30 September 2010

The truth about teaching statements

Almost every tenure-track job ad includes some language that says, “Tell us about your teaching.” Sometimes it’s called a statement of “teaching philosophy,” sometimes a statement of “teaching interests,” or something else.

Those teaching statements are often the weakest thing in the job application, in my experience.*

There are a couple of reasons for this. Many tenure-track applicants have distorted views of teaching responsibilities, because many of them were trained as doctoral students and post-docs at the biggest research institutions. That is to say, institutions with the biggest research programs, the greatest pressure to generate data and publish, and the lowest teaching loads.

Plus, institutions generally doesn’t have to invest in someone’s teaching career in the same way as they have to invest in someone’s research career. Lecture halls don’t have to be renovated for a new instructor, but labs often have to be refurbished for a new researcher. The infrastructure for teaching is already in place.

The result is that job applicants will write research statements that go on for pages, single spaced, with an exhaustive list of references. Documents that show someone has put in a great deal of thought and preparation.

Them, you get a half a page about teaching with no details or specifics. They often wallow in vague generalities, like, “My students will learn critical thinking skills.”

In contrast to the scholarship displayed for the research statements, I rarely see evidence of scholarship regarding teaching. I can’t think of one time where I’ve seen someone refer to the science education literature in their teaching statements, for instance.

Another specific thing you can mention in a teaching statement is whether there are any existing classes in the course catalogue that you might want to teach. There are cases where a department is specifically trying to hire someone to teach an existing class. You can sometimes glean that from the job ad if specific classes are mentioned. We have had positions where one of the listed expectations was, “The successful candidate will teach BIOL 3333,” but when asked to list course they could teach, they don’t mention the one course specifically mentioned in the job ad! Ooops.

The follow-up to that is what courses you’d like to develop. Obviously, both of these require you do your homework, and read the catalogue of the institution you’re applying to.

What am I looking for in a teaching statement?

The level of experience is not critical as long as you have some. Most people applying for tenure-track jobs are going to have experience as teaching assistants (TAs) in labs. Some might have a few guest lectures. Very rare is the person who will have done an entire class.

It is important that you convey a positive attitude about teaching. One of the shocks that I got when I moved to the review and hiring side of the search process was the number of job candidates who give you the distinct impression that they see teaching – particularly teaching undergraduates – as a terrible burden to them. One that they want to get out of as fast as possible.

A lot of job candidates take themselves out of the pool with this contemptuous attitude.

Admittedly, I’m at an institution that is not a research intensive one with a lot of doctoral programs, but I’m willing to bet that many search committees at places with greater research capabilities are not going to ignore bad teaching.

* And what is my experience? I’ve been on search committees most of the years I’ve been here, usually searching for two or more positions a year.

Photo by icentralarkansas on Flickr, and used under a Creative Commons license.

29 September 2010

The Zen of Presentations, Part 36: Prezi

“I only have about six months where this will be really cool, and then everyone else will discover it.”

I thought that about Prezi over a year ago.

This summer, I went to two conferences in three weeks. And I was somewhat appalled by the complete dominance of PowerPoint – for posters as well as presentations. Of all the talks I saw at two conferences, the talk I gave at the International Association of Astacology meeting was the only one that didn’t use PowerPoint.

I used Prezi instead. It was only the second time I’d done so. But like the first time, people were slightly in awe. “How did you get PowerPoint to do all that zooming?” they asked.

I’d smile and reply, “Simple. I didn’t use PowerPoint.”

PowerPoint emulates 35 mm slides: a series of individual images, one after another. PowerPoint has allowed animation of the images, but you’re still basically using the computer as a fancy slide carousel.

Prezi emulates a whiteboard: you get one surface to play on. But it escapes some of the limitations of the medium by combining the whiteboard with a magnifying glass, allowing you to zoom in and out to particular locations at your pleasure.

Why have I only used Prezi twice, when I’ve gotten such a “Wow” response? Because it’s not right for every job. Even experts like Garr Reynolds and Nancy Duarte (replying to Garr on Facebook) seem to be trying to figure whether or not there are any real advantages to using Prezi over other media. There is, as far as I know, just one book about using Prezi – and it’s in Dutch. (Which is great for them, but not so hot for me.)

What sets Prezi apart from PowerPoint (or most other techniques) is the zooming. I’ve seen zooming used two ways.

Some use zooming as a fancy transition that PowerPoint doesn’t have. It’s a wasted opportunity, and such presentations are often called “dizzying.”

Where Prezi starts to rock is when you use it to show whole / part relationships. In other words, you’re zooming in and out of a single thing as though you had a physical camera that zooms in on a part of a larger object, or pulls back and reveals something is just a piece in a larger puzzle.

Here’s one we did earlier, as they used to say on the cooking shows.



This kind of story works extremely well in Prezi. The map ties it all together, and gives everything a spatial context. You can see how big a move going to McGill in eastern Canada was compared to going to grad school, for instance. I couldn’t tell the story as effectively in PowerPoint.

I’ve learned, though, to try to make each individual step rather small. If you go from a long way out to a long way in in one step, you will rightfully earn the “dizzying” label. Here’s another version that zooms straight from one place to another.



I don’t think it’s as effective as the one above it. Of course, both could be improved if I had higher resolution maps, but as “proof of concept” demos, they work well enough.

In the first example, notice that I don’t jump from Lethbridge to Killarney to the University of Victoria. I pull out from one some distance, in steps, before I start to zoom in to the other. In the second, I go straight from one location to the next. You don’t get as strong a sense of the context as the first one. (I think Prezi may have been optimizing their zooming rates; this one doesn’t seem to race from location to location as fast as I thought I have seen before. But maybe I’m imagining things.)

In biology, I can think of lots of different examples where Prezi would be fantastic at showing whole / part relationships.

  • Starting from a whole organism, zoom down to tissues, then specific cells, then maybe even molecules. (We biologists are always obsessing about “levels of analysis.”)
  • Showing relationships between organisms in phylogenetic trees. You can show the entire tree, then look at particular clades, and individual species within a clade.
  • Timelines. I could imagine some very cool things you could do with geological time.
  • Ecosystems and food webs.

Prezi is not a PowerPoint killer. There are many kinds of stories that don’t have any spatial relationships, and Prezi’s only advantage is novelty. As more people discover Prezi, that advantage will wear off. But for cases where you have a story that does have some spatial elements, Prezi is unmatched.

Related posts

No more slidesters, interlude: Making presentations more like posters

Rhett Allain has a nice list of Prezi pros and cons. Ed Yong mentions that the lack of slides allow him to change things on the fly more than PowerPoint. And Ted Curator Chris Anderson does a great talk using Prezi.

28 September 2010

Tuesday Crustie: From mighty oaks...

...come acorns.


A common barnacle on the Pacific coast of North America, the white acorn barnacle, Balanus glandula.

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

27 September 2010

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

Almost two years ago, I gushed over Nancy Duarte’s book, Slide:ology. She has now written her first book, Resonate.

Yes, you read right. Her second book came out two years ago. Sort of like how the first Star Wars movies came out a couple of decades after the later films.

Duarte describes Resonate as the prequel to Slide:ology. And she’s right. Resonate is the one to read first, because it is about the reason for giving a presentation: to change people’s minds, to persuade, to take action. In contrast, Slide:ology is more about design of visuals: the things that you work on once you’ve know what you want to talk about.

At the core of Resonate is her thesis that all good presentations have a common structure. Great presentations start with “the way it is.” Then, they make repeated contrasts between “the way it is” and “the way it could be.” Finally, great presentations end with a call to action, and a promise that new, greater things are possible.


It’s simple, but don’t dare think for a second that it’s stupid. Scientists will probably appreciate the repeated analysis that Duarte has done to show that this structure is variable and rich. It’s similar to how stories can follow the same basic plot structure, but differ profoundly in almost every other way.

Another unexpected inversion is in how Duarte conceives of the importance of story. She has something more in mind than anecdotes or telling a narrative with a clear beginning, middle, and end. The presenter’s role is not to be someone like Sherlock Holmes, who unravels the plot and explains it to Inspector Lestrade (the audience). If I may jump genres...

The presenter’s role is to be Ben Kenobi. *

It takes a little while to get used to this view. At first, it’s somewhat paradoxical to think of the person given a presentation as a supporting character. After all, this sort of character is not usually the most popular one in the movie. Everyone wants to be the central character. You are not.

These short summaries do not to the justice to the richness of these concepts, and there are many more besides. She talks at length about her work process for developing presentations, and how to persuade people (taking some cues from Randy Olson along the way), for instance.

Duarte has again written a deep book. Wonderful.

Related pages

Book website

* Duarte herself uses a different example from the Star Wars series, but I think Ben is a little closer to the part of the presenter than the example she uses.

25 September 2010

A draw?!


Close games are exciting, but this...?

24 September 2010

With or without you

Earlier this year, Dr. Isis discussed the following situation.

A trainee (student, post-doc, what have you) finishes up data collection a collaborative research project. The project would not have been possible without help from the collaborator, who made substantial contributions to the design and data collection of the project.

The trainee starts writing it all up for publication, then tries to get input from the collaborator, but hears nothing.

Trainee tries emailing, contacting, all sorts of goof faith efforts to get input from collaborator. Still nothing.

Should the trainee go ahead and submit a paper anyway? If yes, with the collaborator’s name or without?

There was a fair amount of discussion on this in Dr. Isis’s blog (which I was participating in). A decent number of commenters said that the lack of response from the collaborator was reason enough to submit the article without the collaborator’s name on it. The best known guidelines for authorship say that if you don’t participate in writing, you shouldn’t be listed an author.

A case pretty darn close to this showed up on the Retraction Watch blog earlier this month.

It did not surprise me that the journal editor took the side of the omitted authors in that case.

23 September 2010

A whole new type of flower porn

ResearchBlogging.orgOkay, so males in search of sex are not always that discriminating. We’ve seen that males that mate with females that will kill and eat them. We’ve seen males that will court other males. But not recognizing that something doesn’t even belong to your own kingdom is close to the record, and we saw that with some male insects that copulate with flowers.*

Previously, only orchids were known to trick insects into copulating with them. It’s thought that this is a way to enhance pollination. Now, a new tease has been found.


As you can see, Gorteria diffusa has a lot of variation in its flowers. It turns out that male flies are very attracted to some forms of these flowers, to the point that they will try to mate with them. And yes, Ellis and Johnson have the blackmail tapes.

While wasps only occasionally try to mate with orchids – but flies will try to mate with some forms of these daisies up to 75% of the time. It’s not clear yet if the males learn to avoid these flowers. And, unlike the orchid case, the authors haven’t found any evidence of the male flies releasing ejaculate, so the flies are mainly wasting time, not genetic material.

Another difference between the orchid story and this species is that the daisies actually give food rewards. So within this one flower species there is a wide range of strategies, ranging from honest (“I’ll give you food if you’ll do me a solid”) to deceptive (“Actually, you won’t get offspring from this”). This promises to allow for lots of fascinating experiments.

Reference

Ellis A, & Johnson S (2010). Floral mimicry enhances pollen export: The evolution of pollination by sexual deceit outside of the Orchidaceae. The American Naturalist. DOI: 10.1086/656487

Flower photo by buildingadesert on Flickr. Used under a Creative Commons license.

Related posts

Tricking wasps with flower porn

* Still not the record holder for males with the lowest standards, though.

22 September 2010

Who was that mysterious stranger?

A few weeks back, I joked about the proliferation of new blogging networks. But such networks are useful, and particularly with the launch of Scienceblogging.org, there was a bit of fear that indie bloggers would be pushed into oblivion.

But today I noticed this on Scienceblogging.org:


Someone has created an aggregation of unaligned neuroscience blogs (including this one) called “Neuroghetto” so that posts can be featured on the Scienceblogging.org home page. This was indeed a very nice thing to do.

I’m not sure who to thank, though. It was all done without me knowing.

While I’m here, I want to point to Dave Munger’s excellent analysis of men and women scientists blogging.

Update: I have since learned it was Twiter user sarcastic_f who created the feed. Thanks, guy! That was a fine bit of work. And thanks to Mo and Bora for setting me right!

Scientists Behaving Badly: The Complete Series

Retraction Watch is veritable goldmine for case studies of scientific ethics. Or a motherlode. I’m sure some sort of mining metaphor is appropriate.

There are a lot of blogs that take pride in mythbusting, examining overblown claims, and exposing bad science, and yes, Ben Goldacre’s blog of that name is one of the best examples. But often these deal with claims that are about distortions created by others about valid research, or are examining the weaknesses of projects that are still part of the scientific record.

Retraction is an effort to expunge something from the scientific record entirely. If a journal article gets retracted, it is usually because something has gone very, very, badly wrong. It is among the biggest repudiations that scientists are likely to face, and I daresay is usually initiated by the journal rather than the author.

Having many retractions in one place, with commentary and some investigation, is incredibly instructive. You get to see the pitfalls that people fall into. Some are are unforeseen, and some are holes that people dig for themselves.

It may be one of the most important blogs about scientific research that has yet been created.

21 September 2010

Tuesday Crustie: Tippie-toes


I’m so sorry that I don’t know the species name of this amazing land crab. But this one is too great not to use.

Photo by bob in swamp on Flickr; used under a Creative Commons license.

20 September 2010

Post-publication peer review


“Do you think they’ll notice?”

Last week, I got an email that started off poorly:

Please accept our apologies if we have caught you at a busy time.

I am, and you just wasted another two seconds of it with that useless line. Crud, when you’re bulk emailing researchers, don’t try to convince us that you are all that concerned about our time.

The point of the email was to inform me of a bold new scientific publishing venture! I thought, “Oooh, okay, I’ll bite.” And then the very next line, they lost me and I wriggled away from the bait.

Guaranteed publication of your research within 48 hours of submission

Sorry, can’t take it seriously.

One of the defining characteristics of all academic writing is peer review. Editors and other professional researchers try to filter out mistakes and errors (and, occasionally, cranks).

Yet you publish everything? Forget about being credible as forum for scientific publication, that’s not credible in any form of publication. That has a name in the book business: it’s called “vanity press.”

They try to anticipate the objections, and claim they are still peer reviewed.

Peer review takes place post publication in an open and transparent manner

What?!

Reviewing something after it is published is missing the entire point of peer review. I want someone to act as a filter. I want someone to have made a good faith effort to ensure that the article is not a hoax, a crank, or meaningless.

It’s incredibly tempting to send in a hoax article to see if their “post-publication peer review” calls it out as gibberish.

Now, I do admit I was pleasantly surprised by one aspect of this whole thing. I was completely expecting the punchline, where they revealed a submission fee for publication. This is being used effectively by some credible journals, and as scams by others. So this caught me off-guard:

No cost to authors or readers.

Anything free is worth what you pay for it.

With no fees to anyone, I have to wonder how they plan to sustain the effort and archive articles. I worry about the long-term preservation of research with every online journal, even the most successful and established ones. I’ve been online long enough to have seen stuff (mostly non-academic) lost forever.

I am in favour of experimenting with new models of scientific publication as much as the next guy. But if I saw someone who listed an article on this website as a peer-reviewed publication for an application, grant, or anything, it would go to the bottom of the pile instantly. I’m not accepting this as a valid publication model. And I can’t quite imagine the mainstream research community is going to accept it, either.

Disguising vanity press as “post-publication peer review” is going to be as successful as disguising a mobile phone tower as a palm tree. People aren’t going to be fooled.

Photo by purpletwinkie on Flickr, used under a Creative Commons license.

18 September 2010

Concealment breached

As I mentioned earlier this week, I have been having a good year for publications. Last week, I had one article accepted on Tuesday. I submitted another on Friday.

This prompted one of my peers to say, “You are a machine!”

About four separate people have said this to me this year.

Damn it. They have noticed. Perhaps it is time to give up trying to blend among the humans.

17 September 2010

Pay attention to your State Board of Education candidates

Oh, Texas State Board of Education. You’re the gift to blogging that never stops giving.

Because the Texas State Board of Education is an elected position, there are a long series of run-offs to determine which candidates will be placed on the final ballot. The Austin Chronicle is looking at some of the candidates who hope to serve as representatives, and the story starts with a blunt opening, describing Austin as home to:

(T)he University of Texas... workplace of many of this state's most brilliant minds, who are achieving groundbreaking research in such fields as biology, physics, and history.

And right here, on this side of the window, right-wing Christian conservatives have been toiling for several years now trying to undermine, educationally and politically, much of those scholars' work.

Unsurprisingly, as reporters know this is a bellweather question, candidates are often asked about the teaching of evolution, if they don’t volunteer it outright. Here’s one of the candidates, Marsha Farney, who some were hoping would represent a more moderate Republican point of view:

“My faith is not shaken by evolution. ... It should be taught as a theory.”

The Chronicle characterizes many of her statements as vague, and I think that qualifies.

It also profiles incumbent Board member Ken Mercer, who’s made an appearance or two in this blog before for statements he’s made about the teaching of evolution.

16 September 2010

Inclining the playing field

You have two grant proposals in front of you.

One is a researcher at an primarily undergraduate institution that isn’t well known outside of its region, but this particular person has had several years of producing a string of publications in international journals. In fact, this person has pulled together a few colleagues, and they have a good collaboration going.

The other is a researcher at a major research university that is recognized internationally, and has been publishing, but at nowhere near the rate of the first researcher. He’s plugging away at his own lab with his own doctoral students, and not really working with other faculty in his institution or elsewhere.

Dame Nancy Rothwell would have us believe that the right thing to do is to give the money to the second researcher. He may not be as productive as the first, but that's not important, because the best institutions have to be maintained.

The Times Higher Education reports:

If the coming cuts in higher education spending were so severe that Hefce was forced to choose between protecting funding for top institutions and islands of excellence, the latter should lose out, she said.

To put it another way, people do not count; only institutions do. Individual initiative does not count; only maintaining prestige does. And the status quo never, ever changes.

There’s a message from a king worried about his crown.

As research dollars tighten, watch for more and more vested interests making more and more efforts to stop people from competing for the resources that the established places have had to themselves for a long time.

Hat tip to Chris Atherton.

What am I doing right?

There’s that moment in the first Spider-Man story when Peter Parker gets his first clue that he can do things he couldn’t do before.


Wouldn’t that be a strange, heady mix of elation and “What the...?!” Because you’d have to be thinking, “I’ve done something amazing... and that is not normal!” Wouldn’t you be worried by something so far out of the bounds of your normal experience, no matter how cool it was?

Earlier this week, I got another acceptance letter for an article from a peer-reviewed refereed journal. I now have more articles in press than ever I’ve published in an entire calendar year – and that’s on top of what I’ve already published this year.

I don’t mind telling you – it’s freaking me out a little.

It is just that far beyond what I’ve managed to achieve before that I am thinking about how this happened, what do I do for an encore, can I keep up the pace, should I be trying to publish fewer papers in better journals, will anyone notice, will anyone care, can I maybe use this momentum to have a decent crack at some funding for projects instead of paying out of my pocket... It’s a whirlwind in my head.

What, you thought all those crazy thoughts stopped after tenure and you get to relax? Well, it sure as hell hasn’t been that way for me.

15 September 2010

Comments for first half of September 2010

Manner of Speaking has a great suggestion for taking two slides out of your talk – usually ones at the end. I suggest a third one to remove, at the beginning.

Michael Tobis at Only In It For the Gold suggests academics are becoming like royalty, but not in a good way.

Detective Christie Wilcox tracks down the claim that bull sharks have insanely high levels of testosterone at Observations of a Nerd.

Monofilia describes the evolution of giraffe necks, and makes an obligate but perhaps overused quote from an historic biologist.

Dr. Becca has an enemy.

Scicurious at Neurotic Physiology considers the role of Carl Sagan in contemporary science communication, which is something I wrote about last year. (It’s probably the single most popular post on this blog, thanks to appearing in Open Lab.)

Make your saving throw versus CON

One of the problems of being in a bureaucracy is that administrations change more often than the main line of employees. In a higher education setting, administrators come and go while the faculty remains.

This means that you have to put up with seeing bad ideas over and over again.

And you know what? Willpower is finite. Thus, one’s ability to present the same points over and over again calmly may also be finite. Your mental endurance is tested over and over again.

And when you keep being forced to make those saving throws over and over again, you live knowing that at some point, you’re inevitably going to roll a 1.

Photo by Dr Stephen Dann  on Flickr, used under a Creative Commons license.

14 September 2010

Texas Governor wades back into Texas K-12 science standards debate

You know, I was actually worried that I would not have anything to blog about the Texas education system and evolution for a long while.

As if on cue...

The San Angelo Standard-Times has an interview with Governor Rick Perry.

Explain where you stand on evolution-creationism being taught in school.

I am a firm believer in intelligent design as a matter of faith and intellect, and I believe it should be presented in schools alongside the theories of evolution. The State Board of Education has been charged with the task of adopting curriculum requirements for Texas public schools and recently adopted guidelines that call for the examination of all sides of a scientific theory, which will encourage critical thinking in our students, an essential learning skill.

The Governor’s personal beliefs are his, and I have no interest in arguing those. But he is wading into an incredible mess when he suggests that it be taught in schools along evolution. That would be illegal, following the U.S. Supreme Court decision Edwards v. Aguillard.

It is the prerogative of state governors to rail again national laws and argue they should be changed. Welcome to federalism. But that the Governor would knowingly support an illegal policy is another matter entirely.

Another candidate for the job of Governor, Bill White, answers the same question:

Educators and local school officials, not the governor, should determine science curriculum.

Hat tip to Pharyngula.

Tuesday Crustie: The Loch Ness beauty


This picture of Cypria ophthalmica was taken off the coast of Spain, but this little animal is also very common in Loch Ness, Scotland, and probably much else besides.

Photo by Proyecto Agua** /** Water Project on Flickr, used under a Creative Commons license.

Textbook identity

One of my colleagues got an email from a student peeved that we had switched our introductory biology textbook. The student was annoyed by the cost, and that there were no used copies because it was a new text.

The student had apparently compared the new book and the old, claiming that there were only minor changes in content at most. Putting aside how much the student could actually determine about the content of two books weighing in at close to 1,000 pages in the first two weeks of class, what interested me was that the student thought only about the physical object.

One of the things that is most impressive about contemporary textbooks, however, is the wealth and richness of their online resources. I doubt students consider those at all. (A few years ago, before textbook publishers set up websites, texts would often come bundled with CDs. I heard that when the students sold the books back, the CDs would often still be in the little envelopes bound into the books, untouched, with many students completely unaware it had been there.)

Getting an online resource is like getting an extended service warranty: it’s not something that you can see or hold in your hand when you walk up to the counter. I wonder if there are psychological studies of how people value such purchases.

Textbook publishers are facing a lot of problems. I’ve said before that textbooks probably can’t survive in their current form, and in some ways, the online resources the publishers are offering indicate that the publishers are moving in the right direction.

But emails like the one my colleague received show that the psychological inertia is huge. If there is anything made of atoms, it seems students will focus on that one thing and think about nothing else they might be getting along with those atoms pulled from trees.

Related posts

eTextbooks
Antiquated, heavy, expensive
Why textbooks have a bad rep
The textbook conundrum

13 September 2010

Want to be immune to deadly poison? It’ll cost you

This animal could kill seven people.


No wonder it looks a little smug.

That newt could well be thinking, “Sure, you might try and eat me, but when your brain stops, I’ll have the last laugh, sucker.”

And it wouldn’t be kidding.

ResearchBlogging.orgSome rough skinned newts (Taricha granulosa) have something in common with poison dart frogs, blue-ringed octopus, and pufferfish. They all contain within them a poison called tetrodotoxin.

Tetrodotoxin is a neurotoxin that stops neurons from initiating action potentials. It’s most famous as the stuff that makes fugu, pufferfish sushi, notoriously tricky to prepare and serve, because if you do it wrong, eating it kills.

Some garter snakes (Thamnophis sirtalis), however, have evolved the ability to resist tetrodotoxin – which lets them eat newts with impunity. There’s been quite a few studies on this predator-prey arms race, and the latest, by Lee and colleagues, looks at the properties of the neuron that allow the snake to tough out tetrodotoxin.

Using molecular techniques, Lee and company expressed the voltage gated sodium channels (which are critical to starting action potentials) in frog eggs. They used three different kinds of sodium channels, each of which was based on three different snake populations: one with no resistance to the toxin, two others with different mutations that provided resistance.

“Wait! Frog? You never mentioned anything about frogs...” The frog has nothing to do with the ecology here. It’s just a convenient way to get a lot of cell membrane with the voltage gated sodium channel expressed in it.

The ion channels with the toxin resistance were different from the normal ion channels in several ways. It was harder (roughly and loosely speaking) to open toxin resistant channels then normal ones. To be more precise, they needed a larger membrane potential depolarization to reach activation threshold.

The point of a sodium channel is to let sodium pass through the membrane: the more sodium rushes into the neuron from opening the channel, the better. Here again, the normal channels let more sodium though than the toxin resistant ion channels.

Both of these results suggest that the way to make an ion channel immune to a toxin is to make it a crummy ion channel. Harder to open, and it doesn’t work as well when it does open.

This paper talks about the implications of all this in a way that is mostly geared towards ion channel aficionados. Lee and crew are interested in the molecules, not the animals. But there’s been a series of papers before this that have shown resistant garter snakes don’t fare as well as non-resistant ones in various kinds of physiological tests. This does seem to have consequences at the whole animal level.

What I love about this story is that it’s one piece in a much larger puzzle that is becoming a classic in integrative biology. People have studied this predator / prey relationship all the way from the large scale ecology down to this paper on molecules, which might be as fine an analysis as you can reasonably expect to get.

Reference

Lee C, Jones D, Ahern C, Sarhan M, Ruben P. 2010. Biophysical costs associated with tetrodotoxin resistance in the sodium channel pore of the garter snake, Thamnophis sirtalis. Journal of Comparative Physiology A. DOI: 10.1007/s00359-010-0582-9

Newt picture by randomtruth on Flickr, snake picture by squamatologist on Flickr. Both used under a Creative Commons license.

10 September 2010

Science writing as seen by students

In one of my technical writing classes this week, I conducted an informal poll. I gave students the first page of a new article in Cell, and the first printed page of author Carl Zimmer’s blog post based on the selfsame paper.

Then, I asked them what was different about the two styles of writing. Here’s the list they came up with, in the order they arrived at them, with only the last one being my addition.

Journal article Blog post
Rare words Common words
Divided into sections Continuous
Dull Interesting
Scholarly Opinions
Few examples Many examples
Specific General
Forum for scientific debate Not intended for debate
Supported by authors’ credentials Supported by author’s reputation
Concise Expansive

I was interested by the issue of rare words. There were at least eight words on the first page of the journal article that at least one student had no concept of what it meant. From memory, some were “protostome,” “olfactory,” “prebilaterian,” “topology,” “errant.” There wasn’t one word in the excerpt of Carl Zimmer’s article that they didn’t recognize.

Some of the students also thought that scientific journals required people have doctorates to publish in them – which I’ve never seen listed as a requirement for any journal. It was kind of fun to tell them that I’d co-authored a journal article with someone who was in high school at the time we did most of the work.

That students brought out the idea of a journal as a place for debate stands in contrast to this morning’s post at The Scholarly Kitchen about how little debate there is in journals.

Finally, I’m a little worried. Point #3 on this list suggests I am supposed to teach the students how to be boring.

Reference

Tomer R, Denes AS, Tessmar-Raible K, Arendt D. 2010. Profiling by image registration reveals common origin of annelid mushroom bodies and vertebrate pallium. Cell 142(5): 800-809. http://dx.doi.org/10.1016/j.cell.2010.07.043

09 September 2010

Eating your own brain: Ocean of Pseudoscience repost

Southern Fried Scientist decided to feature a week of surreal science related to the oceans. I take this opportunity to be a lazy blogger and repost this piece (slightly rewritten) from May 2008.

ResearchBlogging.orgAdult sea squirts (also known as tunicates or ascidians) are sessile animals. As adults, they really don't move. But if anyone has heard about sea squirts, they’ve probably hear that little sea squirts start life as smart little tadpoles, searching this way and that for a place to land. Once they’ve found the place where they'll spend the rest of their lives, they go through a metamorphosis into the immobile adult.

But as they have no further need of their brain, they eat it.

The punchline is, “It’s rather like getting tenure.”

The facts should never get in the way of a great joke, but the truth is more complicated. The swimming tadpoles are only about a millimeter long, and there are only a few hundred neurons in the entire tadpole (Meinertzhagen and Okamura 2001), of which the “brain” is only a small part. Tadpoles have miniaturized brains.

AscidiansSea squirt larvae do undergo metamorphosis into a adult with a small brains, but it's not the vestigial little thing that the “eat your own brain” story suggests. “In fact, adult ascidians have perfectly good brains, an order of magnitude larger than those of their larvae, and their behaviour is as finely adapted to sessility as that of the larvae to motility” (Mackie and Burighel, 2005).

We’ve learned a lot about how brains work from invertebrates, and their complexity is often underrated.

References

Mackie GO, Burighel P. 2005. The nervous system in adult tunicates: current research directions. Canadian Journal of Zoology 83(1): 151-183. DOI: 10.1139/z04-177

Meinertzhagen IA, Okamura Y. 2001. The larval ascidian nervous system: the chordate brain from its small beginnings Trends in Neurosciences 24(7). 401-410. DOI: 10.1016/S0166-2236(00)01851-8

08 September 2010

Happy Countdown Day!

Today is 10-9-8 (using the international standard for date formatting).

07 September 2010

Carnivals for September 2010

Circus of the Spineless #54 is up over at Hector’s Coat in Your Eye. Hectoring Co-Tillar Lies? Hectocotlyi? Hectocotyli?

The Carnival of Evolution #27 is hosted by 360 Degree Skeptic.

The Carnival of the Blue #40 gets presented by The Saipan Blog.

And no, I did not forget The Carnal Carnival #1, hosted at A Blog Around the Clock, as much as I might like to.

Tuesday Crustie: Pouncing


“Get that thing out of my eyes!”

The lurking Ovalipes australiensis from last week takes on the bright light.

Photo by Saspotato on Flickr, used under a Creative Commons license.

Peer pranking: Review and run

Lots of homeowners have fallen prey to kids who run up, ring the doorbell, and hide before anyone can get to the door to answer.


Of course, that’s the nice version of the prank. Another version involves placing something sticky and unpleasant in a paper bag, and lighting the bag on fire before ringing the bell, so the unfortunate person answering it will stomp on the bag to put out the fire, and end up with feet covered in... stuff.

Sometimes, opening up email with the review on an academic paper feels like very much opening the door to find a flaming bag of poop on your doorstep.

Lately, I’ve been arguing against anonymity in reviews (links below). But recently, I heard about a review process that might make anonymous peer review more agreeable.

A problem with anonymous reviews is lack of accountability: the reviewer generally doesn’t have to answer to anyone for whatever she or he writes. An anonymous reviewer can say downright nasty things about a paper and know that they don’t face anything much more than the authors trying to rebut their arguments when they submit a revised manuscript.

To put it another way, reviews are often like messages in bottles. You don’t know where it’s from. And it’s going to be a long time before you get another one washing up on shore.

I recently heard about how Frontiers journals handle peer review in part.

(A)uthors and review editors collaborate online via a discussion forum until convergence of the review is reached.

I like this idea. Now, instead a reviewer being able to drop a flaming load of, “This paper is too descriptive, doesn’t advance the field, and is boring,” and not having to hear any response for a few weeks, authors come back and say, “Here’s the page and paragraph where we describe the controls that you complained that we didn’t do.”

As it happens, these journals do publish the names of reviewers after articles are accepted. I had mentioned this possibility earlier, but just creating a dialogue may make the need for disclosure somewhat less. I would be much more okay with anonymous reviewing if journals had this sort of dialogue as reviews,

Anything that gets us closer to the sort of collegial back and forth, discussion, give and take that I usually see at conferences and away from the mysterious and inexplicable sniping that I hear people complaining about is a good thing. Dialogue has got to beat unanswerable missives. Instant messaging has got to beat a message in a bottle.

Related posts

nature didn’t want it, so you get it
Vendetta, Part 2
Vendetta
Should we give up anonymous reviewing?

Photo by tormol on Flickr, used under a Creative Commons license.

05 September 2010

No turning back for science

An article with a title like “Science’s dead end” seems like an active effort to troll the science blogosphere. Maybe author James Le Fanu has a point, but a quick search raise doubts as fast as you can type. He’s trained as a medical doctor, not a researcher. And he seems to be a cynical one, having written a piece with a similarly apocalyptic title, “The fall of medicine,” for the same magazine over ten years ago.

The outsider’s perspective is apparent in his first paragraph.

For science this is both the best and the worst of times. The best because its research institutions have never been so impressive, its funding never more lavish.

Yes, it’s so incredibly lavish that funding rates for most American federal agencies are way less than one funded proposal out of ten applications, so that good researchers devote weeks on end to revising and resubmitting in hopes of finding the resources to carry out their research.

Biomedical research alone received $62bn and over the last ten years that figure has almost doubled again, soaring past the hundred billion dollar mark and dwarfing the GDP of a dozen countries.

The National Institutes of Health budget did indeed double in the late 1990s and early part of the decade, but has been slightly declining for most of the decade. Meanwhile, applications have increased substantially over the same period.


From here.

Pose the question, What does it all add up to? and the answer, on reflection, seems surprisingly little—certainly compared to a century ago, when funding was an infinitesimal fraction of what it has become.

Ah, yes, the good ol’ days. The great thing about nostalgia is that there is no clear basis for comparison. I can just as easily bemoan how much manpower and money are poured into making a contemporary Hollywood movie compared to early in the last century, and make similar sighing sounds.

“The original King Kong was made with the special effects being the handiwork of only one talented animator, Willis O’Brien, and is widely regarded as a classic of cinema. The remake a few year ago involved a veritable army of special effects technicians, but is it better?”

Le Fanu spends several paragraphs recapping arguments made by John Horgan, saying that science must reach a point of diminishing returns.

It is difficult, even impossible, to imagine how so comprehensive an achievement can be surpassed. Once it is possible to say “this is how the universe came into being,” and so on, anything that comes after is likely to be something of an anticlimax.

But not everything in research is about surpassing what came before. It’s about contributing. I doubt few budding physicists have career plans that look like this:

  1. Finish doctorate.
  2. Get tenure.
  3. Surpass Isaac Newton.

Science usually advances incrementally. It’s slow and painful, and it’s a tribute to the increasing numbers of scientists that we made the progress that Le Fanu acknowledges we have made.

Le Fanu’s bemoans that genetics can’t tell us why organisms are different – a claim I’ll leave to better geneticists than myself to dissect. He then goes on to the neuroscience, and doesn’t see much progress there, either.

While it might be possible to know everything about the physical materiality of the brain down to the last atom, its “product,” the five cardinal mysteries of the non-material mind are still unaccounted for: subjective awareness; free will; how memories are stored and retrieved; the “higher” faculties of reason and imagination; and that unique sense of personal identity that changes and matures over time but remains the same.

Le Fanu mixes claims of what science could achieve in the future (“it might be possible”) with what we know now (“are still unaccounted for”).

But Le Fanu retorts that we know the answer already.

The usual response is to acknowledge that perhaps things have turned out to be more complex than originally presumed, but to insist these are still “early days” to predict what might yet emerge. ... (B)ut it is possible, in broad outline, to anticipate what they will reveal. ... (A) a million scans of subjects watching a bouncing red ball would not progress understanding any further of how those neuronal circuits experience the ball as being round and red and bouncing.

It would, indeed, be quite sad if the best science could do would be do the same simple experiment a million times. Fortunately, this is not what we do. Problems get tackled from many sides, at many different levels. Some work at the level of networks of cells. Others work at the level of cells and molecules.

But I think Le Fanu is more likely to reject answers as unsatisfactory. Brass and Haggard (2007) have empirical data that certainly seems relevant to the question of free will. One particular brain region, the fronto-median cortex, is a critical point in the decision making process to do something or not.

Think answers along those line would satisfy Le Fanu?

At a time when cosmologists can reliably infer what happened in the first few minutes of the birth of the universe, and geologists can measure the movements of continents to the nearest centimetre, it seems extraordinary that geneticists can’t tell us why humans are so different from flies, and neuroscientists are unable to clarify how we recall a telephone number.

We may not be able to say why a human can remember a phone number, but we can discuss why other kinds of organisms are able to remember certain kinds of information. But again, does Le Fanu really care that we have good explanations of how NMDA receptors can help create long lasting changes in synaptic strength in a variety of organisms in ways that are consistent with memory?

No. Because, near the end, we arrive at the logical conclusion: Mysticism.

(T)he distinctive feature of both the form and “organisation” of life (as opposed to its materiality) and the thoughts, beliefs and ideas of the mind is that they are unequivocally non-material in that they cannot be quantified, weighed or measured. And thus, strictly speaking, they fall outside the domain of the methods of science to investigate and explain.

Wow. Not only a Cartesian dualist, but a vitalist as well. That’s some seriously hard core rejection of science you’ve got right there. There are some dualists out there (for instance, see Hinson 2010 and Anckars├Ąter 2010 responding to Cashmore 2010), but vitalists are an fairly endangered species.

If Le Fanu lived at the turn of the last century instead of this one, he would have poo-poohed that DNA could tell us anything about inheritance across generations, or that action potentials and neurotransmitters could tell us anything about memory, or that electrical activity would reveal anything about states of consciousness. Because, after all, life and mind can’t be investigated by science. He would have written all of that off as a waste of time. And he would have been wrong.

It is Le Fanu, not science, that has reached a dead end.

Hat tip to PolymerPhD for spotting the article that just killed any chance of Sunday morning fun for me.

Reference

Anckars├Ąter H (2010). Has biology disproved free will and moral responsibility? Proceedings of the National Academy of Sciences 107(27): E114. DOI: 10.1073/pnas.1006466107

Brass M, Haggard P (2007). To do or not to do: The neural signature of self-control The Journal of Neuroscience, 27(34): 9141-9145. DOI: 10.1523/jneurosci.0924-07.2007

Cashmore AR. 2010. The Lucretian swerve: The biological basis of human behavior and the criminal justice system Proceedings of the National Academy of Sciences of the United States of America 107(10): 4499-4504. DOI: 10.1073/pnas.0915161107

Hinsen K. 2010. A scientific model for free will is impossible. Proceedings of the National Academy of Sciences of the United States of America: In press. DOI: 10.1073/pnas.1010609107

Photo by bennylin0724 on Flickr, used under a Creative Commons license.

03 September 2010

Peer review pariah

The Scholarly Kitchen discussed how much time and effort go into peer review.

I wanted to get a feel for how burdensome peer-review is in my field, biology. In a thoroughly non-scientific study, I asked a dozen biology professors about their peer-review burden, trying to get a good cross section of people at different stages of their careers and at different types of institutions. The vast majority told me they review around 1-3 papers each month.

That’s a wide range, but I was still a little surprised. I checked the amount of reviewing I had done since starting my current gig, and included both journal articles and federal grant proposals that I had reviewed. I didn’t include textbook chapters I’ve reviewed, since I am asked to do those by publishers rather than fellow scientists.


That little line underneath the “average” is the number I’ve reviewed. I can’t remember refusing to do a review, so it’s not as though I’m being selective. I did decline to reviewing a revision, but just once.

I suppose many would consider me lucky that I have such a light reviewing load. But I am am having a bit of Rudolph syndrome, wondering why I’m not getting asked to join in the reindeer games.

I wonder if the amount that people are asked to review varies systematically. Do faculty at some institutions get asked more than others? Does the average load vary across disciplines? Is anyone trying to compile a dataset on this?

02 September 2010

Your new blog network for today

Previously, in the science blogosphere...


This prompted Ed Yong to comment:

I hear that the drunk guy in the park with a traffic cone is launching his own science blogging network...

Today, I am that drunk guy in the park with a traffic cone.

  • 2 September: The SciZen blog network launches!

It’s a small network, consisting of three blogs for now:
  • NeuroDojo: The blog you’re reading now. Brains, behaviour, and evolution are favourite topics.
  • Better Posters: A blog devoted to the elimination of ugly posters at science conferences.
  • Marmorkrebs: A bit of a niche blog, covering the remarkable marbled crayfish.

Some of you might say, “But Zen! That’s not a network – those are all just blogs you’re already writing!”

Yeah, well, sort of.

Okay, precisely.

You can’t blame an independent boy for trying to get a little attention in the days of Borg blogging, now, can you?

01 September 2010

Texas Higher Education and Creation Research, Part 38

Is this the end?

After 37 previous posts, is this the last I shall write about the Institute for Creation Research’s (ICR) attempt to get a preliminary plan for a Master’s degree in science education approved the Texas Higher Education Coordinating Board (THECB)?

The National Center for Science Education reports that the ICR has “conceded defeat,” and will not be trying any more legal means to overturn the THECB’s decision.

This is not the last we have heard of the Institute, which has run for a very long time. They are continuing to offer a “Master of Christian Education degree,” whatever that is (not snark, I genuinely do not know). If you take that degree, you can do Creation Research as a minor.

It feels weird. In late 2007, I really got serious about science blogging part due to several convergent stories about the teaching of evolution in Texas: the forced resignation of Chris Comer, the tussle over the K-12 Texas Science Standards, and this story. All three stories now seem to have run their course completely.

Eat ‘til you can’t eat no more: Evolution of the pig-out

Eating food is a wonderful activity. Without it, you’d die.

But have you ever gone overboard? Got to the end of a meal and thought:


“I ate too much.”

ResearchBlogging.orgIn the natural world, we’re so used to thinking of food as scarce for animals that we don’t often think about issues associated with animals that eat and eat and eat until they do not eat any more. It is probably fairly hard to hit that satiation point for many species.

On the other hand, some species are well known for infrequent but huge meals. They have to eat as much as they can when they can, because their food source is unpredictable. But how do you get to the ability to eat those large meals? We know the “I ate too much” sensation can be uncomfortable, but could it be costly in evolutionary terms?

Pruitt and Krauel decided to look at these issues of gorging in wolf spiders (Schizocosa ocreata). They collected many young female spiders in Tennessee, and reared them in the lab. To test how much the females could eat in one go, they fed them crickets.

A lot of crickets.

After the spiders were not taking any more crickets, they measured just how much mass the females had taken on in all that feeding. The females varied quite a bit in how much food they could take on, and there is a clear advantage to doing so: their eggs developed faster and they had more of them.

As I alluded to before, Pruitt and Krauel mated their females. They took the offspring and measure how gluttonous they were compared to their mother, and it turns out that the winners of the eating contest tended to have daughters who could also wolf down a lot of food, too. Eating large meals is heritable.

Now we get to the coolest part.

The researcher took those spiders into the wild, and let them loose.

But they didn’t just turn them loose because the experiment was done, oh no. They let them out in to locations in the Tennessee forest. One was covered with nets so that birds – likely the major predators of these spiders – were unlikely to be able to get in.

All their released spiders were marked so they could be identified. Every day for two weeks, they tried to recapture the spiders they released.

When it was all over, they estimated that their eating champions were more likely to survive and have reproductive success... but only in environments where the predators had been excluded. In the more naturalistic settings, where birds were free to zip down and conduct their own experiments in how much birds can eat, the heavy eaters suffered: they more likely to have been picked out of the population.

And the moral of the story is: Life is all about trade-offs. Sure, you can take in a lot of energy in one go... that will make you so slow that you can’t escape when you need to.

Swings and roundabouts, as they say.

This post is part of the National Evolutionary Synthesis Center (NESCent) competition for the Science Online 2011 conference.

Reference

Pruitt JN, & Krauel JJ. 2010. The adaptive value of gluttony: predators mediate the life history trade-offs of satiation threshold. Journal of Evolutionary Biology. DOI: 10.1111/j.1420-9101.2010.02070.x

Top photo by robstephaustralia on Flickr; bottom photo by dishevld on Flickr; used under a Creative Commons license.

Quick update on Hasuer case

He’s not teaching this semester after all.

Comments for second half of August 2010

Abhishek Tawari finds new papers documenting the misuse of the word “homology” by molecular biologists.

The Scholarly Kitchen accuses science bloggers of being sticks in the mud. But was an article on Jesus curing a viral infection really meant as a gag?

Lab Mom at The Thoughest Job You’ll Ever Love discusses what car a professor should drive.

Anonymity in peer review is currently a favourite topic of mine, so I couldn't pass up a chance to comment at the Child’s Play blog by Melodyne.

Lucas Browers did a nice job of covering velvet worms brains.

Razib Khan at the Gene Expression blog wonders, “Why are there so many neuroscience bloggers in biology?”

Dr. Becca exhorts scientists to make websites! People read them, you know!