Dear Virginia

Dear Virginia Heffernan,

Your recent New York Times column, “Unnatural Science,” is mostly wrong. You’re going to catch a lot of flak for sentences like this:

(S)cience blogging, apparently, is a form of redundant and effortfully incendiary rhetoric that draws bad-faith moral authority from the word “science” and from occasional invocations of “peer-reviewed” thises and thats.

If I might mix metaphors, you paint a distorted picture using a broad brush that’s loaded with tar and feathers. There are bloggers who you disagree with? Fine. There are bloggers that you personally dislike and find distasteful? Okay. But to then accuse every science blogger of being a participant in “bloodsport” and engaging in “bigotry”? That’s not fair, Virginia. Possibly even a bit bigoted.

(D)oes everyone take for granted now that science sites are where graduate students, researchers, doctors and the “skeptical community” go not to interpret data or review experiments but to chip off one-liners, promote their books and jeer at smokers, fat people and churchgoers?

There are many examples of science blogs that do lots of interpreting data and reviewing experiments. You only needed to look at at ResearchBlogging.org for a steady stream of posts daily that do just that. (And, incidentally, it’s hosted by the same company that runs Science Blogs, the target of so much of your distaste.) I’m vain enough to think that I do a passable job of reviewing experiments here on my own blog.

While you seem to think that blogs should be nothing but online versions of the “News and Views” section of the large weekly science journals, I think one of the charms of the medium is that it reveals scientists as people. People with passions and interests and frustrations and opinions – including opinions that you may happen to disagree with. As I wrote before:

I would hate for researchers to lose their authenticity in pursuit of likeability.

You are not the first to have concerns that the writing style of a lot of bloggers. Randy Olson made some similar points in Don’t Be Such a Scientist (I reviewed it here). There has been a lot of discussion about civility in the science blogosphere, which was the point I think you were trying to make. The conversation about civility is something that is, and should be, a work in progress.

Many have pointed out, however, that “civility” has often been used as a tool to preserve the status quo, muzzle dissent, and is applied unevenly. Wielding “civility” like a spiked club has been particularly common response to discussion about religion and atheism, which seems to be something of a sore point for you, since you mention “blasphemy,” “religion-baiting”, and “jeer(ing)... churchgoers.” (I was also a bit disturbed how you mention “peak oil” as though you thought it was somehow wrong or untrue.) I am curious, Virginia, as to whether you have ever found similarly disreputable and offensive smears of science by non-scientists (including the religious)? Do the large numbers of people, many religious, who routinely attack my entire scientific field, evolutionary biology, give you any pause at all?

It’s too bad that you spoiled a valuable message about public perception of science by badmouthing so many of my colleagues, and so much of the enterprise.

Yours truly,

Zen

Additional, 31 July 2010: Virginia Heffernan has followed up at Neuron Culture, and has said she has some regret about the post.

The secret life of a banner

When Dr. Becca announced that she wanted a new banner for her new blog, my response was simple:

“Designing a banner sure beats working.”

She liked what I did. Hooray! So let me take you through the  design process. The first step was reading the directions. I fired up Corel Photo-Paint, and set the dimensions to a new page to her specifications.

The picture

Almost everything was dictated by the title, “Fumbling towards tenure track.” The key word to me was “fumbling,” which immediately has some possibilities for a graphic interpretation. When I hear the word “fumble,” I think of the most famous fumble in Canadian history.

Robert Stanfield has sometimes been described as the best prime minister Canada never had. On the campaign trail in the 1970s, he was playing a little football with some of the reporters, firing off several nice passes. He dropped the ball once. And guess what picture made the front page of the most widely circulated newspaper in the country the next day? This one:

The picture is credited with harming, if not destroying, Stanfield’s chance of winning a federal election. Read more about this picture here.

To me, no other picture so completely captures the frustration of a fumble. So I wanted to use that in the banner. The shape wasn’t right to use the whole photo, but I was able to crop it to show just the fumble.

The typeface

Again, the word “fumbling” played into the choice. The typeface couldn’t be something rigid. It needed to have a bit of the unfinished, slightly haphazard, hand-drawn look to it. I simply scrolled down through the list I had, and found about three that fit the bill. I settled on Ripe, a free typeface I’d found through this article. It wasn’t hand drawn, but it did have some of the variation in letter shape I wanted. And I liked the roundness of it, which suggested a little of the playfulness implied by a fumble. (It has some problems with descending letters, like g, p, and q, though.)

The colours

Dr. Becca wanted something that matched this:

(Why she has this as her avatar... well, I suppose that’s her story to tell.)

I used a trick Garr Reynold talks about in Presentation Zen Design (which I reviewed here): use the colours in the photo. Corel Photo-Paint calls this tool the “eyedropper,” while others call it a colour picker or something similar. It measures and copies the colour at a point in the image. The text and background match the avatar, because the colours were literally picked from the avatar’s photo.

The dark yellow lifted from Dumbo’s hat highlighted the key word, “fumbling,” which I also emphasized by making the text larger and by jiggering the placement a little. Dark blue from Dumbo’s skin for the rest of the title, and light blue for the background, and, as the French say, “Voila!”

The result:

Answering seven

Jason Goldman, the editor of the next Open Laboratory anthology and ace writer, pegged me into doing a little chittin’ and chattin’ over at The Thoughtful Animal blog.

Interviews are useful, because they can force you to articulate things that you hadn’t really thought through.

Science confessions: Language

Honesty time.

Over this weekend, I will be getting on a plane to go to the Ninth International Congress of Neuroethology in Spain.

And it’s scaring the hell out of me.

This is not typical for me. I think I’ve said before that conferences are one of the most enjoyable parts of being an academic for me. It’s not an accident that one of the pictures I use a lot is one of me in front of one of my conference posters. Because I’m actually kind of happy.

But this one, I’m just not anticipating as much as I usually do.

Part of it is probably because I was just at a conference last week. And by the end of it, I felt a little ill, with the combination of food and five hours of sleep a night catching up with me. I am wondering if two conferences in three works is going to do me over.

Part of it is that I worry about the carbon cost of conference travel.


But since I promised I’d be honest, it’s the prospect of going to Spain that is getting to me. I’ve been overseas before. I’ve even lived in another country for a couple of years. But this is the first time I’ve traveled to a place where English isn’t a main language.

And it’s going to be a continual reminder of something I’m not proud of: that I only speak English. I believe that being able to carry on conversations in more than one language is partly a mark of an educated, sophisticated person. I know a small amount of French, but it’s not good enough for me to follow or engage in real-time conversation.

I’m going to spend a lot of time feeling stupid when I’m in Spain. And I am vain: I’ve invested a lot of my self-identity in being an academic, an intellectual, and trying to be intelligent. But change the language, and suddenly little kids have more ability than me to navigate around and do things. I’m going to have to rely on the ability of knowledge of others more than I’d like.

But why I am going? Mainly because I will have a chance to see some people that I don’t see very often.

Nature didn't want it, so you get it

The following is a letter I submitted to Nature in response to a recent editorial. They decided not to publish it... so... blog fodder it is!

---

Sir:

I was pleased to read the recommendation that “scientists, institutions and funding agencies must increase transparency wherever possible” (Nature 465, 7; 2010). To that end, I suggest journals such as Nature consider ways to increase the transparency of the peer review process. The practice of anonymous peer review is at odds with the increasing adoption of transparency and accountability by government, private industry, and elsewhere.

Currently, the identity of reviewers typically remains anonymous to the author(s) of the paper during the editorial process. Even after the peer review process is over and the final article of record has been published, reviewers remain anonymous to the readers. This level of anonymity makes it easy for authors or readers to claim that a shadowy cabal of insiders can effectively block publication of science that is technically sound but controversial. Such accusations were raised by some stem cell researchers earlier this year (http://blogs.nature.com/news/thegreatbeyond/2010/02/bad_reviewers_block_good_resea.html). Cases like it show how a lack of accountability in peer review can be used to cast doubt upon scientific evidence, particularly for controversial subjects like climate change.

One every 48 hours

I am not going to be able to sustain this rate, but having two papers go online in four days is a pretty darn nice feeling.

This one went up Monday morning, local time...

Faulkes Z. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.) in the North American pet trade. Aquatic Invasions 5(4): In press.
http://www.aquaticinvasions.net/2010/AI_2010_5_4_Faulkes_correctedproof.pdf (Preprint)

And though the e-pub date is Saturday, I saw this one in my RSS feed today:

Jimenez SA, Faulkes Z. Can the parthenogenetic marbled crayfish Marmorkrebs compete with other crayfish species in fights? Journal of Ethology 28(4): In press.
http://dx.doi.org/10.1007/s10164-010-0232-2 (Preprint)

Publication wise, in my career, yes, this is the best week ever.

This must be how Rick Shine feels... all the time! (Do not look at this publication list, fellow researchers, unless you would like to be reminded of how unproductive you are.)

Next week is going to be boring. Other than the overseas trip... But more on that later.

Less quoted than Newton

If I have seen further than others, it is because I am surrounded by dwarfs.

– Murray Gell-Mann

Quoted here, but the original source of the quote is unknown, according to Wikiquotes

Tuesday Crustie: Down the middle

A particularly striking squat lobster (Allogalathea elegans, which means, “the elegant other Galathea”).

Photo by by TANAKA Juuyoh (田中十洋) on Flickr, and used under a Creative Commons license.

Confidentiality clauses and choices

There’s a worrying discussion of how BP has been offering contracts to faculty members doing research in the Gulf of Mexico... with confidentiality clauses. One of the most interesting aspects about the article by the American Association of University Professors president is that he argues that maybe professors shouldn’t be allowed to take those contracts, even if they wanted to (emphasis added):

The increasing impact of corporate funding on the integrity of faculty research is among the changes higher education must confront. The decision about whether to sign restrictive contracts is not simply a matter of individual choice. It has broad implications for higher education and for the society at large.

I’m not sure what Nelson has in mind here. Let’s say for the sake of argument that such restrictive confidentiality clauses are so corrosive to the research enterprise that that they should not be allowed. At what level do you set policy? At the level of professional societies? Institutional policies? State or federal legislation?

While I agree that the issue is important, I’m not sure whether it warrants anything other than professional disrepute.

Related posts

Privately funded science

So much research

Recently, I’ve mentioned a few posts talking about their “concern” with the amount of research out there, with the implication being that the research must be bad because there is so much of it.

I think one of my forthcoming papers (available as a preprint) is a good example of how there’s more research because our ability to do meaningful research has increased so much.

Simply put, it’s a paper would not have been possible all that long ago.

The goal was to try to get a sense of how long people have been keeping Marmorkrebs as pets in North America. In pre-Internet days, the amount of effort to get at this question would have made it impractical to do. How could you get an answer? Place an ad in a aquarium hobby magazine asking people to contact me? Phone pet stores individually? Travel to meetings? Most likely, it would rely on word-of-mouth reports from fellow scientists at things like the recent Astacology meeting.

Now, there are online tools that made the whole enterprise relatively easy. Online survey tools, online mapping tools, and a little promotion on a few forums, and now I have data that starts to get at the question.

More research doesn’t mean there is proportionately more bad research.

The question now is whether our ability to search and filter the data can keep up with out ability to generate the data. Seth Godin has termed this the big sort, and notes that the cataloguing is just beginning. Likewise, this post talks about what the volume of publishing does for peer review (though I think I disagree with the solution).

Crayfish meeting

Last week, I was attending a crayfish conference. I have written up daily reports over at the Marmorkrebs blog.

• Day 0
• Day 1
• Day 2
• Day 3: Features a very cute little crayfish video
• Day 4
• Day 5

For those of you with no interest in reading about a week with astacologists, here’s my favourite photo from the field trip to the Shaw Nature Reserve.

70% nerd, 57% geek, 26% dork

Your result for The Nerd? Geek? or Dork? Test...

Modern, Cool Nerd

70 % Nerd, 57% Geek, 26% Dork

For The Record:

A Nerd is someone who is passionate about learning/being smart/academia.

A Geek is someone who is passionate about some particular area or subject, often an obscure or difficult one.

A Dork is someone who has difficulty with common social expectations/interactions.

You scored better than half in Nerd and Geek, earning you the title of: Modern, Cool Nerd.

Nerds didn’t use to be cool, but in the 90s that all changed. It used to be that, if you were a computer expert, you had to wear plaid or a pocket protector or suspenders or something that announced to the world that you couldn't quite fit in. Not anymore. Now, the intelligent and geeky have eked out for themselves a modicum of respect at the very least, and “geek is chic.” The Modern, Cool Nerd is intelligent, knowledgable and always the person to call in a crisis (needing computer advice/an arcane bit of trivia knowledge). They are the one you want as your lifeline in Who Wants to Be a Millionaire (or the one up there, winning the million bucks)!

Congratulations!

Thanks Again! -- THE NERD? GEEK? OR DORK? TEST

Take The Nerd? Geek? or Dork? Test at OkCupid

Drugs in the water affecting crustaceans’ precious bodily fluids?

You shouldn’t be able to call a species anything you want.

Yes, biologists switched to using Latin names for species because we recognized that common names were too variable and imprecise. Still, that doesn’t mean that common names are infinitely flexible.

A crustacean story has been making the rounds in the news, and alas, the news stories are often botching the basics. I wish I could be surprised. News stories based on journal articles seem to be a never ending well of things to correct.

The first time I saw the article was at New Scientist. Then I spotted it on the front of The Age here. Then I saw it again time here, which was what finally set me off. But before this post went up, it also got featured on National Geographic and Improbable Research.

I had looked at the article abstract, and I thought, “Wait. The headline said this was a shrimp. The abstract says nothing about a shrimp.”

The sometimes interesting but often irritating Science Daily has a picture of the senior author, Alex Ford (right), holding something I would not call a shrimp. It’s an amphipod. I can only find one other picture of this species on the web, on Ford’s home page here. In fact, the title of the Science Daily blurb was exactly that of the journal article – except that the word “amphipod” had been replaced by “shrimp.”

The Age referred to this beast as a “prawn”, and showed a picture of something normally called a prawn, Penaeus monodon, which is an entirely different beast. And it gave it the lurid title referring to crustaceans “getting high.”

The third article showed a picture of another species (Crangon crangon) that is not even close to the one studied in the paper. And this time, the article referred to the animals becoming “suicidal”!

Does calling an amphipod a “shrimp” or a “prawn” matter? Yes! People eat shrimp and prawns, but not amphipods. Bu changing the common name, you introduce a whole new set of worries and fears about the safety of people’s food. It’s made worse considering that the third article is at a website called “Fish2Fork,” which strongly suggests they think it’s a seafood story.

The paper is actually quite interesting, but it shows neither animals “seeing the light” (title and article 1), “getting high” (article 2) or “becoming suicidal” (article 3).

The behaviours that the authors are testing are the tendency of amphipods to swim towards a light (phototaxis) or tendency to swim up or down (geotaxis). I am guessing the former is where “seeing the light” comes from, but “seeing the light” doesn’t capture the actual behaviour well at all. I would expect “seeing the light” to mean that the amphipods gained some ability to see something they couldn’t before.

The authors didn’t just test the effect of Prozac, but two other drugs, and the neuroactive chemical serotonin (which Prozac interacts with and which is often important to crustaceans), and a natural parasitic infection (acanthocephalans).

Amphipods that were infected with parasites, given serotonin, or given Prozac all tended to be more likely to be attracted to light, and more likely to be swimming upwards. Thus, amphipods are more likely to be out in the water in bright light, where they would be more susceptible to being eaten by predators. This, of course, is what parasites “wants” so that they can infect the next host in their life cycle. Still, this is hardly “getting high” or “suicidal” in the way people think of those phrases.

Further reading of the paper reveals a less straightforward interpretation than the headlines say. Guler and Ford didn’t measure the drug concentrations in the water where they collected their animals. They argue that their values are within the ballpark that other researchers have recorded in “STP effluent”. (I don’t know what “STP” means, because the authors don’t define it. A little help here? You know, for those of us who don’t speak acronym.)

Complicating matters further is that the authors tested five concentrations for the drugs they tested, ranging from 0 to 10 µg per liter, but it seems only one concentration of Prozac (0.1 µg per litre) caused a significant difference in the amphipods’ behaviour. So if we’re taking enough anti-depressants, there may not be a problem?

Finally, they only used males in this experiment, and there is no explanation why.

This paper is interesting, but it’s yet another case of the researchers and press release writers working too hard.





For more fun with headlines, see the stuff I’ve written with Carin Bondar!

Additional: Deep Sea News also got to this one.

Reference

Guler Y., & Ford A. (2010). Anti-depressants make amphipods see the light Aquatic Toxicology. DOI: 10.1016/j.aquatox.2010.05.019

Link love: Are octopuses smart?

Superfast link to a Seed article about octopuses that mentions my former boss and incidentally me.

Not sure how a paper in Current Biology morphed into a paper in Cell, though. Fact checking fail!

Snake eyes

To many, “snake eyes” is a bad bet at the craps table. To some, it’s a GI Joe villain character. To a very small, select group, it’s a minor addition to the oeuvre of Brian De Palma. ^*

Today, I want to look at the most literal meaning of the term imaginable. But, since this is a biology blog, you could probably guess that I was going to end up talking about the eyes of snakes.

I’m willing to bet that when most people visualize snake eyes, they think of something with a vertical slit for a pupil, like the animal shown here. Such eye look a little scary to humans, because we have circular pupils. Snakes aren’t the only animals to have such pupils; many cats do, too. Why do some animals have vertical pupils, and some have circular pupils?

Brischoux and colleagues set out right away to correct one idea that many people have about vertical eyes that is wrong: it’s not for night vision. They set out to test other hypotheses about the function of pupil shape using snakes as their subjects. One reason for using snakes is that the pupils vary considerably, so compare the animal above to the one below (click to enlarge).

Admit it: it looks friendlier with circular pupils, doesn’t it?

The pupil shape appears to be related to day and night, but in a different way: You can close a slit pupil much tighter than a circular pupil. The yellow snake above has its pupils shut down quite far. This might be advantageous to an animal that normally moves around at night to prevent it from being temporarily blinded by bright light in the day.

The authors also suggest that a vertical pupil may be less recognizable then a round one, making it advantageous for ambush predators who use camouflage. The authors don’t mention that many prey species also use camouflage, and following that logic, might also be expected to have slit pupils.

Brischoux and colleagues coded out about 100 snake species, categorising their pupil shape, type of foraging, and time when the animals were most activity. They found that most snakes fell into a fairly small number of positions in the possible range of values: sit and wait ambush predators that hunted at night tended to have vertical pupils; snakes that actively foraged during the say tended to have circular pupils.

What I don’t get about their figure above, though, is why the data points are scattered. Look at the trio of dots on the lower right corner. Why are they separated? If these are categorical values, all three should be right on top of each other. That implies that they’ve measured something quantitatively, not by category... and if so, where are the value labels for the axes?

Having done all that, the authors admit they still can’t definitively tie pupil shape to any particular adaptive advantage. They suggest some good experiments, such as manipulating pupil shape by retouching pictures to see if this affects how readily detectable an potential predator is. They also point out that many other species vary in their pupil shape, and that similar analyses could be done for those groups, too.

Reference

Brischoux F, Pizzatto L, & Shine R (2010). Insights into the adaptive significance of vertical pupil shape in snakes Journal of Evolutionary Biology DOI: 10.1111/j.1420-9101.2010.02046.x

Yellow snake photo by MrClean1982 on Flickr. Garter snake photo by C. A. Mullhaupt on Flickr. Both used under a Creative Commons license.


^* The film has a special place in my heart, because it was filmed in Montréal when I was living there, and I was able to look in and see the set they had built in the old Montréal Forum when I walked to and from McGill University.

Tuesday Crustie: Bug

Bugs! One I know a little bit about and have published a little research on. This is Ibacus alticrenatus, a slipper lobster. There’s a developing fishery for two species in this genus in Australia, and probably other regions, too.

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

Additional: Hm. Looking at this again, I wonder if this might actually be Ibacus peronii. This angle makes for a dramatic photo, but also makes it hard to tell the species.

As I suspected, I write only like I write

Remember my question about being a stylistic chameleon a while back?

As I suspected, it's rubbish at analyzing text. What I didn't expect is that it is put up by a vanity press publisher.

Neural plasticity isn’t new

A recent post on neuroscience of learning got me thinking about how several people are talking about brain plasticity as though it is a huge revelation of the last couple of decades. From the post:

Only twenty years ago most people in the world of neuroscience believed that the connections between the neurons in your brain were fixed by the time you were a teenager (or even younger)

This is a distortion of history, I think. Ideas about neural plasticity were bubbling around well before 1990s. For instance, Merzenich and Kaas did many experiments published in the early 1980s that showed that if you cut a sensory nerve in a monkey, you saw a major reorganization of the representation of that body in the cortex.

It is true that people thought mammalian nervous systems did not generate new neurons until probably the min-1990s. But then, adult neurogenesis was yesterday’s news to people studying neuroethology, who had been hearing about how new neurons were added to the brains of adult songbirds, like canaries, for years before that (Goldman and Nottebohm, 1983).

Invertebrate neurobiologists had been on the trail of synaptic changes associated with learning and memory a decade earlier (Castellucci and Kandel, 1974).

And, if you think about it, in order for learning to occur and memories to be formed, some kind of change had to be happening at the neuronal level. Psychologist Don Hebb was thinking about how such changes at the neural level might occur back in 1949 (reviewed here).

Previously, people argued about whether those changes were presynaptic or postsynaptic, as though there were only two possibilities. I could make a very long list of ways that neurons might change in response to experience now, and that list shows no sign that it’s reached its limit yet. In fact, less than a month ago, Kuba and colleagues showed yet a new way that neurons can change their propensity to fire: by changing the place on the cell where action potentials start.

We did not suddenly discover plasticity two decades ago. I think the surprise has been not that nervous systems can change, but the number of mechanisms by which they can change.

Additional: Also forgot the work of Nobel laureates Hubel and Wiesel, who studied changes in visual cotices of cats reared under different conditions. Many people thought that it's plasticity, but it's really early in development so doesn't really tell us much about adults.

References

Castellucci VF, & Kandel ER (1974). A Quantal Analysis of the Synaptic Depression Underlying Habituation of the Gill-Withdrawal Reflex in Aplysia Proceedings of the National Academy of Sciences of the United States of America, 71 (12), 5004-5008

Goldman SA, & Nottebohm F (1983). Neuronal production, migration, and differentiation in a vocal control nucleus of the adult female canary brain Proceedings of the National Academy of Sciences of the United States of America 80(8): 2390-2394

Hebb DO. (1949). The organization of behavior. New York: Wiley.

Kuba H, Oichi Y, & Ohmori H (2010). Presynaptic activity regulates Na+ channel distribution at the axon initial segment Nature, 465 (7301), 1075-1078 DOI: 10.1038/nature09087

Merzenich M, & Kaas J. (1982). Reorganization of mammalian somatosensory cortex following peripheral nerve injury Trends in Neurosciences 5: 434-436. DOI: 10.1016/0166-2236(82)90235-1

Canary picture by meophamman on Flickr, used under a Creative Commons license.

Reaching out – way out

Recently, The Daily Show talked about how reaching out to the Muslim world had become one of NASA’s mandates (I wanted to embed the clip, but it’s not working properly). The incongruity (Muslims? Space?) is ripe for humour, of course.

This may not be as far-fetched as it sounds.

I  submit to you that scientific collaboration can occur despite political conflicts.

I submit to you that the United States was never held in higher esteem around the world than at this point in its history:

Privately funded science

David Calquhuon argued on his blog that science bloggers should never be paid. But at least one heading suggested a bigger issue is at stake:

Science and commerce don’t mix

I talked before about how science used to be practiced by the well-to-do, because it ensured analysis unfettered by vulgar concerns like worrying how you were going to feed yourself. This may is one of the reason that public funding has been so highly sought after: it is as close as most scientists can get to achieving the gentlemanly disinterest that is still idolized.

But.

The research community in the U.S. is starving for money. State funding for institutions is drying up, probably for good, and federal funding may not return to old levels in a long time, if ever. Indeed, a story ran talking about how disappointed many researchers were with the current administration – not about funding, admittedly.

Where does that leave researchers?

As it happens, this was also the crux of a case (#6) for the National Ethics Bowl. Again, that it’s a case in a national competition suggests it isn’t clear cut.

Our ethics team came down on the side saying that private money could be acceptable for researchers, with qualifications, the most important one being the independence of the researchers to conduct and publish the results.

The Seed / Pepsi blow-out is an example of the tensions. Some bloggers left. Some stayed. Several talked about how very conflicted they were about what the right thing to do was.

With public money becoming less available, more and more researchers are going to be turning to some manner of private funding. As a profession and as individuals, we basic researchers have not given a lot of attention to this. Requirements to disclose potential conflicts of interest in conference abstracts, say, became common in the 1990s, if I remember right, which is fairly recent in the scheme of things. I am grateful to Mike the Mad Biologist for his discussion about this.

Maybe researchers are hoping that public funding rates will go back to old levels and the problem will go away. I think they’re going to be disappointed.

Texas Higher Education and Creation Research, Part 37

Pharyngula blog points out the newest dodge the Institute for Creation Research is using to get around the lack of accreditation for the Master’s degree: just claim they don’t need it.

At this point, they’ve abandoned any pretense that they’re anything but a diploma mill.

Comments for first half of July 2010

Not Exactly Rocket Science was good enough to give a plug for one of my posts, on axon size.

Mike the Mad Biologist covers a paper that I wanted to do.

The Panda’s Thumb expresses puzzlement over the ruling against Chris Comer. I try to explain.

Octopus venom! On ice! I had to say something in response to that over at Cephalove.

DrugMonkey suggests professors should think of itself as labourers, and consider collective action. I note it’s not an option round these parts.

I like this post at The Ethical Paleontologist.

EcoPhysioMichelle on C6-H12-O6 wonders what the three flying vertebrate lineages are.

Life and death and sex choices in mantids

If ever there was a time to be careful about who you were going to mate with, it would probably be when there was a good chance you were going to die in the attempt.

And we’re not talking about some sort of heroic situation where the male has to endure hardships to get to the female. We’re talking about situations where the female herself is the threat.

“Fair princess, I have arrived to...”

CHOMP. Nom nom nom.

A lot has been written about the cannibalistic tendencies of praying mantises. Indeed, a recent New Scientist article called male mantids “the poster boy of risky sex.” Why the female tend to eat their mates seems to have a lot to do with them being aggressive hunters that pretty much try to eat anything. But we’re more concerned with the males’ response to that behaviour, rather than worrying about what causes it in the first place.

Barry tests the hypothesis that males pick what females to mate with in part by sensing chemical cues that the female gives off. In part, this is a replication of a previous study in the lab in more natural settings.

To give the males something to choose between, Barry split the females into two groups: one got fed three times as much as the other, so you would expect these would be attractive to males for two reasons. First, they should be in better condition, and second, they should be less hungry, and hopefully less likely to strike out at males.

To prevent the males from using visual cues, the females were placed in cages that were covered. Barry also put out empty control cages (which never attracted males). As expected, the males were significantly more likely to end up in cases containing well fed females.

After the males chose, Barry examined the number of eggs in the ovary to determine fecundity. This is a bit tricky, as you would expect that there’s going to be a correlation between feeding and fecundity, which was the case. But, Barry did find that when males did choose the poorly fed females, they picked ones that had mature eggs. When exposed to eggs alone, however, the males never ended up in those cages.

I suppose one question raised here is: How expensive is it to make a pheromone? Insects are famous for being able to detect and respond to small quantities of pheromones; if so, it may not take much to bring in a mate. Does food restriction shut down the chemical pathway, or are the males very sensitive to concentration levels of pheromones?

Reference

Barry KL. 2010. Influence of female nutritional status on mating dynamics in a sexually cannibalistic praying mantid Animal Behaviour. 10.1016/j.anbehav.2010.05.024

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

I am a stylistic chameleon

Several fellow bloggers have been playing with the tool called, I write like. Interesting idea, but suspect execution. My book review yielded this result:

I write like
George Orwell

I Write Like by Mémoires, Mac journal software. Analyze your writing!

On the other hand, a post about bats suggested this:

I write like
Edgar Allan Poe

I Write Like by Mémoires, Mac journal software. Analyze your writing!

My analysis of ethics puzzled me completely:

I write like
Chuck Palahniuk

I Write Like by Mémoires, Mac journal software. Analyze your writing!

Killifish vision?

I write like
Isaac Asimov

I Write Like by Mémoires, Mac journal software. Analyze your writing!

Either I am veritable virtuoso of style, or this writing “analyst” is pulling names out of a hat.

Headline Hogwash, Part 3: Superbugs in sharks!

My colleague Dr. Bondar and I continue our trilogy of press release punditry! We examine a recent headline, and test whether the headline stands up to having two people with doctorates reading the original pper reviewed, technical paper.

This one is fun. Superbugs! Sharks! What unholy alliance have these two formed?

Previous entries in the series

Part 1
Part 2

Tuesday Crustie: Tricolore

I normally don’t feature pictures of individuals where I can’t name the species, but this blue, white, and red copepod was irresistible. The blue bits are eggs, incidentally.

Want more copepods? I’ll plug this recent post in Mauka to Makai about copepod jumping. Relative to body size, they may be the most effective jumper in the animal kingdom.

Photo by kat m research on Flickr. Used under a Creative Commons license.

Book review: Do Fish Feel Pain?

Victoria Braithwaite’s Do Fish Feel Pain? is not a technical book. The type is large and the prose is easy to understand.

I had to read this book, because many of the issues around fish pain are the same as those raised for invertebrate pain (Puri and Faulkes 2010; this post). Fish researchers are about five years ahead of the invertebrate researchers.

Braithwaite’s answer to the question posed in her title is...

Spoiler alert! Click here to read more.

The NSF’s plan for minority students (or lack thereof)

Both Diverse Blog and Fairer Science are reporting that the National Science Foundation (NSF) is considering basically killing funding programs that specialize in supporting minority-serving institutions. Programs that support universities with mostly black and First Nations students, and a planned program for universities with lots of Hispanics (like my own), may be pooled into one program... that any institution can compete with.

I am astonished to hear this, because it was a year or two ago that I was in the same room with two NSF representatives, discussing ways to make a new program for Hispanic serving institutions that would work well.

If they just consolidate all the existing programs and let everyone compete for them, institutions like ours are going to get smushed.

Like a bug.

Competing with a lot of more established research universities for anything is a bit like this:

You’re short stacked, and as the game goes on, the leaders at the table have more resources and more options, and the law of large numbers says you will be slowly ground out of the game more often than you win.

NSF is taking comments until 1 August. I guess I’m going to have to write a memo. Obviously, I have a vested interest in seeing such programs continue.

Hat tip to Biochem Belle. Photo by Rambis on Flickr, used under a Creative Commons license.

PepSeed

I’ve lost the ability to keep track of all the posts on the Seed Media Group / Pepsi story. But I would be remiss if I did not point out the major article in The Guardian excoriating Seed for killing a story that might have embarrassed an advertiser.

That is a much bigger barrel of monkeys than guerrilla marketing a flog. (Aside: DC’s Improbably Science argues that science bloggers should not be paid, ever. I may have more to say on this later.)

Also, Seed CEO Adam Bly started his own blog. He’s not said much so far about the whole blow-up.

Texas Education Agency and Chris Comer, Part 40

When last we left, Chris Comer had filed an appeal on her lawsuit against the Texas Education Agency.

Denied.

The National Center for Science Education reported reported on this last week. (Man, am I out of the loop.)

The fact that Comer and other TEA employees cannot speak out for or against possible subjects to be included in the curriculum ... does not primarily advance religion, but rather, serves to preserve TEA’s administrative role in facilitating the curriculum review process for the Board.

As I mentioned before, I think the lawsuit aimed for too big a claim. If anyone has a legal background, I’d love to know why forwarding an email with “FYI” would be considered a violation of neutrality, which always seemed to me to be the strange thing about this situation.

“You’re not my type!”, echolocation edition

Distinguishing your own species from other species is useful: for one thing, it prevents a lot of potentially embarrassing mating attempts.

“Um. You mean we don’t belong to, er... that is to say... you’re not my species? I am so sorry...”

Awkwaaaaaaaaaaaaaaaaaaaaard.

But how fine a distinction can a species draw? Does it stop at, “You’re not my species,” or can it extend to, “You’re species B, not C or D”? And would species be able to distinguish other species outside of reproduction?

Schuchmann and Siemers tackled these questions by studying the echolocation calls of several related bat species that live in Europe.

Bats use echolocation for, well, location. They are not used in situations where animals are interacting with each other: they are used purely for the bat to get from point A to B without running into trees, and to find food. Even so, the sound that each bat species makes tend to be a little different in pitch. Might one bat species go, “That call is a bit to high to be Rhinolophus euryale, might be Rhinolophus ferrumequinum.”

These, I thought, were very interesting questions. But it wasn’t clear to me how they were going to test it.

The experimental set-up they use reminded me of one that is often used to test the cognitive abilities of babies. Bats, like babies, are easily bored. If you keep presenting the same thing over and over, they stop looking at it. When they detect a change, they react and look towards the new and much more interesting stimulus.

They recorded the echolocation calls of four bat species, and played them back to two (one of them, Rhinolophus euryale, pictured). They kept playing the same call from their own species over and over until the bat stopped responding, then swapped it for a new call.

Bats were very good at detecting when the call switched from their own species to a different species. That isn’t surprising, as it just tells you they can recognize their own species’ calls.

More to the point, when they first habituated the bat to a species different than themselves, and switched the call to yet a third species... the bats were still very good at detecting that difference. So the bats are not reacting with, “Meh. All those other species’ calls all sound alike. Not my species, have a nice day.”

It’s not clear what components of the call the bats are recognizing, although pitch is probably the major one. You could probably do some fun experiments seeing how much you could vary the calls and still have the bats responding. The authors also wonder if these different species might be able to benefit by eavesdropping on other species’s calls. If so, there might be some species that are more worth listening to at some times than others.

P.S. – Dart to the authors for using so many two letter abbreviations for species (Re) instead of writing out species names properly (Rhinolophus euryale)!

Reference

Schuchmann M & Siemers B. 2010. Behavioral evidence for community‐wide species discrimination from echolocation calls in bats The American Naturalist 176(1): 72-82. DOI: 10.1086/652993

Photo by by jasja dekker on Flickr. Used under a Creative Commons license.

How much research should get published?

Kent Anderson of The Scholarly Kitchen looks at how good a filter peer-review is.

The reputation authors garner by being published in a scholarly journal is that he or she has fit through the tight filter on scholarly communications, where only the best of the best gets published.

But that reputation is no longer deserved.

He gives some data showing that papers rejected by one journal appear to get published in some other venue. In doing so, he seems to be taking a position that the amount of research being published is a Bad Thing™. This attitude comes through again:

It’s worth noting that even the advocates who state that the majority of studies should be published also state that filters are vital to making such information usable.

This reminds me all too much of the claim that research is being ruined by bad research, which I talked about here recently.

I’m going to go out on a limb, and make what may be a radical proposition. I am going to suggest that:

Scientists are generally competent at their jobs.

If we admit that most scientists know how to do decent science, then it would seem to follow that most research should be published. I would argue that issues people have with the difficulty of keeping up with the literature is more likely to represent the professionalization of science that took place over the last century. Science was a growth industry, with more and more practitioners. The growth of the scientific-industrial complex has increased the amount of literature, not the loss of quality control, I would argue.

Any veterans out there want to chip in? Is it harder or easier to get published now than it used to be?

In which hermitage pays off

A couple of things I want to boast about. Briefly.

Today, I got a news that another research paper has been accepted and is now in press. This, like another article that is in press, is a Marmorkrebs paper.

I’ve already had two published this year, so these could make it four research articles this year (providing the two latest ones make it out in the next five and a half months). This would be my best publishing year to date.* I still have a few other things in the pipeline that might get published this year, so I have my fingers crossed.

In other news, today I hit the ton on the Research Blogging website. There’s more where that came from, too!

* Of course, some of those projects should have been out last year. Curse you, reviewer #2!

What have we learned? That “advertorial” is a word

A slew of sources are reporting that ScienceBlogs has killed the Pepsico blog. I expect a very long (and maybe angsty) retrospective at the next Science Online meeting.

How'd you get that fat lip?

African rift lake cichlids are among the most famous subjects for the study of evolution. The rift lakes formed recently in geological time, but the cichlids that got in have radiated into a dazzling array of species in short order.

But there are cichlids and other similar recent geological events in the Americas, too, just as interesting!

This research by Elmer and colleagues takes advantage of a lake made by volcanic activity, in Nicaragua. The lake appears to have been formed about 1,800 years ago.


View Larger Map

This crater lake has been colonized by Midas cichlids and a few other fishes. The researchers have done a lot of DNA work here, and based on it, they think the Midas cichlids only got into the lake in the last hundred years or so. This population differs in several respects from the cichlids in the nearest neighbouring lakes.

There are two types of Midas cichlids in this lake: there's a common thin-lipped type (pretty sure this is what's pictured here), and a rarer thick lipped type. This difference in appearance is correlated with diet: the common thin-lipped guys have algae, fish and snails in their stomachs, while the thick-lipped one have arthropods.

Elmer and company argue that this could be a case of incipient speciation here. This is an attractive possibility, given that they seem to have two morphs that have different diets, which could leads to different ecological niches, which could lead to reproductive isolation. While plausible, they could not find any genetic distinction between the nuclear or mitochondrial genes between the two morphs (though they commit the crime of "but it's almost significant" for the mitochondrial DNA).

What needs to happen next? Someone needs to make this lake the focus of a career, and start documenting the populations year in, year out, much like Peter and Rosemary Grant did for the Galapagos finches. There need to be behavioural tests to see if fat-lipped females like fat-lipped males more than thin-lipped ones. There need to be ecological studies to see if these animals are inhabiting different locations in the lake.

If this population truly is this young, we have a great chance to watch speciation happen in front of our eyes.

Reference

Elmer, K., Lehtonen, T., Kautt, A., Harrod, C., & Meyer, A. (2010). Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times BMC Biology, 8 (1) DOI: 10.1186/1741-7007-8-60

Midas cichlid picture by Just Chaos on Flickr. Used under a Creative Commons license.

The history of everything in paint

Set aside ten minutes sometime for this.

BIG BANG BIG BOOM - the new wall-painted animation by BLU from blu on Vimeo.

"BIG BANG BIG BOOM:

an unscientific point of view on the beginning and evolution of life ... and how it could probably end.



direction and animation by BLU

http://www.blublu.org

production and distribution by ARTSH.it

http://www.artsh.it

sountrack by ANDREA MARTIGNONI



many thanks to (in random order):

xm24 bologna, csoa mezzacanaja, ericailcane, robert rebotti, andrea bagni, paper resistance, studiocromie, rifrazioni festival, sasso passo, sibe, festival de cine experimental de maldonado (uruguay), gianluigi toccafondo, orilo, maria de brea, bs as stencil, run don't walk, franco fasoli, modo infoshop, pietro and icone festival, doma, cesare romani, popup festival and all the blu's family

Ethics of ads on science blogs

The unfolding blow-up at ScienceBlogs over the addition of a blog by Pepsico is a good opportunity to examine the ethical issues around some kinds of advertising. I’ve actually spent a lot of time arguing about this earlier this year, because I was helping out our university’s team prepare for the National Ethics Bowl. (My co-author Sakshi was a member of the team.)

Case #12 is a told as a piece of fiction, but it raises a lot of the same basic issues as the ScienceBlogs situation. Briefly, the case describes a company employee who goes around and uses the company’s product in a visible, flashy way, without identifying herself as an employee.

That this was a case for a national competition suggests that the ethical implications are not straightforward.

The response of many people in reading that case was that they thought they would be upset over being the target of guerrilla marketing, but they had a much harder time articulating why.

Part of the difficulty in articulating why people were upset is that, on the face of it, nobody is harmed by this kind of marketing. From a utilitarian position, it can be argued that many people benefit from this, in that they are introduced to products that they might benefit from; the company and its employees might also benefit.

I brought up Seth Godin’s thought on permission marketing. With Godin discussing about respect, it seemed that Kant’s ideas on respect for persons was a useful way to parse this. In essence, the marketer is disrespecting their potential customer, and only treating them as a means to an end.

The other ethical principle that was discussed was transparency. In the Ethics Bowl case, that it was the marketer’s job to display product was not clear. I told the team about cases of flogs (fake blogs), and others mentioned “astroturf” (fake green) marketing efforts by companies.

While several have argued that a blog from a corporation blurs the line between editorial and advertising content, but people’s forceful responses to this blog suggests to me that nobody is genuinely confused by its source: it’s a corporate blog.

More generally, I am not sure that the line between editorial and advertising as clear-cut as some would make it out to be. Newspapers and other outlets have long featured editorial columns from political pundits of all stripes. Many of them are associated with corporations, and promote views favourable to those corporations.

Seed Media Group, on the other hand, ran afoul of transparency by not warning their bloggers about the change. I can’t help but wonder if the response would have been so contentious if people knew it was coming.

In the wake of this, Kevin Zelnio mentioned a website that provides ad free icons. In the wake of the ScienceBlogs / Pepsi kerfuffle, I thought about putting on this site.

But I can’t do it. Use of the icon implies three points. The first one is a stickler for me:

1. That I am opposed to the use of corporate advertising on blogs.

I’m not opposed to ads. In fact, there are certain ads I enjoy, like movie previews. (If you ever see a movie with me, you’ll have to put up with “I wonder what previews they’ll show!”) But right now, there isn’t a way for me to put up ads from places that I choose. (Not that anyone’s ever asked me to run ads on any of my blogs, or is ever likely to do so.) Even if I could, I’m not sure I would.

Meanwhile, Seth Godin comes up with something eerily on point about payola and reputation.

Additional: Forgot to mention: What about the idea of “conflict of interest”? Fair enough. There are concerns about such things in science, but the solution has generally not been to reject all research which has apparent conflicts of interest. (There are exceptions at some publishers, however). The approach has been to declare real and possible conflicts of interest. Funded by a corporation? Be up front about it. And we’re back to transparency.

Sending signals is subtle: Killifish’s favourite colours

Making a clear visual signal is tricky. Consider this traffic signal:

(I totally thought I was going to have to photoshop a stop sign, but no.)

Whether this signal is effective depends on a lot of factors. What's the visual environment like? Some colours stand out better in some lighting conditions than others.

More critically for this discussion, what’s the experience of the person the signal is aimed at? And I mean the term broadly. Is the person colour blind? Has the person grown up in a place with blue stop signs everywhere?

Fuller and colleagues are interested in this question of colour signal, and are studying it in bluefin killifish (Lucania goodei). These fish live in lots of different habitats, ranging from water that is very clear, letting in lots of short-wavelength blue and ultraviolet light, to water that they describe as “tea-stained.” (In one of their experiments, they actually dump instant tea into an aquarium to make the water the right colour.)

The fish are quite brightly coloured, and the males vary in their colours. Fuller and company are trying to work out what factors influence those colours. Is it purely the physics of the environment – certain colours are just more visible in particular light regimes? Is it an innate preference of other fish (mainly females) that matter? Do all the ladies love red fins, say? Or do fish reared in a certain light environment develop a preference for one colour?

Rather than trying to sort this out one at a time, the researchers embarked on carrying out one of the most complicated experimental designs I’ve seen in a long time. Four genetic crosses of parents, two rearing environments, and two testing environments... 16 combinations of variables right there. They measured both the visual pigments expressed by the fish and a feeding-related behaviour: the tendency of the fish to pick at small coloured discs.

That’s not going to be easy to summarize, but let me try.

Visual pigments were affected by the environment the fish were raised in (i.e., clear or tea coloured).

Pecking was also affected by the environment: the fish were raised in; fish raised in clear water liked the yellow more than those raised in tea-stained water.

You’re probably thinking, “A-ha! The changes in the visual pigments explain the differences in behaviour!” Surprisingly, no. The differences in visual pigment expression explained a paltry 3% of the behavioural variation. The important changes are probably hidden somewhere in the visual centers of the brain.

There were also some effects of the setting the fish were tested in, which interacted with the rearing conditions. The authors say that the interactions between where the fish were raised and where the fish were tested is the “unique finding of this study” that is “striking.”

But there’s a problem for the reader in figuring this out. Here’s the graph they present plotting the behaviour (their Figure 5). Look for the open diamonds and the crosses.

That’s right: There aren’t any in the plotted data. D’oh! It snuck past the reviewers, editors, and proofreading authors! (Caveat: Hurricane Alex has curtailed my access to the paper, and it’s possible that the final version has been fixed.)

Of course, one of the problems with this experiment is that while part of the avowed reason for doing it is to explain mate choices, they didn’t measure mating preferences. I’m sure that’s coming. But you need these data on non-sexual stimuli to tell you whether females like certain colours all the time or just for mating.

For instance, human females are often thought to prefer pink. But will that enhance the dating opportunities for this man?

Reference

Fuller, R., Noa, L., & Strellner, R. (2010). Teasing Apart the Many Effects of Lighting Environment on Opsin Expression and Foraging Preference in Bluefin Killifish The American Naturalist 176(1): 1-13. DOI: 10.1086/652994

Stop sign ohoto by Chris Pirillo on Flickr. Man with cat by aBbYhaLO on Flickr. Both used under a Creative Commons license.