03 December 2018

How to create your academic web presence

You’re an early career academic, and you think, “I should have something more professional than my personal Facebook account.” I’m here to help!

I recommend creating your own academic website at a bare minimum. All you need is a clean website that you are obsessive about keeping up to date. It’s practically a cliché that professor websites are five years out of date, so just a regularly updated website puts you ahead of 90% of the academic pack! Colleagues and prospective students will appreciate it.

Your university’s IT depertment should be able to provide you with server space to host webpages. That’s currently how I host my home page. But Seth Godin has a good idea here: get a simple blog and set up one featured post with your basic contact information. Then you don’t have to worry about someone else hosting your stuff, or your URLs changing because your university’s IT reorganized their directories. Of, for that matter, having to transfer everything if you move from one institution to another.

It’s also helpful to have a website with an easy-to-remember name. My website’s domain name is not provided by the university; the name just redirects to the university location. There are lots of domain name providers. I used to used GoDaddy, but got driven crazy by their wesbite, which has all the restraint of someone competing for “Best Christmas decorations in the city” award. I have been a happy customer of I Want My Name for years. Their interface is clean and simple, and their prices are reasonable. Again, having your own website name makes it less likely to change if IT reorganizes your university website.

I code my own home page using very basic HTML. Basic HTML coding is actually pretty simple. I learned by viewing the code of other people’s websites. You can do this on most browsers by choosing “View source,” although the underlying code of webpages now is so much more complex than it used to be that this might not be a great way to learn. I’ve been able to do a lot without getting into style sheets (CSS) and more recent stuff.

(A side benefit of learning HTML was that it has helped significantly in teaching online. I know how to make my online class material consistent and clean.)

I use HTML-kit (build 292, which is free) as an HTML editor, but there are many more available. I used to use what became SeaMonkey (also free). I recommend against using Microsoft Word. Word adds huge masses of mostly useless code, making pages far bigger than they need to be.

If you don’t want to learn HTML, there are online services that create websites. I used Wix to create a website recently. It looks great, but Wix is very fiddly, and it took a ton of effort to make it look as pretty as it did. You can have Wix websites for free, but then the website runs ads. You can pay to have ads removed. Of course, other services are available.

Moving from a basic website to social media is a big step up, and this is the one most where you are most likely to run into option paralysis. There are so many things you can do, how do you pick one one to do? It’s okay for that answer to be “None.” Pick ones you actually use or enjoy. If you hate Twitter, start a blog. Or get on Instagram if you dig photography.

But there are tricks to streamline some of the work in creating a web presence. For instance, the Better Posters blog has a Twitter account that is completely automated. I set it up through IFTTT (short for "if this, then that").

06 November 2018

Pick one conference to go to every year

Because I have science attention deficit disorder (science ADD) and am not independently wealthy,
there is no conference I go to each and every year. The only one which I have made a point to go regularly for the last few years has been the Society for Integrative and Comparative Biology, because I’m a committee chair. (Which reminds me I have some bookings to make.)

Over the years, I’ve been to the meetings about evolution, ecology, crayfish, crustaceans, natural history, coastal research, neuroethology, animal behaviour, neuroscience, parasites, and more. Because I have been living in Texas, a reasonably popular conference venue, my strategy has been to wait for meetings to come to me so I don’t have to travel and increase my conference carbon footprint.

This is a bad thing for me.

In the last few years, I’m coming to the realization that my capricious conference selection might be not the best strategy for professional opportunities.

I got to thinking about this after reading Terry McGlynn’s post about the shock and awe of going to the Neuroscience meeting.

As soon as I walked into the poster hall, I was like ZOMG. HOLY MOLY. WHAT THE WHAT.

Ginormous cannnot do justice to explain the scale of this endeavor. Here’s an attempt: Imagine that scene at the end of Raiders of the Lost Ark, but instead of wooden crates, it’s an endless morass of posters upon posters, in which one of those slots is where you have the honor to have your work visible for a few hours.

Terry worries about the size of the conference being alienating. I have felt alienated at conferences, but it’s never been conference size made me feel that way.

Now, I started going to Neuroscience meeting when it was about 60% of what it is now, so I’m used to the scale of the bigger than big conference. And I’ve never used conference size as a factor for deciding what meeting to go to. Both large and small meetings can be great.


In the last few years, I’ve gone to new meetings I’ve never been to before. What put me off and made me feel excluded, particularly as an established mid-career scientist, were constant reminders that there you are not one of the people who come to this meeting every year. There are in jokes made during symposia, keynotes, and talks to things that happened in previous years. It’s very clear who are “conference buddies” that see each other every year.

(Part of this is probably my own damn fault, since I can be quiet, grumpy, or both. I’m working on this.)

But the point is that those conference regulars have clearly built a lot of social capital and created important professional networks that I haven’t.

And the moral of the story is:

Pick one conference that you like. Large or small, doesn’t matter. Go to that conference every year as religiously as you possibly can. Something to present or not, doesn’t matter. You will start building that group of conference buddies that will improve your conference experience (no more lunches alone!) and will become better known in your field.

External links


Huge conferences and the potential for alienation and isolation of junior scientists

01 November 2018

“How can you trust it when it changes all the time?”

“How can you trust science when it changes all the time? One day you hear you should eat margarine and not butter, then the next week you hear the reverse!”

I see variations of this claim fairly regularly when I’m reading about the neverending discussions about evolution and religious creationism. I sympathize. People want certainty, and science is not always great at providing it in the short term. Give a lot of scientists 50 years or more, and we can often provide pretty good confidence, approaching certainty.

While “science changes, but the Bible doesn’t” is mainly appealing to emotion, I’ve actually always appreciated the “Things mean what they say” aspect of Biblical literalism as an intellectual position. It’s honest. Give me an outspoken young Earth creationist over a hand-waving, insincere “intelligent design” proponent any day. I obviously disagree with the the whole “inerrant” part of Biblical literalism, not to mention the absolute refusal of Biblical literalists to update positions in light of new evidence. Still. Sticking to your guns on interpretation of text? I respect that.

But the next times someone pulls out “You can’t trust that ever-changing science,” I have a new riposte.

May I please direct your attention to American Evangelical Christianity of the early twenty-first century.

Because this particular branch of Christianity is now providing an object lesson in the fact that while the text of the Bible may not change, its interpretation sure does. And this is exactly what’s going on in some Protestant churches in the US now.

Diana Butler Bass, an American church historian and scholar who focuses on the history of the American church... said, white evangelicals are motivated by a willingness to read the Bible non-literally when it comes to passages about, say, caring for the poor.

Over the past few years, she’s noticed what she called “a very slow theological turn within the evangelical community to redefine what seemed like very basic ... verses about the care of the poor and caring for the outcast. On one hand, they might say, ‘Oh, you know, Jesus was born of a literal virgin’ ... but when it comes to these verses about the poor and about refugees, in particular, all of a sudden, literalism disappears.”

Suddenly, she said, she noticed a “new sort of interpretation that’s floating around in evangelical circles about [verses in the Bible where Jesus exhorts care for the poor]. And the interpretation is Jesus does not mean everybody. That Jesus only means that you’re supposed to take care of the ‘least of these’ who are in the Christian community.”

The context of this article is about political policy, not science, but nevertheless... if your position is that the Bible literally means what it says, you have to apply that to the whole text. You can’t say the story of Genesis takes place in seven days of 24 hours length and then say the whole prohibition against tattoos (say) is just a big misunderstanding.

Tattoo of Leviticus verse against homosexuality next to Leviticus verse forbidding tattoos. Quote: "If you're going to read the Bible, read the whole thing."

While I can respect the intellectual honesty of Biblical literalism, it’s hard to respect people who extol it without practicing it.

External links

The Bible says to welcome immigrants. So why don’t white evangelicals?
The Year of Living Biblically

11 October 2018

Why do people think humanities are easier than science?

I believe that all scholarship is hard. But people think humanities are not as hard. You rarely hear about students who “can’t cut it” in medieval literature and change their major to organic chemistry because they think it’s easier. But the opposite change of majors is practically cliché.

Maybe one of the reasons people view humanities as easier is because they are more familiar with it, because they have grappled with it longer, because teachers aren’t scared of using the original text.

We teach Shakespeare’s plays full on in grade school, for instance. We give students the complete written text of his plays and poems. We teach them despite the language used being far from common today. It’s only because of Hamlet that I have the faintest inkling of what a bodkin is. Understanding Shakespeare is hard. But it’s taught in schools to young people without hesitation. We teach even older stuff written in more archaic language, sometimes (albeit often with translations).

But what about Shakespeare’s scientific contemporary, Galileo? I doubts many schools have students read direct translations of Sidereus Nuncius (Starry Messenger) in full. Instead, students get summaries of science in textbooks that are far removed from the original texts.

Teaching science using only textbooks is like teaching literature using only CliffsNotes or teaching film studies using iMDB synopses. Yeah, you’ll learn something, but you’re also missing a lot. Some might say you’re missing the point entirely.

I’m willing to bet most students don’t get tasked with reading original scientific literature until well into a university degree. So is it any surprise that they can’t understand scientific papers compared to reading literature? They’ve had maybe the better part of a decade receiving instruction on how to parse out a literary text, but almost no instruction on how to make sense of a scientific text.

Because of this, students often don’t understand the process of argumentation that goes into science. They don’t understand how many things are suggested before being demonstrated. They don’t understand science as a process instead of facts. These are not new complaints, but the solution most people veer towards is to have students do more “hands on” work to get a sense of how science is done, not to have students read original science.

The writings of scientists are trivialized next to their discoveries, and maybe it shouldn’t be.

22 September 2018

Giving octopuses ecstasy

California two-spot octopus (Octopus bimaculoides)Nobody told me it was “Drug an invertebrate week.” But not only has a story of lobsters getting pot rather than going into pots made the round, now we have octopuses getting another recreational human drug. The story, according to headlines, is that giving ecstasy (MDMA) to octopuses makes them act more socially. And everyone’s comparing octopuses to ecstasy fueled partygoers at a rave.

It’s a nice narrative, but there isn’t enough evidence to conclude that.

There is some genetic analyses of MDMA receptors in this paper, but all of the interest in the press is about the behaviour experiments. The authors gave the octopuses the drug. The octopuses’ behaviour changed. The popular press is interpreting that behaviour in a cutesy way, using terms like “hug” and “cuddle” in headlines. (Even publications like Nature who should know better.)

That’s a problem. Octopuses hunt prey by enveloping them with their web and tentacles — effectively “hugging” them, if you will. Being eaten is rather different than cuddling. The authors provide no videos in the paper, just two still images (below), so you can’t see the behaviour in detail.

Photograph of Octopus social interaction under the saline condition on left and MDMA condition on right.

The sample size for the behavioural experiments is 4 or 5, as far as I can see. That’s tiny.

It’s worth noting that the behavioural changes were not always the same.

In addition, pilot studies in 3 animals indicated that higher submersion doses of MDMA (ranging from 10-400 mg/Kg) induced severe behavioral changes (e.g., hyper or depressed ventilation, traveling color waves across the skin or blanching, as well as catatonia or hyper-arousal/vigilance) and these animals were excluded from further analysis.

Dose-dependent responses are not at all unusual, but again, it makes the simple story of “MDMA means social” more complicated.

I do appreciate that this paper has an Easter egg for people who read the methods:

Novel objects consisted of multiple configurations of 4 objects: 1) plastic orchid pot with red weight, 2) plastic bottle with green weight, 3) Galactic Heroes ‘Stormtrooper’ figurine, and 4) Galactic Heroes ‘Chewbacca’ figurine.

But which Stormtrooper, people?


Which Stormtrooper?!

The paper is interesting, but it’s not getting attention from popular press because it’s particularly informative about the evolution of social behaviour. It’s getting attention because of the novelty of giving drugs to animals, and the “Oh look, animals are like us!” narrative.

Additional, 24 September 2018: Another interpretive problem. Normally, in an interview on CBC’s Quirk and Quarks, Gul Dolen notes octopuses overcome their asocial behaviours for mating. Dolen cites this as reason to think that there could be a way to “switch” the octopuses’ behaviour using a drug. So mating behaviour is the natural “social” mode for these animals.

But the octopus under the basket was always male, because the researchers found octopuses avoided males more than females.

Three of the four octopuses tested were male. (I had to dig into the supplemental information for that.) So most of the observations were male-male behaviour. I don’t know that homosexual behaviour has ever been documented in octopuses. A quick Google Scholar search found nothing.

A Washington Post story revealed that the authors’ wouldn’t even talk about some of the behaviours they had seen:

The authors observed even stranger behavior that they did not report in the study, Edsinger said. He was reluctant, even after extensive questioning, to further describe what the octopuses did, because the scientists could not be sure if the MDMA had induced these actions.

This is problematic. This suggests the behaviours in the paper are deeply underdocumented at best. And it seems to be done on purpose, because it doesn’t fit the authors’ narrative. This, combined with the description of behaviours at different doses, it further suggests that rather than “prosocial” behaviour that the authors and headlines are pushing, the exposure to MDMA is making octopuses behave erratically, not socially.

Reference

Edsinger E, Dölen G. A conserved role for serotonergic neurotransmission in mediating social behavior in Octopus. Current Biology 28(3): P3136-3142.e4. https://doi.org/10.1016/j.cub.2018.07.061

External links

Octopuses on ecstasy: The party drug leads to eight-armed hugs
This is what happens to a shy octopus on ecstasy
Octopuses on ecstasy just want a cuddle
Serotonin: octopus love potion?


Picture from here.

20 September 2018

Giving lobsters weed

I’ve been studying issues roiling around the question of “Does it hurt lobsters when they go into a pot?” for about a decade. After ten years or so, you get a little jaded. I’m used to seeing the same bad arguments. I’m used to it popping up and making the rounds in news about twice a year. The first time this year was when Switzerland put laws into place about lobster handling. This is the second.

And I’ve got to say:

That’s new.

A Maine newspaper is reporting on a restaurant owner, Charlotte Gill, is sedating lobster with marijuana.

I am pretty sure cannabis as a sedative not been the subject of any peer-reviewed scientific papers on crustacean anesthesia. But a quick Google Scholar search (thank you thank you thank you Google for this tool) shows that spiny lobsters and other invertebrates have cannabinoid receptors (McPartland et al. 2005). This makes the technique plausible on the face of it.

The behavioural effects reported were interesting.

Following the experiment, Roscoe’s (the experimental lobster - ZF) claw bands were removed and kept off for nearly three weeks.

His mood seemed to have an impact on the other lobsters in the tank. He never again wielded his claws as weapons.

I am surprised by the apparent duration of the effects. Weeks of behaviour change from a single treatment? That seems long compared to soporific effects of marijuana smoke in humans doesn’t seem to last multiple days.

Earlier this week, Roscoe was returned to the ocean as a thank you for being the experimental crustacean.

I’m not sure of the ethics of this. Will Roscoe the lobster, who has apparently forgotten how to use claws, going to become a quick meal for a predator? A lobster without claws in the ocean is just bait (Barshaw et al. 2003). Releasing Roscoe may doom him!

I am a little concerned by what seems to be Gill’s quick dismissal of other techniques:

In Switzerland, the recommended method of cooking the crustacean is to electrocute it or stab it in the head before putting it in the boiling water.

“These are both horrible options,” said Gill. “If we’re going to take a life we have a responsibility to do it as humanely as possible.”

I don’t know if she has anything but intuition to support that opinion. There’s research on electrical stunning, and the results so far are mixed. Fregin and Bickmeyer (2016) found shocks “do not mitigate the response to external stimuli,” but Neil (2012), Roth and Grimsbø (2016), and Weineck et al. (2018) found electric shocks seemed to knock down neural activity effectively. But the impression I get is that using shock is tricky: you need different protocols for different animals.

It’s also worth noting that a new paper by Weineck et al. (2018) showed chilling was effective as an anesthetic, which the Swiss regulations forbade. Research I co-authored (Puri and Faulkes 2015) showed no evidence that crayfish responded to low temperature stimuli.

Of course, another complication around this technique is its legality. The legal landscape around marijuana in the U.S. is tricky. Marijuana is still regulated federally, but certain states permit different kinds of uses. The article notes:

Gill holds a medical marijuana caregiver license with the state and is using product she grows in order to guarantee its quality.

This is interesting, but it’s not clear to me that this is a more cost effective or humane way to sedate a lobster than what many crustacean researchers have been doing for a long time: cooling on crushed ice.

Hat tip to Mo Costandi.

References

Barshaw DE, Lavalli KL, Spanier E. 2003. Offense versus defense: responses of three morphological types of lobsters to predation. Marine Ecology Progress Series 256: 171-182. https://doi.org/10.3354/meps256171

Fregin T, Bickmeyer U. 2016. Electrophysiological investigation of different methods of anesthesia in lobster and crayfish. PLOS ONE 11(9): e0162894. https://doi.org/10.1371/journal.pone.0162894

McPartland JM, Agraval J, Gleeson D, Heasman K, Glass M. 2006. Cannabinoid receptors in invertebrates. Journal of Evolutionary Biology 19(2): 366-373. https://doi.org/10.1111/j.1420-9101.2005.01028.x

Puri S, Faulkes Z. 2015. Can crayfish take the heat? Procambarus clarkii show nociceptive behaviour to high temperature stimuli, but not low temperature or chemical stimuli. Biology Open 4(4): 441-448. https://doi.org/10.1242/bio.20149654

Roth B, Grimsbø E. 2016. Electrical stunning of edible crabs (Cancer pagurus): from single experiments to commercial practice. Animal Welfare 25(4): 489-497. https://doi.org/10.7120/09627286.25.4.489

Weineck K, Ray A, Fleckenstein L, Medley M, Dzubuk N, Piana E, Cooper R. 2018. Physiological changes as a measure of crustacean welfare under different standardized stunning techniques: cooling and electroshock. Animals 8(9): 158. http://www.mdpi.com/2076-2615/8/9/158

Related posts

Switzerland’s lobster laws are not paragons of science-based policy

External links

“Hot box” lobsters touted
Maine restaurant sedates lobsters with marijuana
New England marijuana laws – where it’s legal, where it’s not and what you need to know

19 September 2018

“Best” journals and other unhelpful publishing advice

The Society for Neuroscience recently posted a short guide for publishing papers for early career researchers. It makes me grumpy.

Aim for the best journal in your field that you think you can get into, as a general rule.” This ranks right up there with Big Bobby Clobber’s hockey advice, “The key to beating the Russians is to score more points than they do.” “Publish in the best journal” (or its sibling, “Strive for excellence”) is incredibly unhelpful for new researchers, because they don’t know the lay of the publishing landscape. They will rightfully ask how to recognize “best” journals. In academia, notions of “best” are often highly subjective and have more to do with tradition than actual data. This tweet led me to this article:

When Elfin was first charged with creating a ranking system, he seems to have known that the only believable methodology would be one that confirmed the prejudices of the meritocracy: The schools that the most prestigious journalists and their friends had gone to would have to come out on top. The first time that the staff had drafted up a numerical ranking system to test internally–a formula that, most controversially, awarded points for diversity–a college that Elfin cannot even remember the name of came out on top. He told me: “When you’re picking the most valuable player in baseball and a utility player hitting .220 comes up as the MVP, it’s not right.”

Elfin subsequently removed the first statistician who had created the algorithm and brought in Morse, a statistician with very limited educational reporting experience. Morse rewrote the algorithm and ran it through the computers. Yale came out on top, and Elfin accepted this more persuasive formula. At the time, there was internal debate about whether the methodology was as good as it could be. According to Lucia Solorzano, who helped create the original U.S. News rankings in 1983, worked on the guide until 1988, and now edits Barron’s Best Buys in College Education, “It’s a college guide and the minute you start to have people in charge of it who have little understanding of education, you’re asking for trouble.”

To Elfin, however, who has a Harvard master’s diploma on his wall, there’s a kind of circular logic to it all: The schools that the conventional wisdom of the meritocracy regards as the best, are in fact the best–as confirmed by the methodology, itself conclusively ratified by the presence of the most prestigious schools at the top of the list. In 1997, he told The New York Times: “We’ve produced a list that puts Harvard, Yale and Princeton, in whatever order, at the top. This is a nutty list? Something we pulled out of the sky?”

When people talk about “best” journals, this almost always ends up being code for Impact Factor. The article mentions these second.

Consider impact factors, but don’t obsess over the number. There are many excellent medical and biomedical specialty journals considered top tier in their fields that have relatively low impact factors. Don’t let the impact factor be your only data point when deciding where to send your paper.” This gives me another chance to point to articles about the problems of this measure, like this and this. It’s so flawed that authors should think about it as little as possible.

Look at the masthead. Are the people listed on the editorial team who you want reading your paper? Do they represent your target readership?” This is deeply unhelpful to new researchers. New researchers do not know the lay of the land and probably are not going to recognize most of the people on editorial boards. Recognizing that network takes time and experience.

Read the aims and scope. Does the journal’s focus align well with your submission?” Finally, a good piece of advice. I would have put this first, not fourth.

Do you and/or your university care whether you publish in open-access journals? Some institutions will put a high value on an open-access paper, so don’t underestimate the importance of this preference.” Again, probably unhelpful for early career researchers. Doctoral students and post-docs may very well change what institutions they are affiliated with, maybe multiple times.

Is your research ready to be published? Do you have a compelling and complete story to tell? While there is a great deal of pressure to publish frequently, don’t slice and dice your research into many small pieces. Consider the least publishable unit, and make sure yours is not too small to be meaningful.” I’m kind of godsmacked that “Check to see if it’s done” is presented as advice. The notion of a “complete story” is deeply problematic. The data don’t always cooperate and answer a question cleanly. There are many projects that I would never have published if I say on them until they were as “complete” as I wanted. Here’s a project I sat on for eight years because it wasn’t “complete.”

External links

How to Publish for a Successful Academic Career