Storytelling in science, part 2

Earlier this week, I commented about the importance of stories, and how denialists of science have a lock on the “little guy fighting the establishment” story. I mused about what the counter story is to that.

As much as I hate to suggest this, I think I have one.

Zombie apocalypse.

You face an world of dangers that are slow and stupid but many and unrelenting. You have limited resources. If you let your guard down, that’s it. If you don’t have the weapons and some knowledge and a little technology, you’re done.

The zombies are the natural world, always throwing up little surprises like a new strain of H1N1 virus. We are finding out to our peril that some of our resources really are limited, or pose their own threat, like fossil fuels.

Scientists?

We’re the ones with shotguns and a stash of shells, baby.


We have decided to fight and we might just be able to help a lot of other people. When the shit hits the fan, the chips are down, you want scientists on your side, because they just might be the only thing standing between you and a a messy end.

(And for the record, I repeat: I hate zombie fiction! But happy Hallowe’en weekend, anyway!)

Picture from here. And yes, I put this up in full knowledge that I will never be one tiny fraction of that bad-ass.

Earning it versus enforcing it

I wonder if students realize how deflating it is for their instructor when, in a class with 20 registered students, only three students show up on time for the start of the class after a couple of months.

Some would say that I haven’t earned the student’s attention, and that I haven’t put in enough effort to make the class so completely engaging that my students couldn’t imagine being any place else three days a week at 8:45 am besides my classroom.

But you know, I can only juggle chainsaws for so long.

Laura Bergalls, over at More Than PowerPoint, talked about the need to earn attention:

A modern audience uses modern tools. As a presenter, I need to learn to adapt my style to fit their needs. Why should the audience have to pacify my selfish needs for their attention? Why should I force my audience to stop using tools that let them learn and share information?

Indeed, Olivia Mitchell encourages presenters to embrace things like Twitter.

As a presenter, I agree. As an educator, I am torn over this.

On the one hand, I do try to make a talk something that is enjoyable rather than painful, and I do want to earn that attention.

On the other hand... What if I have evidence that laptop use in class hurts student performance? (There is.) That multitasking hurts learning? Should I just let them have their laptops running (and let everyone fight over the two or three seats in the room near a power outlet)?

I think doing nothing in that case is irresponsible of me as an educator. It makes me feel that I have given in to the wasteful “sink or swim” teaching technique, where absolutely everyone is on their own for everything at all times. As an educator, I don’t think it’s selfish of me to make a student aware of behaviours that are not productive to their learning. “I notice you haven’t been in class much” or reminding students to turn off their phones or even banning laptops are ways to try enforcing attention. I wonder if they are occasionally necessary to use in an educational setting, even as I try my damnedest to earn their attention.

Storytelling in science

When I saw the silent film version of The Lost World, I was amazed at how it set the template for monster movies for decades. Watch The Lost World, and you can see the mold being set for King Kong, The Beast from 20,000 Fathoms, Godzilla, Varan the Unbelievable, Valley of the Gwangi, Gorgo, Cloverfield, and on the list goes.

It’s something that Randy Olson talks about in Don’t be Such A Scientist (which I reviewed here): there are a few really strong story narratives that we love to hear over and over again. If you want to have an audience for your science, it helps to know what those are, and tell people a story they want to hear.

I’ve had questions have been bugging me about this. First, why do we seem to have such a limited range of narratives that resonate and stick with us? Why do we love hearing the same basic story over and over again? Can we create new stories that are as powerful as the “hero’s journey”?

Second, do stories have opposites?

I think I need some examples to explain that question.

I read once a claim that any effective messages in advertising or branding has an opposite. If one business advertises low prices, its competitor sells quality. If one corporation pitches itself as family friendly, the other says, “Grow up.”

A recent post on the Respectful Insolence blog talked about a dubious magazine article, and blogger Orac noted:

Journalists do so love that cliché, don't they? It's an irresistable (sic) hook, cliché or not. People love reading about issues that we thought to be true but – surprise! surprise! – turn out not to be true. ... Framing an issue as arguing that conventional wisdom is wrong and highlighting a couple of “lone voices in the wilderness” warning, Cassandra-like, of impending disaster represent a time-honored journalistic trope, not to mention a story structure that goes back thousands of years to, well, Cassandra at least.

Same analysis over at Effect Measure:

Our main point was that it was a straw man argument built around the narrative device of the brave, mavericky truth teller who is shunned by colleagues and has to eat alone at conferences.

The “I’m an oppressed little guy fighting against a hide-bound establishment” is a story that you see when you look at denialists of all stripes.

What’s the counter-story? If the denialists are able to get such mileage out of claiming that they are oppressed by an evil conspiracy (even when they’re not), surely there’s some story that can be used to illustrate the slow, hard-won accumulation of evidence that is the way most science progresses.

Tuesday Crustie: Peek-a-boo!

Hermit crab (Pagurus bernhardus).

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

The princess and the perfume, a hermit crab fairy tale

Once upon a time, there lived a princess in a far away land. The princess was young and fair, and this drew the attention of a knight. Though the knight was strong, the princess loved him not.

Enraged, the knight captured the princess and held her in his castle, and told her cruelly that they would soon be wed.

The princess was not strong enough to escape the knight, though she tried many times. Still the knight kept her, guarded in his castle.

But though the princess was not powerful or strong, she was clever. She realized that while she may never be strong enough to defeat the cruel knight, surely there was someone else in the kingdom who was powerful enough to defeat the knight. But how could she find a champion?

Feigning interest, the princess told the knight she wanted to create a perfume, whose wonderful scent would mark her wedding day. The knight eagerly supplied her with all she requested, and with that, the princess created a magic perfume.

From the highest tower of the knight’s castle, the princess let her magic perfume be carried by the winds throughout the kingdom, knowing that strong men who caught the scent would be compelled to follow it back to the castle and challenge the knight...

---

Male hermit crabs often get what they want by being bullies. Males of the species Pagurus filholi (pictured) attempt to monopolize mating access to females by guarding the females, often for several days. Females are not physically able to challenge the males, so what can they do to ensure that they have the opportunity to mate with the fittest males? Okamura and Goshima suggest that the females incite a riot among rival males by releasing pheromones into the water.

This paper contains six short experiments. Several revolve around using “pheromone water,” which is just water that an female unmated female had been kept in; the actual chemicals that might be involved in the signal are unknown.

The authors also made simulacra of guarding pairs by using a live male, gluing a typical shell that a female might have, onto the male’s claw, which is apparently a pretty good visual imitation. To get the smell right, they stuffed the “female” shell with cotton batting containing seawater or some variation of the “pheromone water.”

In the first two experiments, they show that more fights break out when a guarding pair of crabs, or a reasonable simulacrum thereof, is introduced into a collection of males than if a lone male is introduced. Males will normally fight, but if there are chemicals indicating there is a guarded female around, they will fight longer, which is the main evidence for a female pheromone that encourages male competition.

The third experiment tries to ascertain which sensory cues the males are using to detect guarding pairs. If able to see, the males are more likely to be aggressive if there is also a pheromone cue in the water. They found no difference between sewater scent and putative pheromone, however, if the non-guarding males were blinded before the imitation guarding pair was introduced. The blinding of the males makes this experiment difficult to interpret, because they literally cut the eyes off. It would be a cleaner experiment if the effect was reversible (say, by temporarily painting the eyes with something opaque), so it could be tested if the same animals that did not respond when blinded would then respond if they could see. Also, there is an error in the text for this experiment: the words say an effect is not significant, but the statistics listed says it is.

The crucial experiment is the fourth. When there is water from an unmated female is introduced into a tank, males fight longer than if sea water, or water from a mated female (one with eggs) is introduced into the tank.

The last couple of experiments are “dotting the Is and crossing the Ts” experiments. Experiment five tests responses of lone males to just the pheromone-containing water, and finds guarding of uninhabited shells increases when males are exposed to pheromone water compared to sea water. It seems that there is a greater response to pheromone water collected from a guarding pair than a female that had been guarded, but was not guarded at the time the water was collected. Again, it is a little difficult to interpret, because there are three treatments, the text is a bit ambiguous as two which treatments differ from the others.

The final experiment shows that when fighting breaks out between males, the biggest males tend to win, and take over the “guarding” position of the female. No surprise there, as body size is almost always the major factor determining fight outcomes in crustaceans.

That there are so many short experiments makes me a little annoyed that the standard journal practice of separating methods and results means that there is much flipping back and forth between the two. It would be much more readable if each experiment was discussed in total, in on part of the text.

This is a very interesting social system where it seems that the females are both powerless and powerful. They are powerless in the literal sense that they cannot resist being guarded by males. But they are powerful in the sense that they encourage and exploit male aggression, presumably in an attempt to ensure they are guarded by the highest quality males.

Reference

Okamura, S., & Goshima, S. (2009). Indirect female choice mediated by sex pheromones in the hermit crab Pagurus filholi Journal of Ethology DOI: 10.1007/s10164-009-0188-2

Photo from here.

Reading Week panel on Darwin

Last night, I had the fun of participating in a panel discussion at a local community college for their reading week. The organizer had picked evolution as the theme, because we are nearing the 150^th anniversary of the publication of On the Origin of Species.

To my surprise and delight, the auditorium was packed.

This did cause us to start quite a bit late, as the organizer was fretting about the possibility of us violating a fire code, and set off to find more chairs. But spirits were so good! In his introduction, organizer Jerry Freeman mentioned some video on the net* where people were singing “Happy Birthday” on Darwin Day, and somebody started singing it, and the audience joined in for an impromptu birthday song to Charles Darwin.

I was the first speaker, and I talked a bit about all the fantastic transitional fossils that have been found in the last 150 years, how we’ve got a much better handle on genetics and heredity and DNA, and how we’ve developed methods to assemble and test phylogenetic trees, which have allowed us to make trees like this.

Because this was Reading Week, I was asked to read a little evolutionary writing, and I though reading something from Origin was too obvious. Instead, I picked a favourite paragraph from the last page of Stephen Jay Gould’s magnum opus, The Structure of Evolutionary Theory, about what evolutionary biology would be like if Darwin had not existed:

(W)e would have experienced the same biological revolution without the stunning clarity, illustrated by wonderfully apposite metaphors, of a complex central logic so brilliantly formulated, and so bristling with implications extending nearly forever outward, at least well past our current reckoning. In this alternate world, we would probably be honoring a different and far less compelling founder by occasional visits to a statue in a musty pantheon, and not by constant dialogue with a man whose ideas live, breath, challenge, taunt, and inspire us every day of our lives, more than a century after his bones came to rest on a cathedral floor at the foot of whatever persists in the material being of Isaac Newton.

I was followed by a talk on evolutionary thinking as related to human sex and aggression, and a philosophical one on how Darwin’s ideas had changed our sense of telos, or purpose.

The audience made it awesome on a stick. Awesome on a stick dipped in chocolate.

Thanks to all who attended.

* I think he might have been thinking of this one.

Tuesday Crustie: Take me to your leader

A porcelain crab, Petrolisthes elongatus. The photographer titled it, "The face of the alien," and more than a few aliens in old movies did look very crustacean inspired.

Picture by user Nuytsia@Tas on Flickr. Used under a Creative Commons license.

Looking at the genitals of naked mole rats

Since Heterocephalus glaber are naked mole rats, they shouldn’t mind anyone looking at their sex organs, right? I mean, they’re naked, so it’s not like they’re ashamed or anything.

Seney and colleagues noticed that male and female naked mole rats had very similar looking sex organs. Naked mole rats happen to be famous for having a social system that is very much like social insects, with normally a single reproductive adult female and non-reproductive workers. They wondered if this unsual similarity might be related to the social structure of the mole rats.

Rufus notwithstanding (below), naked mole rats are obliged to live in social colonies, and will die if alone, so they couldn’t really do an experiment. Instead, they went looking for another species that showed some similar social features, and found the Damaraland mole-rat (Fukomys damarensis). It also lives in colonies, but the colonies are smaller, meaning more individuals, on average, reproduce. Seney and colleague predicted that the Damaraland mole-rat should have genitals that were more similar in males and females that other, non-social mole rats.

In short, that’s pretty much what they found. Out of six features they authors examined, the Damaraland mole-rat resembled the non-social mole rats on three measures, the naked mole rats on one, and sat in the middle on two.

Interpreting these results hinges upon the relatedness of these species. The authors note that sociality has either evolved more than once, or been lost more than once within the family. The authors argue that the naked and Damaraland mole rats “seem” to have evolved sociality separately, but the information presented in this paper don’t do a great job of convincing here.

The authors also note that the naked mole rat situation seems to be the reverse situation to hyenas. Hyenas also have very similar genitals, but this seems to be because the females’ genitals have been masculinized to resemble the males’. Here, the males’ genitals seem to be feminized to resemble the females’. It’s not at all clear, however, what the relevant selection pressure, or lack thereof, is that is creating similar genitals. It’s slightly surprising that even the “king” males in a naked mole rat colony, that actually do breed, stills has genitals that resemble the females.


Reference

Seney, M., Kelly, D., Goldman, B., Šumbera, R., & Forger, N. (2009). Social Structure Predicts Genital Morphology in African Mole-Rats PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007477

A doubting collection of blog posts

A new blogging anthology is planned for early next year: the Skeptical Blog Anthology. You can find more details, and a link to a submission form, here.

Warrior caste

Does the difficulty of reverse evolution mean evolution is impossible?

My recent post on reverse evolution included some recent work by Joe Thornton. I was not aware that his work had been discussed in the context of creationism. Thornton’s response and description of his work has gone up at Carl Zimmer’s blog, The Loom.

Should we give up anonymous reviewing?

Has anonymity ever elevated the level of discourse?

A recent blog post describes the toxic effect of anonymous online chatter on a conference:

I felt sorry for the conference organizers, who were obviously reading the BackNoise chatter. They started out the day with enthusiasm, energy and confidence. They visibly sagged as the day wore on, making almost apologetic comments to the audience in between speakers.

It reminded me of famed British anatomist Richard Owen.

Owen was, by all accounts, a real piece of work. He was undeniably brilliant, tutor to royalty, critical in establishing institutions like the British Museum, but he was also just plain nasty.

Owen wrote a review of On the Origin of Species by Charles Darwin that proves that snarkiness was invented long before the 20^th century. Most famously, Owen talked about his own work but feigned objectivity by writing about himself in the third person:

In his last published work Professor Owen does not hesitate to state ‘that perhaps the most important and significant result of palæontological research has been the establishment of the axiom of the continuous operation of the ordained becoming of living things.’

Indeed, Owen’s review has a lot of the sort of backchannel nastiness that prompted Stacy Williams to write the post that started us off. Owen was able to do this because at the time, book reviews were published anonymously, for reasons that sound fine in theory: “The reviewer has to feel absolutely free to say anything.” Eventually, the practice of anonymous scientific book reviews faded for reasons that I haven’t been able to trace.

To this day, however, review of technical papers are almost always anonymous to the authors of the article being reviewed. Even journals that argue that they are trying to do science publishing in a new way, like the PLoS family of journals, keep peer review anonymous. The argument is the same as used to be used for book reviews: “The reviewer has to feel absolutely free to say anything.” Stories like Owen’s review and the effect of anonymous and pseudonymous writing on the internet suggests anonymity is more likely to breed invective than constructive criticism.

Arguments for keeping reviews anonymous include that a slighted author may take some sort of revenge against a negative reviewer. Is there anyone in a research field who is so powerful that they can completely prevent a researcher from publishing in all journals and prevent someone from getting any funding?

The scientific community is no longer a clique of wealthy Victorian gentlemen publishing in a scarce number of journals, where angering the wrong people could block you from publication. If privacy is dead, maybe anonymity should join it.

Geek space

From Finite Attention Span.

Retracting a paper when the science is sound

The most recent issue of PNAS has an editorial explaining why they required a paper that appeared online to be retracted. It’s a situation that is, as far as I can tell, without a clear precedent.

The paper, which has four authors, was published online at the end of August. Apparently unbeknownst to some of the other authors, one author signed an agreement with the National Institutes of Health (NIH) not to publish data arising from the project until near the end of September.

Nobody is denying that there’s a problem here. But was retraction the best or only option?

Retraction is a serious business. It is a formal expunging of a paper from the scientific record. In theory, that paper should never be cited. It’s all very mannered and Victorian: “We shall never speak of this again.”

Previously, when I’ve seen papers retracted, it’s usually been due to a problem with the science, where questions have been raised about the truth of the data (due to error or scientific naughtiness). Occasionally, there has been some other sort of weirdness that has resulted in retraction, but in all cases, only two parties have been involved: the authors and the editors.

This situation adds a strange new wrinkle: the ethical violation involves a third party. And as Newtonian physicists learned, three body problems can be insanely difficult. There are many questions arising from this action.

Nobody is questioning the science presented in the paper. Because retraction was usually reserved for papers that were wrong, it ensured the scientific record remained free of known error. That purpose is not served by retraction here.

Can this paper be published in another journal at a later time? Retracting a paper for an ethical violation other than those related to the integrity of the data or text is so rare that I have no idea if there will be any issues with trying to publish the results elsewhere later.

Only one author signed off on the embargo, but three more people are suffering the consequences of the retraction. This seems to be an offshoot of the standards for authorship established by journal editors: Every author is responsible for every claim in the paper equally. Authorship conveys equal responsibility for everything in the paper.

Except that again, the problem is not with the text. The problem is with an agreement entered into with a third party. If NIH’s policy is being violated, shouldn’t NIH be the one responsible for enforcing any consequences of breaking embargo rather than the journal? Maybe this journal’s action was requested by NIH, but if so, the editorial doesn’t say.

The whole situation seems analogous to someone not paying his power bills and having his car, and the cars of his business partners, repossessed.

The editorial course of action seems unsatisfying. The Adventures in Ethics and Science blog raised a similar point. It seems that when dealing with scientific misconduct, there are only two options: a slap on the wrist or the firing squad. That, I think, is the heart of the problem. Editors have an limited range of tools to deal with ethical violations. The editors can either “wag their finger” at the authors, which could be seen as complicity with an ethical violation, or retract the paper, which could be seen as swatting a fly with a hammer.

I’m all for dead flies, but I hate the holes in the wall. There’s got to be room for sanctions that are less destructive.

Update, March 2010: The Embargo Watch blog follows up on this story.

Reference

Schekman, R. (2009). PNAS takes action regarding breach of NIH embargo policy on a PNAS paper Proceedings of the National Academy of Sciences, 106 (40), 16893-16893 DOI: 10.1073/pnas.0910317106

Comments for first half of October, 2009

Over at Neurotopia, I talk a bit about whether PLoS One is really as accepting of negative results as they claim to be.

People don’t recognize Chewbacca? Reminds me of when Anita made the mistake of mentioning tribbles in class.

I get all pedantic on poor Olivia Mitchell for a neuromyth about reptile brains.

Problems of reality or perception?

Randy Olson often says scientists are handicapped by their blind obsession with the truth.

Rory Sutherland puts it this way:

And this shows that engineers, medical people, scientific people, have an obsession with solving the problems of reality. When actually most problems, once you reach a basic level of wealth in society, most problems are actually problems of perception.

I love that quote, but you should do yourself a favour and watch his whole TED talk. It is brilliant.

And I’m not just saying that because it features Shreddies. (Homesickness trigger.)

Everybody click the tortoise!

In mid-July, a preprint about stickleback size appeared in the journal Evolution.

In August, I wrote a post about it.

Now, a new column in SEED magazine has some material from that post. It also refers (and links to) my more recent post on Komodo dragons. And it’s featured even on the home page! Check out “Evolved for extinction.”

Typecasting someone with an identity crisis

I occasionally ponder what my scientific discipline is. It’s one of my Science Scout badges.

If you’re a reader of this blog, you’d probably think I’m mostly an evolutionary biologist. That’s what I write about most here.

My institution hired me as a neurobiologist, and that’s the key class I teach.

Editors seem to think I’m a carcinologist. Of the half-dozen papers I’ve been asked to review for journals in the last few years, every single one has been a crustacean paper. Despite that I have five peer-reviewed publications on non-crustaceans, I seem to be getting these taxon specific papers. They usually but not always have some behavioural or neuronal element, which does make sense, because my research is about nervous systems and behaviour.

I feel like an actor who’s been typecast. “You keep sending me these comedy parts, but I can do drama! Don’t deny the world my definitive Macbeth!” I keep getting sent crustie papers, but I’m egotistical enough to think I can review a much wider range of stuff.

Fellow scientists, do you mostly get asked to review papers that feature the organism that you study, regardless of the intellectual problem? Or am I reading too much into this?

$1.75 million dollars

My institution just put up a press release was just issued concerning the Title V grant I mentioned almost two weeks ago.

Graduate School awarded $1.75 million to transform graduate education - UTPA News

I should explain that the shirt was not in reference to the grant. It was the promo shirt made my the Office of Graduate Studies to promote all the graduate programs here. I joked with Sylvia (right) during the photo shoot that I was “appearing in uniform.”

Shared via AddThis

Tuesday Crustie: Red mantis

I suspect stomatopods, also known as mantis shrimp, like this Gonodactyllaceus randalli, will get more than their fair share of representation in this feature. They have the most complex eyes in the animal kingdom, and no doubt is that is partly because they are looking at each other. Amazing colours, with reflection in the parts of the spectrum that humans can’t detect, and patterns using polarized light that humans are insensitive to.

By user prilfish on FLickr, used under a Creative Commons license.

Face it: Being a scientist can really rock

Last week, I wrote a post about how many obstacles there are to creating a research career. My colleague Dr. Farris rightfully took me to task, asking, “Seriously though, in how many other ways does this job rock?”

And, as if on cue, I learn that CNN Money has a list of the best jobs in the U.S., and lists “professor” as #3. (Their clichéd choice of picture annoys me, though: A tweed coat?)

The major benefit of the job that is listed is one I heartily agree with: freedom. In fact, it’s so far ahead of everything else that the other listed advantages look utterly lame. Does anyone enter a career for a free gym memberships and a library card?

Not all scientists are academics, and the freedom academics enjoy are perhaps not as great as for people working in industry or government. But there’s still great things about being a scientist.

You get to work with a lot of very, very smart people. It’s fantastic to be around people who are smart. They bring up your game, keep you honest, and help you catch mistakes before you make them.

Many of us are fortunate enough to travel as part of the job. Conferences are often held in great locations. Some of us get lucky enough to live in places we wouldn’t otherwise have had a chance to experience, for degrees or post-docs.

You get the satisfaction of making a contribution, particularly a long-term contribution. One researcher I talked to at the U.S. Department of Agriculture said how much he enjoyed solving real, tangible, immediate problems on a daily basis. It’s the same generosity and desire to help that leads people to be firemen, police, or audition for the Legion of Super-Heroes, but with less physical danger and a more relaxed dress code. (Though there are some scientists who would look spiffing in a cape.)

Being able to say that you made a permanent contribution to your field, or permanently solving a problem, is probably one of the more satisfying about being a scientist. Yes, it’s long, tedious hard work to find out new truths about nature, but once you’ve got it... it’s there for keeps.

Photo by user Sacrifice_87 on Flickr, used under a Creative Commons license.

Technology that fugitives should not use

(Emphasis added.)

Face it: Being a scientist can really suck

There’s a refreshingly honest quote in this blog post, to which I’ve added some emphasis:

“People were questioning why there weren’t more women in science, and I had to point out that we are not going to be banging down the doors to enter a profession that just sounds so awful,” said Wu, who just completed her doctorate at the Pratt School of Engineering at Duke.

The article goes on to talk about the importance of peers, time management, and stereotype threat, all the while ignoring the elephant in the room:

Science careers don’t have a lot going for them.

We have this weird Jekyll and Hyde relationship with young scientists. We tell them over and over that we want more people to enter technical careers. But then we sip the potion, and unleash upon them academic hazing rituals that go on for over a decade.

As another example, I just read an article by Villarejo and colleagues that looked at the development of students’ career interests and decisions. There’s much to be learned in this study, but there is an interesting moment. Here, the authors are Dr. Jekyll:

One novel finding of this study that deserves attention is that many individuals who chose careers as biomedical Ph.D.s had serious misgivings about the practical disadvantages of their career choice, in terms of balancing work and family and the financial insecurity they see as endemic to a career as a science researcher. Although they persevered despite these concerns, the same characteristics repelled others.

Now watch them sip the potion in the very next sentence...

Future studies should explore the personal characteristics that allow some individuals to pursue research careers despite the obvious drawbacks.

Suddenly, BAM! You’re dealing with Mr. Hyde!

Rather than what you might think would be a message to try to address real, recognized problem problems with the scientific career path, they argue for doing a better job of selecting the brave and crazy who succeed by pushing through the pain barrier.

It’s crazy.

The paper lists things that made science careers unappealing:

• Difficulty of getting a good job


• Other jobs pay better


• Getting a Ph.D. takes too long


• Lack of sensitivity to family concerns

No real surprises in that list.

BenchFly blog had a very similar take on completion rates for doctoral programs:

From the statistics, the article goes on to conclude:

“These data underscore the need to pick a graduate school wisely.”

REALLY?! That’s what those data mean? Not, why have less than 60% of students obtained a Ph.D. in under a decade?! Not is a 24 to 34% dropout rate acceptable?! ...

(I)n the bigger picture, this feels like a doctor telling a boxer “The solution for your headaches is Alleve” instead of “stop getting punched in the head.”

The problem with fixing this problem is that it’s about widespread cultural assumptions, which are invisible to most people. It’s like asking back in the 1950s, “How do you make sexism go away?” Many people then wouldn’t agree that it was a problem.

People who want to be scientists are not stupid.

Students in research labs look around them. They don’t see prospects for a lot of money for them. They see post docs in holding patterns, eking out a low pay existence. They see supervisors who spend huge amounts of time writing and administering grants, not doing science. And, perhaps more than anything else, they see people working their arms to the bone.

If anyone is being stupid, it some of us who are in the field now, since we seem to be the ones who are unwilling and unable to acknowledge this.

Additional: Lest you think all is gloomy, make sure to check out the follow-up post.

Reference

Villarejo, M., Barlow, A., Kogan, D., Veazey, B., & Sweeney, J. (2008). Encouraging Minority Undergraduates to Choose Science Careers: Career Paths Survey Results Cell Biology Education, 7 (4), 394-409 DOI: 10.1187/cbe.08-04-0018

Humans do not have reptile brains

A neuro myth needs busting. Again.

At the Speaking About Presenting blog, Olivia Mitchell trots out the idea that we have a three part brain: an old, primitive reptilian brain, a mid brain, and a new brain. I am about to go over and be a pedant and leave a comment that while it’s a great story, it is wrong.

Yeah, I know, there I go with that blind obsession with the truth again.

I wrote a comment on the All In The Mind Blog about this, which I reused on this blog here, but I’ll save you all the bother of clicking the link and just repost it.

The basic premise discussed in this show – that human behaviour has an evolutionary history – is not terribly contentious. The specific model discussed in the program, Paul MacLean’s “triune brain,” is more problematic.

As typically expressed, MacLean’s model suggests that entire reptilian brain has been conserved through the evolution of the mammals, with new brain regions essentially added on to the existing core, like suburbs being added to a city.

There are a few problems with this model.

First, MacLean’s ideas seem to be highly influenced by old ideas that emphasized the “march of progress“ or the “great chain of being.” In particular, the MacLean model seems to be based on the notion that reptiles were the ancestors of mammals. It’s debatable whether reptiles are the ancestors of mammals, however. It may be that the two groups shared a common ancestor, then diverged. It's also somewhat misleading in that it lumps all reptiles together. Snakes, for instance, appear much later in the fossil record than the earliest mammals.

Second, the suggestion that the entire reptile brain is essentially the mammalian hind brain is not supported by modern neuroanatomy. To give an example, in MacLean's model, the limbic system is characterized as a “lower mammalian” part of the brain. There is evidence, however, that reptiles have a limbic system (Bruce and Neary, 1995; Lanuza et al., 1998).

MacLean’s “triune brain” hypothesis may have caught the popular imagination, but it has not proved useful in modern neurobiology.

References

Bruce LL, Neary TJ. 1995. The limbic system of tetrapods: A comparative analysis of cortical and amygdalar populations. Brain, Behavior and Evolution 46(4-5): 224-234.

Lanuza E, Belekhova M, Martinez-Marcos A, Font C, Martinez-Garcia F. 1998. Identification of the reptilian basolateral amygdala: an anatomical investigation of the afferents to the posterior dorsal ventricular ridge of the lizard Podarcis hispanica. European Journal of Neuroscience 10(11): 3517-3534.

Look at all the nines! And all the zeros!

Was checking out the new NeuroDojo icon I’d made for Research Blogging at 3:14 pm on 7 October and saw this...


Which led to a flurry of refreshes in hopes I could catch this...


At about 3:30 pm today.

Hooray!

Valley life explained graphically

This morning I found a site called TrendsMap that breaks Twitter trends out by region.

The birth of dragons

The story goes that cartographers would write, “Here be dragons,” on the places of the map where they had no information. This would only be true in a few areas of the world, namely a few islands in the south Pacific, where Komodo dragons live.

As I talked about in an earlier post, weird things happen to the size of species on islands. Big species get small. Small species get big.

And if there’s one thing that people know about Komodo dragons, it’s that they’re big. It wouldn’t surprise me if Komodo dragons feature on a Trivial Pursuit card somewhere: “What is the largest lizard in the world?” They are the biggest, which means they’re the sort of animal that most people know about, so interested are we with extremes, particularly large extremes. Yet despite this, Komodo dragons were featured on the cover of Last Chance to See by Douglas Adams and Mark Carwadine as an endangered species.

Are all these things – living on islands, the large size, the small range the animals occupy – all connected somehow? That is, did Komodo dragons start out as Komodo wyverns (small dragons) and evolve large size because they were on these small islands? Alternately, did Komodo dragons evolve from “Widely distributed South Pacific” dragons, meaning they were just big from the start?

A new paper by Hucknall and colleagues tries to tease out these possibilities, and suggests that the Komodo dragons’ island home isn’t all that related to their size.

Hucknall and company get to say, “We have the fossils. We win.”

Somewhat to my surprise, Komodo dragons have a fossil record that goes back a good long while. The authors here have fossil going back almost a million years, in fact. Most of this paper is classic comparative vertebrate anatomy; lots of notes of condyles and grooves and the like.

These Kododo dragon fossils are found not just on smallish islands where the species lives now... but on mainland Australia. And the ones in Australia are actually the oldest fossils. Because these fossils are recognizable as the same species, and the fossil timeline starts on the mainland and continues to the islands, the evidence does not support a scenario where the ancestors of the Komodos were little dwarfs that got bigger once they reached the islands.

This paper goes on to analyze several other fossil species, including one unnamed new species. They are all big. Interestingly, one old lineage occurs on mainland Asia, quite some distance from Australia, indicating that this particular line of very large lizards was very widespread across the Old World. This particular paper doesn’t address where the group might have originated form in the first place.

The sad news is that the range, population, and number of species of these lizards are all ghosts of their former selves. We value these animals enough that they will probably be kept in zoos indefinitely, but it would be a shame if that became the only place they lived.

Reference

Hocknull, S., Piper, P., van den Bergh, G., Due, R., Morwood, M., & Kurniawan, I. (2009). Dragon's Paradise Lost: Palaeobiogeography, Evolution and Extinction of the Largest-Ever Terrestrial Lizards (Varanidae) PLoS ONE, 4 (9) DOI: 10.1371/journal.pone.0007241

Tuesday Crustie: Look to the right...

A dotillid crab, Ilyoplax pusilla. From Toho University Tokyo Bay Ecosystem Research Center.

Evolution back and forth, from snakes to molecules

“Progress” and “evolution” are inextricably linked in many people’s minds. Evolution is always moving forward. From molecules to cells to invertebrates to vertebrates; from fish to reptiles to mammals to us. There’s a lot wrong with those ideas, but the underlying question is worth asking: Can organisms go back the way they came?

Louis Dollo thought not. He suggested that once a feature was lost in a lineage, it could never be regained. Enough people agreed with this suggestion that it became known as “Dollo’s Law.” A couple of recent papers address whether Dollo’s suggestion was a correct one.

The first paper, by Lynch and Wagner, tests Dollo’s Law at the organismal level. It follows previous suggestions that reptiles have flip-flopping between egg-bearing and live birth. These were only suggestive, because scenarios with no reversals were just about as likely as those without.

The boa family Boidae may provide a strong test of whether evolutionary zig-zagging occurred with egg-bearing. Boas generally give birth to live young, but two do not.

It is possible that these egg-layers were the earliest species to branch off from the rest of the family, which then evolved live-birth, but if so, there should be a raft of other features marking them as very divergent from all other boas.

As is typical now, most of the features examined are DNA. Much of this paper details relationships between many genera of boas, with the specific question about egg-laying being a rather small cookie in what is obviously a much bigger systematic meal. Disappointingly, one of the two-egg-laying boas, Eyrx muelleri (pictured), is not included in this analysis.

The genus Eryx is not an early branch within the boa family, however. The one egg-laying species examined here, Eryx jayakari, is nestled firmly in the middle of the boa family tree, which strongly indicates that its ancestors were live-bearing boas.

Showing that reversals happened does not answer why or how they happened. Lynch and Wagner do discuss some of the selective pressures that may have led to these particular species re-evolving egg-laying. Both live in desert environments, which could be a key factor in what led to the loss of live birth.

A major question for understanding reversals is just how similar the re-evolved feature is to the original. To qualify as a true reversal, the similarities would have to be very extensive and detailed. Otherwise, this may not be a case of reversal, but of convergence instead. The authors note that other snakes have a small tooth to push through the eggs when hatching, but hatchlings in these two boa species do not, indicating that the boas have not wound the clock back entirely or exactly.

Understanding whether this is reversal rather than convergence will probably require doing detailed anatomy of the reproductive organs of a lot of snakes. DNA is great for understanding the relationships between species, but it will probably only be by looking closely at the actual organisms that we will be able to understand the chain of events that might lead groups back the way they came.

A second paper, by Bridgham and collegues, argues that at the level of molecules, Dollo may have been on the money. They ran models of the evolution of a molecular that binds to the hormone cortisol. According to their model, the cortisol receptor was derived from receptors that bound to a much wider range of molecules. The new receptor, then, is a specialization of generalists.

When they took the modern receptor, and experimentally changed several key mutations back to the predicted ancestral state, they got a molecule that bound to... nothing. Bridgham and company’s explanation is that in addition to the key mutations that made the modern receptor possible, there were other changes in the rest of the molecule that. These “background” changes were not obviously related to the molecule’s ability to bind to the hormone, but, in the context of a long, complex molecule where the parts interact to give the receptor it shape, those changes were enough to prevent the experimentally modified receptor to bind to hormones.

Interestingly, the authors stress that these background changes make it unlikely for the molecule to revert back to its ancestral condition... but then they proceed to do it (their Figure 3a). Sure, the chain of events needed to revert the molecule back is longer and less probable. The ratchet they propose for molecular evolution may be a slightly slippery one.

In a sense, both papers show that the argument about evolutionary reversal is not whether it is possible or impossible. The question is not whether reversals happen, but how often they happen. Reversals could be rare. And the frequency of reversal may differ depending on what level of organization you’re looking at. It could be easier in whole organisms than in molecules, or vice versa.

This post is part of National Evolutionary Synthesis Center (NESCENT) competition for the Science Online 2010 conference.

References

Bridgham, J., Ortlund, E., & Thornton, J. (2009). An epistatic ratchet constrains the direction of glucocorticoid receptor evolution Nature, 461 (7263), 515-519 DOI: 10.1038/nature08249

Lynch, V., & Wagner, G. (2009). Did egg-laying boas break Dollo's Law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae) Evolution DOI: 10.1111/j.1558-5646.2009.00790.x

Picture from here.

Hanging tough

My last review article has slipped this month by a notch to #3. It’s now spent four straight months in the Top 10 list at Brain, Behavior, and Evolution.

Latest Carnival of Evolution

I’ve got a couple of posts up at the new Carnival of Evolution, but check it out for much more fine science writing.

V for victory... and five... and an old 80s SF series...

I’m the grad program coordinator for my department. I spend a lot of time trying to improve our grad program.

That task might have gotten a bit easier this week.

My university has received a big, chunky Department of Education grant to create graduate opportunities for Hispanic students. It’s a Title V grant (hence the post title). I will probably have my fingers fairly deep for that program for the next few years, I think.

The picture? Just amazed that people thought V was worth redoing. I doubt anyone will be able to match Diana’s fantastic bitchiness (wonderfully played by Jane Badler, R).

Poor physics...

This graphic shows what people respond when they hear the word “science” in free association tests. From Dr. Kiki’s blog, The Bird Brain.

Happy to see biology looming so prominently, but have no idea why. Odd that physics doesn’t make it on the board.

Comments for second half of September 2009

Neurotopia has thoughts arising from Randy Olson’s book, Don’t Be Such a Scientist. I contend Sci missed an obvious reason why more people want to be physicians than scientists.

On Genomicron, I was able to get in a timely comment about a confirmation of an evolutionary prediction.