Tuesday Crustie: What’s bigger than a giant?

This picture was making the rounds last week after being reported by the BBC:

The BBC did not mention a species name, and the infographic below suggests that it’s an unknown. On the CRUST-L listserver, however, the general agreement was that this was Alicella gigantea, the biggest known amphipod. This is a deep water, rarely seen species.

This infographic prompted Rebecca Watson to quip:

If you’re wondering how big Superprawn was, this image clearly shows he was about half the size of New Zealand.

Not a heck of a lot is known about its biology, though all signs point to it being a scavenger. The few times its been photographed, its often been on bait. Its mouth is shaped to take in large bites of food, and about 90% of its innards consists of the midgut. Many of the specimens have been retrieved from the guts of fish, so these animals aren’t big enough to escape predators.

Alicella gigantea is collected in the Atlantic, too. It’s thought that they are the same species, but to my knowledge, no DNA work supports that. Several people on the Crustacean discussion list were explicitly skeptical of the idea that something this wide-ranging would be the same species. Indeed, one person noted that differences between the Atlantic and Pacific populations were noted some time ago.

References

De Broyer C, Thurston MH. 1987. New Atlantic material and redescription of the type specimens of the giant abyssal amphipod Alicella gigantea Chevreux (Crustacea). Zoologica Scripta 16(4): 335-350. DOI: 10.1111/j.1463-6409.1987.tb00079.x

Barnard JL, Ingram CL. 1986. The supergiant amphipod, Alicella gigantea Chevreux from the North Pacific Gyre. Journal of Crustacean Biology 6: 825-839.

Death on campus

I was probably just getting into my office this morning when a woman was found dead near the building I work in.

The police are calling the death “questionable.”

I know nothing more than what’s here: the police are investigating, my building is closed, and classes are cancelled today. As I type this, I just saw a tweet that there is no indication that anyone else is in any danger.

I am trying to figure out how it was that I knew nothing until students started sending me text messages asking about class this morning, while I was sitting at my desk with my email open. I went first to the university’s police department website: nothing. I went to the “alerts” link to find today’s date and a directions to check the university’s home page for more details.

There were no more details on the university’s home page.

I checked Twitter. I follow my institution’s Twitter account, but for those mysterious unknown reasons, the tweet had not shown up in my timeline. Checking the university’s Twitter feed finally led me to a link to a Facebook post confirming what my students were asking me.

Only about an hour after students initially contacted me did I see anything official in my inbox. How the alerting system failed to alert me to something like this is worrisome.

Additional, 10:51 am: Initial local newspaper report.

Additional, 11:25 am:



Update, 11:59 am:

On the university’s Facebook page and in my Twitter search the main point of discussion is: “Why doesn’t the university cancel every class and lock down the campus?” I think this reaction is in response to the initial description of the death as “questionable,” with many people making the connection that this means “murder” and not “accident.”

Working on a Storify of this situation.



Update, 4:32 pm: Some faculty were allowed back into the building, under police escort, to retrieve items from offices and check on status of things in labs. There is a very good chance that the building will be closed until at least noon tomorrow, depending on how far the investigation progresses today.

The Pan American student news site has a story releasing “more details,” which are not really any more details. Indeed, it’s slightly weird that they say this was a woman who appeared to be in her 20s, and then:

It is not yet clear whether the person is a student or faculty member.

There are not faculty members in their 20s at our campus. So what they’re probably trying to say is that it’s not clear if she was a member of the university community.

Update, 5:08 pm: Email came in a few minutes ago that the Science building will be closed tomorrow until at least noon.

Update, 6:29 pm: My initial Storify of the reaction to the death.

Update, 8:54 pm: The local newspaper has a reasonable summary of the day’s events. There was no evidence of stabbing or shooting, but some students are still thinking “murder.” Perhaps the main factor in this still being an ongoing investigation is that the woman had no identification.

Update, 7 February 2012: This morning, the woman was identified as a local high school student. The Science building reopened this afternoon, although all classes were still cancelled for the day. There is still no word on autopsy results.

Update, 7 February 2012, 6:02 pm: The woman’s death has been judged to be a suicide. So very, very sad.

Update, 7 February 2012, 10:26 pm: The news article linked to above has been expanded significantly. It’s just a heartbreaking story. She had talked about suicide before, including that very day, and hurt herself. I have continued updating the Storify, where some of the reactions well, do not give me solace.

Photo from here.

Be eaten, make glowing fish poo, profit!

Why glow if you don’t have eyes to see?

Glowing takes energy. Down in the deep ocean, energy is in short supply, so why would bacteria do this? Bacteria don’t have eyes. It’s not like they’re going to be able to use it to find stuff. And these bacteria are not living in another organism, so it’s not as though they’re glowing in some sort of mutual trade with a host.

These bacteria only glow when they’re in large numbers, close together (quorum sensing), however. This gives a clue to what might being going on. A new paper by Zarubin and colleagues conducts several experiments to test the hypothesis that these deep sea bacteria are glowing because they want to be eaten.

You might think getting eaten is not a productive thing to do. The idea is: bacteria light up when they’re in large enough numbers to signal decent food. The bacteria themselves might not be the food, so much as the article they’re attached to.

The bacteria use the insides of their consumers as a way to disperse themselves throughout the ocean. It’s already been shown that a fairly large number of these glowing bacteria can survive passage through the gut. But that alone doesn’t provide enough a strong test of the hypothesis that the bacteria glow to advertise themselves as bait.

First, the team tested whether animals preferred glowing bacteria by putting two bags in a big tank of predators. One bag contained glowing bacteria; another contained same species, but with a mutation that prevented the glowing. Decapod and mysid crustaceans went almost all for the glowing bacteria. But it’s not a universal attractor; copepod crustaceans ignored both bags of bacteria.

Brine shrimp (Artemia) would start to glow after swimming in these bacteria, and their guts started to glow after the shrimp ate the bacteria.In the picture below, you can see Artemia in plain light, and after 30 seconds in the dark. The light is dim, but they do indeed glow.

There is a problem here, though: they switched the species eating the bacteria. They don’t say whether they tested if Artemia were attracted preferentially to the glowing bacteria. You can show a plausible chain of events, but to “close the loop” on this story, you’d have to use the same bacteria eaters all the way through. The authors justify this partly by convenience (Artemia are easy to rear in large numbers) and partly by saying that this allows them to see the effect better. Brine shrimp don’t have escape behaviour. Thus, this removed possible confounds of an interaction between the glowing and any movements caused by escape responses. They also say that one of the mysid species glows after contacting the bacteria. They don’t show data for that, or give any citations, however. Their convenience came at the cost of ecological plausibility.

The glowing Artemia are much more likely to be eaten by fish – about ten times more likely. They tested this by putting Artemia in tanks with ring-tailed cardinal fish (Apogon annularis, pictured), which is nocturnal. And after the cardinalfish eat these brine shrimp, the bacteria do fine. They make it all the way through the fish’s digestive system, and they make the resulting feces also glow (though probably not brightly). The authors also tested the feces of other bacteria eaters – the Artemia and mysids – and they also tend to glow.

What I’d like to see next is some indication of whether the zooplankton are getting any nutritional value from eating these bacteria. Are the bacterial consumers being tricked into wasting time consuming “empty calories” that will just pass through their guts without benefit? If so, why haven’t the zooplankton wised up to this? I mean, how embarrassing would it be to be punked by bacteria? Or is these a “selfish herd” sort of situation, where a small proportion of group members are lost, but the risk to individuals is so low? And is there any manipulation of the plankton behaviour by the bacteria, similar to the way large parasites often work?

Reference

Zarubin M, Belkin S, Ionescu M, Genin A. 2012. Bacterial bioluminescence as a lure for marine zooplankton and fish Proceedings of the National Academy of Sciences 109(3): 853-857. DOI: 10.1073/pnas.1116683109

Apogon annularis picture from here.

Jumping spiders still have use for muscles

You can’t push on a rope.

This is why you typically need two muscles to get things done. Muscles only shorten; if you flex a joint, you can’t expand your muscles to push that joint back to its original position. You have to pull a different muscle, with different insertion points, to get that limb back to where it was. For instance, you have biceps to flex your forearm, and triceps to extend it.

Spiders have always been something of a puzzle, because many of their limb joints have unpaired muscles. This is particularly true of the joints far from the body; the joints close to, and on, the body have more usual paired muscles.

On the face of it, this should mean that their joints should only be able to go int one direction. But spiders are agile predators and their limbs are moving back and forth rapidly.

Many spiders use hydraulic pressures to snap their limbs back into position after a muscle has moved it. This has been quite well investigated in a few small species, but Weihmann and colleagues reckoned it was worth re-investigating in a larger spider. They took a big spider species, Ancylomete concolor (pictured), and studied the forces the legs exerted when this spider jumped.

Some of the math and methodology is a little hairy (no pun intended), but this picture helps:

In short, if the spiders are using hydraulics (as small spiders do), the forces from the tip of the leg should be directed forward. If the spiders are mainly using the paired muscles in the joints close to the body, the forces should be directed much more upward.

Wiehmann and company find that their results are much more in line with the jump being powered by muscular contraction than hydraulic pumping. They’re not saying it’s entirely muscle, though, just that muscles are contributing more than the hydraulic factors.

The team briefly takes a stab at the bigger question: why mess around with all the hydraulics in the first place? Why do spiders not have paired muscles all the way through their legs, like sensible insects and crustaceans? Weihmann and company speculate that because spiders are obligate, active predators, that the loss of extensor muscles means that there’s more room for big, powerful flexord muscles – just the things to grab and grapple and subdue prey.

Reference

Weihmann T, Gunther M, Blickhan R. 2012. Hydraulic leg extension is not necessarily the main drive in large spiders. The Journal of Experimental Biology 215(4): 578-583. DOI: 10.1242/jeb.054585

Photo from here.

Reporting on that non peer reviewed stuff

Brian Kreuger writes about the recent media coverage of the latest findings on the arsenic life:

Reporting on data that has not gone through the peer review process as if it were truth is not responsible journalism.

I have also been shocked, shocked, I say, to see a paper deposited in arXiv being reported around the world by researchers and journalists alike. Nobody commented that it hadn't been accepted in a peer-reviewed journal.

Except I'm not talking about Rosie Redfield’s arsenic life paper.

I'm talking about the reports of faster than light neutrinos from OPERA.

Did we hear howls of outrage from the physics community over the coverage of the story? More like chirping crickets. Physicists were right there in the thick of the discussion.

This is an example of the differing cultures of the fields. Physics has developed a pre-print culture where people stake their claims with manuscripts. Biology has developed a culture where people stake their claims with final publications. But cultures change, and it’s individual cases like this one that provide a lot of the push to change.

Just because biologists normally only make findings public very near the last step in the publication change does not change that anything made public at any stage is fair game for reporting.

Dr. Redfield made her work public earlier than others would have done. Unusual, but I cannot see the ethical issue with reporting on information that she has voluntarily shared. Indeed, if her work does not pass peer review, the reporting that is going on right now can add context to that story.

For that matter, journalists have covered results presented at scientific conferences for decades. I have never heard serious suggestions that conference reporting is unethical.

The arsenic life story itself tells us that because a paper has been peer reviewed does not make it automatically credible to other researchers. Biologists on the whole weren't convinced by the claim.

The Zen of Presentations, Part 49: Buying credibility

Credibility, expertise, mastery of the subject, call it what you will: it consistently weighs heavily in separating great presentations from okay presentations.

True credibility is something you have to build. You have to develop a consistent track record of saying and doing smart things. It's a long, hard road to build that trust.

It's only natural that people look for short cuts.

Beginners and students, acutely aware of their own limitations of experience or knowledge, often to buy credibility. There's two common tricks that people try.

The first is to pull out the swanky clothes. This is not a terrible thing to do, since it usually helps make the speaker feel better and more confident. But if you are with audience members that know you, there might not be that big a bump in credibility. When I teach a seminar class, I can usually tell who is presenting that day, because they're dressed nothing like the way they've dressed in the previous month. Instead of track pants and hoodies, suddenly there are skirts and shirts that might comfortably hold a tie.

The second is to talk in a way that a person normally does not talk. This is nicely spelled out in this post about writing, but it's just as true for presentations (original emphasis):

(S)tudents tend to make the kind of mistakes in the formal research paper that they do not make in informal writing (such as blogs) that the sociolinguist William Labov found among working class speakers aspiring to be middle class: use of the word “whom” in situations where it is ungrammatical but sounds fancy, use of semantically incorrect but pretentious vocabulary (“Thesaurusitis”), longer sentences that lack punch but sound “upper class,” lack of demonstrative language, vague construction that lacks a point (“In this essay it shall be argued that...”).

A student giving a jargon filled talk is reacting much like a blue collar worker trying to fit in with a bunch of suits.

Of course, we know how this turns out. We've read this book and seen this movie: George Bernard Shaw's Pygmalion and its musical offspring, My Fair Lady. Henry Higgins tries to buy credibility for Eliza Doolittle by teaching her received English. But even as her pronunciation improves, she still gives herself away with every word she says.



You can fool some of the people some of the time when you try to buy credibility. But if the veneer scratches, even a little, things can fall apart almost immediately. This is particularly true in academic settings, where most of the audience has been highly trained to question, pry, be on the lookout for bullshit, find the weakness in the ideas and arguments, and attack any helpless underbelly.

When you try to buy credibility, the price you pay is in your authenticity. And I'd say that's also pretty important in giving a great presentation.

Related links

The Zen of Presentations, Part 37: What makes a good speaker?
Do you like me? Or any scientist?
The Zen of Presentations, Part 29: The shirt on your back

Comments for second half of January 2012

Back in 2011, Ed Yong and Jerry Coyne covered a paper on treehoppers helmets – here and here, respectively – that is now being disputed.

Scicurious defines neurotransmitter. I distinguish it from “neuromodulator.”

Drugmonkey reignites the great reference battle, which I covered here.

I make a brief cameo at Embargo Watch. Little did I know my little tweet about a dinosaur nest would ripple out to an interesting little story about publishing.

Jerry Coyne looks at open access, and somehow thinks this means “not peer reviewed.” Open access advocates, take note: people keep making it imply things that it does not (e.g., must be free to publish, must be non profit, etc.).

Neuroskeptic has a great summary of an article on face detection.

Texas passes the science test

The Austin American Statesman is reporting that Texas gets a passing grade for its K-12 science standards. It’s a C, to be exact. But who’s doing the grading? The Fordham Institute, which the article describes as a conservative think tank. The American Statesman article says:

“The high school biology course is exemplary in its choice and presentation of topics, including its thorough consideration of biological evolution,” according to the report being released today.

But the evaluation also found that evolution is largely absent from middle school and elementary grades, which means that “students are not prepared to learn what they need to learn at the high school level,” said Kathleen Porter-Magee, senior director of the High Quality Standards Project at the Fordham Institute.

The report for Texas is a short, readable four pages. And while the phrase “conservative think tank” conjures bad images of other institutions, this one does not sympathize with creationism or intelligent design. Here’s a clip (my emphasis):

(T)he seventh-grade standards mention the Galapagos finches, giving the impression that the Darwinian paradigm is being presented. Unfortunately, it is not. Instead, the example of the finch Geospiza fortis apparently refers to studies by Peter and Rosemary Grant on beak size in this species, made widely known by Jonathan Weiner’s Pulitzer Prize-winning book, The Beak of the Finch. Creationists often distort these important findings to argue that Darwinian macroevolution does not occur—instead, microevolution does.

The Austin American Statesman article continues:

Steven Schafersman, president of Texas Citizens for Science and a longtime critic of the board’s conservatives, said the Fordham analysis overlooked some glaring problems with Texas' standards.

He pointed to a separate examination from the National Center for Science Education that found Texas’ standards contain “creationist jargon” and “reflect political and religious agendas, rather than good pedagogy and strong science.”

There are reports for every state, here.

Tuesday Crustie: Ode to a sand crab

With two presentations on sand crabs this month (including one over the weekend, which went very well), sand crabs have been on my brain. Another thing that’s been on my brain is this quote from Martin Palmer in a presentation to the World Wildlife Fund late last year (hat tip to Randy Olson):

We never use a word unless you can show us a poem in which it’s been used. Because if people don’t love it enough to include it in a poem, it probably means it means nothing to them.

Because I want people to care about sand crabs, I found a poem that hung on the wall of the lab in graduate school. It was written about Emerita (Emerita analoga is pictured) rather than the Lepidopa benedicti which were the main focus of my talk, but what the heck.

Ode to a sand crab

A short ode to thee, my dear friend the crab
Whose life I once thought must be rather drab.
On the whole unexciting, most boring and bland
What joy could one find living life in the sand?

I walked by the shore and saw crabs by the score
And felt in my heart a great need to know more.
So I queried the crab, without being too forward
Of her constant displacement both seaward and shoreward.

She seemed quite surprised that I should inquire
Why crabs stay where they stay, rarely lower or higher.
We looked at each other eyeball to eyestalk,
And I listened intently as she started to talk.

“If we stray to high, we’re sure to be dried
So we make quite an effort to descend with the tide.
But with the fish in the surf, we must stay out of reach,
So we go with the tide when the tide moves upbeach.”

She went on with a sigh, “Ah, the things you should know.
You people, like crabs, should just go with the flow.
The waves bring us food, the sand’s a soft bed
We spend our time eating, preparing to shed.”

I pondered the crab and the crab’s view of fun,
Hiding out from the birds, and the fish, and the sun.
No family ties, no dad and no mum
And a diet consisting of diatom scum.

The difference between us is not so profound
My head’s in the air, and your head’s in the ground.
But Nature, I think, oft tends to repeat;
We all feed and respire, find mates, and excrete.

So what if my skin is so soft and you’re hardened,
You’d think such slight differences ought to be pardoned.
Where Nature’s concerned, there aren’t any norms
A life is a life, in all of its forms.

Paul Siegel, Ph.D.

University of California, Santa Barbara

1983

Shoot the hostage

The movie Speed opens with this memorable dialog between two cops:

Harry Temple: All right, pop quiz. Airport, gunman with one hostage. He’s using her for cover; he’s almost to a plane. You’re a hundred feet away... Jack?

Jack: Shoot the hostage.

The strategy of some scientists to take down for profit publishers, notably Elsevier, keeps edging closer to shooting the hostage. Do anything that is bad for Elsevier, even if a few other researchers get harmed along the way.

The Cost of Knowledge website is gaining traction with its call to not “support” Elsevier journals. Jonathan Eisen went even further towards the “shooting the hostage” strategy. He suggested that scientists not “promote” any article in an Elsevier journal: no blogging, no tweeting, no journal club. He was convinced otherwise, as you’ll see by visiting the post. I complement Jonathan for considering other points of view.

You won’t find my name on that boycott list - yet. I’ve written before that I don’t think it’s fair to refuse to review a paper because I don’t like the journal. (Besides, if I put my name on the list but then reviewed for an Elsevier journals, who would know? Reviews are typically confidential.) I still think the best strategy is slow strangulation. Do not submit papers to those journals. Convince colleagues that there are better venues than those journals.

Shooting the hostage makes for great drama, but such a single-minded “get the bad guy by any means necessary” approach may not be desirable. There’s a reason cops don’t shoot hostages outside of action movies.

Related posts

Pressuring journals you dislike

The Zen of Presentations, Part 48: Funny or die?

To hear a lot of people talk, you’d think telling a joke was as deadly as juggling a chainsaw.

Presenters are often told, “Don’t try to be funny.” This is bizarre to me, given that humour is one of the most often cited features of a good presentation. The thinking seems to be that failed humour is a dangerous thing to a speaker. What is at risk when you use humour? People might not laugh.

There’s two responses to that. First, people not laughing is not dangerous. It might deflate your ego a bit. But it’s not as though if a joke lands wrong, it could take your hand clean off!

And if you hadn’t told the joke? People definitely will not laugh. You have the same outcome with or without the joke.

Second, just because people do not laugh out loud at your joke does not necessarily mean they are not enjoying themselves. Sometimes they may just smile. Their smiles may not be big grins. Not everyone in the room may smile. It can be difficult to pick up those cues that people are enjoying the humour, particularly if you’re in a big room, or a dark room, and so on. Even if you’re not getting the audible laughs, you can still have a room full of people who are much more pleased with your presentation than if you didn’t make the effort.

If you tell a joke and it doesn’t work, and you panic, that is not a problem that comes from telling a joke. That is a problem that comes from poor preparation. Lack of preparation can make a talk brittle, and a presenter unable to cope with even slight deviations from plan.

If you’re not comfortable with humour in the sense of telling jokes, think of humour as used in the phrase “good humoured.” Even if you don’t deliberately say funny things, you could at least smile.

Related posts

The Zen of Presentations, Part 5: Legalized insanity
The Zen of Presentations, Part 37: What makes a good speaker?
The Zen of Presentations, Part 38: What you say vs. what they remember

External links

Live notetaking from the “Science humour” session at Science Online 2012 by Perrin Ireland.



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

Hat tip to Christie Wilcox (here and here).