Tuesd Crustie: Good neighbours

Spotted here.

PACE 2013 Bioethics conference, day 3

The last day of this conference featured a keynote by Ivan Oransky, co-founder of Retraction Watch and Embargo Watch. His slide deck is below. The slides are much better when accompanied by Ivan, who presents with an appealing, slightly dry sense of humour. Ivan’s talk was video recorded, but it is not up yet. Plus, I am not sure how good the sound will be; the mic was off because it was generating a lot of white noise.

To be honest, because I know Ivan’s work and follow many of the issues that he talks about online, I was expecting all this stuff to be old hat to me. But even I learned something that dropped my jaw to the floor.

Journals have always been in the business of selling reprints of single articles. Typically, these are sold to the author, who can then use them to send to other researchers. In the days before PDFs, you would often get little “reprint request cards” in the mail. Because of that experience, it never occurred to me that anyone other than the author of a paper would be interested in buying reprints of articles.

It turns out that medical journals have a huge market for article reprints: drug companies. Journals make hundred of millions of dollars a year selling paper reprints to drug companies. The drug companies distribute these to the pharmaceutical representatives, who in turn give them to physicians to promote whatever new drug the reps are promoting to the physicians.

Medical journals have a massive incentive to publish research articles that show new drugs in a positive light. They have no incentive to publish negative results. Who will buy articles that show something doesn’t work?

The last panel I saw was one on Internet security. It was devoted to a proposal that someone at Microsoft put forward that Internet security could be modelled after public health. For instance, just as an unvaccinated child might not be allowed to attend a school, a computer with the latest anti-virus software might not be allowed to connect to the Internet.

One issue around this is that any sort of public health model always involves a certain amount of coercion, since it only works if you have universal (or nearly so) adoption. This means less privacy, less autonomy, and so on.

Another question is whether public health is the right model for thinking about Internet security. What is the Internet equivalent of the plague or Spanish flu? Perhaps Stuxnet? Most computer viruses are not like Spanish flu, sort of “in the air”; there are more like sexually transmitted diseases, in that it requires very specific action on the part of the user to cause trouble (e.g., opening *.exe attachments; contacting that Nigerian prince). There are places where the analogy breaks.

A final point on the panel was that by buying a smartphone, you are taking on certain obligations. Smartphones are connected, and that means you are part of a community. You have responsibilities above and beyond paying your monthly phone bill.

How Do We Know What We Know? from Ivan Oransky

Here’s a storify pf Ivan’s keynote:

PACE 2013 Bioethics conference, day 2

The PACE conference continues to go well, as far as I can tell. I was not able to spend as much time at the conference today, but a panel on the business of healthcare early afternoon was filled to the brim. I apparently should have been there, because a pharmaceutical representative was apparently making all manner of... interesting... claims about the efficacy of brand name versus generic drugs, among other things.

Cross border shopping for health care: The panel started off with this segment from The Daily Show, which the audience seemed to enjoy.

The Daily Show with Jon Stewart
Get More: Daily Show Full Episodes,Political Humor & Satire Blog,The Daily Show on Facebook

I polled the audience as to how many of them had gone to Mexico for some form of health care (including buying medicine), and at a rough count, slightly more than half had. Dental work of some sort seemed to be very popular, and one of the panelists said that the main reason people went to Mexico was the lack of insurance.

I told the story story of Celltex, a company offering experimental stem cell treatments that have not been approved by the US Food and Drug Administration. The company's first patient was Texas governor Rick Perry. Despite Perry's high profile support, the company has continued to be on the receiving end of controversy. In February, Celltex packed up and moved to Mexico, where it didn't have to put up with the FDA regulations. This raised questions about whether patients should be allowed to seek unproven treatments in other countries. Would a patient who went on medical tourism could lose insurance. Could a physician refuse treatment to that patient if complications ensued?

Another issue of cross-border comparisons that arose from an audience question was the relative pay of doctors. For instance, in 2008, the average wage of an American physicians was about $189,000 after expenses, but a Canadian physician made about $125,000. Thus, not only are patients "cross-border shopping," physicians are, too.

Yerberias: Oh, but this turned out to be an interesting panel. I was moderating it, and it turned out to be an interesting challenge.

"Yerberias" are, as far as I can tell, a distinctly Hispanic cultural institution. They might be described as an intersection of magic shops, herbal remedies, and Christian paraphernalia (note the saint on the door in the picture at right). So the idea was to talk about traditional compared to science-based medicine.

One of the scheduled panelists said that asked someone who knew more about this to replace her, and the replacement turned out to be a naturopath practicioner, Shirley Layton. I mentally did a double take when she started talking about homeopathy as effective treatment. Later, she started talking about "double helix" water that was "aligned" to better pass into cells of the body. I think she also had some unconventional ideas about root causes of cancer. And toxins.

Another panelist was discussing "energy healing."

On the other hand, I was there as moderator, and I am skeptical of these things, to say the least. But my job is to ensure the conversation kept going, the audience members had a chance to ask questions, and not pull a Bill O'Reilly style, "I'm unplugging your microphone."

As it happened, we had another faculty member from biology, Andrew McDonald, who has lots of experience in ethnobotany. He characterized things like "double helix water" as "nonsense," (which was also my take) and spoke strongly about the importance of the scientific method. If you don't have reproducible results, you are involved in faith, not science.

At one point, Layton said something along the lines of, "I have knowledge, but not proof," and McDonald replied, "That is something a quack might say." Layton responded, "I am not a quack" in a way that stopped the poster session in the next room. McDonald said, "I didn't say you were a quack, but that is something a quack might say."

I also brought up the point that a Google Scholar search for "yerberias" returned several papers on things like lead and arsenic poisoning. Layton agreed that this was a problem. This might indicate that there might be a role for greater regulation.

Honestly, I loved this panel because there was a frank exchange of views from people who did not agree with each other. After last year's conference, I thought there was too much agreement, which kind of defeats the purpose of panel discussions.

Photo by cobalt123 and houston mamacita on Flickr; used under a Creative Commons license.

PACE 2013 Bioethics conference, day 1

I spent most of the day at an ethics conference here at the university. Let me give you a brief round up. I didn’t see everything (schedule here), but here’s a round up of some stuff I did see.

Texas cancer scandals: Panel discussion about the woes of CPRIT, a Texas cancer center supported by a state mandate to give $3 billion in research money over 10 years. CPRIT has gone from prominent hiring of Alfred Gilman, Nobel prize winning scientific advisor setting out to create world class peer review system, to grant given $18 million without scientific review, to announcing yesterday that the organizing will be closing in 60 days.

Doctor Google: This was a discussion of potential problems caused by people looking up their symptoms on Google, using cell phone apps, or other online resources rather than seeing a physician. I was surprised by two things. First, everyone in the room admitted to googling their symptoms when they felt sick. Second, the physicians are grateful for this. Both the physicians on the panel said that had changed treatments multiple times based on information that patients found in the Internet.

Freedom to be fat: The New York regulation on large soft drinks was the jumping off point for this discussion on diabetes and obesity. This one had probably the best audience participation (the timing was good to have lots of people in the room). There were a lot of different positions, ranging from “People have autonomy, full stop, and we should not do anything that interferes with that” to some people suggesting regulatory agencies did have a role to play. However, everyone’s favourite solution was “education.” I don’t think this was because it was necessarily the most effective solution, but it is one that everyone can get behind.

Open Access: I was on this panel, and readers of this blog will probably know a lot of the issues we faced. This one didn’t have a great audience participation, as not a lot of people in the room are actively publishing. One interesting moment, though, was when I asked the audience how much it cost to publish a scientific article. One medical physician, in trying to work through the problem, listed the things that would cost money. And he got to, “Paying the reviewers...”

That’s when I stopped him and asked if this was something that happened in medical journals. As far as I know, it doesn’t. Authors write for free, reviewers review for free, many editors edit for free. But it did highlight that unless you are right in the thick of scientific publishing, the issues are not clear to a lot of people.

Healthcare delivery: I got a sense of frustration out of this one. One panelist definitely was working a Tea Party vibe (“government can’t get anything right”), but there were things to learn.

One of the biggest surprises to me was the problem of electronic medical records. Now, as someone who sees nothing but benefits from digital, I was surprised that the panelists said some physicians said they’d quite or retire before dealing with electronic medical records. I asked why, and one answer was that the record keeping actually slows people down, by about 10%. Kristy Lam on Twitter described it thus:

Friends in healthcare talk about the nightmare of pop up assessments on screen. Unwinnable whackamole.

There’s also concerns about the initial cost outlay of putting in a medical record system.

External links

PACE home
UTPA kicks off annual bioethics conference (photo source)

Tuesday Crustie: Belize it or not!

This crab was photographed off the coast of Belize. There are so many brachyuran crabs, I am always in awe of people who can come up with even tentative pecies identifications. This one, the photographer thinks is Mithrax spinosissimus.

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

Better off blind

Eyes are good things to have in the light. But if you lived in the dark... all the time... would those eyes become so much a nuisance that you might lose them?

Animals that live in caves are often blind. People sometimes mistake this as evidence that features can be lost just by a “Use it or lose it” rule. That would be an example of inheriting an acquired character, which doesn’t happen in evolution. Instead, the typical explanation is that because there is no advantage to maintaining eyes if you’re a cave dwelling population, any mutation that messes up making eyes is on an equal footing with the genes for making eyes.

It’s not that there’s an advantage for blindess... it’s just that there’s no disadavantage to it. And eyes are complex things to make, so lots of mutations could interfere with making eyes.

A recent paper by Klaus and colleagues suggests that sometimes, blindness in a cave-dweller is an advantage, not just neutral. They examined a group of crabs (genus Sundathelphusa; pictured, showing most cave adapted at bottom) in the Philippines. These are freshwater crabs, and some live in lakes and rivers and such above ground, and some live in caves. In fact, these crabs invaded caves over half a dozen times in the genus. The repeated examples make for nice natural experiments.

Using a combination of genetics plus the shape of the animal, they found that the eyes of the cave crabs had evolved just as fast as other features. Klaus and company argue that if the loss of eyes was genuinely neutral, you would expect it to be happening more slowly than other features, which are presumably under selection. Instead, the eyes were evolving just as quickly as the other featured, which suggests there is some sort of advantage to being blind.

What the advantage might be... the authors don’t say, surprising. In the introduction, Klaus and colleagues mention the idea that losing eyes “frees up” compuational power for other sensory organs. But they don’t follow that up in the discussion. They don’t even speculate a tiny little bit in the discussion. Other papers have also suggested some sort of advantage to blindness, but as far as I know, nobody has yet come up with a testable hypothesis. That it seems to be the case with both vertebrates and invertebrates suggests that whatever that selective factor is, it is very general.

Additional, 17 April 2013: Another take on this paper is at Mostly Open Oceans.

Reference

Klaus S, Mendoza JCE, Liew JH, Plath M, Meier R, Yeo DCJ. 2013. Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs, Biology Letters 9(2) 20121098. DOI: 10.1098/rsbl.2012.1098

Related posts

Turning light and going blind: A tale of caves and genes
Once more into the cave

Comments for second half of March 2013

The NSF DEBrief blog asks what proportion of awards should be awarded to beginning investigators and undergraduate institutions? (Pushed to comment there by Prof-Like Substance.)

A mole crab post! By someone who is not me! Instead, it is Beach Chair Scientist! Of course I shall comment!

Can formal training fix bad science talks? Leopold Leadership suggests every grad student get formal training on talks. I’m not sure this will do the job.

InBabyAttachMode considers the always vexing issue of work / life balance, given that blogger Dr. Isis is saying she could well be out of academic science in less than year.

The conversation about family friendliness continues at The Barefoot Doctoral.

Good post on scientific publishing in the attention economy.

When is professional development worth it when you’re a grad student or post-doc?

Amy Freitag looks at whether acceptance to grad school means anything if you didn’t get a stipend.

Girls are Geeks look at geeky band names.

On Google Plus, David Brin takes an overly optimistic view of a recent paper on brain imaging of convicts and a recent TED talk on desertification that is apparently going viral, but where the science is questionable.

Running Ponies looks at inky slugs, a research program I’ve talked about before.

Blockbusters and telenovelas: models for science communication

This week has seen a couple of headlines where not surprising things were gussied up to look like very big deals. I’ve already written about the “Darwin had emotions!” headline, and yesterday, a piece about saying “Evolution without adaptation!” was making the rounds. When I read the headlines, I made a face, as it was dangerously close to the sort of “Darwin was wrong!” headlines we’ve seen before. Sure enough, the article is about genetic drift, which is well known to working scientists. The original scientific paper about ring species is interesting,  but the Wired piece was making it seem more unusual than it was.

This is a recurring issue in science coverage. The dominant way people try to push a scientific story into the media is to sell it like this:

Science as summer blockbuster movie. This is the model that sells every story in science as a breakthrough, and that those are the only things worth our attention.

But the reality is that much of science is not about breakthroughs. It’s about slow progress.

For instance, at the recent NESCent conference (Storify here), the ENCODE project was criticized for trying to present itself an important breakthrough finding about junk DNA. The ENCODE team tried to position itself as a summer blockbuster when it wasn’t. There are lots of other examples. Another case in point: that irresponsible Time magazine cover this week, saying it was “now possible” to “cure cancer.” Wrong.

Claims of imminent breakthrough after breakthrough are going to bite us. .
There is a mode for storytelling that is more like most science.

Anyone who has every watched a soap opera or a telenovela knows that on any given day, not a lot happens. Plots advance not in single episodes, but drawn out over weeks, if not longer. The running joke is that someone stops watching a soap, comes back after months or years, and says, “I can’t believe that Robert still hasn’t confessed his love for Alice and broken it off with Britney!” There is a often a huge cast of characters, sometimes with only mildly interacting stories.

Why do people come back to soap operas, and other sorts of long form storytelling, where arcs are drawn out over months or years? The characters.

This is one reason why I think blogging and social media for scientists is so important.

I didn’t realize it at the time, but things like the old Science Blogs site (before the Pepsi implosion), and other independent science bloggers I started following around that time, became my scientific soap opera. There was a cast of interesting characters, each with their own quirks and obsessions. And you could see their progress over time. It’s been great to watch people graduate from their degrees and make it into post-docs, and move from post-docs to tenure-track positions. Some people come, some go, and others make dramatic returns to the blogosphere (though no cases of amnesia yet).

If scientists are willing to present themselves as real people, with their own interests and problems and good times and bad, we don’t need to try to convince everyone that the only reason to pay attention to us is because we’re going to save the world from an alien invasion.

Related posts

No, Charles Darwin was not a robot
Not every radical idea is right
The genius myth
Tales to astonish
Original and transformative
What the Coburn report has in common with arsenic life

External links

Something other than adaptation could be driving evolution
Oh geez, not another exoplanet story
Can science become too big to fail?
Yet-another-genome-syndrome
How pigeons cured my case of YAGS
Worst magazine cover of the year?

A short tale about a very short tail

As I’ve mentioned before, scientists are so conservative that when you see an adjective like “extraordinary” in the title, you should at least open up the paper if you can and have a peek.

I came across a paper titled, “An extraordinary tail – integrative review of the agamid genus Xenagama” in Google Reader ^*. I was a bit curious (and miffed) because I had no idea from the title what kind of organism this paper would be about. All kinds of animals have tails.

I love me spikes and spines and armor on critters, so I flipped out a bit when I learned this belonged to the Xenagama:

That is indeed an cool looking lizard (Xenagama taylori) with a cool looking tail. The genus Xenagama originally contained two species that was defined by this short, club-like, spiky tail. But there’s a problem when you use a single extraordinary feature to classify animals: you might overlook all the other features that tie it to other relatives.

A new paper Wagner and colleagues uses a lot of different tricks to tease apart the evolutionary relationships of the lizards in this genus: morphology, genetics, climate, and so on.

By looking at all the morphology, and not just the tails, they found that a long-tailed lizard previously put in another genus (Acanthocercus zonurus; below) sorts out with Xenagama and not Acanthocercus. Genetic analysis on this species also put it in with the rest of the Xenagama group, although it’s an early offshoot from the tree of these related lizards.

The authors also discovered a new species in the genus, that, like Acanthocercus zonurus, has a reasonably long tail; sort of intermediate between the short known species and the misidentified one. This new species is dubbed Xenagama wilmsi.

It turns out that the short tail of most of the lizards in this genus was something that was obscuring some of the relationships. There were similar problems with data on breeding colours. Some of the males in this group show different colours, which was used in creating their classifications, but the males don’t show those breeding colours all year round.

All of which doesn’t answer the obvious question: why do some of these lizards have these short tails? The tails do seem to have an adaptive function. The two species with long tails seem to be tree dwellers, while the two short-tailed species are rock-dwelling burrowers. Xenagama taylori will use its short spiked tail to close its burrow, which you can see in action below:


How this tail has been molded through development and genetic to get so short would be a great doctorate for someone. While native to northern Africa, some of these lizards seem to be fairly available in the pet trade. Don’t know how easily these lizards would be to breed in captivity, though.

Update, 29 March 2013: When readers think of better titles than me: Malcolm Campbell dubbed this article, “Get shorty.” Brilliant!

^* You know, that allegedly useless service that absolutely nobody needs because all of the people on Twitter and social media are so good at finding stuff that I want to read, yet who somehow let me down on discovering this.

Reference

Wagner P, Mazuch T, Bauer AM. 2013. An extraordinary tail - integrative review of the agamid genus Xenagama. Journal of Zoological Systematics and Evolutionary Research: in press. DOI: 10.1111/jzs.12016

Top photo from here; Acanthocercus zonurus from here.

No, Charles Darwin was not a robot

The BBC has this headline about some new letters by Charles Darwin that have not been published before:

Charles Darwin letters reveal his emotional side

This headline was apparently written by someone who has never read anything by Charles Darwin.

Anyone who has read Darwin’s work could criticise it many ways, but “emotionless” is not one of his faults. There’s passages like his story of holding a beetle in his mouth, showing his self-described “zeal”:

I will give a proof of my zeal: one day, on tearing off some old bark, I saw two rare beetles and seized one in each hand; then I saw a third and new kind, which I could not bear to lose, so that I popped the one which I held in my right hand into my mouth. Alas it ejected some intensely acrid fluid, which burnt my tongue so that I was forced to spit the beetle out, which was lost, as well as the third one.

Or, more seriously, look at what he wrote about his daughter Annie (small snippet):

We have lost the joy of the Household, and the solace of our old age:— she must have known how we loved her; oh that she could now know how deeply, how tenderly we do still & shall ever love her dear joyous face. Blessings on her.—

I could pull many, many other examples. That Darwin had  “emotions” is not a surprise worth a headline. Maybe the BBC is buying into the old cliche that scientists are detached, hyperrational robots. But they should know better.

Tuesday Crustie: Barnacle boat

Lots of animals in the ocean need hard surfaces to settle on. So it’s no surprise to see a log adrift to be occupied. It might be unusual, though, to see driftwood so completely occupied with one main species, a pelagic gooseneck barnacle:

Here’s a close-up:

Photos by alex1derr on Flickr (here; here); used under a Creative Commons license.

Steering into the skid: what can we fix with formal training in grad school?

A couple of years ago, I got into a car wreck. A tire blew out on a truck to my right. It swerved and hit me. I skidded across the road. You know what you’re supposed to do in that situation, right?

You’re supposed to steer into the skid.

I did not. I was unable to correct the skid, and wound up crossing a couple of lanes of the highway. There was no oncoming traffic, and I was fine.

I was trained to do the correct thing and steer into the skid. I took driving lessons. Steering into the skid is what you’re told to do in driving school. I know this intellectually. But it’s not intuitive, you have only a split second to react, and, most importantly, we try hard not to create out of control skids. Skids are rare for people doing routine driving, especially in someplace like Southern Texas, where there are rarely icy roads.

How much time should driving instructors spend training beginning drivers to cope with skidding? There isn’t a simple answer. Someone who wants be a professional driver should get more training. A person whose driving mainly to a daily commute in a warm, semi-arid climate, may not need any training. I never practised steering a skidding car, although I learned to drive in Canada, where icy roads are routine.

Last week, NESCent hosted a conference on journalism and reporting of evolution; something I’ve written about a fair amount here. As a possible solution to improve the situation, Melissa Wilson Sayres wrote:

Best Practice: Formal training in journalism/media communication for graduate students

(Check her original tweet for some discussion.)

This suggestion is well meaning. It’s a tempting suggestion to make for us in academia, since our entire career revolves around training in one way or another.I’ve been guilty of saying, “Every academic should make it a point to get good at... (pet topic).” But such suggestions are hard to do. 

The deeper concern is whether “formal training in graduate school” can what we want it to do.

For instance, there has been a lot of interest in having students receive training in research ethics. Funding agencies love these. Some set aside specific pots of money to supplement training programs so that those programs can include training in ethics. Despite that, the Retraction Watch blog has no shortage of material, and most retractions are due to unethical behaviour on the part of the authors (Fang et al. 2012).

As an instructor, obviously I am not going to say that training is entirely useless. Rather, I am saying that training happens in a larger context. There is a great big ol’ reward system in place in academic science. Academic science rewards you for original peer reviewed journal articles, preferably in a small set of journals with a high impact factors (the “glamour mags”), and grants. The rewards for getting those things are large.

Giving a grad student formal ethics training and expecting them not to be even a little tempted to take shortcuts in their research to get those highly rewarded papers in Nature, or Science, or Cell is like admonishing someone to cut down on calories while leading them through a cupcake shop giving away free samples while everyone’s back is turned.

Similarly, despite training about sexual harassment, there’s still a lot of pig-headed, boorish, sexist behaviour in the workplace. Again, note that I’m not saying that such training is useless, but that there is a lot of  cultural baggage that can’t quickly be overcome by “formal training.”

First, there is no central authority that says, “YEA VERILY, ALL GRADUATE PROGRAM SHALL TEACH...” Trying to implement any formal training across the board is tough, given that grad students are spread across thousands of independent fiefdoms.

And let’s not underestimate how long “communication training” would take. As Karen James wrote:

I’ve been working at (communicating outside a research field) for a decade and still not there.

Graduate students get a lot of formal training already. There has to be a point where we stop adding to their curriculum. We can’t just send students to a workshop, or even a semester long class, then dust off our hands and say, “They’ve been trained.” Communication training won’t matter much until there are rewards and opportunity for people to practice those skills, day in, day out, until it becomes like steering into the skid: when you don’t even have to think it through.

Reference

Fang FC, Steen RG, Casadevall A. 2012. Misconduct accounts for the majority of retracted scientific publications. Proceedings of the National Academy of Sciences 109(42): 17028-17033. http://dx.doi.org/10.1073/pnas.1212247109


Related posts

“We cheated death”

External links

Reporting Across the Culture Wars: Engaging Media on Evolution
Retraction Watch

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

Almetrics and the need for speed

I’ve been playing around with ImpactStory, which I learned about at Science Online and was also featured at the recent AAAS meeting. I like it.

In playing with it, it occurred to me that there is only one reason we need this, and tools like it. Because we need to make decisions relatively fast. With tenure, promotion, and funding decisions typically are trying to evaluate research done in the last couple of years.

If it weren’t for that, I’d wager we’d just use citations to evaluate research contribution. Citations have always been considered a very good measure for how a scientific article has affected the research field. The problem is that citations accumulate too slowly. Altmetrics are starting to tease apart other kinds of impact (interest in the general public). For routine academic decisions, though, would you need anything besides citations if it weren’t for the speed issue?

Additional, 25 March 2013: There are a lot of interesting points in this article, but relevant to this post is this graphic about the probability of being cited in physics:

If I understand this right, the X axis shows the time to first citation and the Y shows the number of citations. As author Kristina Lerman puts it:

A newly published paper is very quickly forgotten. After a paper is a year old, its chances of getting discovered drop like a rock!

This suggests that the situation for traditional citations isn’t as slow and pokey as I might have thought. That first citation seems to be a decent predictor, and a year isn't that long to wait. I would be interested in knowing if there are similar analyses for other scientific disciplines.

External links

Stop publishing so much already!

The audience member that counts most

One of the most common pieces of communication advice is, “Know your audience!” I’m going court controversy by saying that is overrated advice.

Many people have produced substantive works and had only vague ideas about who their audience was. Last year, an article in the Wall Street Journal made this point explicitly about books:

Novelist Scott Turow says he’s long been frustrated by the (book) industry’s failure to study its customer base. “I once had an argument with one of my publishers when I said, ‘I’ve been publishing with you for a long time and you still don’t know who buys my books,’ and he said, ‘Well, nobody in publishing knows that,’ ” says Mr. Turow, president of the Authors Guild.

Yet authors managed for centuries to create books with only the vaguest understanding of who their readers were.

In his memoir, animator Chuck Jones (the man responsible for many classic cartoons with Bugs Bunny, Daffy Duck, Marvin the Martian, and the Grinch) talked about the process of making Warner Brothers classic cartoons. They had no idea who their audience was.

We never stopped to analyze what made our cartoons funny. If they made us laugh, then we hoped the audience would follow.

Stroke of Genius, A Collection of Paintings and Musings on Life, Love and Art

Although they didn’t ignore input entirely. Jones told the story of producer Eddie Selzer in his memoir Chuck Amuck:

He once appeared in the doorway of our story room while Mike Maltese and I were grappling with a new story idea. Suddenly a furious dwarf stood in the doorway: “I don’t want any gags about bullfights, bullfights aren’t funny!” ...

Having issued this angry edict, Eddie stormed back to his office, Mike and I eyed each other in silent wonderment. “We’ve been missing something,” Mike said. “I never knew there was anything funny about bullfighting until now. But Eddie’s judgment is impeccable. He’s never been right yet.” ...

Result: Bully for Bugs - one of the best Bugs Bunny cartoons our unit ever produced.

Remember, the Warner Brother animators worked at a time when everyone went to the movies regularly. There was no marketing or focus groups. Their animated shorts were “add ons” to feature presentations, so there was probably no tracking of box office. Their cartoons were made when was no television. How could the creators anticipate that their cartoons, many of which had fairly adult jokes in them, would become Saturday morning staples for kids decades later?

Looking at it a little closer, the “Termite Terrace” crew made their cartoons to please themselves. They were their own audience.

As you develop a presentation, and as you give a presentation, it is critical that you become your own audience. You always have to be asking yourself, “What do I think of this work?” This is not to say that you should ignore feedback from others; it’s important to be checking your perceptions with others to avoid the Dunning-Kruger effect (unskilled but aware of it).

This also means that we instructors should ask our students, “How do you think you did?” more often. We have to force them to be analyzing their own work before giving it to us.

But if you’re honest with yourself, you’ll have a good idea of when you’re on the beam, when you’ve fumbled, and when you’ve fallen flat on your face.

External links

Your e-book is reading you

SARS a decade on, with a lesson about administration

There have been a few retrospectives the last couple of weeks about the tenth anniversary of the emergence of SARS. There are several articles in the current issue of Science magazine and on their podcast.

A story from that time. This was at a time when the Regional Academic Health Center (RAHC) was not up and running yet. I distinctly remember in a faculty meeting, our then department chair announced that the plans for the RAHC were that researchers there would be doing research on diabetes... and SARS.

All the faculty in the room laughed.

This was so obviously something an administrator said because he or she latched on to what was in the news right then, with no idea of the biology. Lots of epidemics are fleeting. The people in charge were fishing for ideas. I remember someone saying something like, “SARS will burn out before the building ever opens.” And he wasn’t far wrong.

This has remained a great example of why research initiatives should rarely be started by top-down directives. The gap between ideas and practical problems can be too large. There’s too much risk of people on the ground saying, “We need bullets and body armour” somehow being turned into the higher-ups saying, “We’re winning the war on terror.”

Related posts

Who ya callin’ “small”!?
Oh boy, here it comes...
A beautiful white elephant?

External links

The SARS wake-up call
A decade ago, SARS raced round the world; Where is it now? Will it return?

A big vote on a new university

Today is a big day for my institution. A deciding vote on whether to create a new university in south Texas by merging mine (The University of Texas-Pan American) with other institutions here in South Texas.

9:57 am: I’m a bit annoyed that the Texas legislature is only providing a stream through Real Player. God, it’s been years since I’ve used that software.

10:00 am: Opened up RealPlayer. Here we go.

10:05 am: An invocation. Wow. And it’s not even Sunday. Sometimes, I kind of forget how ingrained Christianity is in the official business of politics.

10:08 am: Pledge of allegiance and allegiance to the flag of Texas. And now a Doctor of the Day? I think they really mean Physician of the Day. Do you reckon a Ph.D. has ever been featured as Doctor of the Day?

10:12 am: Not much happening now. House getting called to order.

10:13 am: HR 651, a bill honoring NASA! It’s Space Day at the Texas capital. I’m actually quite glad that this is happening on the same day as our bill.

10:18 am: HR 373, a bill honoring the 80th anniversary of a church in Dallas.

10:22 am: An announcement of the opening day of the Texas Rangers baseball team? Yeah. More evidence that the public stuff is just for show, and the real work goes on in the backrooms and committees.

10:23 am: HR 948, Brezoria County Day at the State Capital. Wow. There are a lot of special days at the state capitol. It must get tiring.

10:26 am: A representative is announcing his mother’s 70th birthday. And there’s a HR 1012 to congratulate her.

10:30 am: HR 1020, homelessness awareness day.

10:37 am: Missed some stuff when someone came into my office. Now seems to be a bill celebrating a newspaper’s hundredth anniversary.

10:38 am. A representative from Brezoria County has five more resolutions... bet they’re all congratulatory for people in Brezoria County.

10:41 am: A representative just called himself “a small country boy.” I think he’s joking. But I’m not sure.

10:48 am: Now a memorial resolution, recognizing a former judge. Starting to feel lots of sympathy to the clerks, who have to read a lot of fairly mundane stuff quickly and accurately.

10:55 am: HR 887, a resolution honoring visitors to the capital. They're peeling through these fast. I wonder if the bill to create a new university will be ripped through at the same pace as these commemorative resolutions.

11:21 am: Someone is in my office again, but I turn back at just the right moment to catch debate on HB1000, with one senator raising concern about whether students trained at the medical school will stay in the state.

11:25 am: A representative says he hopes that in years to come, when people nationwide say, “the valley,” the question will be, “Do you mean Silcon Valley or the Rio Grande Valley?” A somewhat unexpected plug for the research aspect off the bill, rather than on the medical school, where most of the attention is focused.

11:27 am: The vote occurs. Final tally, 149 ayes, and 0 nays. No surprise that it passes, though perhaps the unanimity is. The bill has to have a third reading and go back to the Texas senate, but I cannot see anything that is going to stop this train now.

External links

House Gives Early Approval to South Texas University

Geek love

Squee!

This blog is featured at Girls are Geeks today!

They say lots of nice things about this blog. I’m blushing. Thank you, Girls!

Tuesday Crustie: Texting

Poor hermit crab. He could really use a new phone. Those clicky keyboards are old school...

Spotted here.

Today in cognitive dissonance: celebrating “landmark” openness in a closed journal

A new editorial in The Journal of Comparative Neurology celebrates a paper that goes the extra mile in making its anatomical data available:

(The authors) provide an unprecedented level of access to their supporting data by publishing their full set of experimental outcomes in the form of virtual slides, or whole‐slide images.

The editorial nicely summarizes why archiving data from brain slices is particularly important. Brains are complex structures, and there is necessarily a lot of interpretation of what you see on microscope slides. (How many beginning students mistake air bubbles for amoeba?). Increasingly, many studies rely on stains that fade over time.

For comparative neuroanatomists, you can’t always guarantee that you will be able to get another brain from some interesting species. You can’t just go get a brain from a whale any time you want. There is a tradition of collecting and archiving interesting brains from all kinds of species in comparative neuroanatomy.

The editorial points out the advantages of archiving these data on the Internet rather than in print:

(A) typical virtual slide in the collection would require over 250 square meters of paper if printed at full resolution.

The irony of all this is that The Journal of Comparative Neurology is a paywalled, subscription based journal. And not just any subscription journal, but one with a breath-taking $30,860 price tag. And that’s for Internet access or print. If you want both, be prepared to add a few thousand to meet the new asking price of $35,489.

Guys, if openness and data sharing is good, and the limitations of print are bad, you’ve just made great argument for journals like PLOS ONE, PeerJ, the BioMed Central family, and their like. Why does your journal continue to exist in its current form?

Related posts

Got $30,000 to spare?

References

Gaillard F, Karten HJ, Sauvé Y. 2013. Retinorecipient areas in the diurnal murine rodent Arvicanthis niloticus: A disproportionally large superior colliculus. The Journal of Comparative Neurology: in press. DOI: 10.1002/cne.23303.

Karten HJ, Glaser JR, Hof PR. 2013. A landmark in scientific publishing. The Journal of Comparative Neurology: in press. DOI: 10.1002/cne.23329

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

The costs of being tall: lessons from giraffes

True facts about giraffes!

They’re tall. And I use the word precisely. They’re not just big; their legs are about half again as long as you’d predict based on their mass and bodies of other mammals.

Being tall has distinct consequences for the nervous system. The distances that signals have to travel might mean there is lots of lag between something happening out in the world, the signal getting to the brain, and the appropriate response going all the way back down to the muscles the animals use to move about.

There are ways around this distance problem. You can make axons bigger, which speeds up how fast they can send a signal, but that means you probably have fewer axons, which could mean lower sensitivity on the sensory side, or precision on the motor side.

A new paper by Heather More and colleagues try to figure out how the giraffe’s nervous system deals with all these great distances. They recorded the speed of reactions and the size of neurons in the sciatic nerve of giraffes. The average speed of signals in this giraffe nerve was about 50 meters per second, which is about the same as rats. Rats, it should be noted, are not tall. They’re not even big.

More and colleagues calculated that for a giraffe to be as quick and as responsive as a rat, the speed of signals would have to be around 200 m/s, which is the top speed in the entire animal kingdom (a record held by some shrimps). And to get to that point, their neurons would have to be two and a half times the diameter they actually found in the giraffes.

Looking at the sheer number of axons, More and colleagues also suggest that the giraffe is comparatively at a disadvantage compared to smaller mammals. If the giraffe’s sciatic nerve had the same number of axons for its size as the rat does, it would have about 50 times more axons than what giraffes actually have.

From this, the authors predict that giraffes are working with a bit of a neural and behavioural handicap. They should be less sensitive to the world around them, and slower to respond to it, than smaller animals. But this is still a prediction that needs testing. Getting some giraffes in the lab for the experiments might be a bit tricky.

P.S.—When I blogged about a previous paper with some of the same authors, one criticism in the comments was that the team used conduction velocity of action potentials to measure “responsiveness.” This paper does a much better job of laying out all the different elements that go into determining “responsiveness” in general. That said, they don’t make much progress on measuring all those other elements in this paper, but at least they recognize they exist.

Related posts

The elephant and the shrew, an axonal story

Reference

More HL, O'Connor SM, Brondum E, Wang T, Bertelsen MF, Grondahl C, Kastberg K, Horlyck A, Funder J,  Donelan JM. 2013. Sensorimotor responsiveness and resolution in the giraffe. The Journal of Experimental Biology 216 (6): 1003-1011. DOI: 10.1242/jeb.067231

Top photo by ucumari on Flickr; used under a Creative Commons license.