This is an excerpt of a data set from a manuscript I’ve been working on.
The box shows where half the data live, with a line dividing the boxes marking the median. The small black square in the mean, and the little crosses show highest and lowest data points.
When I submitted the manuscript, I didn’t do any statistical analysis of the data. One reviewer asked me to to a statistical analysis. It was a perfectly reasonable request that I should have anticipated. The reviewer didn’t see the same plot that I have above and didn’t know the data as well as I do.
But it got me thinking. John Vokey, one of my undergraduate professors at the University of Lethbridge,used to refer to some differences as “significant by the IOT test.” IOT was an acronym for “Inter Ocular Test.” In other words, the difference was so bloody obvious that it hit you right between the eyes.
“If the mean for one group is up here with only a little variation, and the mean for the other group is down here with this much variation, what do you need a test for? Why not just say they’re different?”
I didn’t do an analysis because I thought there was no point. In the data above, there is no overlap between the two sets at all. Do you need a statistical test to tell you that those two data sets are different?
It is easy enough to do a simple t-test on the data above.
But does adding the test and p value tell you anything more, or different, than the plot alone? Or is including the p value a statistical “fig leaf”?
Do your thoughts about analysis change when I plot the raw data next to the box plot?
Now you can see more clearly that the sample size is small. But even then, when there is no overlap in the data sets, is there any test or condition that will say those two are not statistically different?
Philanthropy: Up 530%
Research expenditures: Up 56%
Student applications: Up 21%
Based on this, the UT System values money above all.
This is consistent with comments UTRGV president Guy Bailey made to faculty last year. He said he was often asked about what problems the new university was facing. He said, roughly (not a direct quote) that he told people, “I don’t have any problems that money can’t solve.” And indeed, the rest of his presentation talked about how UTRGV could get more money from the state by optimizing patterns of student enrollment. The main times I have seen our president in the news have been when he’s accepting money from donors.
The longer press release is a bit better. The first bullet in the list is student retention rate. That is indeed something to be proud of, considering that retention was something the legacy institutions struggled with. But the next two items on the list are about money.
I find it interesting that I can know I’ve crossed half a million views on a Q&A site, but still have no idea what having a journal’s “Top 10 paper” for a month means in terms of page views, downloads, and so on.
I’m far from the first to note how music locks us into times. You can’t control what songs are playing and popular in any year, and they become indelibly associated with that time in your life.
For me, I can’t think of The Tragically Hip without thinking of grad school. 100.3 The Q, the local Victoria rock radio station, declared The Hip to be their “house band,” so they were kind of ubiquitous on the airwaves when I was doing my doctorate.
When I moved out of the country, I didn’t hear their music any more. I’d heard about Gord Downie’s diagnosis of terminal cancer. But I happened to be in Canada this last weekend, and caught a bit of the Hip’s final show on CBC. I saw people’s reaction on Twitter. Even with my tiny little familiarity with the band and the music, I was awestruck by how they touched people last Saturday night.
I was never actually a big fan of the Tragically Hip’s music. But I always liked this one a lot.
In the middle of a good article, I find this aside:
(Last
semester, we even got a Faculty-wide email encouraging us to write up
our Master’s students’ project work for publication. Because what
science needs right now is more unfinished crap.)
Objection!
It’s terrible to characterize master’s theses as “unfinished crap.” It shows how little regard you hold for master’s students and their work. What have master’s students done to warrant their research being treated with such contempt?
I wish I could say this was surprising, but I have seen over and over again this disinterest in master’s students, their work, and their degrees. Research universities view master’s degrees as the exit route for bad doctoral students. Funding agencies don’t want to support them, because they buy into the “failed doctoral student” narrative, and because master’s are not terminal degrees.
This is another one of those biases that works against the stated aim of many institutions to increase diversity in science. As Terry McGlynn has often noted, under-represented students come from under-represented institutions. Many of the under-represented students we say we want to recruit may not have immediate access to an institution with a doctoral program. They may want to gain research experience in a master’s that may not have be available to them as undergrads (but that undergrad students at the more swanky universities may have already had).
In my role as grad program coordinator, I have been the person sending
those emails asking, “Why we are graduating so many master’s students
with thesis, but we are not seeing papers being published based on that
thesis research?” I send them because we have always had in our program’s guidelines that a master’s thesis should represent a publishable peer-reviewed journal. My rough and ready guide is that a master’s thesis represents one paper, and a doctoral dissertation represents about three papers.
If you think your students’ work is “unfinished crap,” let me suggest to you that it is not always the students’ fault. Maybe it’s the fault of professors who didn’t mentor the student, didn’t support the work, and can’t be bothered to do their job right.
In every case, Voigt is pursuing the arowana. She first hears the name from a law enforcement who is talking to her about the exotic pet trade in New York. She learns that the arowana is a large fish prized by a certain kind of aquarium owner: usually Asian, male, and rich. The latter is the most necessary feature for many arowana owners, because single individual arowanas are fetching hundreds of thousands of American dollars.
That’s not a typo. It’s no surprise that you find arowana gracing the landing page of Aquarama, a trade show for the aquarium industry that Voigt visits early in the book.
Even by the time Voigt visits Aquarama, it’s clear that the arowana is the center of an unusual market, often shrouded in secrecy, and both threats and acts of violence. Again and again throughout the book, arowana are stolen, smuggled, and fought over, both in the professional and literal sense of the word.
The strangeness of it all is compelling for the reader and Voigt, who ends up pursuing this fish through multiple countries and jungles. She’s accompanied by a memorable set of other people, who I found myself constantly googling to see by the time I reached the second half of the book.
The Dragon Behind the Glass is not an academic work, but it almost could have been. Voigt’s research on the pet trade and the science is flawless. There is lots of solid biology and scientific history. For instance, we learn one species of arowana was collected and drawn by no less than the co-discoverer of natural selection, Alfred Russel Wallace, on an expedition to the Amazon that was ultimately doomed. (Sean Carroll’s Into the Jungle describes why in more detail than here. It’s about the only example in the book where I felt Voigt missed a good story.)
I came to this book because of my own research on the aquarium industry. But I was an armchair investigator. I was frustrated by my inability to get a handle on much of the supply chain for aquarium animals (crayfish in my case). Voigt provides that inside view of the production and wholesale end of the aquarium trade, and has many thoughtful asides about the pet trade. She considers the pros and cons of collecting from wild populations, CITES listings, and the paradox of the arowana being “a mass produced endangered species” (a term that applies perfectly to some crayfish in the pet trade, too).
It’s trivia night at the pub! Because I am a non-imbiber, the most fun alcohol ever gets for me is enjoying the names and the bottle designs. I was tickled by this name when I saw it on the menu: “Evil crawfish.”
This was the art before all the brewer’s insignia got added.
Another version of the tells the story behind the name. The same company makes “Eagle Claw Fist.”
Once upon a time a man walked into a bar where a friend of our’s was tending the taps. He tried to order an Eagle Claw Fist, but got it wrong and asked for an Evil Crawfish. When we heard the story, after much laughter, we knew one day we’d make the beer. Finally, here it is, built off of ECF, but cleaner, meaner, less bitter, and dry hopped with Citra, El Dorado, and Mosaic.
I sometimes get emails from undergraduate student here asking if there are research opportunities with me. Partly because I have some bottlenecks in my lab (microscopes are a limiting factor), I can’t have a lot of students in my lab.
I’ve started offering them research opportunities to do data extraction or analysis, rather than data collection. I ask them to extracting data from websites or journal articles, and get them into an analyzable form. For example, getting latitude and longitude coordinates for species locations in the literature. Or compiling weather data.
I never heard from those students again.
I can only speculate as to why they never follow up. But, at a guess, I think they don’t consider working with spreadsheets “real” research. For them, “real” research means having a lab coat on and a pipette in hand, or getting a sunburn out in the field with a notebook in hand.
Students are shortchanging themselves.
First, I suspect that by the time you’re asking someone to compile and analyze
data from some other source, it may be more likely to result in the
student getting their name on a publication than bench or field work.
Second, extracting existing data and putting into a form that can be analyzed
is far, far more likely to be a skill that these students will use
throughout their professional career. Lots of professional level jobs
require working with spreadsheets; very few require running gels.
August is rarely a happy month for academics. Summer is more than halfway gone, we haven’t done as much research or as much writing as we wanted, and classes are going to start gearing up again very soon.
At my university, and public universities across Texas, today marks the start of an even less happy month. Today, 1 August 2016, is the day Texas’s campus carry law goes into effect.
The sign above, on the door leading to the research labs, including mine, went up Friday. The law permits university administrators to set “reasonable rules” for “campus safety.” (Yes, the wording is vague, which caused no end of difficulties in drafting policy, I’m sure.) Consequently, there is a long list of exclusionary zones on UTRGV campus, including labs.
University administators, and many others, lobbied harder against this law than any other I have seen in my time here, but to no avail. It’s telling that private universities were given the option to opt out of the law, and 36 out of 37 did.
We are in the middle of a science news hype cycle.
First, the inflated expectations. Lots of news sources reporting that funds from the Ice Bucket Challenge were used to make a “breakthrough” in ALS. Note that the original press release didn’t say “breakthrough” anywhere in the headline or the main text. It said a “significant... discovery” was made.
We’re now in the trough of disappointment. Serious science journalists are poo-poohing the claim that the results reported can be described as a “breakthrough.” Some are warning that just proves this whole crowdfunding thing is a dangerous idea. Boing Boing, for instance:
As useful as the funds raised by the Ice Bucket Challenge are, they can’t replace the big, institutional, steady spending that has been under assault since the Reagan era.
But I worry that downplaying good new research (which as far as I can see, everyone admits this was) because it’s not a “breakthrough” accidentally reinforces the notion that only the “breakthroughs” matter. It also implies that because the results are not a “breakthrough,” that they are trivial findings. Of course, the “not a breakthrough” article admits:
This is intriguing and important research.
Guys, if you’re going to criticize press coverage for bombastic headlines and burying the qualifiers and nuance near the end of the story, I think it’s fair to ask for the same in return.
Focusing on the resulting science also buries some of the less tangible benefits of the crowdfunding campaign. People had fun
with the Ice Bucket Challenge. People might have learned what ALS was for the first time. Scientists got to do their research were less likely to shut their labs down. Those are positive benefits regardless of whether the money raised led to any particular scientific outcome.
I’ve seen the argument that crowdfunding somehow poses a threat to federal funding since I got involved with #SciFund. What’s been missing every time I see this claim is any actual evidence. I have yet to hear one politician say something like, “We’re thinking of cutting funding to ALS research because we saw the Ice Bucket Challenge was a big success.”
All I see is fear. And I get that fear. Many people’s labs and careers have depended on federal funds for so long that anything that gives the hint of deviating from the cry of “MOAR funding!” is open for criticism.
But what else are we supposed to do?
Yes, we’re supposed to advocate for our science to politicians. We’re supposed to communicate our discoveries to the broader public. We do that. And, in the United States, all that advocacy over more than a decade has yielded us...
A set of flat research budgets in real dollars (check the “nondefense” line). Labs shutting down, and an endless stream of complaints about the amount of time spent trying to get money for research instead of doing research.
It’s frustrating to be told that scientists should not even try any other plan because it might threaten the plan that is not making any progress, even after more than ten years.
You are going to read about a zillion hot takes and think pieces about this game, but remember: the Southern Fried Scientist, Andrew Thaler, got there first.
I’ve been struggling with a frustrating manuscript revision this week.
First, the manuscript was turned back to me because of formatting. I think this was the first time that a journal didn’t send the article out for review just because I hadn’t followed their style guide. In fairness, I had not followed their style guide closely enough, but it wasn’t fixing the reference format that frustrated me.
What frustrated me was that I had submitted the paper months ago, and had been waiting for something to happen. The journal had sent it back for reformatting a couple of days after I submitted it.... but never sent me an email notification about it. I only found out because I logged into the manuscript handling system just before I was about to email the editor saying, “Hey, what’s going on?” I had wasted months waiting for a decision because of that lack of notification.
After I found this out, I talked to one of my colleagues who’d had a similar experience. A paper she’s submitted sat in the editorial system, with no notifying email, because the recommendation was not “Accept,” or “Reject,” but, “We think this paper would be more appropriate to our sister journal.”
The moral of that part of the story is to log in to the manuscript submission system after a week or so to check on your paper.
I made the changes and resubmitted it. It came back again fairly quickly – and I did get an email telling me about it this time – with another style request.
Please eliminate pronouns like ‘we’, ‘I’, ‘our study’, and ‘my study’ throughout your text. Proper technical writing should not use such phrases.
I had a Return of the Jedi flashback:
Han Solo: “Well, why don’t you use your divine influence and get us out of here?” C-3P0: “I’m sorry, that just wouldn’t be proper.” Han: “Proper?!”
First, that little detail about not using the first person is nowhere in the journal’s rather extensive style guide. I would have avoided it if you’d told me not to do that.
With no guidance, scientists copy what they see, and we see thing like this: “The author is of the opinion that it is appropriate to write papers in the third person.” This is ridiculous. I am the author, not a third person.
The insistence that “data” must always be always a plural noun is another example of a stylistic preference that is confused with some sort of “proper” use. I used to believe this, but argument, analysis, and common use has softened my position. The example that convinced me was that we say, “Eight hours is too long to wait.” There’s a plural noun followed by a singular verb, and nobody bats an eyelash.
There is no ultimate authority of what “proper” technical writing is that someone can appeal to. I realize that people disagree about writing style. That’s fine. But asserting that something is wrong or improper is annoying when you can find examples of that style in many journals, and there is no ultimate authority to appeal to.
Update, 13 July 2016: People on Twitter (mostly) agree: first person is technical writing is not a horrible thing to be avoided at all costs.
Arthropods are wonderfully charismatic and photogenic under a scanning electron microscope. Here are a few pictures of Emerita benedicti that my student Claudette and technician Tom took for no reason than they look cool.
The animals were under the microscope for a research project that we have going on. We got some other nice pictures that may make their way into a manuscript. These were just a bonus.
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.
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?!”
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.
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.
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!
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!
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?
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.
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.
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?
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.
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.
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.
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 Biology11(1): 80–89. http://www.herpconbio.org/Volume_11/Issue_1/Rochford_etal_2016.pdf
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.
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.
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.
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.
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.”
