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.”

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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.

Scooped

I discovered today that I got scooped on a project I was working on. I wasn’t very far along on it, but I had some data in the can on it. Alas, there’s really no point in continuing with the project and no way to salvage it. It’s been done.

This is not something I ever expected to happen. I don’t work in a research field that could exactly be called “fast paced.” C’est la guerre.

These problems with publishing are starting to get old. I was scooped today, and my last two papers have been kicked back from journals for various reasons. I want something to get something finished and published, damn it.

Tuesday Crustie: Ghostly claw

The Murray cray, Euastacus armatus. This impressive, spiny species is protected in Australia.

Picture by user Aaron Gustafson on Flickr used under a Creative Commons license.

How moral thinking affects scientific reasoning

On the TED blog, Jonathan Haidt says something important about how people interact with evidence. I’ve added some bolding for emphasis.

We engage in moral thinking not to find the truth, but to find arguments that support our intuitive judgments, so that we can defend ourselves if challenged. The crucial insight here comes from psychologist Tom Gilovich at Cornell, who says that when we want to believe a proposition, we ask, "Can I believe it?" – and we look only for evidence that the proposition might be true. If we find a single piece of evidence then we’re done. We stop. We have a reason we can trot out to support our belief. But if we don’t want to believe a proposition, we ask, "Must I believe it?" – and we look for an escape hatch, a single reason why maybe, just maybe, the proposition is false. So people who have a negative intuitive reaction to Obama, or who are fearful about the enormous changes going on, are already inclined to believe rumors against him and his plans. They hear about death panels and forged birth certificates and ask “can I believe it?” The answer is usually yes, particularly if Fox News raises these questions and brings on experts who claim that the propositions are true. Even if Fox News presents both sides, the fact that somebody on TV endorsed a proposition gives viewers permission to believe it, if they want to. Conversely, Democrats can give rebuttals till they’re blue in the face, but if people are asking themselves “must I believe it” about the Democrats’ claims then the answer they will usually reach is “no.” Logic and consistency just aren't very important when it comes to morality.

Haidt frames this in the context of moral thinking, but my experience is that these exact same patterns occur in areas that have little moral repercussions at all. For instance, what is the moral or ethical issue involved in accepting that twelve human beings have walked on the surface of the moon? Part of this may be fear of science, as Haidt notes that:

(M)aterialism is deeply and profoundly threatening to many people.

Science is 100% materialism, through and through, beginning to end. This means that, according to Haidt, scientists are going to have an incredible problem putting their message across on any subject.

Of course, with many scientific issues, I can absolutely see where people think there are ethical issues involved. Is there is any way to break through this pattern of thinking? Haidt’s response fills me with dread, frankly.

While it is useful to rebut charges and get your arguments out in circulation, you have to understand that arguments and evidence have little impact on people as long as their feelings tilt them against you. You’ve got to create trust and liking first, and then people will be willing to listen. People can believe pretty much whatever they want to believe about moral and political issues, as long as some other people near them believe it, so you have to focus on indirect methods to change what people want to believe. You have to get them to the point where they ask themselves “can I believe it?” about your claims, rather than about your opponents' claims.

The first likable, apparently trustworthy person you meet who exposes you to an idea has a huge advantage of convincing you of that idea, regardless of whether it’s true or not. This supports a lot of what Randy Olson is arguing in his book (reviewed here).

The ray of hope Haidt offers is faint indeed:

People may not be logical, but few of them are crazy.