History of the world (compact version)

The history of the planet in one minute flat, over at Seed Magazine. (Spotted at Why Evolution Is True.)

Geologic time is hard for us to grasp, because the timespans are so vast. Everyone resorts to metaphors of one kind or another for comparative purposes. Verbal ones are okay, but I really like how immediate this one feels.

The feeding frenzy resumes

I have already received multiple emails and read several articles about the hit of money the U.S. federal funding agencies are getting through the economic stimulus package. I was, and, I think, to some degree still am, optimistic, but am starting to feel worried.

In the 1990s, the National Institutes of Health (NIH) budget doubled. Universities have a lot of smart people in them. They saw the money, and they responded. They hired people and put up buildings based on the promise of NIH money. What few seemed to realize is that everyone else had the same plan.

In the 2000s, the NIH budget stayed flat or shrank because of inflation. Suddenly, all those people who were counting on NIH money faced a low probability of success. So even though the NIH budget was about twice what it had been, the number of people chasing the dollars had gone up more than twice, so the chance of successfully getting funding actually went down.

It’s almost impossible for outsiders to know how much angst and pent-up demand there is among researchers over research budgets and grant success for federal agencies. Many departments basically fire people if they don't get federal grants, even though the funding prospects have been so bad. In essence, the NIH is making tenure decisions for many researchers.

I think researchers are going to be so relieved by hearing about the federal budget increases, so excited by the prospect that writing a grant proposal might be a better way to get money than buying a lottery ticket, that there could be a huge surge of new grant applications. I worry that the stimulus package is not going to be nearly enough, and that it will create its own little bubble in the research community.

The fate of flash drives

You wouldn't expect an article on computer backups to contain a good one-liner, but this one does:

Be wary of memory sticks. Once full, they fall prey to the same monster that eats socks.

Sink or swim

ScienceWoman, then Neurotopia, have posts on lecturing that generated a lot of comments. Useful stuff for anyone starting out to teach. I think everyone develops their own answers to lecturing, but I want to point out a couple of broad patterns of thought, using swimming as an example.

You can teach people to swim by throwing them into the deep end of the pool where the diving boards are. Some will learn by this method, but many will drown.

You can also teach people to swim by starting them in the shallow end of the pool and actually instructing them. It’s slower, but you'll probably end up with more people actually swimming by the end of it.

Many university instructors teach using option one. This is frequently supported by statements like they want to challenge the best and brightest students in the class; that they are maintaining the quality of education and refusing to dumb down their instruction; students have to be responsible adults who learn on their own; and so on.

I personally find this a terrible wasteful of human potential.

Incoming publications

A week ago last Thursday, I got both copies of the reprints of my latest article. Yes, I know people are going to download the PDF of my article, but dang it, I still like having the paper reprints. The publisher, Karger, does such a nice job on them... If you would like a reprint, just email me and I'll stick it in the mail.

The same day, I also got an unexpected bonus: a copy of Sean Carroll’s Into the Jungle (see here describing his talk based on material in this book). I got sent a copy because the publisher is hoping to use it as a textbook or textbook supplement, I think.


Monday night, I found out that the Open Laboratory 2008 is now available for sale. Again, I know you can read every entry in their original form on blogs, but the editors did such a nice job on the compilation...


And finally, the actual issue that my latest review is in came into my mailbox yesterday.

I'm not quitting my day job regardless of this estimate

The value of the NeuroDojo blog, according to $timator:

$4,571,815

Check yours?

Um.

No.

There’s no way that’s even close to reality. My blog is not worth $4,571,815. I agree with Beth’s Blog on this one.

If you are attempting to translate benefits into dollar amounts, particularly intangible benefits - make sure you have a credible formula that you can explain to your executive director in under 5 minutes and that is credible.

By comparison, here’s the estimate for the main page of the institution I work for:

$38,413


Check yours?

My blog is not worth 100 times more than my university’s main page ($38,413). Even I don’t have that big of an ego to think so. My blog is also worth more than Richard Dawkins’ main site ($187,860), the Pharyngula blog ($2,361,839), Science magazine ($933,301), the National Science Foundation ($242,149), and the government of Canada ($191,781).

I suspect the issue is that because this blog is hosted on blogger, it’s somehow incorporating values for all of "blogspot" in its calculations, inflating the estimate horribly. My Marmorkrebs blog is valued at $4,570,988, but the main Marmorkrebs page at $254.

They try to explain this, but in a terribly confusing way:

For a sub-domain you have to take under consideration if you are in a (for example) tumblr or blogspot context or in a situation where the sub-domain is an important piece of the main domain otherwise the final estimator value could be higher.

Pardon...?

I don’t think the site maintainers’ main language is English.

Circus of the Spineless #36

Check out the blog carnival of crunchies and squishies at Invertebrate Diaries.

Teaching with Twitter

Twitter is definitely the flavour of the moment. And I’ve succumbed, adding it to this blog, with the original idea that students could use it to check whether I’m in my office or not.

Recently, Twitter head honcho and Blogger creator Evan Williams gave a TED talk (below), which ends with an examination of Twitter feeds about his talk, which prompted this article about Twittering during presentations, which prompted this tweet, which led to me writing this post.

Currently, I ban laptops from my classes, but I use clickers to ask questions and tally feedback.

Now, it’s dead easy to Twitter from a mobile phone. Most Twitter users do it that way instead of through a computer. And I’m willing to bet that 99% of my students have a phone within reach during my lectures.

Consider this scenario. An instructor is giving a talk. When the instructor wants a question answered, students Twitter their response instead of using clickers. Ideally, this would involve some software that could recognize some special symbol or code associated with a class, so that responses could be tallied and a graph could be generated on the fly. I’m guessing that such software isn't out of reach for good programmers. Conceptually, it seems actually pretty simple.

As suggested in the article, students are encouraged to send in their questions by Twitter, which the instructor can check periodically. This allows her to address questions that students have on the fly.

“But why don’t students in the room... you know... stick up their hands and just ask a question?”

First, never underestimate how intimidated students are of their instructor. (I’m becoming ever more convinced this is one of the biggest obstacles to learning.)

Second, sticking up your hand and speaking out gets harder to do as the class gets bigger. If there’s a class of, say, 200 students in a lecture theatre, students may worry that their questions will disrupt the flow of the lecture. This is a legitimate concern. I think everyone will have seen a moment where an instructor can’t answer a question quickly, or some student has something important only to them that they’re fixated on, and the instructor says, “Come see me and we’ll talk after class.”

The potential downside to using Twitter while teaching is obvious. People won’t pay attention. I’m totally unconvinced by the claim that Twittering during a talk helps people focus. And while people may think it’s their right to ignore a boring presenter, it’s a really bad thing to happen in a teaching situation.

I wouldn’t try this in a class of 30 students, say, because ultimately, students do need to learn to ask questions by opening their mouths and saying what’s on their mind.



More thoughts on the so-called “backchannel” here, here. Of course, I find these after I’ve pretty much completed the post above, and feel foolish for feeling that I’ve been ignorant of something going on for a while. I didn't even know the word “backchannel” before this week.

Reassessing a font

My interest in graphics lead me to be very curious about Eco-font when I read about it on the TED blog late last year. Ecofont is designed to cut ink use; the main website claims it can be 20% less.

When I first downloaded and tried it, I was disappointed. It renders very badly on a computer screen, and looks relentlessly washed out and gray. I recently changed my mind, however, when I saw it actually printed. Using a standard inkjet printer and regular font sizes (11 or 12 point), it is quite readable, much more so than on the screen. At larger sizes, however, the ink-saving holes become more visible and legibility starts to become an issue again.

I’m not using it for things that will probably remain digital (manuscripts that will be sent by email, etc.). I do plan on using it for forms and things that I have to print.

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.