30 November 2012

And now, unicorns

Apparently this is cryptozoology week. We started the week with the news about the claim of Sasquatch DNA. We end the week with the announcement of the discovery of a unicorn lair.

In North Korea.

How did the researchers find this? There was a sign:

Archaeologists of the History Institute of the DPRK Academy of Social Sciences have recently reconfirmed a lair of the unicorn rode by King Tongmyong, founder of the Koguryo Kingdom (B.C. 277-A.D. 668).

The lair is located 200 meters from the Yongmyong Temple in Moran Hill in Pyongyang City. A rectangular rock carved with words "Unicorn Lair" stands in front of the lair. The carved words are believed to date back to the period of Koryo Kingdom (918-1392).

That the sign is about a millenium younger than purported event, the riding of the unicorn by King Tongmyong, is not discussed as problematic.

What is weirder to me is that they are putting out a press release for something that is being “reconfirmed.” I could totally go into that press release scheme. “Scientists reconfirmed today that water is still wet.”

And you know, since this means there were unicorns less than 2,00 years ago, that is probably young enough that you could get ancient DNA to sequence, if the preservation conditions were right.

Update, 5 December 2012: Maybe things are quite as surprising it originally seemed. A grad student explains that the translation of the press release was bad. Incredibly, amazingly, bad. For one, the beast was better described as a kirin rather than a unicorn.

Hat tip to Bess Lovejoy.

Hat tip to College Guide blog.

You need an online presence, scientists

Two examples of people giving advice about why you need to get online.

Earlier this week, we hosted a presentation by Sheri Graner Ray, game designer. She is a South Texas native, who attended our university for a couple of years, and now lives in Austin.

Sheri’s advice on getting into the gaming industry? Get on Facebook. Clean it up to a point where you wouldn’t be embarrassed if a potential employer saw it. Then friend people in the business, and update your status once a day. Get on Twitter and tweet twice a day, and retweet and reply to people already in the business.

She asked students in the audience how many were of Facebook. A good chunk of the hands went up. She asked how many were on Twitter. Very few hands went up. Students, you are missing out.

Given her digital emphasis, I was a little surprised that she also stressed the importance of having a business card, calling it another “golden ticket” to networking and employment.

She said so far, four students took her advice. The number she was able to help land jobs in the gaming industry? All four.

Sheri has a series of “Networking 101” posts on her blog that, while geared towards the game industry, have a lot of good tips for students, too.

(The picture at right is my very primitive attempt to sketchnote her presentation. I was also playing with the newest update of Adobe Ideas on my iPad. The update included different pens, brushes, and a fill tool, all of which make it much more useful and fun than before.)

The Action Potential blog at Nature also talks about this. Much of the article is about how the editors are trying to be more inclusive, especially of women scientists. But there’s also this (my emphasis):

The greater challenges are deciding when to follow up on a suggestion to try out someone we don’t know, and identifying potential new reviewers on our own – particularly young scientists. The first stop in the process is usually a Google and/or Pubmed search to check infer expertise. Recommendations from trusted reviewers play a part. An informative lab or personal website helps. We also invest a fair amount of energy in “scouting” personally. We take note when we have had constructive and productive exchanges with authors. When we go to conferences, we make mental notes when presentations impress us, or we have interesting scientific conversations while in line for coffee. Our ears perk up when a veteran referee touts the critical faculties of a senior postdoc. The occasional find has even come through blogs – I have contacted people on the basis of the careful, rigorous thinking evident in their posts.

And here are the top two suggestions:

  1. Have some form of web presence. If someone can’t find you, they can’t follow up on you. This is less of an issue in the US, but I can’t tell you the number of times I’ve looked for someone in Asia and had trouble.
  2. Keep the information on your website current, or if your department is maintaining your web entry, make sure someone’s keeping on top of it. Ensure that your publications, key research interests, and technical expertise are easily accessible.

When called a jackass

When one person calls you a jackass, that person is obviously an ignorant fool.

When ten people call you a jackass, maybe you ought to think about getting fitted for a saddle.

—Source unknown

Photo by plone of Flickr; used under a Creative Commons license.

29 November 2012

A map of pain

Motor homonculusThere are maps of your body in your brain. Some maps represent the control over your muscles. Other maps show the input coming in from your senses. One of the best known sensory maps is the one for touch.

But we might think of everything we feel with our skin as one sense – touch – these are several separate sense. We feel pressure. We feel changes in temperature, and and different neurons handle warmth and chills.

And we feel pain.

While Wilder Penfield published the famous maps of the somatosensory cortex over 60 years ago, it hasn’t been clear if the neurons that we use to pick up pain from tissue damage, nociceptors, make maps in the brain the way other sense do. There are fewer nociceptors in the skin than other sensory neurons.

A new paper by Mancini and colleagues set out to test this. They gave their volunteers either innocuous little puffs of air on their hands, or...

They shot their volunteers with frikkin’ laser beams.

This hurt. Not much, but enough to set off the nociceptors in the volunteers’s fingers. The authors describe it as “pinprick.”

While they were doing this to the hands, Mancini and company were taking brain scans using functional magnetic resonance imaging (fMRI).

If you look at your hand, the middle finger is well, in the middle, flanked on either side by the ring and index fingers.


If there’s a map of nociceptors in the cortex, you should find that same order in the parts of the brain that respond to being shot with lasers. Using the colour scheme above, the blue should always be flanked by red on the one side and green on the other.

And that’s what you see. Check the area surrounded by the dotted white line in the picture:


The team also shows that the responses for the control puffs of air also map out in the same way.

Strictly speaking, the authors only show that there’s a map of the nociceptors of the fingers. Now, to assert that this means there is a full map of the sort that gets shown in textbooks is sort of like saying that because you have a decent map of the Mediterranean, you also have a decent map of Australia. That’s plausible, though strictly speaking, they haven’t mapped the entire nociceptive globe, so to speak.


It’s a nice demonstration that these neurons follow some of the same patterns of organization as other sensory systems. Which does lead to a bigger question: why does the nervous system tend to make these maps instead of some other form of organization?

Reference

Mancini F, Haggard P, Iannetti GD, Longo MR, Sereno MI. 2012. Fine-grained nociceptive maps in primary somatosensory cortex. The Journal of Neuroscience 32(48): 17155-17162. DOI:

Related posts

Classic graphics #3: The somatosensory cortex

28 November 2012

Fallout from “GM food causes cancers in rats” paper

Remember a few months back that there was a paper claiming genetically modified food caused cancers in rats?

A whole bunch of letters to the editors, and a response from the authors, are available as pre-prints in Food and Chemical Toxicology.

Criticisms (mostly)

Barale-Thomas:

(We feel) compelled to point out weaknesses in the paper by Séralini et al. (2012), the number and importance of which make the study reported very difficult to interpret scientifically.

Schorsch:

(R)eporting and analysis of the study as presented in Food and Chemical Toxicology are inadequate and that this contribution is of insufficient scientific quality to be relevant in the safety assessment process

Wagner and colleagues:

(T)his study does not provide sound evidence to support its claims. Indeed, the flaws in the study are so obvious that the paper should never have passed review

de Souza and Oda:

This paper has some relevant flaws from the experimental design, through the statistical analysis and the way the data is presented. In addition, it lacks of some crucial information for the proper understanding and full assessment of the work.

Tester:

I am writing to ask that the paper by Séralini et al. be retracted(.)

Berry:

I was much involved with the problems that followed a similar failure of scrutiny of a paper about the MMR vaccine. This led to real injury to many and emphasized that careful consideration of the validity of results that appear to be outliers, is vital.

Le Tien & Le Huy

(P)resented here below are the three points that may constitute a sufficient ground to request an editorial retraction of the paper.

Panchin:

Analysis of the data suggests that no statistically significant findings of GMM toxicity were presented in the first place.

Grunewald and Bury:

Because of these fundamental flaws, the conclusions of Séralini et al. are not substantiated in any way.

Pilu:

I think that the readers of this important journal should have these answers from the authors to better understand and evaluate the results obtained in this work.

Hammond et al.:

(T)he study cannot be used to support any conclusions regarding the safety of NK603 glyphosate tolerant maize and Roundup® herbicide.

Ollivier:

(O)ne can see that no value reaches the threshold of 7.815 needed for declaring the differences among treatments statistically significant at the 5% level.

Trewavas (With shout-out to science blogger Emily Willingham and her re-plot of the data):

(T)his paper and this journal have dealt the value of evidence-based knowledge a serious blow and it can only be rectified if the paper is withdrawn by the authors with an apology for misleading the public and the scientific community alike

Langridge:

The problems lie at several levels and bring into serious question the quality and standard of the editorial processes in your journal.

Heinemann, noteworthy for its positive tone:

(I)t is my view that the recent study is a valuable contribution to the scientific literature, debate and process of evaluating technologies

Tribe:

Since I last wrote to you, the scope and seriousness of the international scientific criticisms of the Séralini (2012) paper appearing in your journal has made me realise that my comments about the paper do not adequately describe the serious failures that have occurred in the peer review process at FCT.

Williams:

The widely publicised Séralini paper does not survive such scrutiny.

Editor’s response

Wallace Hayes

Peer review does not end with publication. In the event that an accepted manuscript is questioned by the scientific community on the basis that the authors acted unethically, plagiarized, or where there are queries relating to the data or interpretation of the data, the editors will contact the authors to investigate unethical/fraudulent/plagiarized works or the journal editor will invite or accept letters to the editors.

Authors response

Séralini and colleagues

This may explain why 75% of our first criticisms within a week, among publishing authors, come from plant biologists, some developing patents on GMOs, and from Monsanto Company owning these products. ...

We encourage others to replicate such chronic experiment, with more statistical power. Now, the burden of proof has to be obtained experimentally by studies independent from industry. This was recommended by regulatory agencies that have assessed our work in France, even if it their objective is more to regulate products than to review research. GM NK603 and R cannot be regarded as safe as long as their safety is not proven by further investigations.

Related posts

What did you think those film crews were doing in the lab?
Why not retract the rat cancer / GM corn paper?

Building memory by not building molecules

Honeybees are clever wee beasties. If you give a honeybee a scent, then give her food, she can quickly learn to extend her mouthparts when she smells the scent alone. And they can remember this for at least a whole 24 hour day. This is a classic learning test made famous by Pavlov’s dogs. So honeybees are at least as smart as dogs, for this test anyway.

What’s going on in that tiny little head as they learn that some arbitrary smell means food? Usually, neurons need to make new “stuff” to form a memory. Making proteins, for instance, is usually needed for long term memory, but not short term memory.

Actin is a protein that is best known as half of the machinery that powers muscles (myosin in the other), but actin is also a more general component of a cell’s skeleton. In rats and mice and other furry mammals, you need to make actin to get long-term potentiation (LTP), which is a strengthening of the connections between two neurons.

Ganeshina and colleagues injected honeybees with chemicals that blocked the making of actin. You would expect that this would mess up the poor little honeybee’s memory.

But expectations were dashed. These actin-inhibiting drugs made the honeybees remember better, not worse.

The authors’ aren’t sure what’s going on here, but they have a guess.

The parts of the honeybee’s nervous system that learns smell are called the mushroom bodies. These mushroom bodies grow a little as the honeybee gets older, adding in new connections between neurons all the time, regardless of whether the honeybee learns anything or not. These new connections, because they aren’t related to anything the bee learns, would mostly add noise to the neural pathway. And that could drown out some of connections between neurons that are formed or strengthened as the honeybee learns.

The authors seem to think that knocking out the actin production prevents “random” new connections that would form just during normal aging. As a result, the honeybee gets more memory signal and less noise.

This is a story of diversity. This paper reminds us that even when animals can learn the same kinds of tasks, they may not be learning them in the same ways.

Reference

Ganeshina O, Erdmann J, Tiberi S, Vorobyev M, Menzel R. 2012. Depolymerization of actin facilitates memory formation in an insect. Biology Letters 8(6): 1023-1027. DOI:

Photo by BugMan50 on Flickr; used under a Creative Commons license.

27 November 2012

Tuesday Crustie: Bisection

Lobster colour variants continue to fascinate...



From here.

26 November 2012

Sasquatch DNA?

On Sunday night, I spotted an article in Neil Gaiman’s Twitter feed: A lab claiming that it has sequenced DNA from Sasquatch.

Well. That would be interesting, if it were true.

It’s not just the subject matter of the press release that is strange, though. There’s the little fact that it’s for a paper that is in review, not one that has been published. Usually, papers in review don’t get press releases, because goodness knows Reviewer Number 2 has taken a lot of manuscripts out of contention and they never see the light of day.

In fact, I have to admit: I am so pulling for Reviewer Number 2 to take this manuscript down. Preferably with sniper-style precision and finality. As Adam Goldstein indicated on Twitter, this is something that most journal editors would not even send out for review.

A quick search on Google Scholar revealed one article on animal DNA co-authored by the researcher mentioned in the press release, Melba Ketchum: Recommendations on animal DNA forensic and identity testing. This morning, I’ve found another: A low-cost, high-throughput, automated single nucleotide polymorphism assay for forensic human DNA applications.

That Ketchum is a published author on DNA techniques makes me think this is not a hoax. And I’ve smelled sasquatch hoaxes before (see related posts at bottom). This feels much more like... overly enthusiastic interpretation, if I’m being charitable about it.

More details emerged this morning courtesy of @mem_somerville.

The source of the DNA appears to have been from a woman in Michigan who claims to feed blueberry muffins and bagels to Sasquatches on her property. The researcher, Melba Ketchum, also appears to claim to have DNA from angels. This longer article has more details.

I would love some other science blogger to do a post on, “If this were true, this is what the DNA would be like, and these are the reasons someone could get mislead.” On the latter, I can say: I lived through the rush to find dinosaur-era DNA back in the 1990s. There were a lot of papers published in Glamour Mags claiming to have DNA tens of millions of years old. It didn’t replicate. Lots of cases of contamination. This taught me that DNA is much trickier to work with than you might think.

I think Neil himself has a good summary of this story so far:

I do not care if this is true or not. It makes the world a cooler place & it delights me(.)

While I am extremely skeptical of the results scientifically, this is shaping up to be one fascinating glimpse into fringe science.

Update: Apparently, this story has been bubbling in the sasquatch community for some time now. This post is interesting, is that it looks at the business that Melba Ketchum is in. The Better Business Bureau has several complaints lodged against her business for failing to deliver results.

More updates: Back in January, Melba Ketchum applied for copyright for media around “The Sasquatch Project.” (Hat tip to The OpenHelix Blog.) This is not surprising, as we have often seen people with sexy scientific projects try to make money with documentaries (e.g., the documentary on Darwinius).

Another report from back in January motes Ketchum says she has seen Sasquatch personally.

Update, 27 November 2012: I don’t like either of these two news stories. This one is two credulous (“actually proves the existence of Sasquatch”). This one is too mocking (“Like OMG!”). Hat tip to Leonid Kruglyak for spotting both.

Update, 28 November:  Corrections and additional information from Robert Lindsay in the comments.

A attention-grabbing headline:

Boffin claims Bigfoot DNA reveals BESTIAL BONKING

...at odds with a nuanced final paragraph:

El Reg awaits it with interest. While it's easy to chortle at such stories, the scientific method demands that disbelief be suspended until peers have reviews and retested. Maybe it is possible that someone had the one-night stand from hell and we ended up with a near relative – but great claims demand great evidence.

Update, 29 November: Here’s an article from someone else who was responsible for testing sasquatch DNA back in 2005, which I blogged about at the time.

(W)hat exactly might Ketchum have sequenced? Coltman doesn’t know for sure, but he said that it’s easy to pick up human mitochondrial DNA because of contamination, and that the nuclear DNA could represent environmental noise, more contamination of yeast, fungi, or other microorganisms–very common occurrences with any forensic sample. “There are big piles of DNA sequence that come out of any environmental sample that don’t line up to anything,” he said.

Update, 1 December: Here’s an interview with Dr. Ketchum on Houston television.

Related posts

Another cryptozoology disappointment
Smell the popcorn, carny’s coming to town
Hype, hoax, or hope?
More sasquatch honesty than expected
ABout where I expected we’d end up with sasquatch

Temporal harassment

A few other people were writing about career and training practices at the end of last week.

First, I want to shine a light on something that Dr. 24 Hours said on Twitter, in conversation with Dave Bridges. Dr. 24h was commenting on the expectation of many senior academics that their trainees put in unreasonably long work hours, and offered this solution:

Harrassment to keep longer hours. Policed the same as other sorts of harrassment.


It’s one of those things that is so obvious in retrospect, I can’t believe I didn’t frame it that way before. A senior scientist demanding a grad student or post-doc work 80 hours a week, for years, is creating a hostile work environment, like telling racist jokes, or a man pinching a woman’s bum, or making innuendo laden comments.

Realizing that it is harassment gives me hope, for two reasons. First, we have made progress on getting rid of other kinds of harassment. Second, institutions like universities usually have people and procedures to deal with harassment.

Second, I recommend PalMD’s post, “Call me a commie, I dare you.”

The system itself devalues labor, and thereby the people who perform the labor. We perpetuate the idea that medical schools and grad schools must be cut-throat-competitive. This may or may not be true, but this creates a system where laborers (medical and science trainees) are told they are “lucky to be here”, that “there’s a dozen others ready to take your place should you fall.”

Once again, this may or may not be true, but it helps perpetuate a feeling among laborers that their position is always at risk, that they should be thankful for their abusively long hours and any other mistreatment they receive. And they should thank the boss that they get paid anything at all.

Third, in the “Pay us” department, is a New York Times article, “Skills don’t pay the bills,” that shows manufacturers who claim they can’t hire skilled workers... are offering crappy wages.

At GenMet, the starting pay is $10 an hour. Those with an associate degree can make $15, which can rise to $18 an hour after several years of good performance. From what I understand, a new shift manager at a nearby McDonald’s can earn around $14 an hour.

25 November 2012

One meth lab ready to go

Congratulations to Ethan Perlstein. Last night, he accomplished something that I didn’t think would be possible:


Over twenty-five thousand dollars for science!

Ethan ran one of the most ambitious crowdfunding campaigns for a single scientific research project to date. Technically, he was working on the neuroscience of drug addition, but non-technically, he was asking for help to run a meth lab.

If you’d asked me at the start about how much money I thought Ethan would raise, I probably would have guessed about $10,000.

I’ve gone through two rounds of #SciFund myself, and I’d worked very hard to hit my targets ($1,750 combined). With #SciFund, the sweet spot for success seemed to be about $1,000. Bigger projects with higher targets were much less likely to succeed. No single project in #SciFund had ever raised more than about $10,000.

But last night, when the last minute donations started coming in for Ethan’s project? Exciting. When I went to bed, Ethan had less than $1,500 to raise. To be completely honest, I had dreams about checking Ethan’s project on RocketHub. In some dreams he made it, in some, he didn’t.

I was surprisingly anxious to check the tally when I got up this morning.

How did he do it? Ethan hit the bricks, and did a superb job of promoting this project. He got himself in Nature, Scientific American, Talking Points Memo, and others.

Ethan also had the advantage of a great hook. An academic running a meth lab? Shades of Breaking Bad.

This is another important moment for science crowdfunding. One of the most common arguments against science crowdfunding is that crowdfunding will never be able to raise enough money to do cutting edge science. Ethan’s project exemplifies my first* response to that:

No, crowdfunding can’t raise enough money. Yet.

When you look at crowdfunding for the arts and games, it started slowly. It took a few years to grow before there were the big break-out successes.

Science crowdfunding still has not had its breakout moment yet. We still don’t have a Pebble or Double Fine. But Ethan’s project has moved the dial on what is possible in crowdfunding science. Again. That’s important. Every time, we change the conversation about what is possible in crowdfunding science. The success of Ethan campaign helps us take another step forward in convincing skeptics that crowdfunding is part of the future of science.

The only problem is that now Ethan is going to have to repaint his door:


Post script

I would be remiss if I didn’t point out that #SciFund round 3 is running right now. There are 35 projects. Three have made their targets, and seven are more than 50% funded. (My favourite? a crustacean biologist who needs to money to help him travel to a field site in Florida. Sound familiar? I symapthize!)

You should go to RocketHub and support science!

If you can’t contribute money, you can still help by spreading the word about a favourite project! Like it on Facebook, tweet it, tell your friends and family about it!

* My second response to that argument is lots of perfectly respectable science is cheap. Not zero dollars, but much less than typical grant proposals.

23 November 2012

Kill the “scientist as monk” meme

Is The Guardian trolling us?

Yesterday is was a flailing piece that tried to justify the existence of for-profit scientific publishers, and flailed like a beached fish.Today, it’s an article about scientific careers that asks researchers to just accept that society will treat them like crap.

Steve Caplan says that academic research looks like a Ponzi scheme. This charge that is so well known that Ph.D. Comics has parodied it:


In the next paragraph, Caplan anticipates my reply: entry level positions always outnumber the managerial positions at the top. Nobody calls this a Ponzi when it occurs outside academia. Perhaps the problem is that outside academia, you can make a comfortable career in middle management. In academia, there fewer opportunities to have a long term career in the middle of the pyramid.

Yet despite saying academic research looks too much like a criminal scam, Caplan won’t bite the bullet and say that we are producing too many graduate students. According to Caplan, the problem is that we aren’t doing a good enough job at getting people to leave academia.

The problem... is... general failure to inform students (as well as post-doctoral fellows) of their career options and train them for a wide variety of scientific careers, including the many opportunities that exist outside academia.

The reason that people typically embark on doctorates, though, is to become professors. To join academia. To be a working scientist. It’s no surprise that they don’t want to leave because that’s what they set out to do. It seems pointless and a little cruel to get people into programs, then spend a lot of time telling them they will probably have to take on jobs that they didn’t sign up for.

Are other professional programs worrying about this? Are medical schools running workshops on what career options their med students have for when they fail to become physicians? Do law programs train their students for the many career opportunities outside of the legal system?

My first idea... is to provide far better training for students. Many universities are already employing career development plans to help their graduates prepare for a wide range of science-related jobs.

My question is whether that “wide variety of scientific careers” are careers that need a Ph.D. to do. I suspect not. Instead of putting people through an academic wringer that was designed to create professors, let’s create new programs and training that are not doctoral programs. Let’s get those people out in those science-related careers faster and more efficiently.

It’s Caplan’s second recommendation that makes me mad, though.

I am of the opinion that despite dwindling academic job prospects, this country and the world needs more scientists with PhD degrees, not fewer. Although for the most part careers in science are unlikely to lead to high-paying salaries, society benefits greatly from churning out more scientists with advanced degrees. Critical thinkers who have a working knowledge of the intricacies of scientific research can be the very best ambassadors for science. Whether they become politicians, businesspersons or leaders in any other occupation, their support for science could be the key to the future of science. So in some respects, I almost view a graduate degree in science as a form of national (or international) service – poor pay, but something to be proud of and with great benefits for society as a whole.

Screw. That. Noise. I am so sick of the “Joining the monastery of science” and “Science is a calling, you shouldn’t do it for the money” memes. This “scientist as monk” meme is hurtful and deserves to die a flaming death.

As I’ve mentored students, and watched them consider graduate school and scientific careers, it’s become clear to me that a major reason that they don’t want to go into graduate school is because they want to live their lives. They see continuing in university as something that will interfere with them from meeting people (including potential partners), travelling, having families, and enjoying themselves on their own terms.

In other words, I’ve seen that many bright, hard-working students who could get doctoral degrees do not want to be monks and nuns for science. I don’t want to be a monk for science. I set on this path because I thought it was a career that could offer me some long-term stability and a way to keep a roof over my head and food on my plate.

We cannot simultaneously:

  1. Call for more people trained in science, and;
  2. Say people trained in science should be willing to leave the profession they want to join, and accept a crummy standard of living regardless of whether they join the profession. 

These two things are not compatible. You want more scientists? Then FUCKING PAY US. Other professions are not stupid enough to fall for self-immolation, and scientists shouldn’t be, either.

Photograph of Charles Ponzi, originator of Ponzi scheme.

All I needed to know about the Universe, I learned from Doctor Who

What’s the point in being grown-up if you can’t be childish sometimes?!

You can’t change history – not one line. (The First Law of Time.)

Aim for the eyestalk.

Military intelligence is a contradiction in terms.

Nothing is rubbish if you’ve got an inquiring mind.

Have a jelly baby.

A straight line may be the shortest distance between two points… but it is by no means the most interesting.

Logic merely allows one to be wrong with authority.

Of course we should interfere; always do what you’re best at.

You can always judge a man by the quality of his enemies.

When you make a plan, plan in depth.

Computers are really very sophisticated idiots.

Scientists earn their right to experiment at the cost of total responsibility.

There are no other colours without the blues.

Reverse the polarity of the neutron flow.

Somewhere there’s danger, somewhere there’s injustice, somewhere else the tea’s getting cold.


Happy 49th anniversary, Doctor Who!

By me, apparently around 30 January 1994 (that’s the date on the computer file, anyway).

22 November 2012

Academic publishers need better defenders

A new article by Alexander Brown in The Guardian tries to argue that scientific publishers do add value to research manuscripts. But Brown does not help the publishers’ cause.

Let’s see what he lists as services that scientific publishers provide to authors.

Editors help “ensure that research can be universally understood.” By that criteria, editors are failing miserably. I’m a working scientist, and I have problems reading many journal articles in my own field. I have never had a journal editor who has recommended, or made, substantial changes to the text of one of my articles for readability, and particularly not to the point where it could be understood by someone who was not a professional scientist. Any suggestions for improving my manuscripts have come from reviewers, not editors.

Editors help “to recognise emerging fields.” Researchers can do that themselves.

Publishers “create new journals.” That is valuable to publishers, not to authors. There is no shortage of venues to publish in.

Publishers “build and maintain the brands and reputations of journals.” The “brand” of a journal is more valuable to a publisher than an author.

“Developing systems and platforms” to “get the right research into the hands of those who need it most.” And the platforms that I hear most researchers in biology use to find their research are Google Scholar and PubMed, neither of which was created by publishers. arXiv wasn’t created by publishers, either.

Adding metadata, XML generation, and tagging. I’ll spot Brown that one. I love DOI numbers, for instance. But he may be overstating the value. My impression is that if you have machine readable text, just the number of times key words are used in the text will accomplish much of what tags are supposed to accomplish.

Bringing old print archives online. Yes, I’m glad publishers have made their “back catalogue” available. But that is a mainly benefit to scientific readers, not current and future authors.

Depositing works into institutional archives. No publisher has ever even offered to do that for me. I don’t doubt that it happens, but how much does that matter for how many authors?

It’s kind of astonishing that Brown’s listing of ways publishers add value miss almost every major thing that I, as an author, value.

Organizing peer review and fact checking. But there is so little difference in how journals do this, that I think no journal can brag about how much better its reviewing process is. Many entries in Retraction Watch show that journal reviews are often not very thorough. I would love it if there were journals that boasted of having a dedicated fact-checking staff, or advertised that they checked every manuscript for plagiarism, or that routinely sent papers to five authors instead of two, or that guaranteed a 48 hour review turnaround.

Professional typesetting
. Journals do make things prettier than I can do on my own.

Promotion. I have never had a paper that a journal decided was sexy enough to promote. But I see what happens when a Glamour Mag gets behind promoting an article and pushing it to the press. It’s like watching a lion take down a zebra: a display of unfettered power. Seeing a hot article appear again and again over the course of a few weeks shows that this is something that publishers are supremely good at.

Archiving. Institutions do a better job of this than individuals, and publishers have a decent record of this (see “Bringing old print archives online” above). But the fact remains that for profit publishers are not guaranteed to be around forever. Many publishers have been bought up by other companies. Publishers could go bankrupt. Publishers are certainly not the only ones interested in, or charged with, archiving. Google Scholar, PubMed, and university libraries all do this. I am not sure publishers are doing a better job than those entities.

Publishers, if Brown’s giving the best arguments in your favour... you’re in worse trouble than you think.

Lion picture from here.

20 November 2012

#SciFund expedition: recovery edition

“Dream come true” sounds too hokey. “I love it when a plan comes together” sounds too smug.

It was a long week of hard work, much of it hard physical labour, with a lot of mistakes and frustrations. By the end of it, I felt like this:


Ready for it to be over.

But I achieved everything I set out to achieve... in miniature. This is in line with the spirit of #SciFund, since #SciFund was a miniature grant.

I set out for crayfish, and I got crayfish:


I got small animals, little tiny hatchlings. These are going to have to grow for a while before they’re any good to me.

I set out for sand crabs, and I got sand crabs:


I got a small number of animals, less than the number of my fingers. I have enough for to be useful for at least one project.

All the way through the trip I was very aware that this was possible because of the generosity of people who donated to #SciFund. I was frequently updating a blog I created for supporters, and journaling the expedition for an audience made the trip a little less isolating.

Would I have liked to have had a few more data points, the important thing was that I did not come away empty handed. It was wonderful to be out in the field, trying to tackle problems and do things that I had been thinking about for a couple of years. Now I will have to spend a few more months thinking and working before I know what to do next.

Tuesday Crustie: Deeper than did ever plummet sound


This fearsome looking crab, Thyrolambrus efflorescens, is featured in this news article from Nature about how many species are left to be discovered. Ed Yong’s response to this picture:

OH GOD KILL THAT CRAB WITH FIRE

Fear the crustacean!

16 November 2012

When you hear "correlation" at the barbecue place

It's funny what words you associate with your job.

While I was Li'l Red's Cookin' last night, trying to decide what to have, I heard a woman at the table scross the aisle - not quite opposite mine - say "correlation." And I immediately started paying attention. "Correlation" is not the sort of word that comes up in everyday conversation for most people, but that academics say all the time.

I kept listening. I was curious just how "correlation" worked itself into the conversation.

And darned if it wasn't a set of people talking academic research. I wasn't able to make out everything, but I think the woman was a psychological researcher doing some research related to sexual harassment. There was talk about regressions, groups, editors, reviewers, and I sat there thinking, "These are my people." I just never expected to hear that sort of conversation in a barbecue place... when I wasn't involved in the conversation.

When the talk turned to evolutionary psychology, I was very, very tempted to walk over and start making comments. I repeatedly reminded myself that would have been rude.

But I lingered at my table much longer than I had to before I walked over to pay the cashier. Just to eavesdrop.

It is striking how recognizable academese is. It only took me one word to spot another member of the tribe.

(Incidentally, Li'l Red's is a great barbecue place.)

Comments for first half of November, 2012

Through the Looking Flask considers correlation and causation.

Congratualations to Neuroskepticfor becoming the first to publish a blog post into a peer-reviewed journal, with pseudonym!

I make a cameo over at The Contemplative Mammoth, sharing the stage with many other scientists on Twitter dispensing grant writing advice.

15 November 2012

In Florida, ballots and crayfish are counted

I have been in the Fort Lauderdale / Miama area on my #SciFund expedition! I have got to say, field work like this messes with your sense of time like few things can. I've had just two full days here, but it feels more like four or five.

So far, I've been focusing on collecting crayfish, which was the goal for my first #SciFund project. I am finding crayfish, but a lot of them are the wrong species.

You can see a picture of me with one of my captures here. Ah, photographs, always there to remind us how goofy we look. Part of the scruffiness is due to being out in the field in the morning, but I can't blame field work for the expression on my face. Classic. Photo by David Shiffman during my talk the The University of Miami yesterday afternoon.

My talk there was great fun. The crowd was small but apparently one of the better attended ones for this program. And the discussion was excellent. As was the food at the Titanic pub after the talk.

14 November 2012

How to become an undergrad scientist

Last week, Adrian Ebsary tweeted:

Hey SciTweeps - have any links that have good info on how to find and contact profs for research experience as an undergrad?

I have some resources on my home page, but this is a good opportunity to write more about this. I’ve run an REU program, worked with a lot of undergraduates, and published papers with them.

Start early

If you want to do research, be looking for opportunities in your first semester. The sooner you get started, the more likely it is that you’ll have something to show for it before you graduate.

Another reason to start early is that professors can only handle so many students at one time. A professor may be interested in working with you, but say, “Not until some of my current students graduate.” You have to be a squeaky wheel, and keep coming back to ask if things have opened up.

Also, if a professor know you’re looking for something, she or he can often help direct you to good opportunities.

Your institution

Your best strategy for getting a research opportunity depends a lot on the kind of university you are in.

If you are in a big research institution with doctoral students and post-docs, it can be harder to find an opportunity to work in a lab on the campus. The original research is mostly done by the doctoral students and post docs, and professors have their hands full with them.

If you do, that research experience might be just a step above bottle washing. You probably won’t work directly with the professor on a day to day basis, but will instead be working with grad students. This is not necessarily a bad thing, as the grad students and post docs often have more practice and are current with their skill set than the professor.

If you are at a mainly undergraduate institution, you have a much better chance of getting to become a regular in the lab, doing original research. You also have an edge in getting into summer programs.

Summer research programs

There are a lot of undergraduate summer research programs. Funding agencies love them.

These can be great opportunities, because almost all summer programs are explicitly searching for students from all over the place. This means you have a chance to travel someplace very different, work with people of very different backgrounds and styles than you have at your own university.

As I alluded to above, students from undergraduate institutions tend to have a leg up in getting placed into these summer programs, because it is assumed that professors at such universities don’t do much research. (In truth, the amount of research professors at undergraduate universities do varies a lot, but agencies tend to lump them together.)

Summer programs are very structured. This means that you, the student, don’t get a lot of say in who you will work with or the kind of project you do.

Joining a lab year round

You could join a lab that you can work in year round. As noted above, your level of involvement will depend a great deal on the kind of institution and kind of professor you end up working with.

There are several ways that you can get involved.


Honor’s program: Lot of university have an honor’s program that requires a thesis of some sort. This provides a little more structure and support for you and the professor. Not everyone qualifies for these programs or is into the extra commitment the program might require.

Independent study classes: Some universities have classes that allow you to work on a project for academic credit. The good news is that if you do what your professor tells you, you will usually get an A. The bad news is that it costs you money (tuition fees) rather than makes you money.

Volunteering: You might be willing to work just for the heck of it. Speaking as a professor myself, though, I don’t like asking people to work for free, and I am always looking for ways to support students financially.

Programs: There are not as many research programs during the year as there are during the summer, but there are some to be had out there. Keep your eyes and ears open.

Approaching a professor

There is one simple rule that can dramatically increase your chance of having a good conversation with a professor about joining his or her lab for undergraduate research: do your homework. Not your class homework (though you should do that too), but do a little digging into what your professors do. For instance, Namnezia tweeted this about postdocs, but it’s just as true for undergraduates:

SPAM email requests asking for postdoc positions never work people!! Stop sending them! Look for a lab RELATED to what you do.

If you come into my office and tell me you are excited about doing cancer research, and have no awareness that I have never done anything remotely like that, this is not going to be well for you.

Look at the titles of papers that your professors have published. Maybe even read a few. See if you can find things in discussion sections that say, “The next question to be asked in this line of research is...”. You might ask the professor if that’s been done yet. The key thing is: don’t go in cold.

Email a professor in in advance and ask for an appointment. Be clear that you are interested in their research. You may get back a, “Sorry, but my I’m not taking on students.” But if you do, just ask if you can come talk about his or her research anyway. You’d be surprised at how rarely professors get asked by someone to talk about their research. So if you do get that appointment, block off an hour, because if her get going, good luck at shutting her up.

Do not flatter.

Otherwise, you’ll come across like this:


A little creepy and scary. Rare is the scientist who wants a “yes man” student.

Postscript

This might also be a good time to say that last week, one of my undergraduate students, Karina, showed me that she is co-author on a paper based on work she’s done in another lab. Hooray!

13 November 2012

Tuesday Crustie: Caving

This week, I am in Florida to collect crayfish and sand crabs. Florida is a hotbed of crayfish species, with over 50 species, while the much bigger state of Texas doesn’t even top 40. Unfortunately, I won’t have the time to look for all the species, particularly ones like this...


This is the Putnam County Cave Crayfish (Procambarus morrisi). It is critically endangered. It lives one cave. And people are doing things like scuba diving and dumping garbage in the cave.

Photo from here.

12 November 2012

A #SciFund trifecta

I swear to you, this is purely coincidence.

It is purely coincidence that today:

  • I am getting on a plane to Florida on a crustacean collecting trip powered by two rounds of #SciFund support, and...
  • Round three of #SciFund launches!

It’s been a long time coming for my #SciFund expedition. Round 1 was about this time last year. Then, I was so focused on doing the project that I didn’t realize that the crayfish I wanted to collect were a bit seasonal, and the best time to collect them was November.

I will be blogging about my #SciFund trip here, but only a little bit. My supporters from round 1 and 2 will be getting access to s special expedition blog, Amazons and Goliaths, where I will be blogging much more extensively and in a much different format than here.

As for round three of #SciFund, this is the first time I do not have a horse in this race, so to speak. But you should go to Rockethub and check out all the cool projects!

External links

My #SciFund Round 1 project: Doctor Zen and the Amazon Crayfish Civilization
My #SciFund Round 2 project: Beach of the Goliath Crabs

07 November 2012

The new Texas State Board of Education: slightly less radical?

The Austin American Statesman reports:

After Tuesday's elections, the board is made up of five Democrats and 10 Republicans. Of those Republicans, three are social conservative Republican incumbents — Ken Mercer for District 5, David Bradley for District 7 and Barbara Cargill, who currently chairs the board, for District 8.

A few of the right-leaning Republicans have indicated they likely would align at times with the social conservatives, but it will remain to be seen if they will consistently vote with that bloc or not.

I hope this will mean Texas will be less likely to end up in the national news because of the Board’s continual, ideological efforts to rewrite the K-12 school standards.

University of Miami talk

Hey University of Miami! I’m comin’ your way!

This is currently the one and only presentation I’ll be making during my #SciFund expedition. Mark your calendars for next week, 14 November!


Read more here. Thanks to Gina Maranto for making this happen!

06 November 2012

Tuesday Crustie: Psyclops


A page of psyclopoids from a crustacean atlas. Click to enlarge this one to see the subtleties of colour and shape. I’m in awe of the level of artistry that allowed us to record the natural world before cameras were commonplace.

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

05 November 2012

The Zen of Presentations, Part 57: Pocket persuasion

Full disclosure: The book I am about to review below arrived in my mailbox, unbidden, from Harvard Business Review Press. I have no idea why or how my name got on their mailing list, but I thank them.

It’s no secret that I’m a massive fanboy of Nancy Duarte. But I was not frothing at the mouth in anticipation of her new book after she revealed that much of it was contained material from her previous two books.

Much of HBR Guide to Persuasive Presentations is an executive summary of Duarte’s previous two books. As I went through, I often thought, “There’s the presentation structure from Resonate.... ooh, and there are diagram types from Slide:ology.” That said, even in sections that cover old ideas, there are new examples. The book is right up to date, using examples from earlier this year.

The last two sections of the book – “Delivery” and “Impact” – are the ones of most interest, because they have the most new material. There’s a good section on giving webinars and other remote presentations online. How can you give a presentation that people will listen to... when people are much more likely to check email during that time? There’s a discussion on working with an interpreter to deliver a presentation to people who don’t speak your language.

Much of the online science crowds might be interested in her sections on following-up presentations with social media tools. For example, she encourages speakers to create a hashtag for their presentations – but not “canned” tweets. She cites research that people want to determine what’s important, so suggesting tweets to the audience makes it less likely people will use it. There’s also good discussion about the pros and cons of monitoring the backchannel during a conference, for example.

HBR Guide to Persuasive Presentations is a very different beast from Slide:ology and Resonate. The size of the book is something you can readily throw in a backpack or purse, rather than the oversized trade paperback of the predecessors. The production is spare. The pages and pictures are all black and white. The contrast to the visually lush reading experience of Slide:ology or Resonate is dramatic. For me, Persuasive Presentations was less, well, persuasive because it didn’t have that depth and intensity.

As an academic, I’m disappointed that when Duarte talks about research and gives examples, you’re on your own to try your luck with Google to find them. There are no references or URLs anywhere in this book. I’m hoping that this might be remedied in the ebook, but the product description makes it appear that the ebook’s advantage is a video rather than links.

Each section is short. Each one is about the length of a blog post. It’s similar to my own Presentation Tips, which started life as a series of blog posts. Some sections have been put up as blog posts on the Harvard Business Review website, and because they can use colour, they look much better than they do in the book itself.

Despite the brevity, Duarte makes this a more personal book than her previous ones in many cases. She sprinkles personal anecdotes throughout. I get the impression that she’s gained a lot more experiences to share as she’s transitioned from a “behind the scenes” presentation designer to an “on the stage” keynote presenter.

If you have not bought either of Nancy Duarte’s previous books, Persuasive Presentations is excellent value: you can get this one for less than half the price of the other two combined. But this is not a “must own” like Slide:ology and Resonate are. HBR Guide to Persuasive Presentations informed me, but it didn’t delight me.

Related posts

The Zen of Presentations, Part 20: The presentation book you must own
The Zen of Presentations, Part 35: Another presentation book you must own

External links

Ted blog: How to give more persuasive presentations: A Q&A with Nancy Duarte

01 November 2012

Comments for second half of October 2012

Bradley Voytek proposes changing how we handle citations.

Sounding the Sea ponders how we can make biologists better at math.

DrugMoneky asks how many student projects turn into papers.

Matt Shipman examines whether there’s a best length for a piece of writing, particularly blog posts. Many of my most successful posts have been long ones.