Making trees, or; The triumph of molecules

One more quick observation from the Evolution meeting in Austin last week.

Every tree of relationships between species I saw was based on molecular data.

This interested me, because there was a point where there was controversy about whether DNA data could be used to make phylogenies. I seem to remember articles that argued that relationships based on morphological data would generally be superior to those from DNA.

Now, I wonder if the tables have turned so much that if you put up tree based on morphological data instead of molecular data if people would look at it funny. (There would be a few exceptions, obviously, like fossil data.)

Photo by Extremely Tropical on Flickr; used under Creative Commons license.

Evolution 2016, Day 5

Perhaps the highlight of my last day of the Evolution meeting was learning from Paul Durst that you can get fleas off a (dead) mouse by putting the body in a paint can shaker. The next speaker, Matthew Forister, started his talk by saying, “Dead mice in a paint shaker. Tough act to follow.”

Forister also won the “Overly honest methods” award for saying at one point, “Does this have anything to do with the real world? I don’t know.”

Some final impressions of this meeting.

I was surprised by how humourless the talks were. Dead mice in a paint shaker notwithstanding,very few people tried to make a joke. I only saw one Star Wars quote in a talk, even though a social game for students, Evolution bingo, encouraged people to put Star Wars quotes in their talks. I didn’t see any clown noses in the poster sessions, either.

The food and drink was very good. I’ve been at some small meetings that had snacks this good, but not a conference that was this big.

This was probably the smoothest running set of presentations I have ever seen. While I made fun of the chimes, they worked better than conference moderators. People started and stopped on time.

The precision timing of the talks mattered little, however, when you have one talk in room 10-C and the next one in Ballroom C. The distance between them was long enough that it took probably 3 minutes to get from one end of the meeting rooms to the other, so you were invariably missing the starts of talks.

On a related note, sixteen concurrent sessions is too many.

When you see a lot of cool talks using the same sort of organisms, you feel like the stupidest person in the world for not working on them. “Why am I not studying guppies? What is wrong with me?!”

External links

Evolution 2016 bingo card

Evolution 2016, Day 4

Yes, I saw some cool science, yesterday, including some cool and contradictory results on how predators shape brain evolution (big brains are favoured in high predator environments in guppies but not killifish?) and jump right to the big news.

The Society for the Study of Evolution's flagship journal, Evolution, will be moving to an online only journal, with all papers becoming open access two years after publication. Decades of papers, including many classics, will be free to read in early 2017.

The Society is also launching a new online, open access, "high impact" journal in early 2017, Evolution Letters.

Let me be among the first to congratulate the Society for the Study of Evolution for moving their publications toward a superior and more modern way of scientific communication.

And I think I am among the first to pat the Society on the back, because, judging from the reaction in my Twitter feed, these announcements are widely regarded as bad moves. 

People are mad that Evolution won't be immediate open access, that the two year embargo is too long for NIH funded researchers, and that the journal is still being published by Wiley, one of the biggest for profit publishers.

People (including, it must be said, myself) worry that Evolution Letters might as well be titled Evolution Rejects. The perception is that the journal will be a dumping ground for those papers that are not considered novel enough for the flagship journal.

I've been critical before about the creation of new journal that serve no editorial purpose. I worry  Evolution Letters will be one of those. It's not being created to define an emerging field of research, but as part of a business plan. But I have no doubt that it will have an audience. Scientific manuscripts expand to fill the available journals.

I worry that the "54 40 or fight" attitude to open access might be a little counterproductive. While It's   important shift that Overton window, it might be that criticizing good but imperfect progress might discourage people from trying to make any progress at all.

Evolution 2016, Day 3

Obviously, the biggest, most important day at any conference is the one where you present your own research. 😉 First, thank you to all who came and talked to my student Claudette and me about sand crab eyes! The poster is up at figshare, along with some others from the meeting; search for "evol2016".

Observations from the second full day of the conference:

Some rooms were consistently standing room only (afternoon sexual selection session), while other, much bigger rooms were nowhere near capacity.

Lightning talks. There were a lot of these Ignite! style, short presentations. While I love this format, I think that the vast number shows of lightning talks, combined with the funkiness in room size, shows that Evolution is at a transition point in size. I think it's getting too big for talks to be the norm, and in the next few years it will start to transition more to a more poster oriented meeting.

A few talks I saw - just a random sampler, not in any order:

Aaron Owen showed the first example of rapid evolution (over a couple of centuries) in a mammal, an Indian mongoose. This was a finding that was worth having to look at mongoose butt for.

Trevor Fristoe showed that big brains allowed birds to invade variable, harsh climates, rather than harsh climates selecting for big brains.

Speaking of brains, Alberto Corral-Lopez showed that female guppies with big brains were much better at selecting sexy males with lots of colors than their small brained brethren.

Frances Hausers and Sarah Dungan both presented nice work on opsins. Dungan's talk introduced me to "Concept I have to look up and read more about when I get back": intramolecular epistasis. In my notes next to the phrase:  "This seems kind of important." Not going to try to unpack it in a morning after blog post. (Frances was a fan of the Better Posters blog, too!)

Online people I got to meet in person included Scientist Sees Squirrel blogger Stephen Heard, and chat at the pub with gif master Dr. Rubidium.

Evolution 2016, Day 2

The conference began in earnest Saturday, and some of the notable things were about the conference organization rather than the science.

Bells and chimes. To keep speakers on time, the conference is not relying on unreliable moderators. Each talk begins with a "Setting sail" ship bell. Near the end, there's a doorbell sound that makes me want to say, "Avon calling!" In every talk. Sometimes they chimes are are subtle, and sometimes they'll make you bolt out of your seat and yell, "YES MA'AM I'M AWAKE THE ANSWER IS TWENTY!!"

The conference also has the slickest speaker interface for slides I have ever seen. Instead of a series of strewn out files on the desktop, there is a single clean custom interface with talks and speakers clearly labeled.

The talks are kind of strewn out all over the convention center, and can make it hard to hop between talks on time. Ballroom C is a long way from room 10A! And the difference in room size is puzzling. Some rooms seems to seat 50, while the biggest ballrooms seem to seat 500 or more.

LIkewise, there are long keynote style talks and Ignite style talks interspersed in some rooms, with no clear reason for the variation. It does break up the pacing, but makes it harder to plan how to transition between rooms.

I'll have more to say about the poster session in the Better Posters blog.

Some scientific highlights included a talk by Naomi Pierce on ant symbiosis, mainly with caterpillars, but more recent work with bacteria. Yes, people, the microbiome is one of the hot and inescapable topics at this conference. Very fun stuff.

Scott Solomon gave a talk plugging an upcoming book called Future Humans. I think this book will fill an important niche, because I see so many people outside of biology who start biology questions with, "Because humans aren't evolving any more..." NOPE. Solomon's book will be the one stop source to point to people to show what we know about current human evolution.

I saw a lot of talks on sensory systems (I am allegedly a neurobiologist, after all). There were interesting talks on the variation of eyes in butterflies. And an intriguing talk that showed that eye size alone seemed to provide a fitness advantage in water fleas.

I was super pleased to meet some people I knew from social media for the first time, like Jeremy Yoder and Lenny Teytleman. 

And there is the opening chime for Day 3! Time to stop blogging and start note taking!

Evolution 2016, Day 1

I've wanted to go to the Evolution meeting for years. I was so delighted when it practically landed in my backyard this year in Austin.

Of course, because Texas is big, it probably too me longer to travel by car to the meeting from within the state than many others took by flying in. That last mile on I-35 is always a killer (15 minutes to go about a mile).

The opening evening started with a social, where two former UTPA students came up and found me - one who'd been in one of our undergraduate training programs and is finishing up a master's at Michigan, and one who'd done a master's and is now doing a Ph.D. here in Austin. It's so good to see people who are continuing!

Carl Zimmer gave the opening talk, after receiving the Stephen Jay Gould award for writing about evolution. Carl talked about how successful Gould was as a writer, and of his one encounter with him. Carl was working as a copy editor for Discover magazine, and got asked to edit one of Gould's essays. Now, Carl didn't say this, but Gould was infamously protective of his prose. Gould was many things, and even his close friends admitted he could be difficult. Carl said, "I think I got him to change one comma."

Carl's talk mostly focused on the discoveries around human evolution, which have so emphatically shown a point that Gould made again and again: evolution is not a straight line march of progress, but a "luxuriant bush." But Carl noted, rightly I think, that even Gould would not have predicted the wild interbreeding that ancient DNA evidence is showing us. "Call it a bramble, call it an orgy...".

I saw a few tweets suggesting that Carl's talk was too basic for a scientific conference. He did introduce DNA, in case someone had forgotten it. What I think some people forgot was two things.

First, there were a lot of students in the room. A lot of this information would be new to them, or maybe something that a quick reminder of basic s would help them follow.

Second, and I may be mistaken here, I think this talk was intended as a free talk, open to the general public, not just for conference attendees. And there I think it would have been completely appropriate to mention some of the basics that Carl did.

Today's sessions are starting in about six minutes. I hope to have a day 2 report tomorrow!

Neurons older than dinosaurs, and homologous cells

If you look at your arm, you have a single long bone connected to your shoulder, followed by two more long bones, a bunch of little bones that make up your wrist, and a set of fingers.

It’s the same in all the vertebrates. Why that particular arrangement of bones? They’re all inherited from a common ancestor. In technical terms, those bones are homologous.

I was thinking about homology after writing this answer on Quora to the question, “What is the most fascinating thing you know about in the field of neuroscience?” Here’s my reply, inspired by my 2008 paper::

You can identify neurons that are older than dinosaurs.

Not the actual live neurons in an individual, of course, but types of neuron has been inherited for hundreds of millions of years.

Shrimp, crayfish, clawed lobster all have giant neurons that they use to perform escape movements, called lateral and medial giant neurons.

Now, this little guy is Anaspides:

It has lateral and medial giant neurons, too, and it uses them to perform escape movements.

While some call this species a shrimp, it isn’t a shrimp like most people are familiar with. The shrimps and prawns most people know are decapod crustaceans, and Anaspides isn’t a decapod. (This is why you don’t use common names for scientific purposes.) The oldest decapod fossil is about 350 million years old, so these escape related giant neurons must be older than that.

I think it’s awesome that you can identify neurons in species that are separated by at least 350 million years of evolution. It makes me appreciate deep time.

After writing this answer, Namnezia pointed out that ion channels are even older. Ion channels are molecules, and it struck me:

We talk about homologous organs, like the arm bones I mentioned above, all the time in biology.

We talk about homologous molecules, mainly sequences of DNA and the proteins they make, all the time.

But the escape neuron answer I gave above may be a little unusual because I am talking about single, identifiable cells as homologous. It struck me as interesting that we routinely talk about homology in levels of organization above cells, and below cells. But outside of identified neurons in neurobiology (and invertebrate neurobiology at that), people rarely talk about homology at the level of single cells.

The only other examples of cells that people called homologous were few. You can talk about homologous cells in C. elegans and other nematode worms, because those small animals have predetermined cell fates in development, and we can map every single cell.

Is the cellular or tissue level of organization different from molecules or organs in terms of our ability to identify distinct homologs? Or have we just not looked closely enough?

Reference

Faulkes Z. 2008. Turning loss into opportunity: The key deletion of an escape circuit in decapod crustaceans. Brain, Behavior and Evolution 72(4): 251-261. http://dx.doi.org/10.1159
/000171488

Picture from Anaspides, a Living Fossil

Hello Atlantic! Here are my answers to your questions about funding

The Atlantic recently ran an article about science funding that asked for scientists to write in and answer three questions. So, I did. These were my answers.

How did those years of flat (National Institutes of Health, NIH) funding affect you or your colleagues, if at all?

The difficulty in attracting funding affected our students. When I took students to conferences who were considering looking for doctoral positions, they were disheartened by how much of the talk was about whether a lab could get funding.

Flat NIH didn’t affect me or my colleagues much, for two reasons.

1. My university is an emerging research institution, so there is not a huge amount of federal funding in general. Faculty here haven’t reached the point of being competitive for the stand alone R01 research grants that are the bread and butter of many biomedical research labs.
2. My department is not a biomedical department. The National Science Foundation and other organizations are generally better funding fits than the NIH for us. (And it is a bit annoying when reports treat the NIH as if is was the only funding agency for all of biology. There are huge swathes of biology that NIH doesn’t touch.) 

Have you even noticed the 2016 increase?

Nope.

(Other researchers often get annoyed at me when I say declining funding rates haven't affected me personally. They badly want to show solidarity, and impress on people that the funding shortfalls are hurting science – which they are, and I agree with. But it doesn’t affect all of us equally.)

And what would more funding mean to you?

My institution is determined to add many new doctoral programs, including biology. I’good thing that would creating new opportunities for underserved minority students in my region, instead of this:
ve had many discussions with my colleagues about whether this is a good idea, given the steady decline in funding success rates. More funding might convince me that a new doctoral program could be a

Additional: Moments after I posted this complaining how NIH is so often presented as the only game in town for biology funding, what do I see but a tweet from the Society for Neuroscience presenting NIH as the only game in town for biology funding. Sheesh.

Contact your representatives today and ask them to make the case for a strong research funding level for NIH.

If you’re going to all the trouble of contacting your federal representative to support neuroscience, why not mention other agencies that fund that discipline? Like the National Science Foundation?

Related posts

Happy sequestration

External links

NIH Funding: It’s Personal

The cages we scientists make for ourselves

 
“We need to change incentives!”

Ah, how many times I have heard some variation of that phrase in describing scientific publishing.

With the creation of UTRGV, my department was forced to create new evaluation documents for annual review, for merit and tenure, and so on. Creating policy documents sounds dull, but I was quite excited by this. You don’t get many opportunities the scrape away all the junk that accumulated over the past few decades that nobody could be bothered to change. This is not an opportunity that comes along every day.

I argued to change our department’s incentives structure. I had a few things I wanted to accomplish.

• I wanted us to reward open access publication and data sharing.
• I wanted to broaden the range of things that could be considered scholarly products to include more than journal articles.
• I wanted our evaluation document to reflect that the current world of scientific publishing is largely online.

My arguments did not convince my colleagues. Mostly.

People voted in favour of rewarding people for editing a book (which was previously missing from our list), or getting a patent. Progress!

People did not vote in favour of reward sharing datasets (e.g., on Figshare) or computer code (e.g., on Github), although those votes were close. Promising.

The discussion over rewarding publication was revealing.

Previously, we had given multipliers for whether a paper was published in a regional, national, or international journal. I proposed that instead, we give more weight for an open access journal article, and less weight for an article that appeared in a print only journal (e.g., not available online).

There were two arguments against rewarding open access papers.

The first was “But it costs money.” I pointed out that many open access journals charge nothing, or have fee waivers. I was also not sure why “I have to pay” was seen as a problem, since one of the legacy departments has long rewarded people for each scientific society they belong to, and that’s an out of pocket expense to get a reward, too.

The second objection was prestige. I provided links and papers to support the arguments of the benefits of open access, the pitfalls of Impact Factor, and that reprint requests don’t cut it compared to genuine open access. But they were not swayed.

Ultimately, it felt like asking my colleagues to image a world where a PLOS ONE paper was worth more in an evaluation than a Nature paper was like asking them to picture a reddish shade of green. They just couldn’t imagine it.

The department voted against the new multipliers.

So the next time you hear, “We just have to change incentives for scientists,” remember that these existing incentives are often ones that many scientists actually want. They are in a cage of their own making and could leave at any time, but won’t.

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

No mystery how invaders cross oceans

I hate it when news organizations act boggled when there is no reason to be.

Man-Eating Nile Crocodiles Found In Florida, And No One Knows How They Got There

Obviously, the “man-eating” thing is a bit overblown and lurid, but it’s that second half that bugs the heck out of me.

Nile crocodiles are large (hence, potential “man-eaters”) animals that live in Africa. There is one way, and only one way, that they got across the Atlantic Ocean to wind up in Florida.

People moved them.

They didn’t swim. They weren’t carried off by flying rocs and dropped off. They weren’t picked up in some freakish weather event. (Though Crocnado would be an awesome name for a bad SyFy movie, if sharks hadn’t got there first.)

Sure, maybe we want some more details about who did the moving and why. The article goes on to suggest someone thought a Nile crocodile would be a great pet. The technical paper notes:

Over the last decade several large groups of C. niloticus have been imported from South Africa and Madagascar for both zoological display (e.g., Disney’s Animal Kingdom) and the pet trade, with the latter being the most likely introduction pathway for these individuals.

Saying, “Nobody know how they got there” is a lame dodge of responsibility. It’s just another example of humans messing with wildlife. We need to recognize that, and not absolve people through “mystery.” A few years ago, I heard someone on a radio show say something like, “Our pets have become family, and wild animals have become our pets.” We need to get over this notion that almost any type of animal can be a pet.

Hat tip to Andrew Thaler. Update: Andrew rightfully points out:

The specific mode of each introduction is hugely important. Accidental release from a zoo? Illegal exotic trade? Unintentional transmission via shipping? Those details matter, and we don't know yet.

That’s a fair comment. Those details are important. They may be more important for those of us studying the pet trade or working on policy than it is in a general news story. In a general news story, more good might be done by spreading the message, “Don’t keep exotics.”

Reference

Rochford MR et al. 2016. Molecular analyses confirming the introduction of Nile crocodiles, Crocodylus niloticuslaurenti 1768 (Crocodylidae), in Southern Florida, with an assessment of potential for establishment, spread, and impacts. Herpetological Conservation and Biology 11(1): 80–89. http://www.herpconbio.org/Volume_11/Issue_1/Rochford_etal_2016.pdf

External links

Man-Eating Nile Crocodiles Found In Florida, And No One Knows How They Got There


Picture from here.

Research underemployment

In general, people in science get doctoral degrees because they want to do science. But the opportunities to do so after grad school and post-docs have shrunk dramatically.

Karen James wrote about the prospects of being an unsupported scientist. Shortly after, Terry McGlynn talked about the prospect of self-funding research. Both are expressions of a common frustration: more people are getting trained to do science, but after that “training period” is over, there’s less money for research per scientist than there used to be. It’s getting tighter and tighter, with no end in sight.

While I was turning this over in my mind, two questions came to me.

Who is to blame?

The answer, of course, is nobody is to blame. Funding agencies, states, and universities each have their own, often contradictory, sets of goals and incentives. On science social media, most of the talk rotates around the policies federal funding agencies, neglecting the role of the states, incentives for institutions, and that some trends occur with no help from funding agencies. (For instance, those agency policies don’t seem to account for the growth in master’s degrees.)

The last one – institutional incentives – is is not looked at enough. If I were a university president, even knowing the oversupply problem, if I had a chance to create more doctoral programs, I would do it. There are just too many advantages. You get higher university rankings and more money.

For instance, look at the Carnegie classifications of universities. Their first pass on classifying universities as research (R1, R2, R3) is based on the number of doctoral programs. In my state, the Texas Higher Education Coordinating Board groups universities by the number of graduate programs, number of graduate students, and research expenditures. (The last is another potentially corrosive influence.)

Why is number of graduate programs and students used to measure research output? It assumes that faculty perform no research outside of supervising doctoral students. Why not number of publications or scholarly products? Universities collect that data. Heck, I’ve lost count of the number of times my university has asked me for my CV.

Obviously, there are potential pitfalls in systems intended to measure academic productivity. But consider what would change if universities were classified more by what research they put out instead of how many training programs and students they have.

Using the number of doctoral programs as a proxy measurement for amount of research capacity of a university is like using the Impact Factor as a proxy measurement for the quality of research articles: deeply, if not fatally flawed for most purposes, but survives because it’s convenient. The difference is there’s no shortage of researchers, editors, and others writing articles and editorials pointing out that the limits of Impact Factors.


Why are there so few solutions suggested to address these problems? 

Everyone likes to support “training.” Nobody’s going to get fired for putting money into training, since education is one of those rare areas that pretty much everyone wants to be seen supporting.

People with doctorates have some of the lowest unemployment rates in the U.S. There’s very little concept of underemployment and no balance sheet for missed opportunities. That makes it a tough sell to convince politicians that people with a Ph.D. are a group in crisis.

Like the weather, everyone talks about Ph.D. oversupply, but nobody know what to do about it besides dressing for today and hoping it’ll chance to something nicer soon.

External links

Karen James’s Twitter rant
Self-funding your research program
Refusing to be measured
In the future, all research will be funded by Taco Bell

Building a winning trivia team

Trivia night!

A local pub, Grain to Glass, hosts trivia night every Tuesday. I got invited to join a team over a year ago now. Our team consistently does very well, thank you.

I’ve thought a lot about why our team does so well. I’ve concluded it’s because pretty much everyone on the team is different. We have Americans, an Englishman, and a Canadian who’s lived in Australia (me!). Just that geographic diversity helps a lot. Our ages from youngest to oldest covers probably 20 years. Our professions are different. We have both men and women. My strength is science and movies, but I suck at sports... which a couple of other team members know very well.

If we had someone who kept up with current pop music, we’d be unstoppable. (Why are there so many questions about One Direction?!)

This same applies to departments and institutions, too. Diversity can build a better team.

Personalizing PDFs: reclaiming a personal touch on reprints

As a grad student, one of my keys to my development as a professional scientist was getting acquainted with the relevant literature. Because I be old, this was all done on paper, and largely consisted of raiding my supervisor’s files and photocopying her reprints. Some of her reprints were signed, often with short little personal notes on them.

When I started to send off reprint request cards in the mail, I started getting back a few of my own signed reprints. I liked the personal touch, and I tried to put a personal touch on my own paper reprints when I mailed them out.

Of course, email requests and PDFs supplanted posted reprints (thank goodness!). I would never want to go back to managing huge file cabinets full of photocopied reprints, but I kind of miss that personal touch. I realized, though, that there is a way to reclaim it.

If you can edit PDFs (which you can in Adobe Acrobat), you can insert test anywhere you want using the “Tools.” You can use a typeface that has a handwritten look (say, something from comic letterer Blambot) to make it distinct and separate from the main text of the paper.

You can place a signature file, like a scan of your signature on paper, using “Fill & Sign.”

It takes only a minute or two. You can make a personal message, and thank the person requesting your reprint by name. While it might not entirely capture the charm of the ink on paper, but it shows a bit of effort. And maybe it can provide some of that sense of personal connection to a community that I felt as a grad student when I was looking through my supervisor’s filing cabinets.

And the cycle repeats

Today is the last day of class for the Spring semester, which kind of means it’s the end of the first regular academic year at UTRGV. Okay, sure, there is summer session, but really, most of us faculty have a nine month salary, so our pay stubs say this is the end.

Where are we with UTRGV? Ugh. It’s still in beta testing. There are still many weird, unsettled (and unsettling) things going down for my liking. There’s an obsession with instant growth, and a lot of parachute candidates for administrative positions. Could it have been better? Sure. I suppose it could have been worse, though.

Meanwhile, speaking of education, Texas is set to review its science standards again. Slate has the story. Notably, author Zack Kopplin writes:

Via public records request, Slate obtained the full list of 545 applicants. Many seem up for the task, including the employees of the Perot Museum of Nature and Science in Dallas, scientists from Houston’s energy industry, the president of the Micropaleontology Press, science-assessment specialists from the textbook publisher Pearson, and hundreds of K-12 science teachers or college professors.

I was one of those hundreds of educators who applied, by the way. I’ll let you know if I get picked, but I think the odds are long. As the article says:

Members of the Texas State Board have full discretion over whom they want to appoint to the review panels—and history shows they often pick creationists.

In other words, here we go again. At least because this is happening in summer, I should have time to blog about it.

And it’s also Star Wars day! I won this glass at the pub last night during trivia.Thanks, Grain to Glass! They made both Light Side and Dark side glasses. Only Dark Side glasses were left, but I would have picked that one anyway. I’m definitely a Sith.

I won it knowing what “AT-AT” stands for. (Gloss for the non-Star Wars fans: The AT-ATs were these things, introduced so memorably in The Empire Strikes Back.)

“AT-AT” stands for “All Terrain Armored Transport.”

External links

Scientist vs. Creationist: Who will get to update Texas’ science standards?

Evolution journal retracts old science because new science is better

Retraction Watch is reporting on a case where the journal Evolution is retracting a paper, against the author’s wishes, because the author’s new research was better than the old (now retracted) research.

This is a bad move by the editors, for multiple reasons. Retracted papers still get cited, though. And maybe, in this case, that’s a good thing.

Tueday Crustie: Maintenant en couleur!

Here’s a treat. The Biodiversity Heritage Library has digitized one of the first books to show crustaceans in colour! It’s from 1754. As with much old work, it’s an interesting mix of the scientific and artistic. Many of the crustaceans are immediately recognizable from their general shape, but there is a lot of detail work that is... what’s the word... fanciful.

For instance, this is without a doubt a ranid crab of some sort:

Though I have never seen any crab with such a regal looking plant on its carapace before. It also appears to have four eyestalks.

Here we have a slipper lobster:

And a spiny lobster with antennae so spectacular it required a special fold-out plate!

And, oh yeah, a mermaid. With tiny little arms.

The Christie’s auction listing notes:

Renard never visited the East Indies and was completely reliant on information supplied by Fallours and other returning travellers, and, clearly worried by brilliant colours, fantastic shapes and habits of his subjects, felt it necessary to include affidavits from various eye-witnesses testifying to the accuracy of the depictions. Despite these declarations, his work was dismissed at the time as being largely fantasy. However, writing over one hundred years later, Bleeker remarked that, 'Although these figures are partly exaggerated and partly unrecognizable, it later proved that practically every one of them is based on a natural object'.

For more on this fascinating book (and the conviction that mermaids were real), see here.

Hat tip to Raven.

External links

Poissons Ecrevisses et Crabes, de Diverses Couleurs et Figures Extraordinaires, Que L’On Trouve Autour Des Isles Moluques, et Sure Les Côtes Des Terres Australes
Glasgow University Library Special Collections Department Book of the Month, January 2002: Louis Renard,
Poissons, Ecrevisses et Crabes
Christie’s auction description

Tuesday Crustie: Winning the war

I recently discovered the TV show Skin Wars on Hulu. It’s one of those, “Make some cool really fast” competition shows like FaceOff, Top Chef, or Project Runway. In this case, the topic is body painting. The show’s had two seasons, with a third starting up next month. But this was the last winning entry that clinched season two for Lana!

The craziest recommendation form I have ever completed

As a professor, you write recommendations for student regularly. One came in this morning, so I started filling it out. First questions were pretty standard, asking you to rate students compared to others you’ce interacted with.

One struck me as oddly worded: something like, “Student will do the right thing when no one is looking.” Um... if this student does these things when no one is looking, how can anyone know?!

But then I got to the question (click to enlarge):

Which of the following achievements may be applicable to your student's future: Select all that apply.

Options include “Astronaut,” “Nobel prize,” “US Supreme court justice.”

And you can pick “All that apply”! “I’ll be Secretary of State and run a pro sports team!” “I’ll be Fortune 500 CEO and an astronaut, becoming the first entrepreneur in space!” These are the kind of career ambitions you might have when you’re eight. But for evaluating university students? No. These achievements are so rare and capricious that it makes no sense to ask someone to say that a student is likely to achieve these.

I thought, “This is the craziest, least realistic question I have ever had to do on a scholarship recommendation.”

Then I saw the next question, and I had to throw out my previous record holder for craziest, least realistic question I’ve had to answer for a scholarship recommendation.

If you fast forward 10-20 years, who would these student most closely resemble?

Options on the first screen include Barack Obama, Elon Musk, and Charles Darwin.

Options on second screen include Marie Curie, Mother Theresa, and Oprah Winfrey.

Options on third screen include Rosa Parks, Thomas Edison, and Rita Moreno.

There are some people in that list I would use if I wanted to diss a student. Some of the politicians come to mind.

The way this recommendation was going, I expected the next question to be, “What is this student’s mutant superpower?”

These questions are dumb. I get that a scholarship organization wants students to aim high and achieve and all, but geez. These are not realistic career expectations. And it’s not a helpful way for professors to try to characterize what they think the student’s good and bad qualities are.

A pre-print experiment: will anyone notice?

In late February, there was a lot of chatter on my Twitter feed from the #ASAPBio meeting, about using pre-prints in biology.This has been the accepted practice in physics for decades.

My previous experience with pre-prints was underwhelming. I’d rather have one definitive version of record. And I’d like the benefits of it being reviewed and edited before release. Besides, my research is so far from glamorous that I’m not convinced a pre-print makes a difference.

Following the ASAPbio meeting, I saw congratulatory tweets like this:

Randy Schekman strikes again: yet another #nobelpreprint - Richard Sever

Marty Chalfie on bioRxiv! That’s Nobel #2 today - Richard Sever

Yay, Hopi Hoekstra (@hopihoekstra) just published on @biorxivpreprint - Leslie Voshall

Similarly, a New York Times article on pre-prints that appeared several weeks later focused on the Nobel laureates. I admit I got annoyed by tweets and articles about Nobel winners and Ivy League professors and HHMI labs and established professors at major research universities using pre-prints. I wasn’t the only one:

 I wish this article didn’t erase the biologists who have been posting to arXiv for years.

If pre-prints are going to become the norm in biology, they can’t just work for the established superstars. Pre-prints have to have benefits for the rank and file out there. It can’t just be “more work.”

For example, I think one of the reasons PLOS ONE was a success was that it provided benefits, not just for superstars, but for regular scientists doing solid but incremental work: it provided a venue that didn’t screen for importance. That was a huge change. In contrast, new journals that try to cater to science superstars by publishing “high impact” science (PLOS Biology or eLife and Science Advances), while not failures, have not taken off in the same was that PLOS ONE did.

I decided I would try an experiment.

I don’t do the most glamorous scientific research, but I do have a higher than average social media profile for a scientist. (I have more Twitter followers than my university does.) So I thought, “Let’s put up a pre-print on biorXiv and see if anyone comments.”

I spent the better part of a morning (Thursday, 25 February 2016) uploading the pre-print. Since I had seen people whinging about “put your figures in the main body of the text, not at the end of the paper,” I had to spend time reformatting the manuscript so it looked kind of nice. I also made sure my Twitter handle was on the front page, to make it easy for people to let me know they’d seen my paper.

I was a little annoyed that I had to go through one of those clunky manuscript submission systems that I do for journals. I had to take a few stabs at converting the document into a PDF. biorXiv has a built-in PDF conversion built into it, but the results were unsatisfactory. There were several image conversion problems. One picture looked like it came out of a printer running low on ink. Lines on some of the graphs looked like they had been dipped in chocolate. Converting the file to PDF on my desktop looked much better. I uploaded that, only to find that even that had to go through a PDF conversion process that chewed up some more time.

biorXiv preprints are vetted by actual people, so I waited a few hours (three hours and thirty-nine minutes) to get back a confirmation email. It was up on biorXiv within a couple of hours. All in all, pretty quick.

I updated the “Non-peer reviewed papers” section of my home page. I put a little “New!” icon next to the link and everything. But I didn’t go out and promote it. I deliberately didn’t check it on biorXiv to ensure that my own views wouldn’t get counted. Because the point was to see whether anyone would notice without active promotion.

I waited. I wasn’t sure how long to wait.

After a day, my article had an Altmetric score of 1. biorXivpreprints and three other accounts that looked like bots tweeted the paper, apparently because they trawl and tweet every biorXiv paper. (By the way, “Bat_papers” Twitter account? There are no bats in my paper.) The four Twitter accounts combined had fewer followers than me. Looking at the Altmetrics page did remind me, however, that I need to make the title of my paper more Twitter friendly. It was way longer than 140 characters.

Four days later (29 February 2016), I got a Google Scholar alert in my inbox alerting me to the presence of my pre-print. Again, this was an automated response. That was another way people could have found my paper.

Three weeks has gone by now. And that’s all the action I’ve seen on the pre-print. Even with a New York Times article brought attention to pre-prints and biorXiv, nobody noticed mine. Instead, the attention is focused on the “established labs,” as Arturo Casadevall calls them. The cool kids.

I learned that for rank and file biologists, posting work on pre-prints is probably just another task to do whose tangible rewards compared to a journal article are “few to none.” Like Kim Kardashian posting a selfie, pre-prints will probably only get attention if a person who is already famous does it.

Update, 18 March 2016: This post has been getting quite a bit of interest (thank you!), and I think as a result, the Altmetric score on the article reference herein has jumped from 1 to 11 (though mostly due to being included in this blog post).

Related posts

The science of asking
Mission creep in scientific publishing

Reference

Faulkes Z. 2016. The long-term sand crab study: phenology, geographic size variation, and a rare new colour morph in Lepidopa benedicti (Decapoda: Albuneidae) biorXiv. http://dx.doi.org/10.1101/041376

External links

The selfish scientist’s guide to preprint posting
Handful of Biologists Went Rogue and Published Directly to Internet
Taking the online medicine (The Economist article)

Picture from here.

Tuesday Crustie: Paddy

I love this design, although since the only native Irish crayfish is the what-clawed crayfish, I kind of wish this guy had some patches of white on his claws.

This design is by Jen, who has this page with a whole whacking big stack of crustacean design! I suppose my only complaint is that the “lobster” and “crawfish” look mighty similar to one another.