immoral and wrong to inquire about compensation? Plus, it was obvious me that I was supposed to be honored by the request..

After all, Dr. Important Person does it for free so what’s my problem? Listen, I ain’t him and he ain’t me. Folks have reasons – finances, time, energy, aligned missions, whatever – for doing or not doing things. Seriously, all anger aside…this rationalization of working for free and you’ll get exposure is wrong-headed. This is work. I am a professional. Professionals get paid. End of story. Even if I decide to do it pro bono (because I support your mission or I know you, whatevs) – it is still worth something. I’m simply choosing to waive that fee. But the fact is I told ol’ boy No; and he got all up in his feelings. So, go sit on a soft internet cushion, Ofek, ‘cause you are obviously all butt-hurt over my rejection. And take heed of the advice on my khanga.

You don’t want none of this

Thanks to everyone who helped me focus my righteous anger on these less-celebrated equines. I appreciate your support, words of encouragement, and offers to ride down on his *$$.