29 March 2013

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?

28 March 2013

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:

Xenagama taylori

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:

Top photo from here; Acanthocercus zonurus from here.

27 March 2013

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.

26 March 2013

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.

25 March 2013

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 ca, 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.

22 March 2013

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!

21 March 2013

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

20 March 2013

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?

19 March 2013

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.

18 March 2013

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:

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:

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

17 March 2013

Fans can turn on you

If there ever was a Kickstarter that resulted in a second season of Firefly, what do you want to bet that fans would watch it and say, “The old stuff was better”?

Seen this happen many times. Genre fans are fickle.

There are an advantages to having one short, beautiful run of a series. Seal it away and be done with it.

16 March 2013

Comments for first half of March, 2013

I make a cameo in our Office of Grad Studies blog about a recent mentoring workshop.

The Science Online 2013 music video by my sister from another mister, Carin Bondar, went up! I make a cameo:


You may not quite see what I’m doing in my second brief clip, but when Carin pointed her camera at me, I reached into my pocket, and unfolded a piece of paper to show to her:


Deep Sea News covers a familiar article: sea cucumbers eating through the back door.

Dynamic Ecology examines peers, mentors, role models, and heroes.

The Cellular Scale examines bald assertions in manuscript reviews.

Prof-Like Substance asks how much funding undergraduate universities should get for research. He’s asking particularly about the National Science Foundation.

15 March 2013

Internet services or Internet utilities? More thoughts on the death of Google Reader

The week began with me writing that I could not have written my latest research paper without two services from Google: Google Alerts and Google Analytics. The week ends with me writing about Google pulling a service that I use in my work routinely. Irony.

To go even further, last night listening to the Science podcast, I hear a story about how a team showed you can predict interactions between available drugs before this is recognized by the American Food and Drug Administration. How do they do this>? Using data from Google.

The raises a question. How useful does a service have to be that a company has a moral obligation to keep a service running? How widely used does something have to be before it stops being something that a single private company should control?

Imagine if Google decided that it wanted to get out of search. Sure, some people would say, “Hey, no big deal. DuckDuckGo and Ask all exist. Meybe even Bing could become relevant.” But let’s realize that for many people, Google’s search engine practically is the Internet. And Google data is being used for scientific research in a way that other services are not.

Many have pointed out that we can’t expect free services to last. Someone has to pay. Usually, people think of ads or subscriptions, and stop.

We may need to start thinking about some core functions of the Internet not to be handled only by services that individual companies can do as they want with. We may need to think of starting to establish chunks of the Internet utilities. And utilities are things that get regulated. There is a reason why we don’t have a hodge-podge of private roads. Common, stable, public infrastructure matters.

For instance, Google Scholar was largely anticipated by PubMed. PubMed’s problem for me is that it is too focused on biomedicine, and there aren’t equivalent services for other fields. But that it is a publicly supported utility means I have much more confidence in its permanence than I do for Scholar.

You might notice that these arguments about services used by scientists parallel arguments made about the products made by scientists (i.e., open access publishing). In both cases, the concern is about having the stuff scientists need to work being controlled by private business. Perhaps supporters of open access need to start putting as much emphasis on Internet services, like Google, Google Scholar, and Google Reader. After all, we’ve already seen one tool for academic referencing, Mendeley, look like it will be bought by Elsevier, a for profit publisher. Mendeley pushed open data sharing, and was lauded for it. Elsevier might not have the same ethos.

Are there services on the Internet that are “too big to fail”? They should be identified sooner rather than later. And we should think about how we can create thriving, stable ecosystems of those services, not ones that can disappear at a moment’s notice.

External links

Paging Dr. Google
Elsevier in advanced talks to but Mendeley
Why RSS still matters

14 March 2013

The terrifying death of Google Reader

Yesterday, I learned about Google’s decision to do away with Google Reader. My first reaction was: How am I going to work now?

I use Google Reader practically every day in my research. I cannot begin to tell you how big a difference Google Reader has made to my work flow. Almost every scientific journal has an RSS feed, and I have a great heaping bucket of them in Reader. Being able to go to one place instead of many enabled me to scan so many more articles in so much less time.*

Plus, Reader allowed me to search back in old posts. I can’t count the number of times I thought, “I remember reading that in a blog, but not which one” and find it by searching Reader.

I’ve seen some people argue that we don’t need Reader in the age of social media. Why get an RSS feed when the hivemind recommends the good stuff? Where do you think the hivemind finds the stuff to recommend? From people who are monitoring their RSS feeds. I am often aware of stuff in my feed days before I start seeing recommendations on Twitter, say.

Since I’m apparently going to have to get used to life without Reader, I’ve been looking at alternatives. So far, I’ve only come aware disappointed and more impressed by Reader’s good design. Reader’s split screen, with list of feeds, then updated individual posts, and the spacebar to mark a post and move to the next one, allowed you to get through a lot of stuff fast.

I tried Feedly. I got sick of how little I could see on the screen and constant clicking to get around. Newsblur and The Old Reader are choking on importing my old feeds, and I have so many feeds that entering them all in again by hand is not an attractive option.

But putting aside all this inconvenience, my bigger worry is now about the other Google services that have made their way to the center of my life as a scientist.

Blogger and Google Scholar. I have a decade’s worth of writing here on Blogger, with three active blogs. I’ve written about Scholar before, and it has just gotten more and more useful over time, with features like analytics for articles, author, and journals, and new article alerts. I use it extensively.

If those services shut? What then? I’d be screwed.

Google seems to have a lot of forward looking group of people. It seems to be one of the few companies that believes in conducting, and supporting, original research. It is a company that has promoted itself as having a forward-looking vision.

But there is something perverse about creating tools that genuinely work and improve other people’s ability to do work (including research), then take them away without an alternative. It would be like Henry Ford introducing the automobile, than discontinuing it and telling everyone they should go back to their horses and buggies. 

* Before you say “Just use PubMed,” PubMed’s not as great for us outside of biomedicine.

Update: Slate draws attention to Google Scholar, too, and makes a similar point to me.

Or how about Google Scholar, the academic papers search engine? Sure, this extremely useful service is in keeping with Google’s larger mission to make the world’s knowledge universally accessible. But Google does not display any ads in Scholar, and I can’t think of any other way it’s padding Google’s bottom line. So might it, too, disappear some day?

External links

Why Did Google Reader Die?

13 March 2013

One vote down, one to go

The Texas Senate passed bill SB 24 to create a new University of Texas institution in the Rio Grande Valley, as reported here, by a wide margin.

The reporting is already starting to annoy me. Why is the headline, “Senate approves medical school for Valley” instead of “Senate approves new university for Valley”? Or how about “Senate approves The Texas Academy of Mathematics and Science in the Valley”? The latter is in there. Nobody had ever mentioned before, even though it’s a big part of the Senate bill.

House bill 1000 is the House of representatives version of the bill, and it’s here. If I’m interpreting it right, it will be voted on on 19 March 2013.

First legislative vote on new Texas university

My institution’s Facebook page (?!) is reporting that the Texas Senate will be voting today on SB24 , a bill to create a new university in the Rio Grande Valley. The Senate will convene at 11 a.m., and proceedings can be watched live here.

12 March 2013

New university out of committee

Our student newspaper reports that the bill to create a new university in south Texas is now out of committee. We still do not know when we will know if the bill will even come up for a vote in the legislature, however. The bills are supposed to go to Calendering Committee next, which gets to decide when the bills go to a vote in the legislature.

It has been interesting, to say the least, to be interviewing job candidates for positions now. The conversation keeps coming up as to what it might be like in a new university, but nothing is certain. Every conversation about the prospects for a merge is an exercise in hedging your bets.

Tuesday Crustie: “Can you tell us what happened?”



This one positively screams for a caption contest.


Spotted here. Hat tip to Miss MSE.

11 March 2013

“Blogging for the long haul” session up!

Back at the end of January, I co-moderated the session “Blogging for the long haul” with Scicurious at Science Online 2013. The session went very well, judging from the audience feedback we got. It is now available for your viewing pleasure here, along side many other excellent sessions

Watch live streaming video from scienceonline at livestream.com

The masks that Scicurious and I are wearing shall remain unexplained.

I also make a cameo appearance in the “Identity” session (co-moderated by Scicurious and Kate Clancy), at about the 9:00 mark. This is followed a few minutes later by Danielle Lee, which I blogged about here.

Related posts

Science Online 2013: “Blogging for the long haul”
Using advantages

How much is that crayfish in the window?

I could not have written my latest paper without Google Alerts.

I can’t remember when I set up Google Alerts for “Marmorkrebs” and “marbled crayfish,” but it goes back to at least 2008. Given that I set up the Marmorkrebs home page in late 2007, that was pretty clever of me, though I say it myself.

In 2009, I set up a survey on the Marmorkrebs home page that ran throughout the year (I blogged about this process here). I was very familiar with a the problems of surveys. I learned a lot about them during my undergraduate degree, where I majored in psychology. People have to be willing to come to you, and those people, being volunteers, are not necessarily representative of the general population.

Now, with so many ideas, it’s difficult to pinpoint or remember the origin of the idea. But late in 2009, a paper was published in Nature that you could predict flu outbreaks fairly well by tracking things like how often “flu symptoms” was typed into Google. (This led to this online resource.) I think the led me to the idea of using the information being delivered through the alerts to keep track of the locations where people were keeping Marmorkrebs as pets.

This project changed a lot as it went along. Initially, almost all I was concerned about was the locations where people were keeping Marmorkrebs. I had the date, the city, the American state or Canadian province.

As the project went on, and I kept collecting data, I kept expanding what I was recording. What were people calling these crayfish? (This may have been prompted by seeing made up species names.) What were people doing with them? Are the same people cropping up over and over again? And how much is a crayfish worth on the open market?

The problem was, when I went back... there was a lot of link rot. Craigslist entries came down fast, and I often couldn’t find them. It was only late in the day that I started the practice of turning every web page I could into a PDF so I could archive the entry. In retrospect, I could have done all this so much better.

Creating this paper was a little bit like making repairs on a plane while it was still in flight.

That makes the other thing I’m trying with this paper a little nerve-wracking. I decided to put the entire spreadsheet (slightly cleaned) I used in this paper up on figshare. Now, for reasons I have just described, this is not the cleanest data set out there. All the more reason to be transparent about how the set was put together, and make it available to check. I’m also happy to share PDFs of particular entries in the spreadsheet, as I expect link rot will continue to take its toll on the entries in the list.

I did some more analysis for when I presented this work at the Society for Integrative and Comparative Biology meeting in January, and I found a few more interesting things that were too late for the paper, and are probably not substantive enough for the next pet paper I’m working on. To continue the metaphor above, I am still not sure the plane has landed, and I’m still trying to fix it.

References

Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16

Faulkes Z. 2013. How much is that crayfish in the window? Online monitoring of Marmorkrebs, Procambarus fallax f. virginalis (Hagen, 1870) in the North American pet trade. Freshwater Crayfish 19(1): 39-44. http://dx.doi.org/10.5869/fc.2013.v19.039

Faulkes Z. 2013. Online monitoring of Marmorkrebs in the North American pet trade: figshare. http://dx.doi.org/10.6084/m9.figshare.645344

Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, Brilliant L. 2009. Detecting influenza epidemics using search engine query data. Nature 457(7232): 1012-1014. http://dx.doi.org/10.1038/nature07634

Related posts

Tracking Crayfish Zero: the threat of pet crayfish

08 March 2013

Is it an experiment?

“Is this a study, or is this an experiment?”

I ask students this question a lot, both undergraduates and master’s, and they struggle to find an answer. This surprises me, given that experimental evidence is arguably the gold standard for scientific evidence. That is not to say experiments are the only scientific evidence; there are many fields of completely respectable science where you can’t do experiments easily.

The difference between an experiment and a study is manipulation. That is, did the scientist actively change something, or just collect data from the world as it is?

For instance, sampling DNA from fifty species of fish to determine the relationships between them is a study, not an experiment. Observing a hundred thousand galaxies to see how many are red shifted is not an experiment. Searching for a predicted transitional fossil in geographic starta of a certain age is not an experiment. Those are all studies, not experiments.

If a human being actively intervenes in a system somehow, then you have the potential for an experiment. Adding a chemical to a mixture, removing a nutrient from a diet, showing pictures to an undergraduate, or changing how you word a survey question are all experimental conditions.

An experiment does not necessarily mean you have a control group. You can have an uncontrolled experiment. That’s not ideal, but it still qualifies as an experiment.

You can also have a natural experiment, where there has been a intervention, but not by people. The qualifier is important there, as it points out that a natural experiment is something slightly, but importantly, different from a normal experiment.

The difference between an experiment and a study should be as important a distinction to as the difference an hypothesis and a theory.

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

05 March 2013

Tuesday Crustie: En pointe!


The legs on this Dungeness crab (Metacarcinus magister) look like they could double as letter openers!

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

04 March 2013

Flipping the funnel

I have a theory why some people thrive more in social media than in social situations.

In a lot of face to face interactions, we are expected to generate a lot of inconsequential formalities first, and only later get to anything important. You have to be willing to spend a lot of time wading through small talk before you can drill down to something more interesting.


In social media, however, the pattern is often reversed. You discover a voice because that person says something interesting and, remarkable, or note-worthy. From there, you gradually learn about that person’s quirks, passions, and their trivia.



ne model involves cutting away at small talk; the other lets it grow organically. I’m not saying either one of these is a better way of communication; just suggesting that this difference exists, and some people might prefer, or be better at, one over the other.

01 March 2013

Asking, connecting, trust, and crowdfunding

Crap. Amanda Palmer just made me cry.

How? I watched this talk:


After a morning of debating the potential of crowdfunding on Twitter, and trying to write a tough post about being left behind and reinvention, this talk just brought so much clarity.

“Is this sustainable? What about donor fatigue? What about people not funding the Very Important Research?” I’ve answered a lot of those kinds of questions, but Amanda’s talk reminded me, powerfully, that those are just... details. I should be crowdfunding, for the same reason I blog: to share.

Thank you, Amanda, for the reminder of our mission as I look forward to the next round of #SciFund.

External links

Neil Gaiman’s journal: The art of asking
Amanda Palmer: The Epic TED Blog, part one: It Takes a Village to Write a TED Talk.
Ryan Dancey on Amanda Palmer (Facebook post): “Instead of trying to figure out how to get millions of people to HEAR you, figure out how to get tens of thousands of people to LOVE you.”

Happy sequestration

Earlier, Science magazine asked, “How will #sequestration affect you?” In response, I tweeted this picture:


And I said:

I’ve had to build research program without regular funding. #sciquester makes little difference to me.

Yes, it’s glib and impolitic. The scientific community wants everyone to present a united front on research funding. Yes, sequestration cannot be good for the scientific enterprise in the United States.

The question was about how the sequester would affect me personally, but some reactions from people who wanted to talk more about the prospects for sequestration and research generally. Indeed, a lot of the reactions being compiled at the Science Now website here are comments about general policy decision, and not reactions from individual researchers about how they personally will be affected.

But... damn it, I’m so tired. I am so tired of being marginalized in these conversations. I am so tired of the theme of “imminent crisis.” I am so tired of the lack of awareness that a lot of scientists got left behind by the funding agencies long ago.

I look around my department, where nobody regularly gets the stand alone research grants that are the bread and butter at a lot of places. It’s certainly not for lack of trying, but there’s history and infrastructure issues that are hard to beat. We have been mostly running on training grants (because we have a lot of Hispanic students). We’re doing research, and I’m proud that we’ve kept the wheels turning without the sort of federal research grants that has so many of my peers in a panic over losing.

Personally, if you’d asked me when I started this job if I thought that I’d be able to get grants for my research, I’d have said, “I think it’ll take me a few tries, but I think I can do it.” Well, that hasn’t happened. So I’ve had to re-invent myself, my expectations, everything, from almost the ground up. It’s been a decade-long battle to redefine myself as a scientist. I’m still not done.

But, to paraphrase Gunny Highway (Clint Eastwood) in Heartbreak Ridge:


Reinventing yourself professionally is long, and hard, and it sucks. So if you’re worried about the effects of sequestration on your lab... you might want to start that project now.

Additional: It was pointed out to me on Twitter that some of the undergraduate training grants I mention are supported by federal funds. Yes, and they could well be affected by sequestration. The point I was fumbling to make was that in our department, we developed ways to support research that didn’t revolve around individual research grants. Those individual research grants are, as far as I have seen, seen as much more desirable than undergraduate training grants at a lot of universities.

For example, when I had one undergraduate training grant, I went to a meeting of PIs holding those grants in biology. Several people from major research universities griped that their faculty didn’t want to participate in those program unless there was summer salary for the faculty. Contrast that to my experience, which is that we want those training grants badly, because they truly allow us and our students to get stuff done.

Just another example of different perspectives. Which one gets heard more often in these sorts of discussions?

(By the way, the line in the picture was a reference...)

Comments for second half of February 2013

Drugmonkey tackles science crowdfunding. I appear in the comments, not entirely of my own accord.

Aviva, writing at News in the Age of Participatory media, compares science writing to sports writing.

What’s the point of a Ph.D.?” Good question, Biochem Belle!