29 May 2006

The blog as art

NeuroDojo structure graph
Neuroethology.org structure graph
Zen's UTPA webpage graph
Zen's hobby page graphThe graphics on this page shows the way a webpage is written. The first one on the left is the page you're reading (prior to making this post, which should change the structure slightly). I suspect that many Blogger-driven blogs will look the same, due to common blogger templates and such.

To the right of that, with lots of red, is the structure of the International Society for Neuroethology webpage, which I oversee but did not write. The preponderance of red indicates a lot of tables being used to structure the page.

Interestingly, but not surprisingly, authors seem to have distinct styles. The third and fourth graphs are both pages I created -- my academic home page (left) and one of my hobby pages (right). The substantial amount of blue and orange in the bottom two graphs shows that I like links and text, respectively.

The original description of the project, and a link to make a graph of any website you want) is here. It's really quite fun to watch the program run, as the graphic "grows" out, very quickly at first, then finally settling down to a pattern. More discussion, including some very helpful interpretation, is found on this discussion thread on Edward Tufte's website.

27 May 2006

Lies that scientists tell

I wrote previously that honesty is a core value for scientists, but that doesn't mean that scientists don't engage in, shall we say, "spin."

  • "This work could have practical applications." Maybe it will and maybe it won't, but that's not why you did the research, is it, you fibber? You did it to test the dominant theories. It might be a dominant theory in the field that you want to support, it might be a little upstart theory that you think makes no sense or attacks your findings. Most scientists are scientist entirely because they love the ideas. It's the engineers' job to worry about practical applications.

  • "I'm just following the data." The idea that scientists are dispassionate observers does not, in any way, jive with my experience woking with scientists. I've seen and read too many arguments from researchers studying the origin of bird flight to be convinced otherwise. (It seems, from a distance, to be one of the most polarized, divided into us and them warring intellectual camps that you'll find anywhere.) Scientists I know are very often emotionally attached to their theories. After all, as I mentioned a while ago, people like to have their beliefs confirmed. But if you understand science in a deep-in-your-bones kind of way, you know that you have to try to murder your darlings. You have try to strangle your absolute best to see if they really hold up.

  • "Introduction - Materials and Methods - Results - Discussion/"
  • This is the standard format of scientific papers. It's supposed to reflect the order of events that goes on in performing research. Ha! More like, "Methods, preliminary results, more methods, results we had to throw out because equipment broke / animals died / grad student didn't take measurements when he was supposed to / supervisor didn't take measurements that she was supposed to, more methods, statistical analysis of results so far because the poster for the upcoming conference is due next Tuesday, more methods trying to fix the criticism you got from the conference poster, results that you might actually be able to trust, start researching discussion, write introduction to make it seem that this experiment was designed to test a theory that you weren't even aware of until you started researching the discussion."

(This post inspired by several similar ones over at Guy Kawasaki's blog.)

Why a book?

As I mentioned last time, I'm working on a book manuscript. Why am I doing that instead of, say, writing a technical review article for a journal? There's several reasons, but it boils down to public relations.

Books get attention.

Science, Nature, American Scientist, Animal Behaviour, New Scientist are all journals that I read that have book reviews every issue. Just a few off the top of my head. Some even have occasional special book issues. There are many books that even though I've never read, I've read so many reviews about them that I have a decent idea of their arguments and what they're about.

Write a book and you might get invited to talk about it on Quirks & Quarks or the Science Show. Heck, the last third of The Daily Show would not exist if it wasn't for authors plugging their books.

Likewise, relatively few people ever go in and wander around an academic library, pick up a journal with an interesting cover and skim a few abstracts. People go into bookstores and do that all the time.

Sure, the blogosphere is making an ever-increasing impact over the past few years. And there's no getting away from the importance of peer reviewed refereed journals in making or breaking scientific careers. But if the goal is to explain something about my field to those outside it -- which it is -- I think a book may be the best way to go.

It's easy to keep up with my 200 word a day target right now (see graph). This is partly because I'm still at the point where I'm fleshing out a structure and deciding what I want to talk about. It's also partly because as I'm writing, references are going in. References add quite a few words, but don't require any talent on my part except deciding which is the right one to put in and where.

There's going to be two hard parts. One is going to come when I start hitting the limits of what I know from my general background, which will mean I'll have to find a lot of old articles to learn what I don't know. The second is going to be the point where I have the structure in place and I have enough words (or, more likely, more than enough), and have to figure how to say it all in a way that a non-researcher can not only understand, but enjoy.


Meanwhile, I actually had research going on in my lab this week. We finally have tunicates back, so my HHMI undergraduate student Veronica is doing some experiments with them. My graduate student Sandra got the tax return cheque that she needed to fix her rattling car, so she can now drive into the lab. Both she and I are trying to replicate some results for a manuscript that we're revising for a journal. The reviews were positive, but the referees asked us to try to refine a couple of figures.

I hope Sandra has more success than me. I set up one experiment Wendesday, and needed to finish it Thursday. I had meetings almost all that day and I wasn't able to get into the lab until quite late. And the experiment has not worked at all. I didn't get a single datum, nothing that would help the manuscript revision get off.

24 May 2006

Now that I'm on track I can tell you

Spalding Gray, in his monologue movie Monster In A Box, talked about being in Los Angeles and asking random people (the person behind the checkout counter, someone in line in the grocery store, whoever), "How's your screenplay going?"

The usual response: "How'd you know?!"

Everyone secretly working away on their story. I feel a little bit like that now.

I can't remember whether to blame this one Neil Gaiman's blog or Stephen King's writing memoir, but I think it was one of those two who wrote that if you can write 200 words a day for a year, you've got a novel at the end of one year. Somehow, that little piece of advice has ferreted itself away in my head, and I've decided to give it a try.

I'm trying to write a book. Not a novel, not a work of fiction, but a scientific book. (I don't have enough imagination for fiction.) The idea to write a book has been rolling around in my head for a while now. Originally, the idea was to do a review article for some journal, but somewhere along the road, I thought this might work as a full-blown, proper book.

At the end of the semester, I decided to try to get it off the ground. I was promptly waylaid and did nothing on it for several days. But I'm keeping track (that's the graph -- I am that geeky), and trying to keep to that goal of 200 words a day. It's taken until today to get to about where I should be.

I'm hoping that by posting about this process, it'll help to force me to continue steadily writing. 'Cause now someone might, you know, be watching. I know, weird, but I can't explain it better than that.

I'm not going to tell you what the book's about yet. It's too early. After all, I am often overly ambitious and this might just fall apart and I never finish it. But it's better better to try stuff than not try it.

Do i whiiiiiiiiiiiiiiiiiIIIIIIIne?

While browsing the always enlightening Panda's Thumb, I followed a link from there to the equally fine Aetiology and finally a weird editorial on MSNBC.

First, the subtitle says, "Evolution debate doesn't help doctors confronting difficult medical decisions." I think most people with some biological knowledge can immediately think of one case where understanding of evolution would inform a medical decision: do you prescribe antibiotics or not? If you understand evolution, you're more likely to understand why using antibiotics willy-nilly is a bad idea. Antibiotics kill bacteria -- most of them. Some, by natural variation, resist the antibiotics, maybe taking more to kill them. They survive and reproduce. Congratulations! You've created a selection pressure on bacteria that leaves us with antibiotic resistant strains in the long run.

In the first paragraph describes how he was thinking about this as his kid graduated from med school. While I'm always happy to hear about a student completing achievement, it's not at all clear why physicians and medicine is getting dragged in here so forcibly. Tara Smith already pointed out in Aetiology, scientists are not here just to teach medical students, gunfunit.

He wants scientists to talk about values. Hey! I did that a couple of months ago. And I will argue to him that the value of honesty requires that biologists continue to "whine" about intelligent design: because a lie left unchallenged gains the perception of truth.

Besides, I'd prefer to think that I whinge.

21 May 2006

Ancient enemies continue their battle

I live right across the corner from the Edinburg Baseball Stadium. The year I moved here, 2001, was the year the Edinburg Roadrunners debuted. They won the league championship that year, and again in 2004. Imagine my surprise when I walked by the front of the stadium as I routinely do, and saw a sign up proclaiming that the baseball stadium was home to the Edinburg... Coyotes.

Sheesh. Don't they know coyotes never catch roadrunners?

(With appreciation to the late, great Chuck Jones.)

Couldn't resist. Actually, the Coyotes are actually the winners this time. The poor Roadrunners are defunct, as is the league they played in. More on the Roadrunners / Coyote dispute here. And, joking aside, the Coyotes did win earlier this week.

Thinking scientifically

We are living in an age where people routinely ignore facts and ideas that are inconvenient or uncomfortable to them. It's easy to do: people like to have their beliefs confirmed, not challenged. (If I had stayed in my original field of psychology, I think I would be studying the psychology of belief.) But of course, the natural world doesn't care what we believe. Hence, the need for scientific thinking. Here, I wanted to put together a few short points geared towards helping someone think a little more like a scientist.

What is the evidence? This is a crucial first question to ask about any claim. We all have a tendency to trust, and to take things presented to us at face value. That's why it pays to stop, give your head a shake, and say, "Waitaminute. This is all very interesting, but does it have anything to back it up?"

Extraordinary claims require extraordinary evidence. This is an extension of the first point, but it's important enough to merit its own paragraph. As I mentioned above, we like to confirm our beliefs, so there's a real temptation to "clutch at straws." You compile all the evidence in favour of a belief, and ignore all the problems and contradictions the evidence presents. For instance, there's lots of evidence that the Loch Ness Monster exists. Now, hear me out! The problem is that the quality of the evidence is weak compared to the claim. Eyewitness reports are notoriously unreliable; most pictures of the monster are ambiguous. (That's for the pictures that have not been revealed as outright hoaxes.) Saying, "There is a large undescribed animal present in a Scottish loch" is a big claim. To convince me of something that big, you're going to need something equally big to prove it.

If you didn't manipulate anything, it's not an experiment. In an experiment, someone deliberately manipulates something. In the simplest form, you set up two groups, and you make it so one one group gets a treatment, another doesn't. Experiments are important for science because they can establish causal relationships. But research does not necessarily mean an experiment was done. A "study" does not mean an experiment was done. That's not to say it's bad science or weak evidence -- not at all. But there's a limit to what you can conclude, because...

Correlation does not imply causation. Just because two things go together does not mean one caused the other. Now, it's a strong hint that one might cause the other, but that's about as far as you can take it without an experiment. You see correlation and causation confused all the time. Watch any political show. "Since we introduced tax cuts, unemployment went down." The implication is clear: tax cuts caused the change in employment rates. They may have done, but it's very difficult to prove that causal link.

19 May 2006

A goal

That I can be as good a looking Canadian scientist as David Suzuki.

A trip to the island, but no beach time

Went to South Padre Island today, and this time, I wasn't there digging up the beach. Instead, I was there for a networking lunch at a little conference my buddy Mike (King Midas) Persans was hosting on plant membranes. While I had nothing to do with plant membranes, they had one of the program directors from the NSF there. I welcome a chance to hear the sounds directly from any goose that might one day lay a golden egg.

If nothing else, I did confirm that an impression I had was not just a hallucination on my part. The NSF has plenty of programs for undergraduate research, and doctoral research, but ignores Master's students. Since I coordinate a Master's program... well, you can see where my (self-)interest in such things lies.

18 May 2006

Aw, maaaaaaaaaaaaaaaaan...

Had my wallet stolen tonight out of my gym locker. Locker door was forced open. Major hassle. Enough said.

Additional, 27 May 2006: I phoned all my credit card and bank card phone numbers the evening of the theft, Thursday night. Discover Card had a new card in my hands by Saturday morning. Chase Master Card and my Bank of America bank card didn't hit my mailbox until Wendesday. Just in case you're wondering about replacement services.

16 May 2006

Best research article title of the month

"Twenty-eight retinas but only twelve eyes: An anatomical analysis of the larval visual system of the diving beetle Thermonectus marmoratus (Coleoptera: Dytiscidae)" by Karunyakanth Mandapaka, Randy C. Morgan, and Elke K. Buschbeck in this month's Journal of Comparative Neurology.

13 May 2006

New technical work online

My latest research article, another on a digging crustacean, can be found here. Or at least, you can find the abstract there. And if you've got $25 burning a hole in your pocket, you get the option of buying a reprint of the whole article. Digital object identifier 10.1163/156854006776952874 -- accept no substitutes!

I'm slowly starting to get my head back up to look around and see what's going on since the semester officially ended yesterday. I should have many more updates over the next few days.

12 May 2006