29 October 2011

Lost and found

You may have to embiggen this image by clicking to see the fine print...


(There are some witty pranksters on my campus.)

28 October 2011

What degree plans tell you about departments

These are real degree plans that students get at three different departments at my institution. (Click to enlarge.) They may provide a little insight into the mentality of the type of individuals in each kind of department.

Biology gives students a checklist.


Mechanical Engineering gives students a flowchart.


Computer Engineering give their students... whatever the heck this is supposed to be.


Eeeeiiiiiiiii! My eyes! My eyes!

Remember this the next time your computer crashes or does something bizarre: it was built by people who could understand that.

27 October 2011

Choosing a grad program, the short version

Sometimes you have to simplify.



Deciding on a grad program is a complicated choice. Do you pick based on the institutional name? The program? The advisor? Here’s a way to simplify your decision.

Which program will pay you the most?

Money talks, bullshit walks.

I’m not saying you should choose only by that criterion. But it is a quick way to shake out who wants you the most.

26 October 2011

Saying “Yes” (sometimes)

Assistant professors are often advised they have to say, “No.”

Don’t serve on committees. Talk your way our of as much teaching as possible. Do the absolute minimum you have to unless it will benefit your research. Just keep saying, “No” to, well, pretty much everything.

I admit that I said “Yes” too much during my probationary period. But you know what? I am glad I said yes to a lot of things. In my department, the majority the faculty for the better part of a decade have been tenure-track. There was just not enough tenured people on the ground to get everything done. If the tenure-track faculty left everything up to the tenured faculty, the department would have suffered.

When you listen to someone who preaches following your own self-interest all the time, remember the risk. If you keep saying “No” to working with other people, you can end up being a hermit who owns a lot of guns and has all your cash stuffed in coffee cans under the mattress because you haven’t worked with anyone else and don’t trust them.

In other words, a crazy misfit.

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

24 October 2011

Sound over picture

As you may have noticed, I’m participating in the #SciFund Challenge.

One of the main things you need for the challenge is a video. This made me nervous. I’ve shied away from video for this blog, but taking part in the #SciFund Challenge has forced the issue.

What I have learned from making my own video and watching other #SciFund videos is that an undervalued part of a good video is the audio.

Film schools are always telling their students, “Film is a visual medium.” But I like what director Nicholas Meyer wrote for a 1993 box set of the Star War soundtracks:

(S)ound always dominates picture. If you are in any doubt, simple drive around in a car with the radio or cassette player blasting and look out the window. The nature of the music affects the mood of what we are seeing. It is never the other way around. If you play happy music, even some fairly squalid and dispiriting surroundings seem more cheerful. If you play sad or ominous music, the most agreeable vistas assume a sinister aspect.

This shouldn’t surprise me, because I am, after all, a total soundtrack nerd. And I’ve been stuck with poor to middling audio before. But I have gained a deeper appreciation for the sound mix.

What I have learned:

Your computer microphone isn’t good enough. Sure, a lot of laptops and desktops have built-in cameras and mics for video chat and the like. But if you’re just sitting at your usual distance from your computer, your voice will sound small and tinny, and there will be a lot of hiss and background. And if you have a different mic for voice-over of pictures or videos, the difference in sound quality and intensity will be distracting and noticeable.

You can’t just talk. Normal speech is filled with hesitations and pauses. This is okay in conversation, but it’s noticeable in a short video clip. And those pauses chew up valuable time. Every second on a YouTube clip is a second that someone might leave to see what’s happening on their Twitter feed. You have to be the best version of you.

For example, good movie commentaries are scripted, not improvised:

One condition which Toho insisted on was that a script of the commentary be submitted to them for approval. This turned out to be one of the best things that happened to us. ... Reviewing the first draft, I quickly understood the merits of having a script. While it would be easy to just talk about the film, it would be just as easy to overlook important subjects by getting lost in the moment and running out of time, and it was also vital that certain comments be timed to images on screen.

You need split second timing. I was constantly fiddling to get the pictures and the sound lined up the way I wanted. In some cases, tenths of a second made the difference in synchronizing the two so that the effect was cool. Being out of sync by fractions of a second made it look so much worse.

Recording voice overs in small bits helps. Short sound bytes are easier to align to particular points in the video, particularly if (like me) you’re stuck using very basic, free video software.

If you want to make a good science video, buy the best microphones you can get your hands on.

Additional: Coincidentally enough, today sees a post called 10 common video storytelling mistakes (and how to avoid them). And the number one mistake?

.01 you don’t prioritise sound

I’m actually gonna stick this one at the top because it’s probably the most common mistake. I’ve seen far too many video stories where the interview is practically inaudible, drowned out by traffic, air conditioning or something else. The cause? Not using an external microphone.

Audiences seem quite happy to tolerate poor quality pictures – they don’t mind mobile phone footage for example; but they will not tolerate crappy sound. End of. Invest in a good quality clip microphone for interviews and a Rodemic or similar for on board sound.

21 October 2011

Coming soon...


Jump! Fish are surprisingly good on land

ResearchBlogging.orgIt’s another new fish out of water paper!

I’ve written about terrestrial fish, and fish the beach themselves for long times. Mosquitofish (Gambusia affinis) don’t take their air time as seriously: they seem to use land as refuges for short times, and then flip back into water. But while on land, they have to jump to get around, and eventually back into the water.

In a nice little paper, Gibb and colleagues describe the jumping behaviour of these fish on land. To test if mosquitofish have any particular behavioural specializations for this jumping behaviour, they also tested zebrafish, which nobody has ever reported routinely jumping out of the water.

To my surprise, once on land, these two fish species showed no important differences in the jumping behaviour. The mosquitofish took off at a slightly lower angle, and didn’t tumble as much as the zebrafish, but the similarities between the fish are much greater than the differences.


One possibility is that the neural circuits involved in this behaviour are the largely the same as those responsible for rapid escape responses (C-starts). These neurons are well known, and involve famous giant neurons called Mauthner neurons. It would be interesting to see if the neural circuit is perhaps a pre-adaptation for these jumps on land. This paper shows that C-starts are different in the timing of their movement than the jumps on land, but that does not completely rule out the involvement of some of the same neurons in bothe behaviours.


How widespread is this ability to move around on land, even if not much better than hit-and-miss flopping around? Mosquitofish and zebrafish have been separated for a long time, so most fish might be able to jump on land in a coordinated way.

Reference

Gibb A, Ashley-Ross M, Pace C, Long J. 2011. Fish out of water: terrestrial jumping by fully aquatic fishes. Journal of Experimental Zoology Part A: Ecological Genetics and Physiology: In press. DOI: 10.1002/jez.711

Photo by davidhofmann08 on Flickr; used under a Creative Commons license.

Related posts

Being a fish out of water changes you
Conquest of the land, a la Chubby Checker


19 October 2011

Dancing with the invertebrates

If Peter Parker does whatever a spider can... he must be one hell of a dancer. And there’s some evidence for that.



(I will admit, that is not exactly what I expected to find when I Google searched for “Spider-Man dancing.”)

This video of the peacock spider (Maratus volans) went up early in March. It blew me away.





Finally, there’s a scientific paper that starts to describe this astonishing behaviour.

If you’ve just watched the video above, you can appreciate how restrained the scientific writing style for journal articles is. Instead of, “Wow! You have got to see this!”, we get, “Research on animal courtship has demonstrated that males of many species produce elaborate multi-component signals spanning more than one sensory modality.”

It’s not until the third paragraph in that Girard and colleagues let a little wonder slip in, calling the peacock spider, “an exceptional example” of spider courtship.

The paper contains a very detailed verbal display of the behaviour, and I don’t envy the task the authors had. Describing behaviour with just words is terrifically hard. Things start getting more interesting scientifically when they start to get to the parts of the courtship display that can’t be seen: vibration. I particularly love some of the names they give these signals. They call one kind of vibration signal... rumble-rumps.

Rumble-rumps! How can you not smile at that? And another kind is called crunch-rolls.

The vibrational seems to be a very important part of the courtship display, as these start when the male is still a long way away from the female. The authors note that this is very different from some North American spiders in this group, where the vibrational signals seem to ramp up when the males and females are quite close to each other.

Given the opening of this paper, I was rather expecting that there would be some suggestion about which of all these cues the females are important for the females. Unfortunately, there is not found in this paper. To get the best filming condition of the male courtship, the experimenters resorted to pulling a dirty trick on the males: they weren’t courting live females, but rather dead females, mounted into a life-life posture. I know it sounds slightly creepy, but animal behaviour scientists have been resorting to such tricks for many decades. Imagine the poor little male spider’s thoughts: “I’m dancing my fan off here! Sheesh, what more do females want?”

This is such a rich behaviour that it’s no doubt going to take years and years of research before we begin to understand it.

Reference

Girard M, Kasumovic M, Elias D (2011). Multi-modal courtship in the peacock spider, Maratus volans (O.P.-Cambridge, 1874). PLoS ONE 6(9): e25390. DOI: 10.1371/journal.pone.0025390

(The creator of the YouTube videos, J├╝rgen Otto, is not an author on this paper, but is thanked for helping to collect specimens.)





Breakin’ Spider-Man from here; balletic Spider-Man from here.

18 October 2011

Tuesday Crustie: Performing arts


This hermit crab, carrying a replica of Constantin Brancusi's Sleeping Muse, has become a star at the Frieze Art Fair in an installation called “Recollection” by artist Pierre Huyghe.

Jessica Hamzelou describes the piece thus:

The idea is that the natural interactions between the creatures - or performers - will create a story for viewers. While I sat watching the scene, I did see what looked like a brief tussle between two arrow crabs - a struggle for alien territory, perhaps? Or maybe an attempt to impress the regal, art-adorned crab king?

Learn more at this article at New Scientist (may require registration).

12 October 2011

National Fossil Day, 2011

Happy National Fossil Day!


Everyone should have a fossil. I am fortunate enough to have this lovely one on my desktop, within arm’s reach.

Related posts

Last year, I featured the portable fossil I keep for emergencies.

11 October 2011

Tuesday Crustie: She’s a lady


A lady crab (Necora puber, I think, although the photographer identifes it as Polybius puber).

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

10 October 2011

Planning is essential; plans are useless

People are often advised that it’s important to have a plan, particularly in scientific careers. In my career, though, I have been more impressed at how much it has been shaped by events that I never could have predicted.

As an undergraduate, I got started in research because I walked through a door, was having a discussion with Jennifer Mather (who I was talking a class with), she mentioned a research project she wanted to do, and I said, “That sounds interesting.” I was recruited practically on the spot to work on the project! So my research career got kickstarted by walking through Jennifer’s door.

Meeting with my doctoral and post-doctoral supervisors had a similar feel. I never could have planned to have worked with the people I did. I didn’t plan to work with crustaceans for my Ph.D., or crickets for a post-doc. I didn’t know the people I worked with extremely well before traipsing off to their lab; I took a bit of a leap of faith in deciding to work in someone’s lab.

I published two papers on tunicates entirely because I met Virginia Scofield in the hallway outside my office, and we got on well.

More recently, I talked about how I ended up co-authoring an ecological modeling paper and a parasite paper. Neither of those papers would ever have happened if there wasn’t the right person down the hall whose door I could walk into.

My career is not completely wu wei. I sought out opportunities like scholarships and awards, and made plans, too. I did have a plan for my post-docs: I wanted to a post-doc outside of Canada, then a second one in Canada. I got the Canadian and international experience, but in the reverse order. But I had to be open and flexible enough to read the signs and follow them where they led.

You never know who’s going to walk through your door next. They might change everything.

(“Planning is essential; plans are useless” is a paraphrase of a U.S. army saying, popularized by Dwight Eisenhower. A variation of it is, “No plan survives contact with the enemy.”)

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

08 October 2011

Carnivals for October 2011

It’s October, and you know what that means? It’s Zelnio month!

Kevin is hosting Carnival of Evolution #40 at EvoEcoLab.

Kevin is also the overlord of Circus of the Spineless. Circus of the Spineless #66 is hosted by Wanderin' Weeta. Kevin is looking for hosts for future editions of the Circus; email him.

Isn’t that, like, a conflict of interest or something...?

07 October 2011

Pressuring journals you dislike

Mike Taylor at SV-POW exhorted scientists to stop reviewing for journals that are not open access.

Sorry, but I’m not stopping.

I say this not because of any great love for “for profit” publishers, but because I don’t think it will hurt them.

If I don’t review an article, who do I hurt? I hurt the scientist(s) who submitted the paper. A journal editor is going to keep looking for reviewers until they have them. Indeed, they have to. I want you to imagine what you would think and feel if you got back a reply from a journal saying, “I’m sorry, but we cannot publish your paper, not because we find any fault with your science, but because we cannot find a willing reviewer.”

If I don’t review a paper I could review, all I am doing is needlessly dragging out the review process, making it more difficult for the scientists submitting their results.

For whatever reason, they picked that journal to publish in. They don’t deserve to become pawns in someone else’s game.

If you don’t think a journal deserves your support, don’t submit papers to it. Submit your paper elsewhere, especially if it’s good. Encourage others to submit their papers elsewhere, especially their best papers. The glamour magazines like Science, Nature, and Cell thrive on the high-profile articles that drive up their impact factors, keep their brand in the eyes of both scientists and journalists.

Don’t tear down the castle. Build a more livable city instead.

05 October 2011

I’m in Nature!


If you don’t blink, you’ll find me making a very brief cameo appearance in this Nature article on retractions by Richard Van Noorden.

823 days: A tale of parasite publication

It’s unusual that I can pick exactly how long a project took from beginning to end. This time, I can: 823 days.

Day 1: 4 July 2009


Since 2006, I’d been examining the nervous system of shrimp (for a project that is still ongoing – sigh). When I looked at the nerve cords under the microscope, I kept seeing odd little bits that I thought were caused by some problem with the fixation or clearing process. I realized that was wrong when on 4 July 2009, I took this video:



Okay, those slight odd looking bits in the nerve cord didn’t have anything to do with staining. They were moving. They were something alive inside the nerve cord.

Well. That was unexpected. Also, slightly freaky.

Here’s my notebook entry for the day:


(And yes, I am well aware of my terrible handwriting and other problems, thank you very much.)

Soon after, I went down the hall and showed this stuff to the man on the right in the photo below.


This is my co-author Brian Fredensborg, who is a real parasitologist. He had joined our department a couple of years previously. I showed him what I had. He didn’t immediately say, “Oh, yes, that’s a [name], and it’s well known that they live in the nervous systems of crustaceans. Not very interesting at all.” This was a good sign. We were both interested, for different reasons, in what the heck was going on here.

Day 4: 7 July 2009


Brian gives me a tentative ID of the beasts we’re dealing with: larval tapeworms. I record in my notebooks, “Possibly PROCHRISTIANELLA PENAEI or PARACHRISTIANELLA or POLYPOCEPHALUS.” Brian seeks out some help in narrowing down the possibilities from a colleague, and he hears from one of his colleagues that the last guess is the right one.

But the project had to wait. Neither of us had the time to follow it up immediately, and all our students at the time were already deep in working on projects of their own.

Enter the woman on the left.

Day 59: 31 August 2009


The last day of August in 2009 is the first day of class for the Fall semester. I am teaching my neurobiology class, and though I didn’t know it at the time, one of the students registered for the class is Nadia Carreon. We had some good conversations in that semester. This good relationship in class helps paves the way...

Day 200-317: Spring 2010


After the semester is over and neurobiology is done, Nadia comes into my office and asks about the possibility of doing a research project before she graduates. We sit down in my office, and I throw out a whole whack of half-baked ideas that could be turned into research projects, including the mystery shrimp parasites. Nadia thinks the parasite project is cool, so we walk down to Brian’s office and I introduce them to each other.

Everything looks good, so we start to plan a project that Nadia can complete over the summer that will, we hope, be publishable.

Days 318-422: Summer, 2010


And we are go for data collection! We plot, we plan, and we set up a way to gather data at the Coastal Studies Lab. We fiddle with webcams. We figure out ways to tag the animals so we can track them individually. I pull out a big honkin’ heavy mechanical cell counter – made of metal and that makes a very satisfying click every time you press one of the keys – to aid in the counting of all those parasites.

(For the record, I wish to apologize to Nadia publicly: I had no idea just how many parasites were going to be in those shrimp. I never expected that one shrimp alone might have 500 parasites infecting it.)

Proving the old adage, “If it weren’t for the last minute, nothing would get done,” much of the planning takes place in May and June, while a lot of the actual data collection happens late in August.

Day 451: 27 September 2010


We do get a first pass at data gathered over the summer, and get it together in time for a poster at the HESTEC science symposium. The poster wins third place in the undergraduate poster competition.

The analysis and writing continues at a slow but steady pace through the fall semester.

One moment I particularly liked was when I finally got the big, massive spreadsheet of all the behavioural data. For whatever reason, in my research, there are very few “Aha!” moments. There’s a lot more sneaking suspicions followed by a long period of trying to convince myself that what I think I’m seeing is actually what I’m seeing.

As it happened, we had a little bit of data destruction problem. Some of the last video shot was unusable. Brian and Nadia and I had talked about whether we might need to run some more behavioural tests on shrimp, but we still had a decent sized number of animals. We decided that if we didn’t see significant differences, we might run some more. But if it was significant, but it saw significant differences with the smaller sample, we could start writing up in earnest.

There was so much data here, there was no way to get a sense of whether there were going to be any trends associated with infection rates. So I was quite excited to run the first analysis, because I had no idea how it was going to turn out. ... and see significant differences in behaviour!

Day 533: 18 December 2010


Nadia graduates with her bachelor’s degree in biology!

Brian and I are committed to writing and finishing this manuscript before the year is out. The main reason is that Brian is expecting to become a father for the first time in very early January. This gave us very strong incentive to finish, because, as I said to several people, “I don’t know of anyone who has ever said, ‘Yes, we just had a baby. And my productivity has gone through the roof!’”

Day 545: 30 December 2010


Manuscript submitted! Happy New Year!

Day 609: 4 March 2011



Nadia gives the first presentation of this story to the larger scientific community at the Texas Academy of Science meeting. This poster later appears on the Better Posters blog.

Day 633: 28 March 2011


The manuscript is accepted. On the first submission, without any revisions. This has never happened to me before. Holy cow. And the pre-print goes up the same day!

Day 704: 7 June 2011


I present an updated version of the Texas Academy of Science poster at The Crustacean Society meeting in Honolulu. The new data makes this poster 33% bigger than its predecessor.

Day 823: 4 October 2011


The paper finally moves from “pre-print” to published status! And now, I have a paper in a parasitology journal, which was never something I expected to happen. Hooray for collaboration and academic freedom.

Day 824: 5 October 2011


“And on the eight-hundredth and twenty-fourth day, he blogged.”

But wait! We’re not quite done yet! Nadia continued working on this project a bit on a volunteer basis through 2011 after she graduated. We have more data, that we hope will eventually become part of the first follow-up paper.

Day 864: 14 November 2011


Come meet Nadia and myself at the poster session for the Faculty for Undergraduate Neuroscience at the Neuroscience meeting! 6:45-8:45 pm in the Grand Ballroom Central and North in the Renaissance Hotel.

There you have it. The long, winding road from an initial observation to a final, pretty, published article, with brushes along the way of both the thrill of victory (“No revisions?!”) and the agony of defeat (“The video’s gone?!”). It’s also fairly typical of research at undergraduate universities, I think, in that things can wait for a long time because you’re just waiting for a student to pick up the project. And I was surprised in writing up this retrospective to be reminded that stuff gathered even early in the project can be useful:

I took the picture in Figure 1a on Day 1.

Reference

Carreon N, Faulkes Z, Fredensborg BL. 2011. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology 97(5): 755-759. DOI: 10.1645/GE-2749.1

Faulkes Z. 2007. Motor neurons involved in escape responses in white shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 47(Supplement 1): e178. DOI: 10.1093/icb/icm105

04 October 2011

Tuesday Crustie: Neural

Crayfish are on a photography contest roll.

Last week, I showed Michael Bok’s winning picture of Louisiana red swamp crayfish (Procambarus clarkii).

Same species, but a rather different view...



These are neurons that connect to the big muscles in the tail that the crayfish use to swim with – and that so many people and predators find so tasty. The staining technique is called cobalt backfilling. This is many pictures compiled into one. It’s a “stack” of photos merged into one using Helicon Focus, which I wrote about here.

Why do I have all the stuff defacing the image? Because I want people to see the full sized, pristine image in the calendar!

This picture is going to be featured in a fundraising calendar for the J.B. Johnston Club. The J.B. Johnston Club is an organization that meets right before the Neuroscience meeting. They have a student travel award that they are raising money for. Kara Yopak had the idea of creating a calendar with twelve months of images of neurons, brains, and organisms. This is such a great idea, because neurons are always beautiful.

The calendar will be on sale at this year’s J.B Johnston Club meeting. Thirteen images, 8½ × 11" on glossy paper, all for $20!

You want one, don’t you? Email Kara Yopak to inquire about how you can get a copy! If you won’t be in Washington, DC for the J.B. Johnston Club meeting or Neuroscience, tell her were you are located so she can work out the posting details.

I don’t know what month this image will be. I’m kind of hoping for February.

03 October 2011

The Science Cheerleaders at HESTEC Community Day 2011

Almost a year ago, I wrote a post about the Science Cheerleaders. It was one of the first of many posts around the science blogosphere about the team, and one of my more widely read posts, I think.

Little did I know that less than a year later, I would be sharing the stage with them.

I was so pleased to work with the Science Cheerleaders at HESTEC Community Day. The weather was cooler than normal - rain for the first time in a long time! - but there were still consistently good crowds to see the Science Cheerleaders’ show.

I was able to surprise them when they learned that even though none of them had been to UTPA before, they had a connection with us. The cameraman on their popular YouTube video, Brandon Garcia, was a UTPA alumnus.


After each show, I talked a little bit about the Craywatch citizen science project that I have at the Science for Citizens website. I did it a little differently each time, but the last time I said something like, “You know what cheerleading has in common with science? You have to work hard at it to get good. I went to school a long time to become a professional scientist, and you might think you can’t do science if you don’t have fancy degrees. No! All you need is an inquiring mind and a willingness to learn. If you don’t like crayfish, there are hundreds of other real research projects that you can help with.”

The Cheerleaders got asked to be part of a lot of photographs, and signed almost as many autographs.


This tiara’d women is Laura Eilers, the choreographer.


Ringleader Darlene Cavalier takes a picture.


Thanks so much to Darlene, Laura, Melissa, Heidi, Sammi Jo, Sandra, Ada (making her Science Cheerleading debut, if I remember right) for letting me be part of the act.

Hooray for the Science Cheerleaders!

Additional: The view from the cheering side.

01 October 2011

Comments for second half of September, 2011

Sea Monster looks at a blog favourite, the mimic octopus.

Tales of the Genomic Repairman looks at the funding of science, particularly “people versus projects.”

A brief history of the squid giant axon preparation at Take It To The Bridge.