I’m tryin’ here

Nature exhorts in this week’s editorial:

(R)esearchers would do well to blog more than they do.... there are societal debates that have much to gain from the uncensored voices of researchers. A good blogging website consumes much of the spare time of the one or several fully committed scientists that write and moderate it. But it can make a difference to the quality and integrity of public discussion.

I agree with the time sink comments, and sympathize with the thought that it impacts on the quality of discussion on science. This is one reason why, in the last 15 months or so, I’ve really tried to step up the level of writing in this blog, with more frequent and substantive posts.

On the other hand, Chris Mooney wrote of blogs in Slate:

The science blogosphere is, of course, booming—but... the blogs are unlikely to reach very many citizens who aren't already science lovers. And what would be the effect if the blogs did get to a wider audience? The semi-finalists in the recent “Best Science Blog” of 2008 contest were a site that questions the reality of global warming and PZ Myers’ Pharyngula—ground zero for a potent mix of pro-evolution advocacy and uncompromising criticism of religion.

I'm getting mixed signals here.

To head back to the Nature editorial, some comments can be found here. I think the biggest obstacle to scientists blogging is when colleagues say things like this (from commenter Michael Nestor):

We all need to get back to finding the cure for cancer instead of talking about finding it.

Translation: Waste of time. Go back to the lab. Get data. Build the better mousetrap and the world will beat a path to your door.

But I don’t think all science works that way. Nor should it.

The example is telling: “Cure cancer.” Yes, that’s a worthy goal, but it’s an extraordinarily unusual in the amount of public interest about it. What about all the other science? Is there a hint of, “If people don't care about your science, it’s your own fault for not choosing the right research questions?” Or am I being overly sensitive in detecting a little philistinism in such arguments?

If we’ve learned anything from 400 years of organized science (and it is the 400^th anniversary of Galileo looking through a telescope, as good a place as any to mark the birth of science), we rarely know in advance what the right questions are.

Psychedelic bouncing frogfish

I love me some wild new species, and this time, it’s a fish. I’ve read somewhere about this one before (maybe Quirks & Quarks? – yup, that was it), but the formal paper has now come out. The Age has a news story here.

And here are some videos.





Crazy, man.

The Zen of Presentations, Part 24: Slidesters

Many people have discussed the deficiencies of "sliduments": PowerPoint printouts that are given instead of actual, detailed prose documents. See also here.

Another misuse of PowerPoint is to use it to create large posters. My experience has been that PowerPoint is abysmally suited for this task. That said, I have not used the 2007 version of PowerPoint that was released along with Windows Vista, but I have suspicions that at least some of the problems I had are still true. The main reason I suspect this is that I deal with posters for HESTEC from our department every year for the last four. And every year I am horrified by the PowerPoint posters. People only do this because they know PowerPoint and think it’s “Good enough” for the task. My reaction is much like that of William T. Riker: “‘Good enough’ never is.”

In the last version, PowerPoint was limited in how big a poster it can make. Some conferences give several feet of space, and PowerPoint couldn't reach the large sizes.

PowerPoint is also wretched at typesetting and handling complex layouts. It’s harder to change even basic paragraph settings like line spacing in PowerPoint than Word. Perhaps the fatal flaw is that the heart of any poster layout should be a consistent grid, and setting up a grid in PowerPoint is very difficult. Consequently, I see many posters where I’m willing to bet no two items on them are actually aligned. They’ve been roughly kinda sorta eyeballed.

Strangely, many who use PowerPoint have an much superior tool at their disposal: Publisher. It’s part of the standard Microsoft Office package, but not many people are aware of it. It uses many of the same commands and logic as the other Office software that people know, so its lack of popularity is all the more surprising. Publisher has its limitations, but the improvement over what one can do in PowerPoint is huge.

There are many, many websites now that are devoted to improving the design of slides. I’m a big fan of many of them; they perform a very useful service. But maybe it’s time for a few dedicated individuals to take up the cause for poster design.

What are you good at, and what do you suck at?

Hot on the heels of my Intellectual Styles post comes, "What are you good at?" seen at Sciencewomen and Uncertain Principles.

You are in a room with a bunch of other female faculty/post-docs/grad students from your university. You know a few of them, but most of them are unfamiliar to you. The convener of the meeting asks each of you to introduce yourself by answering the following question: "What is one aspect of your professional life that you are good at?"

While I think it's important to recognize what you're good at, I think the flipside is also important, so I'll throw this out for comments:

What are you good at, and what do you suck at?

Professionally, I think I'm pretty good at presentations, writing, and graphics. I suck at routine organization and cleaning.

Tricking wasps with flower porn

Orchids are lovely flowers and if you think they’re just a bit sexy, you're not alone. In fact, for some wasps, they’re very sexy. As sexy as any female wasp.

It’s well known that flowers use many methods to attract insect pollinators. Many flowers have nectar. Some smell horrible, and are pollinated by flies and other insects that tend to feed off dead things. And some look like female insects, and deposit pollen on males when they come into investigate. What this paper by Anne Gaskett and colleagues show is that the insects are fooled more completely than anyone previously thought, to the point where they not only copulate, but ejaculate. This paper came out several months ago, and got some attention in the news media (e.g., here, here, here, here).

Showing that males have ejaculated is fairly simple, and actually a relatively small part of this short paper. There are some more interesting issues here.

These cases of mistaken identities are costly to the insect. Even setting aside the major finding of this paper, there’s simply the cost of the males wasting time. So you would anticipate that over time, male wasps will “push back” and try to avoid being tricked. There is an experiment that tries to show that wasps learn to avoid copulating with these orchids, but the experiment has several odd features.

The researchers first observed over 100 wasps in the field, and noted how many approached the orchids, copulated with them, and so on. They have no way of knowing the animals’ experience in the field. They then brought 30 of those wasps into the lab, presented them with a fresh orchid, and observed their response. This mix of field and lab observations raises questions: What if the effects are due to the handling or the differences between artificial and wild conditions?

More puzzling still, the researchers then took only 14 of the wasps for a third trial, giving all the remaining wasps fresh orchids again. It’s not at all clear why the sample size changed for the second exposure in the lab.

Their results showed that wasps became less likely to copulate with an orchid after they had already been exposed to one, suggesting that animals were learning to avoid the orchids. But the interpretation is problematic here, especially considering that to be pollinated, the same wasp must visit at least two orchids. The wasps in their experiment dropped from about 90% copulating with the orchid to about 30% copulating after only one (known) encounter with a flower – which seems a pretty precipitous drop-off is the goal is to get one wasp to visit twice. That said, loss may be tolerable if those males that do visit a second orchid have very high likelihood of pollinating the flower.

Interestingly, the paper also shows that most of the orchids that engage in this sort of deception are pollinated by haplodiploid insects. Without going into detail, haplodiploidy means that males in these species are laid from unfertilized eggs; females are laid from fertilized eggs. So, strangely, orchids, by “cutting in” on the female insects’ mating possibilities, the orchids may be ensuring a greater number of males in the wasp population that can serve as pollinators. If female wasps don't mate (because all the males are out satiating themselves with orchids), all the females can do is... lay eggs for more males.

It’s a hothouse of treachery and manipulation out there, I tell ya...

Reference

A. C. Gaskett, C. G. Winnick, M. E. Herberstein (2008). Orchid Sexual Deceit Provokes Ejaculation The American Naturalist, 171 (6) DOI: 10.1086/587532

Why textbooks have a bad rep

Seth Godin writes:

Demolish the textbook market as soon as possible(.)

Why would someone actively urge demolishing an industry devoted to improving knowledge? Surely there are other industries more worthy of immediate replacement. (Yeah, I’m looking at you, fossil fuels!)

Traditionally, people whinge about the cost of textbooks. But I don’t think that alone is the issue, considering that many of them will happily spend much more on other things. The issue isn’t the cost, it’s their value.

I think one of the problems with textbooks is that, by definition, they are compilations of established knowledge. We have a fairly long established idea that over time, established knowledge becomes public domain. This is particularly true of scientific ideas. Indeed, some may argue that this is the entire point of science. So people really wonder why they should have a compilation of stuff where the core materials are often quite literally decades old.

This problem for textbooks is going to get worse as more old information gets put online. For the kind of science found in introductory textbooks, sources like the much reviled Wikipedia are decent starting points.

Textbooks are going to have to reinvent themselves. They’re going to have to stop being mini-encyclopedias on a topic, and offer something else. I’m not sure what it’ll be. Maybe the future lies with textbooks that offer personal perspective, opinion, a plan, or a point of view.

Intellectual styles

I'm fascinated by how scientists have different intellectual styles. Some are methodical, others disorganized; some are great in the lab, others excel at interpreting data.

This post at The Quantum Pontiff reminded me of this question, presenting an idiosyncratic listing of different types of intellectual styles.

I became aware of different intellectual styles when one of my professors told a story about how several grad students were sitting around a table, chit chatting. One said he loved coming up with the questions to ask. Another said she loved the actual experiment, when the possibilities seemed infinitely variable. A third said, “No, it’s the numbers,” and enjoyed the process of running through the data, looking for the patterns. And the last enjoyed the writing, the pulling all the threads together into a final form.

Then they looked at each other and agreed that they should all write a paper together.

Another neurobiologist I met said the thing that he loved the most was listening to action potentials on an speaker. “I never get tired of that.”

The thing that keeps me going are the beginning and ends of the process: I love the ideas, and I love communicating them. The actual gathering of data, I have to admit, I sometimes find a bit of a grind. I particularly get frustrated running replicates. I know they're important, and I know I have to do them, but typically, when I running a replicate experiment, I usually have a very good idea of what the answer's going to be.

For my fellow scientists: What’s your favourite part of the research process?

I like my students

Some of them, anyway. ;)

Why online teaching hasn't taken over education

I use the web for teaching a lot. Pretty much have since I started in my current gig. But I've never done a completely online course, for a lot of reasons. And I was always skeptical of the notion that students would start getting degrees from universities far from where they were living online. The Age has an article about why so few students find totally online teaching appealing.

A quick list of why online degrees haven't taken off:

• People crave real social interaction.


• Lack of self-discipline and study skills (mainly an undergrad issue).


• Questions of legitimacy of online institutions.


• Students have only superficial technical skills.

What a dentist believes

The Texas Observer has a profile of Don McLeroy, the dentist who chairs the Texas State Board of Education who is a Young Earth Creationist deeply involved in setting Texas Science Standards. The title ("The Curious Faith of Don McLeroy") and the first paragraph give s sense of the articles tone:

Don McLeroy’s story, and his thinking, are more complicated, and more telling, than those bare facts suggest.

There's a fair amount of interesting things here. Here's one:

McLeroy insists he doesn’t have any desire to have creationism taught in classrooms. “It’s a religious philosophy,” he says. “It doesn’t belong in schools. Same with intelligent design. Evolution is the scientific consensus, so we’ll teach that.”

You know, I'm willing to give McLeroy the benefit of the doubt here. Maybe this limited thing is what he personally is trying to accomplish. But what seems to be missing is an acknowledgment of the possibility that some people will see "strengths and weaknesses" as an invitation to teach religious philosophy.

But McLeroy believes that at some point, perhaps in 10 years, perhaps in 50, a new scientific revolution will reveal that “the creationists’ crazy ideas” are actually right—just as quantum mechanics and relativity overturned the tidy world of classical physics.

I wonder, historically, how many people who said "History will vindicate me" actually were vindicated by history...

“Well, if he feels there’s such a controversy,” says Eugenie Scott, executive director at the National Center for Science Education, “then he should address it at the university level. That’s where new science is made. To expect high school students to evaluate ‘controversies’ in cutting-edge evolutionary biology before they have a solid grounding in science is ridiculous.

“We don’t do that with any other science. Would you teach kids about the controversies in string theory before they learned basic physics?”

This line of thought reduces McLeroy to near-speechlessness. “But ...” he sputters when I call him for comment on Scott’s point, “It’s not ... it’s not true. There are real problems with it. How can we teach our kids something that’s not true?”

Sorry, Mr. McLeroy – it is true. And the author, despite a fairly sympathetic tone that paints McLeory as a relatively nuanced thinker, goes on:

What McLeroy doesn’t seem to understand is that science education is all about teaching kids things that, strictly speaking, aren’t true. When I learned about relativity and quantum mechanics in college, I learned that the classical chemistry and Newtonian physics I had been taught in high school were, at best, approximations. That they really didn’t do that great a job of describing the way the universe works. That, in a sense, they were lies.

Science and music and Karl

You may not know much about the scientific publication business, but I'm willing to bet you know something about the music business. You probably know that the traditional music industry is having panic attacks about people downloads and piracy (just like they used to be having panic attacks about cassette tapes).

Both the music industry and scientific publishing are currently undergoing a Marxist revolution. I'm grateful to Jay Rosen, speaking on this Scence Talk podcast, which reminds us that Marx said that a revolution occurs when the means of production change hands.

Scientists and musicians face two, dramatically different problems. The first is creating something wonderful. The second is putting that in the hands of someone who cares.

The creative process is not necessarily easy, but you can often do a lot without that much investment is special equipment. Even so, as the creative process became professionalized, some aspects of the creative process were out of range of most people. While anyone might compose a song with a beat-up acoustic guitar, not everyone had could afford to have their own recording studio. Anyone can have an excellent scientific hypothesis, but not necessarily the right tech to test it.

The second one used to be really, really hard. Musicians would have to tour, but couldn't go everywhere their fans were. Recorded music required mass production, and no one person could afford to make a factory to press vinyl records or send them to radio and retail shops, so a huge middle management sprung up to connect musicians to their fans. Scientists with completed ideas would have to go to conferences. Research publications required specialized distribution, but no one researcher could afford typesetting and layout services and buy a printing press and send journal issues to libraries around the world, so a huge management sprung up to connect scientists to their peers.

Now the "means of production" (distribution, really) is totally changing hands. The middleman is facing extinction. Now, musicians can make their own music in their homes and put it directly in the hands of their audience. See this example from Brazil. Researchers are slowly, slowly, slowly waking up to the same idea. The internet means everyone has a printing press and a distribution network.

This story suggests that open access doesn't guarantee wide dissemination. I think this is historical inertia. The journals run under the old model still do a fine job, and still have prestige. So it remains to be seen how whether there will be a boody coup or a quiet revolution.

Podcasting lectures works

New Scientist reports that students who listen to lecture podcasts can do better than those who actually sit their butts in seats for class. But there's an important qualifier...

Students who downloaded the podcast averaged a C (71 out of 100) on the test – substantially better than those who attended the lecture, who on average mustered only a D (62).

But that difference vanished among students who watched the podcast but did not take notes. Students who listened to the podcast one or more times and took notes had an average score of 77, McKinney says.

As always, much replies on the students. The authors note that with the podcasts alone, some -- in fact, most -- of the students listened to the podcast more than once. So what may be going on here is, in part, a simple repetition effect. You have more opportunities to learn something if you are exposed to it more thane once.

The original paper is here.

NSF's on Twitter!?

I didn't expect this. A Twitter feed from a government research agency? Seriously? I had been reading about how some companies were trying to use Twitter and mostly failing with Twitter as they had with almost all social networking, so this caught me off-guard.

Do male crickets shorten the lives of female crickets?

One of the deep insights from evolutionary thinking in the fields of ethology, animal behaviour, behavioural ecology, and sociobiology is that males and females often have distinctly different best interests when in comes to reproduction. Now, it’s very easy to made wild extrapolations about this, particularly regarding humans, but there are many examples of the general principle. Of course, when you're looking at any individual case, the devil is always in the details.

This paper, by Green and Tregenza, looks at whether male crickets (Gryllus bimiculatus; sometimes known as “bimac” in cricket labs) manipulate female crickets by transferring special seminal proteins along with sperm when the copulate. The underlying idea is that it is in the best interest of the male for the female not to mate with other males, because this would cut into the first male’s reproductive success. Thus, a male that can change a female’s behaviour or attractiveness or what have you so that she is less likely to mate would have an evolutionary advantage.

Green and Tregenza test this idea by taking spermatophores from several male crickets and making a liquid that they injected into the females. As a control, they injected a different group of females using a physiological saline (water and a few salts that are similar to that inside the cricket).

One of the potential shortcomings of this study is that these were not delivered into the reproductive tract, which obviously would be the case with actual mating, but into the abdomen directly. On the one hand, this is clearly not a natural situation. On the other hand, it does help test whether any effects are due to the physical act of mating rather than actual chemical signals.

The authors find that there are two main effects. Females injected with the mix of seminal proteins walk forward less, and they have shorter lives. The females in both conditions lay about the same number of eggs. Green and Tregenza also looked at other factors, like responses to male song, but found no significant differences. From this, they conclude that the seminal proteins are having manipulative effects on the females.

The discussion does talk about the suggestion that the injection of chemicals is causing a general immune response, but they downplay this, saying that they would have expected to see a greater decline in female’s orientation if there was a general immune response. But it seems a fairly frail argument. This experiment could have made its case much more strongly by adding one more control group.

Imagine that you have the hypothesis that the secret ingredient in a particular cola flavoured soft drink – let’s call that secret ingredient, say, 7X – causes burping. So you give one group of people glasses of water to drink, and one group the one brand of soft drink. The latter burps more. You thus conclude that 7X causes burping, right? Not so fast!

A soft drink is a complex concoction of carbonation, sugars, and flavourings. Water is not. What you would really want as a control is a soft drink with everything but 7X, either instead of, or in addition to, water.

In this paper, a complex protein mixture is being compared to a physiological saline. The implication is that the effects are due to particular proteins generated by the males that function to manipulate the females. But it may be that this is simply an effect of injecting a complex mixture of proteins, and there is no protein specific to males that is having this effect. A second control containing proteins unrelated to crickets, like bovine serum albumin (BSA), would help to sort this out this possibility. Or, use seminal proteins from a distantly related cricket species. If this was really a case of sexual manipulation, you would predict that only the proteins from the same species would have a significant effect.

Reference

Kelly Green, Tom Tregenza (2009). The influence of male ejaculates on female mate search behaviour, oviposition and longevity in crickets Animal Behaviour DOI: 10.1016/j.anbehav.2008.12.017

Which companion are you?

Dagnabit, I just can't resist quizzes like this one...

Connectome comment

PLoS Biology has published a comment from me about the paper, "The Interscutularis Muscle Connectome." This is the same paper I recently discussed here.

Shadow life and "less than inevitable"

This story in The Age predicts that we'll have evidence of life on other planets within four years. But, the argument goes, we probably won't find anyone to talk to, according to Alan Boss:

"Whether the life we find is intelligent is, however, less than inevitable. Intelligent life seems to be fleeting. In terms of the universe it only exists for a fraction of time."

Boss was apparently speaking at AAAS, as was Paul Davies, who coins the interesting term "shadow life" (analogous to a shadow cabinet, I suppose). Davies suggests that that there may be life here on Earth that evolved independently of all the life we already know. Certainly we've seen life living in places nobody expected, but so far, it all seems related. It'll be a tough haul to look. I wouldn't want to be the one writing the grant proposal.

"I seek funding to travel to the most extreme reaches of the planet to look for something that might not exist and that we might not recognize even if it does."

If shadow life exists, it would, like life on Mars, weaken the prospects for the search for extraterrestrial intelligence (SETI), since it either would show that the origin of life does not inevitable lead to the formation of a highly intelligence species capable of using advanced technology.

How geeky am I?

+++ Total Geek......................................≥25%

I scored 33.72781... very close to a major geek.

---

Geek Test Results
You are 60% geeky.

Not bad. Maybe you spend a little too much time with your computer, but at least you have friends. You do have friends, right?

The current average score is: 32.15%

Fact: 20.15% of people who took this test claim to have attempted to build a robot.

---

68% Geek

---

Your result for The How Geeky Are You? Test...

The Geekiest

Congratulations! You scored 82% on dorkpoints, higher than 95% of your peers.!

You're the nerdliest of the nerdy. The dorkiest of the dorky! You make other geeks tremble in your prescence! See you at the next convention!

Take The How Geeky Are You? Test

What would Darwin think?

There's been a tremendous amount of good stuff about Charles Darwin this week in honor of the 200^th anniversary of his birth. That said, there's been one frequent question interviewers have been posing that I want to take on.

"What would Darwin think about... the interest in his birthday / his theory / the current state of biology / etc.?"

This is always a question I've disliked, because the whole point of deep thinkers is that they came up with answers that surprise you. Plus, almost every answer I've heard has said something like, "Oooh, I'm sure he'd be very pleased / excited / interested." Frankly, those answers seem just a bit too pat and easy.

Since nobody really knows what Darwin would have thought about current biology, let me suggest some alternate ideas...

Darwin, a naturalist to the core, would be horrified by how few biologists are engaged in observing the natural world. He might be highly critical of biologists working in labs with, say, cell lines who no appreciation of the organisms they originated from.

Darwin, fortunate to be independently wealthy, would be shocked at how contemporary scientists are forced to work on a thousand tasks at once. Darwin could speak about the importance of uninterrupted time in developing ideas, and might be convinced this would be a superior method of inquiry over doing grant writing, teaching, grant writing, revising manuscripts, sitting on administrative committees, and grant writing.

Darwin, by all accounts quite shy, would be embarrassed by the amount of attention he is receiving. He probably be the first to give credit to the many other researchers who have contributed to evolutionary biology.

Finally, Darwin might well be saddened that arguments he had during his lifetime, and which, in many cases, he correctly answered in his own writing, are still viewed as serious problems, instead of being matters that have been settled ten times over.

Setting the bar low

Gail Patricelli is quoted in New Scientist as saying:

The males are trying to copulate with cow pies all day.

This from an article about courting birds.

And on that thought, happy Valentine's Day.

Muscle innervation is not a connectome

Since the word "genome" entered the lexicon, mainly on the heels of the Human Genome Project, there has been no shortage of people trying to cash in on the idea of "-omes." The idea is that an "-ome" is a complete catalogue of all... something. So we have budding fields like proteomics (all the proteins in an organism), and, in my own field, neuromics (all the neurons in an organism) and now, connectomics (all the neural connections in an organism).

Lu and colleagues purport to have a connectome. That's what the title says, after all. This is, unfortunately, misleading. This is innervation of one muscle. It's detailed, yes, but it's no more a "connectome" than sequencing one gene is a "genome." I suppose, though, that "Motor innervation patterns of the interscutularis muscle" is less likely to land you a spot in a high-profile journal than a title using, "connectome."

Putting my irritation with the unwarranted title aside... what's to learn here?

The authors used a genetically modified mouse that expressed a fluorescent protein in all its motor neurons. Then, they used confocal microscopy techniques to reconstruct the paths of multiple motor neurons leading to a small muscle in the head. Neither of these techniques are particularly groundbreaking in principle, but there's no doubt that achieving this level of high detail would have required a lot of patience. From there, there's lots of math and models, but it boils down just to looking closely at what they saw.

The authors summarize their main findings as these.

The more muscle fibres a neuron innervates, the bigger the twitch. Although this is presented as a conclusion, the authors didn't actually measure twitch generated by muscles in this paper, so there is still more physiology.

The bigger the neuron, the more muscle fibres it innervates. Not a huge surprise, considering that there will be more demands to create and transport chemicals to the tips of the nerves if there are more synapse.

Every motor neuron follows its own unique path, and it's often a path loaded with detours. This speaks to the development of muscle innervation being quite loosely controlled. Again, no big surprises, as there'd been a reasonable amount of evidence showing that axon guidance is something that tracks (say) chemical gradients, rather than any sort of precise pathfinding or lock and key mechanism.

Perhaps surprisingly, it's probably going to take a long time before these methods are successfully applied to many invertebrate species, particularly arthropods. Although invertebrates have fewer neurons, the way they connect to muscles is much more complicated.

Reference

Ju Lu, Juan Carlos Tapia, Olivia L. White, Jeff W. Lichtman (2009). The Interscutularis Muscle Connectome PLoS Biology, 7 (2) DOI: 10.1371/journal.pbio.1000032

361

Scientific American reports on a recent paper estimating the number of stable extraterrestrial civilizations in our galaxy.

361.

More or less.

I previously wrote about the probability of intelligence evolving. On this and related biological points, Forgan says, "The model now enters the realm of essentially pure conjecture..." Which is typical research publication speak for, "We have no idea. None whatsoever."

Trying to make the Texas State Board of Education accountable

In the Houston Chronicle, two Texas state representatives describe legislation intended to put in some periodic reviews of the Texas State Board of Education.

As scientists and educators across Texas and the nation mark the 200th birthday of Charles Darwin with calls for a renewed commitment to science education, the State Board of Education continues to engage in narrow theological debate about the validity of evolution. ...

To ensure that the SBOE works as it should, we have filed legislation to place the board under periodic review by the Sunset Advisory Commission and hold them accountable for their performance, just as we do the Texas Education Agency and other state agencies.

The decisions of the SBOE not only impact millions of young lives on a daily basis, but impact the economic progress of our state as well.

For these reasons and many others, the public has a right to full disclosure and oversight.

The board has escaped such scrutiny for far too long. The disregard for educators, instructional experts and scientists can’t continue.

Good luck, then. You'll need it.

In praise of evolutionary trees: a personal gallery

Charles Darwin's On the Origin of Species By Means of Natural Selection contains exactly one picture (here).

It's an evolutionary tree, a visual depiction of relationships between organisms. Such a relationship is now known a phylogeny, a word that Darwin coined. The point Darwin is trying to make with it is not the one that most people associate with evolutionary trees; Darwin was trying to emphasize what he called his Principle of Divergence. Nevertheless, trees have become more broadly representative of the entire evolutionary enterprise.

In that vein, and because variation is a key theme of evolution, I thought I would present the trees I've published in my research papers, with some commentary, for Darwin Day. I don't pretend that my trees are anywhere near as impressive as, say, David Hillis's massive, beautiful supertrees, but I present them here nonetheless.

There are two scientific stories being told here. One is about digging (figures 1, 2, 3, 4 and 6), and the other is about escape responses (figures 5, 7, and 8). I've grouped them in chronological order, however.

Figure 1.


This figure represents, well, bafflement. Not on my part, but on the part of the taxonomists. At the time, carcinologist Fred Schram memorably described the phylogeny of this group (Reptantia) as a "morass." Nobody had much of an idea of who was related to what, so instead of nice two way splits... a five way free-for-all. Original dissertation here (be warned, it's big!).

Figure 2.


This tree is nice and simple, and lends itself to using diagonal lines. Original paper here.

Figure 3.


This tree is considerably more complex. I'm trying not only to show the taxonomic groupings, but key features. The angle of the diagonal lines isn't terribly aesthetically pleasing to me, but I was trying to make the figure as compact as possible. Original paper here.

Figure 4.


Getting featured on the cover is always a nice ego boost. On this one, there's an ancestor nestled at the bottom of the tree, the earliest known decapod crustacean. Original paper here.

When I showed this figure to the editor, Glenn Northcutt, when he was visiting our campus, he asked, "Why are the animals pointing to the right?" He explained that in vertebrate anatomy, there was a long tradition of the anterior always being to the left. I'm pleased he published the figure anyway. Still...

Figure 5.


You'll notice everything facing left from here on in.

This one has even more species, with various traits in the branches. It was just easier to make straight lines instead of diagonals. Original paper here.

Figure 6.


That this one is back to diagonals is indicative of how long that paper sat waiting for me to revise and put it into the hands of editors! It was actually created well before the one above. Original paper here.

Figure 7.


Similar to the one before last, I think this one offers a few improvements in presentation. More of the taxa names are properly aligned, for starters. This and the cover are probably my two best looking trees. Original paper here.

Figure 8.


These two trees were the most complicated I've had to make yet. I was trying to show more groups of animals and more features. The size of this thing meant that I had to "chop the tree down" and show it horizontally, and that I couldn't show little icons of the animals, as I had done before. I really like putting in the pictures, because in some of my papers, they're about the only indication of what the organism looks like! But there was no possibility to do that and have any hope that the thing would fit on the page.

The other thing I like about this is that it shows that a tree is really an hypothesis. There are two trees, because there are two major competing hypotheses. There are similarities between them, and it turns out that both of them give the same "punch line" for my story anyway, which is multiple, repeated losses of certain neurons. Original paper here.

One thing I'm rather pleased with is that I've never re-used a tree. I've always redrawn them, always trying to look at each one afresh and make decisions appropriate for that tree. I hope these trees give a glimpse of the importance of evolutionary thinking in the research that I do.

Charles Darwin's first evolutionary tree (pictured) was not the first -- that honour lies with Jean-Baptiste Lamarck. nor was he the first to make the creation of trees rigorous and following explicit, testable rules -- that distinction lies with Willi Hennig. Nevertheless, I think we should celebrate evolutionary trees as part of Darwin Day because they represent one of the most important elements that Darwin brought to biology: history. Or maybe "deep time" is a better term.

Organisms have a past, and that past matters. That ancestry helps explain features of organisms that may otherwise be inexplicable, and it gives us a way to make predictions about organisms that we have not yet studied.

Perhaps more importantly, trees remind us that life is ancient. Organisms have been engaged in the struggle for existence on this planet a long, long time. Even the two centuries since Darwin's birth is a paltry handful of heartbeats in evolutionary time.

Before I go, I have one last tree. I did not create this one; I am grateful to Neurotree for this information. Since today is Darwin Day, an event that bills itself as a celebration of science and humanity, let me add in some personal connections. It's a reminder that the scientific community is, from a certain point of view, very small.

Figure 9.

8 Steps:

Zen Faulkes (The University of Texas-Pan American)
was a post-doc for

|

David L. Macmillan (University of Melbourne)
who was a grad student for

|

Graham Hoyle (University of Oregon)
who was a research assistant for

|

Bernard Katz (University College London)
who was a post-doc for

|

John Carew Eccles (Australian National University)
who was a grad student for

|

Charles Scott Sherrington (University of Oxford)
who was a post-doc for

|

Michael Foster (University of Cambridge)
who was a grad student for

|

Thomas Henry Huxley
who was a collaborator, friend and colleague of

|

Charles Robert Darwin (Independent)

Darwin created the foundation for evolutionary biology; Huxley created the biological curriculum for universities of his day; Michael Foster was a pioneer in physiology; Sherrington stood at the precipice between general physiology and neurobiology; Eccles, then Katz, strode into neurobiology; Hoyle stepped into the realm of invertebrate neuroethology using insects; Macmillan, while still a neuroethologist, preferred crustaceans as subjects; and I try to follow as best I can.

Descent with modification, indeed.

Research paper title of the moment

How could you not click a link to read a paper with this title?

Martinez-Solano I, Lawson R. 2009. Escape to Alcatraz: evolutionary history of slender salamanders (Batrachoseps) on the islands of San Francisco Bay. BMC Evolutionary Biology 9: 38. doi:10.1186/1471-2148-9-38

Love the title, but the ideas in the paper seem pretty interesting, too. The idea is that the salamanders were on the islands before they were islands! They were inhabiting hilltops when the water level was lower, then got stuck as rising water levels turned hilltops into islands.

Putting food on the table, science style

Stephen Quake, subbing in for Olivia Judson, has a superb column in the New York Times detailing how science currently runs: tax money and the very occasional private foundation.

For instance...

It strikes me as one of the ironies of modern life that professorial faculty... accept such a brutal free-market approach to their livelihood. If they can’t raise grants to support their research every year, they won’t get paid. So not only do they have to worry about publish or perish, it’s also funding or famine, in the very real sense that without a grant there might not be food on the family dinner table!

Fortunately, I am in a position where my base is not dependent on my getting grants. But let me add that there's a spillover effect. I have a grant for undergraduate researchers. I have the potential to have a big impact on the pay going to a set of students. And being responsible to bring in money for other people is also pretty stressful.

Google takes on journals?

The reaction to this will be interesting... At first glance, it looks like Google is firing a shot across the bow at, oh... pretty much every scientific research journal.

As long as big journals provide a useful service, this tool will only enhance their effectiveness. But the more they take months to review our publications, and the more they give unqualified reviews, and the more they force us to clear irrelevant hurdles prior to publication, and the more they lock up our works behind fees and copyright transfers, the more this tool will provide an alternative to their services.

Update, 14 August 2014:After years of silence, Wired has an article that picks up this thread as a rumour.

Google is allegedly working on a free, open access platform for the research, collaboration and publishing of peer-reviewed scientific journals.

Blog swarm!

I have never heard of the concept of a blog swarm before, but I'm in! The Blog For Darwin project caught my attention, and I'm planning on participating... come back Thursday!

Quotes that scientists hate: Part 1

Mark Twain blamed Benjamin Disraeli, but, as far as I can find, nobody has found when Disraeli said:

"There are three kinds of lies: lies, damned lies and statistics."

I hate that quote. Or, to be more accurate, I love its humour, but I hate how it gets brandished around like a club.

I was reading about possible lottery fraud, and this comment popped out at me:

Statistics can be shown to mean whatever they want.

Whenever someone wants to dispute a finding that relies on numbers, Twain's quote is never far from the surface. People bring it out as though it were some logical proof or eternal verité, instead of being a punch line.

For the non-scientist, numbers are slippery, unpredictable and untrustworthy things. You can't look them in the eye. You can't question their motives.

For scientists, numbers are the real deal. You dispute the interpretation, the analysis, the experimental design, what have you... but it is highly unusual to dispute the numbers. One saying goes, "Interpretations may change, but the data should be valid forever."

Fortuitously, this article in New Scientist makes a similar point. When climate scientists say "Very likely," they are expressing a confidence that the probability is more than 90%. In comparison, nearly half of non-scientists thought the probability was less than 66%.

Such things tap into of important differences between how non-scientists and scientists approach problems.

Vestigial icons

Quick! What's the icon circled in red mean?

"Save," right?

Now, what does that icon depict?

It's a 3½" floppy disk.

When was the last time you used a 3½" floppy disk?

I'm guessing it's been about 5 years since most people have touched one.

So why is that still showing up as an icon for "save"?


I wonder how long it'll be before that 3½" floppy fades as a symbol for "save." What will replace it? Will it be a flash drive icon, or perhaps something less computer centered, like a bank vault?. I wonder if there are computer users now how recognize that it means "save," but not why it means save.

The textbook conundrum

I don’t know what to do about textbooks.

On the one hand, textbooks are obsolete. They had a very clear and useful purpose: to summarize relevant technical research, originally published in disparate technical papers piecemeal across hundreds of journals, in one place in a reasonably authoritative manner. If a student wanted to learn about the basics of a subject by reading the original papers, it would have been a phenomenally daunting task. It would take days scouring through compilations like the Zoological Record and Psychological Abstracts to find the key papers. Even then, many papers would be may have published in journals that not even all university libraries had.

Internet resources should have killed textbooks dead about five years ago.* More and more and more research papers, even quite obscure ones, can be found online. And there are specific databases and search engines devoted to scouring only those scientific sources, like Google Scholar. And the researchers themselves are making their knowledge more available online. Now, I can usually get up to speed on a topic in a couple of days – a task that used to take me weeks.

On the other hand, I hear things like this all the time:

The #1 habit successful people share with me is this: They read books to learn. They do it often and with joy. It’s cheap (or free, at the library or online) and portable and specific.

That particular riff is from Seth Godin.

Below, Chris Anderson talks about the importance of starting to read again after the .com bubble burst in 2000. (It’s about 4:50 in, but it will have more impact if you listen to the those preceding 4 minutes.) It comes up again at about 11 minutes, where Anderson says, “Books kind of saved me in the last couple of years.”



Over and over and over again: There is something valuable and important about reading. It leads to deeper, more reflective thinking. Particularly books.

So I’m completely conflicted. Students are notoriously recalcitrant to buy textbooks. They don’t see value in them (by which I don't just mean the often extreme cost). But I think they need the sort of deep thinking skills that they get from reading.

* Maybe textbooks are dead, and they’re just twitching.

Everybody gets an A

In Spider Robinson's Mindkiller, a professor at Dalhousie University who starts off one of his semesters telling all the students in his English class (James Joyce, if I remember right) that they will all get an A. He tells students this because he wants students to be there because they are actually interested. The section concludes with something like, "The students who remained looked mighty interested."

In idle moments, I've contemplated doing this myself. I've considered whether I could possibly get away with it.

But I never expected to find someone with the chutzpah to actually do it.

University of Ottawa professor Denis Rancourt gives everyone As. The result?

In December, the senior physicist was suspended from teaching, locked out of his laboratory and told that the university administration was recommending his dismissal and banning him from campus.

Firing a tenured professor is rare in itself, but two weeks ago the university took an even more extreme step: When Prof. Rancourt went on campus to host a regular meeting of his documentary film society, he was led away in handcuffs by police and charged with trespassing.

"Sneak out while the adults aren't looking"

Our local newspaper has a story on who educators in our part of Texas are viewing the recent vote on K-12 science standards.

Science teachers in the Valley didn't experience much pressure from local districts or the community on how to teach evolution.

Perhaps that is because most people in the Valley are Catholic, and the Catholic Church — as well as mainline Protestant denominations of Christianity — have backed off from the evolution debate, said Bob Soper, a retired science teacher and an ordained minister with the Episcopal Church.

Kathryn Tabb has some things to say about the teaching of evolution.

Darwin preferred the outdoors to the schoolhouse and once confessed, "Observing, thinking & some reading beat, in my opinion, all systematic education." My guess is that Darwin would urge the children of Austin to take advantage of all the mayhem to sneak out while the adults aren't looking--and, equipped with magnifying glasses and notebooks, take to nature and draw their own conclusions.

Good advice, considering that the governor of Texas reappointed creationist dentist Don McLeroy to chair the State Board of Education, and his shenanigans seem set to extend... how long are these appointments?

Go boss!

My undergrad supervisor, Jennifer Mather, spoke at TED today. A liveblogged summary is here.

If we can understand [octopus] intelligence, we can understand just how different intelligence can be and can manifest.

My jealousy continues unabated.

Hispanics in science from an outsider on the inside

The Extrovert Scientist asks a question I've had to think about a lot since moving here:

What’s the deal with the disparity of Latins in the sciences? It has to be a cultural thing because I know for a fact there are numerous opportunities for scholarships. Some organizations are virtually begging for Latins to apply in the STEM disciplines.

I'm reposting, with a little revision, my comments from that thread, because I am a lazy blogger:

Caveats: I’m at an institution (seen from above here) with about 85% Hispanic students, but I'm not Hispanic. Some of these may be regional attitudes, rather than Hispanics across the board. Still, I think the following factors might play into the lack of Hispanics in science. I'm certainly not saying they're unique or unusual to Hispanics, but I think they may be exacerbated compared to anglos.

• People who are good academically are pressured to pursue high paying professional careers (e.g., health professions). You may say, "Everyone wants their kid to be a doctor," but many Hispanics come from regions that are not well off, and this seems to make people gravitate to careers that have cash and clearly defined respectability.


• Family ties make people unwilling to move from a region to pursue an academic career. Academic careers usually requires several moves from institution to institution, with no easy guarantee of ending up close to family home.


• People are pressured to get jobs sooner rather than later. Even the value of years of “not working” for an undergraduate degree can be a hard sell. Heck, even convincing families to let kids finish high school required a cultural shift.


• We’ve seen students — usually female — whose partners or family seem determined to sabotage the students’ prospects for continuing in education. In at least one case, there was no doubt: a family forbade one of our students to leave the area to pursue a degree after her bachelor’s. Sometimes this argument is over familial obligations, but other times seems to be motivated by a lot of macho bullshit.

More commentary over at On Becoming a Domestic and Laboratory Goddess.

Who you callin' doctor?

One addendum to the issue of calling people with academic doctorates doctors.

There is one set of people who I would refuse to call "Doctor", and it's exemplified by this article.

Laura L. Callahan was very proud of her Ph.D. When she received it a few years ago, she promptly rewrote her official biography to highlight the academic accomplishment, referring to it not once or twice but nine times in a single-page summary of her career. And she never let her employees at the Labor Department, where she served as deputy chief information officer, forget it, even demanding that they call her "Doctor." ...

"When she was running around telling people to call her 'Dr. Callahan,' I asked where she got her degree," says Richard Wainwright, a computer specialist who worked for Callahan at Labor for two years. "When I found out, I laughed."

This, I suppose, is the twisted flip side of the situation with Jill Biden's doctorate. This civil servant Laura Callahan got her degrees from a non-accredited institution, a.k.a. a diploma mill. Anyone who insisted on being called "Doctor" because they had a degree from a "prestigious non-accredited university" (as they frequently call themselves)... my response might be very similar to the one described above.

More commentary on Dr. Isis's blog On Becoming a Domestic and Laboratory Goddess (here and here). Note: The comments to those posts are lively and frequently profane. But this comment from Ben in the latter post got me thinking:

In general society, people who are smarter than you are more dangerous than atomic bombs.

The original doctors

Cluelessness from the Los Angeles Times:

“My feeling is if you can’t heal the sick, we don’t call you doctor,” said Bill Walsh, copy desk chief for the Washington Post’s A section and the author of two language books.

Yeah, because fact-checking and veracity at newspapers is so last century. It’s all feelings.

At issue is whether Jill Biden (pictured), wife of American Vice President Joe Biden, “deserves” to be called “Doctor” or not. I’ve blogged about this before, so this sort of stuff is no surprise. Disappointing, but not surprising. I still like Russell T Davies’ answer to this sort of small mindedness.

But what I love about the blogosphere is that there’s someone who will not only point out that this is wrong-headed, but give a fairly detailed analysis to drive the point home. From GrrlScientist:

Long long ago (in the early Paleozoic), Islamic law awarded the first Ph.D. degrees in the 9th century; a “Doctor of Laws” degree. Then in the middle ages (shortly after the extinction of the dinosaurs), the Ph.D. or Doctor of Philosophy degree (Latin; philosophiæ doctor, meaning “teacher of philosophy”) was expanded to include all fields of scholarship except theology, law and .. medicine. Let me repeat this in tiny words for the journalists in the crowd: the Ph.D. became THE most advanced academic degree awarded by the vast majority of the English-speaking world and it is required for those Doctors pursuing a career as a university professor or researcher in most scholarly, academic or scientific fields. By comparison, medical practitioners (have) been known as “doctors” only very recently.

More commentary at:

• DrugMonkey
• Uncertain Principles
• Terra Sigillata
• Adventures in Ethics and Science
• Pharyngula
• The Questionable Authority
• The Austringer
• Citizen Sugar
• Oh! Industry

I also have to agree with several of the above commentators that this whole thing shows up some fairly blatant sexism. Women with doctorates of any variety are far, far less likely to be referred to as “Doctor.” Sad to say, I've seen this in play on my own campus.