31 December 2010

Pacifists or pugilists?

“They’re very gentle.”

I met Silvia Sintoni in front of her poster at the International Congress of Neuroethology in Vancouver in 2007. I was very interested and excited to talk to someone working with the all-female marbled crayfish, Marmorkrebs. I talked with her about how they housed the animals in her labs. She told me they kept most of their animals communally, which surprised me slightly, because I thought of crayfish as aggressive.

Crayfish fighting has been the subject of much research since the 1950s. And when I kept Louisiana red swamp crayfish (Procambarus clarkii) together, there would often be murders, particularly when one molted.

Silvia assured me that these animals were not terribly aggressive – though I wondered if there might be a little projection of traditional human female characteristics onto the crayfish.

But another paper also mentioned low levels of aggression in Marmorkrebs, basically as an anecdote. And when I got my first Marmorkrebs in my lab to start the aquarium, on one of the first days, I came in to find three or four of the adults all hiding under the same piece of clay pot – which was not something I had seen other crayfish do!

Marmorkrebs interacting

After a few days, though, I too k the picture above of some fighting in my new tank. The girls were not completely averse to fighting!

It was just a natural and obvious thing to see if people’s impression matched up to reality. Were these marbled crayfish less aggressive than other crayfish species?

This became the project of my co-author Stef (more formally Stephanie A. Jimenez), seen here presenting some early results at the 2009 Ecological Society of America meeting.



We explored a lot of ideas that didn’t quite make it into the final paper. In particular, Stef ran one fairly lengthy experiment that we were never quite sure what to do with, because it failed to replicate a result from another lab. And I’ve learned from experience those are... problematic... to get published.

As it was, this paper didn’t have the easiest time finding a home. But I’m pleased it did find a home and hope you enjoy it.

Massive thanks


To all my students this year, who helped me have one of the best years of my career:

Sakshi, Stef, Unnam (all with papers published or in press), Nadia, Sandra (both with papers in review), Jessica, Karina, and Samantha (no papers yet, but watch out editors! They could be coming your way in 2011!).

Thanks for your hard work, guys.

Reference

Jimenez SA, Faulkes Z. 2011. Can the parthenogenetic marbled crayfish Marmorkrebs compete with other crayfish species in fights? Journal of Ethology 29(1): 115-120. http://dx.doi.org/10.1007/s10164-010-0232-2

Other stories behind the papers

Crayfish zero
Crustacean nociception

30 December 2010

My record holds

Submitting a manuscript makes a nice holiday treat to myself, not to mention my co-authors. It’s helpful to know that the very productive year I mentioned back in September isn’t coming to a grinding halt quite yet.

My record for peer-reviewed, original technical papers in a year – the bread and mutter for professional scientists – is three. I’ve managed it twice before. Once in 1997, which were all from my doctoral degree. And again in 2006, when I cleared off some manuscripts that had been lingering from a post-doc several years earlier.

This year, I was hoping to break that personal record. But I’ve ended up with three again. Sort of.

I’ve had several papers in press for some months now, and I kept hoping that one of those would make it into publication before the year end. And one did, just last week... except it has a 2011 publication date on it.

D’oh!

I just can’t bring myself to count for this calendar year.

And there’s only one other paper that could come out any second. But with less than two days to go, I’m not hopeful. (If it comes out in January and has a 2010 date on it, then I’ll feel vindicated and consider the record broken.)

Of course, I also had a post in the Scientific American Guest Blog, a letter in Science, and a selection in Open Lab 2009. And blog posts. Oh yes, I blogged. It certainly hasn’t been a bad year, writing wise.

So with one paper already in the can for 2011, two papers in press, a book chapter in press, and three manuscripts in the hands of editors being reviewed, let’s see what happens if I push this...


References

Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450.
http://dx.doi.org/10.3391/ai.2010.5.4.16

Puri S, Faulkes Z. 2010. Do decapods crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. http://dx.doi.org/10.1371/journal.pone.0010244

Jimenez SA, Faulkes Z. 2010. Establishment and care of a laboratory colony of parthenogenetic marbled crayfish, Marmorkrebs. Invertebrate Rearing 1(1): 10-18.
http://inverts.info/content/establishment-and-care-laboratory-colony-parthenogenetic-marbled-crayfish-marmorkrebs

Jimenez SA, Faulkes Z. 2011. Can the parthenogenetic marbled crayfish Marmorkrebs compete with other crayfish species in fights? Journal of Ethology: 29(1): 115-120. http://dx.doi.org/10.1007/s10164-010-0232-2

29 December 2010

The cloud is fickle

Following up on my recent concerns about archiving, stability, and the scientific record, I was disturbed to read this:

Yahoo! is shutting down Yahoo! Video next year. March 2011. March 15, 2011, to be exact. They will delete all user-generated content on that day.

Yahoo! Video was the second-most used video hosting site behind YouTube. Number 2! And all of it, all video, is going to be deleted. Thousands and thousands of videos, many of which are likely hosted nowhere else, completely gone.

With my original post, I was trying to argue that it wouldn't take civilization ending to pose archiving problems. All it would take would be slow, creeping link rot.

The closing of a major video service isn’t quite the collapse of Western civilization. But it’s more than link rot.

28 December 2010

Tuesday Crustie: Terrible claw

Everyone knows “dinosaur” means “terrible lizard.”

Meet Dinochelus: “terrible claw.”


ResearchBlogging.orgAlthough it’s described as a “lobster” in the paper’s title, it’s more of a size that most people would describe as a prawn, or maybe even a shrimp. It’s maybe 10 centimeters long.

I’m pleased that this animal has a prehistoric type of name,* because its claw reminds me of nothing so much as the gaping maw of dozens of reconstructions of marine reptiles. It’s stunning. Click the photo to enlarge; this one is worth viewing full size.

The picture of that claw is so striking, I was hoping that the species description by Ahyong and colleagues might give some glimpse of what this highly impressive appendage was used for. For competition between individuals? For hunting? It certainly looks like it could hold very slippery prey in place!

Sadly, there is no hint of speculation about how this claw is used by this crustacean. This isn’t surprising, as it was found by dredging and trawling during the Census of Marine Life. The authors comment on how the claw makes it possible to identify even damaged specimens, so it’s likely that several arrived at the surface in poor condition. So some lucky grad student will have to travel to the Philippines to do a doctoral thesis on the behaviour of this beast!

Reference

Ahyong ST, Chan T-Y, & Bouchet P (2010). Mighty claws: a new genus and species of lobster from the Philippine deep sea (Crustacea, Decapoda, Nephropidae) Zoosystema 32(3): 525-532

* I’m less than thrilled by the species name. It’s D. ausubeli, named for Jesse Ausubel, who gave money to the Census of Marine Life. I’ve never been a fan of naming species after people; I much prefer names to reflect something about the biology of the organism. (Of course, I’ve already admitted I have genus envy.)

27 December 2010

My first academic citation

As I mentioned, I was recently on a The WorldScience podcast for a “Music in Science” segment. In doing the interview (which was much longer than the aired segment), I told another story about how music was relevant to me. Since it didn't make the interview there, I reckoned I would tell the story here.

It was music, not science, that got me my first academic citation.

In the early 1980s, we were still in the Cold War. And pop music picked up on the tension – as it does.



I was working on the student newspaper, The Meliorist, mostly writing entertainment pieces: movie and record reviews (yes, there were still mostly records then). Somewhere along the way, I got the idea of writing a feature article on protest songs.



I wrote it, did some cartoons for it. It was a two page center spread in the paper.



Later – I can’t remember how much later – two of my friends walked into my apartment, reading something from a book. It took a few minutes from me to untangle what they were saying, because they were fairly enthused. The book was The Emerging Generation by Reg Bibby. (The cover below is a reprint; I remember my copy as being mainly white and blue.)


Dr. Bibby had come to the newspaper office to give me a signed copy of the book, but I wasn't in.

The book was describing Canadian teenagers of the early 1980s: their values, attitudes, opinions, and so on. One chapter was on what made teenagers happy, and one of the most consistent answers was, "Music." My feature article on anti-war songs was given, not just a mention, but was the basis for a whole paragraph. It was used as an example of how teen music wasn't just, "I love you, yeah yeah yeah," but could have more substance.




It was a great plug, and showed that you never know how what you write is going to ripple out and have effects that you don't anticipate. Things you think are for the moment, to be forgotten in a week when the next paper comes out, sometimes have a longer shelf life.

I was never quite able to figure out how to add that to my CV, though.

24 December 2010

Flashback: Christmas, 1977

Through the usual chain of improbable internet connections, I got interviewed for PRI’s The World Science podcast. There is 30 minutes and 17 seconds of much other good stuff, but obviously, I want to talk about my bit, 30:18 in. They have a regular “Music in science” feature, and I got to talk about my interest in film soundtracks.

This segment probably went out this week because there was holiday angle to the story I told. My interest in film music all started when my parents gave me two pieces of vinyl for Christmas in 1977:



Thanks to Elsa Youngsteadt for the interview and the deft editing! It came out really well!

And thanks, Mom and Dad, for the presents over the years.

May you all get a gift under the tree that you’ll remember over three decades on.

23 December 2010

Christmas days (n=12)

On Twitter, Eskay started a 12 days of Christmas for the labbies. But because all twelve days can’t fit into 140 characters, I thought I would summarize:

On the twelfth day of Christmas, my PI gave to me:

Twelve knockout mice
Eleven magic plasmids
Ten new citations
Nine microarrays
Eight lanes of reads
Seven western blots
Six linear models

Five perfect gels!

Four pipettes, three replicates, two tubes of Taq
And a p-value of point oh three!


And just for a little more holiday feeling...


And people wonder why I love comics.

Picture found at Lady, That’s My Skull.

22 December 2010

Violin vs. piano!

It's time to play... Pros and cons!

Violin

Pro: Compact and portable.

Con: Never one to be found in a swanky hotel lobby.

Pro: Played by Sherlock Holmes.

Con: Not as sexy as a cello.

Pro: Easier to make a sound imitating the screeching of cats.

Con: No cartoon character has ever had a violin dropped on their head.

Piano

Pro: "Ticking the ivories" sounds dirty and can be used in pick-up lines.

Con: Player pianos. (Do you really want to learn something that a perforated roll of paper can play?)

Pro: All the notes are laid out in a nice, orderly sequence.

Con: The instrument of choice when the villain ties the heroine to the train tracks before foreclosing on her mortgage.

Pro: No spit valve.

Con: Always being left out of the marching band.

Hm. The listing wasn't as definitive as I hoped it might be.

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

Scientific publishing and tree-shaped frosted sugar cookies

1. Short and long term


“Short term” versus “long term” are locked in an unending battle in our heads.

Long term loses. A lot. Just look at this talk from Dan Ariely:



We discount the future. Even though I might be worried about my weight and health, it doesn’t help much when there’s a tree-shaped frosted sugar cookie in front of you right now. While I want to try to reduce my carbon footprint, I am still planning on going to scientific conferences.

2. Clouds are not solid


We are a society that likes to convince ourselves that we need to be mobile. That we need to be able to work and be in contact anywhere, even if we spend most of our time in a small number of physical locations: home, work, and the commute between them. This fascination with mobility has been fueled, and fuels, electronic devices: laptops, iPods, iPhones, and Kindles.

This interest is also driving a desire to move to cloud computing. Why store files locally when you can store them in online services that you can get to from anywhere? Dropbox has been nothing short of a revelation to my work habits for just that reason. It is absolutely brilliant in the short term.

But over the last few weeks, we’ve seen a weakness of cloud computing. Other people control your data. Not you. And they can take it away at any time. That Amazon stopped hosting Wikileaks is one interesting example.

As more people move to cloud services, there is every reason to think that a few private companies will control most of them, because they are the ones who can afford the infrastructure. We have seen over and over that these companies don’t always act in the best long-term interests of... well, anyone. Including themselves.

3. A tangent on romance


This reminds me of this post about dating profiles, and in this case, white women:

It's also amazing the extent to which their list shows a pastoral or rural self-mythology: bonfires, boating, horseback riding, thunderstorms. I remind you that OkCupid's user base is almost all in large cities, where to one degree or another, if you find yourself doing much of any of these things, civilization has come to an end.

I bring this up because it’s easy to poke fun at the idea of civilization coming to an end. In discussions about online publication, there is a strong undercurrent of, “This is the way things are done now. We have the internet, and we are never going back. Ever.”

Sean Connery can tell you that “Never” is a long time.

So maybe civilization doesn’t collapse. It wouldn’t take civilization collapsing to cause problems to a lot of people. There are several online services that, if they were to close today, could take a decent chunk of my scientific work with them.

If Blogger closed up shop, I would lose over eight years of writing spread across some 2,000 posts, and I don’t even want to think of how many words. And I’m vain enough to think that this would be a loss not just to me, but to other people.

4. Archival quality


Not enough researchers are thinking hard about archiving. I was thinking about this as I walked in to work this morning, and coincidentally enough, someone forwarded this article on Twitter. Here’s a sample:

You are a nanomolecular biologist who is attempting to find a cure for a new disease. You would love to get your hands on the computational research of those who worked on a similar strain of the disease back in 2010, but that data is no longer available. Although the computational power that is available to you is far greater than that which was used in 2010, much of the effort expended over the lifetimes of those scientists who committed their research to digital files is lost.

Ironically enough, you can, however, read Linnaeus’ hand-written field notes from nearly 500 years earlier.

As an example, I wanted to give some lectures on bat echolocation. I had seen Catherine Carr’s talk at the International Congress of Neuroethology on the subject, where she showed some brilliant videos of this. I went to her web page and found a list of movies. I particularly wanted to show the beam aiming movies. I was excited!

Until I tried to get them to play.

None of the ones I wanted worked. They had been encoded using Indeo codec, which was no longer supported by Windows or by QuickTime versions later than 7.5.5.

The web page had a 2005 date on it. So in about 5 years, this very interesting information had rotted into unusability.

This story had a happy ending. I emailed Dr. Carr, she had one of her students update the movies, and I was able to show them to my students.

As I’ve asked before, when was the last time you saw a floppy disc?

5. Acceleration


Don’t get me wrong: I am not saying that we should stay just with paper. The opportunities to learn and accelerate discovery are too tremendous if we adopt the new technologies. Chris Anderson talked about this (also in the January 2011 issue of Wired).



My short term brain – the one that has consumed way too many tree-shaped frosted sugar cookies this week – loves online journals, loves TED talks, loves all that he has been able to learn though this online technology.

My long term brain still has this niggling feeling that sooner or later, some online science publisher is going to go under, or some remote hard drive will crash, and take a lot of scientific research with it. My long term brain worries about making sure this information continues to enlighten, as it has enlightened me.

If you’ll excuse me, I have to send some reprints to the archivist at our library.

Right after I eat this tree-shaped frosted sugar cookie.

How hard is it to read this blog?

Google allows you to look for things by reading level now, using their advanced search options. So I did a search to see how tough the going was here:


And watch out for that last 1%. I know it’s around here somewhere...

Want analyses of other blogs? Why, Colin Schultz has you covered at CMBR. This blog’s score (1.87) is a little on the low side for science blogs.

21 December 2010

Tuesday Crustie: Philosopher or devil?


This burrowing crayfish, Cambarus diogenes, shares a name with a Greek philospher – although admittedly one with a sour outlook. But it is often called the devil crayfish. I am presuming that the burrows it digs remind people of the traditional location of the underworld.

Photo by Mean and Pinchy on Flickr; used under a Creative Commons license.

20 December 2010

Who will fight for linguistic justice?

ResearchBlogging.orgEnglish is the de facto language of science, so those who aren’t native speakers are at a disadvantage in publishing science. A couple of letters appeared recently in TREE discussing this issue, with the first, Miguel Clavero, saying that the predominance of English has created “linguistic injustice.”

All the costs of having a common international language in science are borne by NoNES (non-native English speaking - ZF) scientists, implying unfair cooperation in obtaining a common good (i.e. a common language).

Clavero paints a somewhat lopsided picture of the costs, however.

(T)o have your publishable science published you should ask a NES (native English speaking - ZF) scientist friend to help you (bearing the risk of losing all your NES scientist friends)(.)

In Clavero’s scenario, the author is the one who is bearing all the cost: the extra time writing in a foreign language, plus the cost of alienating friends. He does not address the “cost” that a friend incurs in agreeing to help the author. I might argue that helping may not be seen by people as costs at all; as the old saying goes, “That’s what friends are for.”

Clavero would like to put much of the burden on journal editors and associated editorial staff to make sure that articles are in the best written form possible. From his letter, he does appear to have encountered many cases where English speaking editors and reviewers puts in additional time and effort to make the paper better.

In a letter in response, Guariguata and colleagues argue that the problem may not be as severe as Clavero suggests. They argue:

(T)he overall burden should not fall on the editorial teams of the journals as it is not good use of either an editor’s or reviewer’s time.

Here, I disagree somewhat. It is not just a good use of an editor’s and reviewer’s time, it is one of the things they should be expected to do.

As a reviewer myself, I do try to help authors fix wording and language issues. It often makes up most of my comments on reviews, in fact. I sometimes have to admit defeat, though, where there are just so many suggestions and corrections that I just give up. There is a point of diminishing returns.

While I accept some responsibility a reviewer, the main responsibility should reside with the authors. It shouldn’t be a secret to yourself that you didn’t grow up speaking English and don’t speak or write it on a daily basis. You should be self-aware enough to look for help. People do not become scientists by accident, after all. Researchers protesting that they have to communicate in English is little like an actor protesting that he doesn’t want to memorize lines.

That said, I do appreciate the problem that many people don’t decide they are going into scientific careers until they in their late teens or early twenties. They’re well past the stage that it’s very easy for them to learn a language. (But then, who hasn’t ignored lessons that would have helped us later, if only we’d have known?)


P.S.—I used these letters as the basis for a final exam in my biological writing class. I asked my students, “Who should bear most of the brunt for making scientific journal articles readable? The authors, editors, reviewers, or someone else?” Because I made my students write about this, it’s only fair that I do so, too.

For what it’s worth, the vast majority of my writing students thought that the authors of an article bore the most responsibility for making it readable English. A much smaller number placed the bulk of the responsibility on the journal editor. None placed the primary burden on the reviewers.

References

Clavero M. 2010. “Awkward wording. Rephrase”: linguistic injustice in ecological journals. Trends in Ecology & Evolution 25(10): 552-553. DOI: 10.1016/j.tree.2010.07.001

Guariguata M, Sheil D, Murdiyarso, D. 2010. ‘Linguistic injustice’ is not black and white. Trends in Ecology & Evolution. DOI: 10.1016/j.tree.2010.11.001

Obscure geek reference: Picture of Cypher, a superhero whose power was the ability to understand all languages.

17 December 2010

Pay per view science

There’s a nice article on the pressures facing academic libraries that delves into costs and the commercialization of knowledge. I agree with much of what Robert Darnton says is there, but wanted to play Devil’s advocate:

(T)hose publishers add very little value to the research process, and most of the research is ultimately funded by American taxpayers through the National Institutes of Health and other organizations.

First, a challenge to those who think publishers add little value: try publishing your own journal. It can be done, and is getting easier all the time. But it is hardly a trivial matter. PLoS is not a “two people in a garage” operation by any stretch of the imagination.

Second, I’m getting a little tired of the implied argument that because much science is funded by the American National Institutes of Health (or some other federal agency), all science should be free to Americans. (In fairness, Darnton doesn’t make that argument explicitly.)

If a research project is not funded by U.S. taxpayers, why should the scientists have to make the results free to the American public?

Some journals that normally have paywalls offer an open access option for authors. Maybe we should have the reverse, too: open access journals could have an option that allows independent researchers to charge for their science. A $1 fee through PayPal, say, that would go directly to the researchers.

Maybe this could become a new way to fund research: pay per view fees on articles that went straight to authors could help fund the next projects.

You’re not done


Putting up one wanted poster doesn’t make you tough on crime.

And putting up one static PDF doesn’t make you engaged.

Engagement is a process. It’s not something you do once before heading back to the lab.

16 December 2010

Meritocracy and democracy. Also, money.

I’m late to the party on the fallacies in this Slate article about the lack of Republicans in science.

It is no secret that the ranks of scientists and engineers in the United States include dismal numbers of Hispanics and African-Americans, but few have remarked about another significantly underrepresented group: Republicans.

I’ll point it out, because nobody else seems to have done it: You can’t choose to be Hispanic or African-American; you’re pretty much stuck with it. You do choose what party you vote for. You can even change your mind about it. Multiple times.

So if people would like to see more scientists voting Republican, it would be helpful if... say... Republican politicians didn’t start initiatives asking people to identify waste in scientific agencies. Unsurprisingly, other researchers have not reacted well to a Republican effort to question the value of research supported by the National Science Foundation. I’m not even going to try to find other links; there are too many.

I agree that there could be reforms that would save money in research agencies. Did you know that there is a law preventing NSF grant holders from buying airplane tickets on a foreign airline if an American carrier is available, even if the cost of the foreign airline is lower? Pure protectionism.

Did you know there is no mechanism for grant holders to send unspent money back to NSF. Thus, if a researcher is very efficient and does the work under budget, it means nothing?

On a related topic, Dan Hind argued in New Scientist (registration required) that there’s a case to be made to let taxpayers have input into science funding:

If we are serious about science as a public good, we should give the public control over the ways in which some - and I stress “some” - of its money is spent.

I must admit, I am slightly intrigued. To listen to some politicians, the public would sink that money into space and dinosaurs.

Would people choose to sink money into cancer research and other projects that promised short term practical benefits? Or would there be a chance for some kinds of research to actually come out ahead, because it engages people? Remember that science stories, often long ones, are among the most emailed at the New York Times.

The current incarnation of the American Republican Party has way too much hate for smartypants to make it feel welcoming to scientists, but that doesn’t mean that scientists should reject everything they say.

Comments for first half of December 2010

Arsenic life


Byte Size Biology looks at blogging on the controversial claim for bacteria living without phosphate. He wonders if anonymity issues are why more people don’t make these posts.

Berkeley Science Review reported very positively on the arsenic life story, even after a couple of days of criticism of the paper’s conclusions.

Embargo Watch looks at NASA’s division of “real media” and “blogs.” NASA aren’t the only ones who have problems seeing that there isn’t a difference any more.

Larry Moran referred to the name of the arsenic tolerant bacteria, GFAJ-1.

Ed Yong wonders if he did enough to critique the arsenic bacteria paper, and how other journalists could have done better.

The Curious Wavefunction suggests journals should have a section for speculative ideas.

The Promega Blog also looks at how the arsenic life story serves as a lesson for science communication.

Rosie Redfield asks if journals could compile all the external links about a paper.

People who dared blog about things other than arsenic life


Biochem Belle writes about personal statements and leadership. I don’t know what she was thinking; December was supposed to be arsenic month.

Dr. Becca gears up for an interview.

Hannah asks who’s reading her blog Culturing Science and why. I have a simple answer.

Gerty-Z discusses “chalk talks” – which will probably continue being called that even after whiteboards have replaced chalk everywhere – which are apparently routine in some areas.

Scicurious makes a guest post on Science of Blogging about writing under a pseudonym.

Finally, not a comment of my own, but a pointer to Thoughts in a Haystack, which found my post on the evolutionary origin of bone useful.

15 December 2010

Living out loud

Johnny Blaze got it right:


“You can’t live in fear.”

It never occurred to me to blog as anyone other than me.

Of course, when I started blogging, there weren’t a lot of other scientists blogging. There was no model to follow or pattern to emulate. (This might explain why the first years of the blog... failed to find an audience.)

What are the advantages to blogging as yourself, under your real name? One advantage is that you can cultivate some of the patterns of behaviour that serve people well in face-to-face conversations. Knowing that you’re accountable for everything you put out there can help you to remember to shut up sometimes. Not to insult people gratuitously. To make a point without making an enemy.

And it always seemed to me that being a scientist was supposed to be about accountability.

As John Wick wrote somewhere, “You own every word that you speak.” I’ve tried very hard to live up to that ideal. That’s not to say that I’ve never annoyed or offended anyone; I have. My hope, though, is that in the long haul, being accountable and willing to admit mistakes will put my balance on the positive side.

Some people avoid being online because they want to be “off the grid.” If you’re a scientist, this is a fool’s errand. Your name is in Google Scholar, on your university website, and who knows how many other places.

If you don’t use your name, you forfeit control over it. Marketers like to say that your brand isn’t what you say about you; it’s what other people say about you. Everyone googles everyone else. If you leave it to others to define your web presence, you might not like what they say. By blogging under your own name, you can actively shape your digital destiny.

I also wonder if one unspoken reason people might not blog under their own name is the fear, not that people will notice, but that they won’t.

External links

14 December 2010

Tuesday Crustie: Darkfield


An ostracod. Love seeing the antennules on this one!

Picture by Specious Reasons on Flickr. Used under a Creative Commons license.

13 December 2010

Woo hoo! I lose again!

NESCent has announced the results of the 2010 evolution blogging competition!

Congratulations to Danielle Lee (for How some females respond to nuptial gifts) and Neil Losin (for Do mother birds play God?)!

The lonely places: Where could life exist, but doesn’t?

ResearchBlogging.orgOur planet is covered with life. Birds fly over Mount Everest; ecosystems thrive at hot vents at the bottom of the ocean. And the more we have looked, the more and more weird places we find organisms living in places we thought was completely uninhabitable.

Given all the interest in the idea that life could exist without phosphorus, this new article by Cockell is extremely timely. Cockell points out that if we want to understand life, we have to pay attention not just to where life is present, but to where it is absent.

Think about it: where is there no life on this planet? Clearly, there are some places that life cannot be sustained at all. The inside of an active volcano comes to mind. Indeed, volcanoes might a source of what Cockell calls “vacant habitats,” places where life could live, but currently doesn’t. But “sterilization” events are perhaps not very informative, as most places become recolonized.

Cockell is after bigger game, namely places that are routinely uninhabited by life. He doesn’t provide any clear examples of such places on Earth outside of disaster areas where life is temporarily eradicated.

Indeed, we may have a problem even identifying a vacant habitat on Earth. Given that life is so ubiquitous, are “extreme” habitats without life because life cannot be supported at all? Or is it within the realm of life’s capabilities, but there isn’t life in that niche?

Then, Cockell gets more speculative, wondering if other planets might have vacancies for life. He logically divides the possibilities into planets where life never originated (so the whole planet is vacant), and those for which life did originate, but was either localized or wiped out.

To my surprise, although Mars comes up tangentially, Cockell doesn’t make much of it. It seems to me we know enough about the Martian landscape to make a reasonable guess that at least some of it could support terrestrial life. Science fiction fans will no doubt know of many books describing the terraforming of Mars. (The article does have a box dealing with the ethics of introducing life into vacant habitats.)

The perpetual speculation about whether there is microbial life on Mars suggests that Mars is a vacant habitat, in at least one sense. I wrote this a while ago (and it remains one of the favourite things I’ve ever written), shortly after the “Martian meteorite” (McKay et al. 1996) had been announced as a possible indication of past life on Mars:

There is a more depressing side to the announcement of possible past Martian life, however. Mars may be an entire biosphere that has gone extinct. We find living organisms living and often thriving in our planet’s most hostile locations, so terrestrial life appears marvelously tenacious and resilient. There is no evidence of life on Mars now, suggesting that if life originated on the red planet, it never managed to get a toehold: No macroscopic organisms, no increasing complexity, no smart Martians carved out by the forces of natural selection.

While as a biologist, even microbes would be a spectacular finding, the question of whether habitats are vacant for complex, multicellular life is almost as interesting. And if Mars is ever found to support microbial life, why doesn’t it support macroscopic life?

References

Cockell CS. 2011. Vacant habitats in the Universe. Trends in Ecology & Evolution. 10.1016/j.tree.2010.11.004

Faulkes Z. 1997. Is intelligence inevitable? In: The UFO Invasion: The Roswell Incident, Alien Abductions, and Government Cover-Ups (eds. K. Frazier, B. Karr, J. Nickell), pp. 303-312. Prometheus Books: Amherst.

McKay DS, Gibson EK, Thomas-Keprta KL, Vali H, Romanek CS, Clemett SJ, Chillier XDF, Maechling CR, Zare RN (1996) Search for past life on Mars: possible relic biogenic activity in Martian meteorite ALH84001. Science 273: 924-930. http://dx.doi.org/10.1126/science.273.5277.924

Picture of Tycho crater by Michael Karrer on Flickr, and used under a Creative Commons license.



10 December 2010

Captain Green Mom saves the day!

One of the classes I taught this semester was Biological Writing. As I understand it, the way a lot of my colleagues teach this class is that it is very focuses on some traditional academic writing. I think some of my colleagues even have students write mini grant proposals.

I wanted to shake things up and expand things to scientific communication. I was inspired by the student videos at Shifting Baselines (masterminded by Randy Olson, author of Don’t Be Such A Scientist, which I reviewed here). So, I asked my students to pitch an idea, then make a short video. The target was to make the video one minute (excluding credits).

This project had some issues as a project, mainly arising from that it is necessarily a group project. Group projects are always tricky because of social loafing and so on. I don’t know quite yet how to refine it if I do it again.

But...

They rose to the challenge! (This is not the only video project from the class, but is the only one that students put on YouTube.)



Someone wrote someplace that the boomers and Gen X watch TV, but millenials make TV. This is a good example. I talked with my students about story, but all the technical stuff – the sound, the effects, the editing – they worked that out themselves.

09 December 2010

GFAJ-1: Get Fighting And Jousting!

Felisa Wolfe-Simon and NASA have copped a lot of flak for saying repeatedly they aren’t going to address criticisms of their arsenic bacteria paper anywhere but in peer reviewed journals. Even the most recent response says:

We invite others to read the paper and submit any responses to Science for review so that we can officially respond.

At first, I wondered if the team’s attitude towards blogs is another case of the “Nothing matters but papers” attitude. I don’t think it is, since it doesn’t align with them holding a press conference.

I almost get the sense that they think that debating science bloggers would be like wrestling with a pig: they’ll get dirty and the pig would enjoy it.

I have a little sympathy here. I get the sense that there are a lot of people who want to see...


Thunderdome!

Two scientists enter! One scientist leaves!

People love gladiatorial combat. It might not have to be physical, but a scrap is fun to watch. Let’s be honest: it’s exciting to follow the arsenic life story, because you have so many interesting elements. Hype! Embargoes! Egos!

It would be a heckuva a lot of fun to watch if @ironlisa (Felisa Wolf-Simon) and @RosieRedfield (author of a highly read critique) decided to have a “frank exchange of views” on Twitter. As of this writing, though, neither is following the other on Twitter. (Me? If someone cared enough to write about some of my research, I’d probably be following them.)

I’m also a bit sympathetic because I could appreciate wanting to think before wading into this. The team has already been criticized for moving too fast. Ed Yong asked:

(H)ave any of you scientists engaged w/ commenters on other people's posts about your work? If not, why not?

I replied that I have done so, when Scicurious blogged about a paper I co-authored (mentioned here). But that was easy, as the comments were straightforward ones.

I don’t know if I’d have been so ready to jump in and respond to commenters if I was getting told, “This paper shouldn’t have been published.”

And if I did decide to wade into an argument with someone who was that convinced that my work has so little value, what response could I give? Do I just say, “Oh, I’m sorry, I’ll start work on the retraction”? I don’t think I would, for all kinds of reasons. The chance that I’d say something stupid and intemperate and that I might later regret might be fairly high.

There are many, many, many ways that this story could have been handled better. But even if they did it for the wrong reasons, not jumping into the ring and playing, “Let’s have you and them fight,” might be the first smart decision.

Additional: Dr. Isis has some similar thoughts on this matter.

Related link

Science Show feature has some audio with Dr. Wolfe-Simon, which is notable for confirming that the name of the arsenic-tolerant bacterial strain, GFAJ-1, is indeed an acronym for “Give Felisa a job.”

08 December 2010

Questions posed by grad schools

If you’re applying to a grad program, here are couple of questions you might find on an application.

Describe your professional goals you hope to achieve by pursuing a graduate degree.

Translation: “What job do you want after you finish your degree?” Or, to be even more blunt: “What do you want to be when you grow up?”

First sentence should be something like:

“I want to work to be a [ professor / technician / researcher / patent lawyer ] in a [ teaching university / research university / community college / state government / federal government / start-up company / pharmaceutical company ], because....”

The rest of your response should flow from that first sentence.

Here’s another question you might get.

Describe why you are interested in your chosen field of study.

This question uses sleight of hand. I think it’s what it’s trying to find out is not your reasons as much as whether you have a “chosen field of study.” It’s a subtle way of asking if you have an understanding of what is currently being researched. Are you engaged with an intellectual problem? Have you read any research literature?

That means your first sentence should be something like:

“I want to study cell biology / ecology / herpetology / evolutionary biology / animal behaviour / taxonomy / molecular biology, because...”

The more specific you can be about the field in the first sentence,
the better. For instance:

Good: “I want to study microbiology, because...”

Better: “I want to study extremophile archae that live in high temperatures, because...”

Still better: “I want to study enzyme stability of extremophile archae that live in high temperatures, which several faculty in your department work on, because...”

07 December 2010

Tuesday Crustie: Sea of green


A porcelain crab (Neopetrolisthes maculata) trying to hide in an anemone from a photographer.

Photo by Boogies with Fish on Flickr. Used under a Creative Commons license.

06 December 2010

Your yawns and your dogs

ResearchBlogging.orgIn humans, yawning is contagious. Heck, I’ll bet just looking at the title and first sentence of that post triggered a couple of yawns somewhere in the blogosphere.

A couple of years ago, a report that dogs could “catch” the yawns of their human owners made a big splash in the news media. Here’s a particularly provocative headline:

Dogs ‘may be able to read their owner’s minds’

When you yawn, and then I yawn, you know that I am reading your mind.

While the headline is over the top, it relates back to an hypothesis that the paper made that yawning might spread from humans to dogs because dogs have some level of empathy with humans.

I’m going to jump to the punchline of a new paper by O’Hara and Reeve about this: There is almost no evidence that yawning spreads from humans to dogs. What’s more, this is the second study to fails to replicate the finding that made all the papers.

To go into this in a little more detail, they author were playing around with the idea that dogs catching human yawns might be evidence of dogs’ empathy with humans. If that was the case, you might expect a dog living with an owner presented with a human yawn might yawn than a dog in a pound.

No difference.

You might expect a dog to yawn more if her owner yawns than if a stranger yawns.

No difference.

You might expect more empathy between two dogs (being the same species and all) than between a dog and a humans, so dogs seeing another dog yawn would be more likely to respond with a yawn than to a human yawn.

No difference.

And so it went. There were other comparisons, but O’Hara and Reeve found only very weak evidence that dogs were picking up on any yawns at all. They found an effect only when pooling all the yawning stimuli conditions, and then only for dogs in a rescue shelter, not dogs in their owner’s home. That sort of inconsistency makes me think it might be a false positive, since there doesn’t seem to be a strong reason that dogs in a pound would be more susceptible to catching yawns than other dogs.

This study is almost certainly not going to get the attention that the original one did. “Dogs catch your yawns” is a more compelling story than “Dogs don’t catch your yawns.”

That said, O’Hara and Reeve suggest a great experiment about catching yawns that doesn’t seem to have been done yet:

Do dog owners catch their pets’ yawns?

Related post

When is yawning contagious?

Reference

O’Hara S, & Reeve A. 2010. A test of the yawning contagion and emotional connectedness hypothesis in dogs, Canis familiaris. Animal Behaviour. DOI: 10.1016/j.anbehav.2010.11.005

Joly-Mascheroni R., Senju A., & Shepherd A. (2008). Dogs catch human yawns Biology Letters, 4 (5), 446-448 DOI: 10.1098/rsbl.2008.0333

Picture by marlana on Flickr. Used under a Creative Commons license.

03 December 2010

Carnivals for December 2010

Encephalon, the neuroscience blog carnival, has returned from wherever it had gotten to, and #81 is being hosted by A Blog Around the Clock.

Circus of the Spineless #57 is hosted by Wanderin’ Weta.

Carnival of the Blue #43 is hosted by Deep Type Flow.

And lucky last is the Carnival of Evolution #30, at This Scientific Life.

02 December 2010

A new form of DNA


This is way cool. Even though it isn’t aliens.

If you want serious coverage, go to Ed Yong and Carl Zimmer, who explains the skeptical point of view.

Additional: More criticism of the paper.

Reference

Wolfe-Simon F, Switzer Blum J, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PCW, Anbar AD, & Oremland RS. 2010. A bacterium that can grow by using arsenic instead of phosphorus. Science. DOI: 10.1126/science.1197258

Indie spirit

A lot has been written about the second Rock Stars of Science campaign. Chris Mooney is keeping tabs: One, two, three, three and a half, four.

In a way, the pairing of these particular scientists and these particular musicians is apt. In both fields, these are Famous People. They who run big operations with big money.

In short, these are people who have Made It.

But for every headliner, there’s a brilliant session musician who only people in the industry know. There are the friends in their garages practicing and bands crisscrossing the country in second hand vans. Singers who hold down day jobs to hold themselves over between gigs. These can be musicians of high caliber, have a thousand true fans, but will never hear their song on the radio.

I want an Indie Bands of Science campaign.

I want something to celebrate the grad students who are still trying to break into a science career, the overworked post docs, and the profs who run labs on shoestrings.

In many places, the value of faculty members is being judged by their monetary value alone. How much grant money can you bring in?

This is a like judging the quality of music by the number of iTunes downloads. By that measure, one of your favourite musicians is “objectively” not as good as the Glee Cast, Ke$ha, or Justin Beiber.

For faculty members, it’s an embarrassment not to have funding. Nobody exactly brags about it. But maybe it’s time for people to speak out and say when they have produced science without grant support.

For instance, if you look through the acknowledgments of my newest paper, you won’t see any funding agencies mentioned. That’s because the paper is self-financed: I paid for everything out of my own pocket. Here’s the cost breakdown:

  • Domain name renewal for Marmorkrebs.org: $32.61 (3 years)
  • Domain name renewal for MarbledCrayfish.org: $20.38 (2 years)
  • SurveyMonkey Pro: $39.80 (two months)
  • Publishing fee for open access journal: $200.12 (may be some bank fees for wire transfer in there)
  • Grand total: $292.91.

I could have shaved it down to $230.94 or so if I was counted the domain name renewals for one year, didn’t bother with the alternate domain name, and if I’d been more efficient downloading and analyzing the SurveyMonkey data. I suppose I could have hacked it down to less than $100 if I was willing to put it in a journal behind a paywall, but I wasn’t willing to do that. On the other hand, it doesn’t include any costs of the computer or software I bought, as those work on innumerable other projects.

A lot of science cannot be done this cheaply. But there is often almost an assumption that all science – or maybe all science worth doing – is supported by taxpayers. Many arguing for open access publication say something like this repeatedly. Some funding agencies may track how many papers came out of their awards – and frankly, some of those numbers are scary, with over a million dollars going into the production of some papers.

But nobody tracks self-financed science. Nobody even acknowledges efficiency, let alone rewards it. I would love to know how much science gets done because someone simply eats some or all of the costs because it’s faster and simpler to open their wallets than get and manage a grant.

Let’s celebrate the indie spirit.

Reference

Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16

Shiny Toy Guns picture by Nirazilla on Flickr. Used under a Creative Commons license.

01 December 2010

Reverse dumpster diving: Republicans and National Science Foundation spending

Michael Faraday, the story goes, was once asked by a politician what good electricity was. Faraday reportedly said, “One day, sir, you may tax it.”

This might explain why the American Republican party is uninterested in science,  since so many of them seem to see no benefits to any taxation, ever. Meanwhile, Republicans are asking people to look for “wasteful” projects in the National Science Foundation.

What is bothersome is that the web page is very... directed. There is a preconceived idea about what is “wasteful.”

In the “Search Award For” field, try some keywords, such as: success, culture, media, games, social norm, lawyers, museum, leisure, stimulus, etc. to bring up grants.

At the end of this, you know a Republican politician is waiting to say, “Look at all the wasteful spending on these subjects that people identified... using the criteria that we suggested they use to look for wasteful spending.” Talk about a self-fulfilling prophecy.

What they don’t tell people is the size of the NSF budget. Go look at Jess Bachman’s “Death and Taxes” poster of the US Budget, and find the NSF.

It’ll take a while.

Because it’s hard to see.

Because it’s tiny.

If you really want to save people some money, one could argue that the place to start would be the place where the most money goes. Shaving off a couple of percentage points of the costs of some agencies could well save more than the entire NSF budget.

The site also makes it sound like the NSF is just awarding money to any random crap that happens to be out there. It doesn’t tell you about the entire peer review process, and how these projects represent only a small fractions of submitted proposals.

Third, there is a clear way to submit “suspect” links, but no way to submit a comment in support of the NSF.

Of course, attacking funded research projects is a venerable political trick. Sarah Palin criticized fruit fly research; John McCain criticized lobster research.

While Michael Faraday’s taxation answer fall upon deaf ears in the Republican Party, let me remind them of another version of the story.

“What good is electricity?”

Faraday replied, “One might as well as what good is a newborn baby.”

Oh, Republicans, why do you hate the babies of science?

One fish, two fish... Can fish count?

Quick! How many dots?


You can do that fast, right? You don’t even have to count.

In comparison, as fast as you can, how many dots?


That’s much trickier, isn’t it? Slower. You have to count.

The first, “at a glance” way of determining the number of things is called subitizing.

ResearchBlogging.orgA new paper by Bisazza and colleagues takes a look at these abilities in guppies. Guppies, like many other fish, have a behaviour that is sensitive to numbers of things: joining a school of other fish. Bisazza used this behaviour to test guppies abilities to distinguish quantities.

And, for an added twist, they looked at how the behaviour changed over time. Little (one day) guppies were able to tell 3 from 4... but not 4 from 8. Or even 4 from 12! “Four” seems to be the breaking point. Adult guppies, however, can tell 4 from 12. This suggests that these fish have a mechanism for distinguishing small numbers, but not larger ones, even when the differences between the numbers are substantial.

The guppies abilities to distinguish sizes gets better as the guppies get older; they hit adult abilities at about 40 days of age. Interestingly, though, practice matters. Guppies reared in pairs improve in their abilities to distinguish large from small more slowly than guppies reared in tanks with many companions.

You might argue that this doesn’t represent counting in any real sense – this could just be amount of “visual space” that objects represent. That is, guppies distinguish large from small. The researchers tried to control for that, using a tank set-up so that the lone fish being tested could only see one other fish at a time. That seems to eliminate “size” as a proxy for counting.

While Bisazza and collegues emphasize the evidence for there being a small number subitizing system and another for larger numbers, I’m actually most fascinated by the entire social aspect of this. I wonder if the improvement in discrimination would be seen in other situations. Would fish that could discriminate large from small schools also be able to discriminate large from small numbers of food items, say?

P.S.—There are 23 dots in the second picture.

Reference

Bisazza A, Piffer L, Serena G, & Agrillo C. 2010. Ontogeny of numerical abilities in fish. PLoS ONE 5(11): e15516. DOI: 10.1371/journal.pone.0015516

Photo by Tartaruga33 on Flickr. Used under a Creative Commons license.

Comments for second half of November 2010

Scicurious wants to know how well she’s doing at writing for non-scientists. Later, she asks what makes a good basic science blog.

At The Rogue Neuron, Andrea Kuszewski takes up the cause of the Science Cheerleaders, with my previous blog post on them, and another by SciCurious figuring rather prominently. Living LabSpaces also comments on the Science Cheerleaders. And don’t forget Genegeek, who brought curling into the discussion!

The other popular post I wrote was on academic myopia of publishing peer-reviewed papers. Biochem Belle had another riff on this. Kevin Zelnio at Deep Sea News managed to link this back to the Science Cheerleading discussion, too.

Angry by Choice has suggestions for applying to grad school. Students: Every program is different, so you have to do your homework.

Peter has a great story on Science of Blogging of how he benefited from blogging about his research. But is it typical?

Not so much a comment, but a pointer to a SEED column by Dave Munger on poisons that referred to one of my posts on tetrodotoxin resistance in snakes.