Evolutionary gems

Nature has just published a freely available PDF about evidence for evolution called, "Evolutionary gems." This is their first official issue of 2009, which will be (in a few hours) the 200 anniversary of Charles Darwin's birth and the 150th anniversary of his "abstract," On the Origin of Species by Means of Natural Selection.

And I mention this mainly because it's interesting, but secondarily, by doing so, I reach an nice even number of posts for this blog this year: 300.

Now, I'm off to pick up posters for the SICB meeting.

Dissertation variation

Over at Uncertain Principles, check out the comments section in the post about whether doctoral students should publish papers before defending their dissertation. It's very interesting, because, as I mentioned in my comment, I had never heard of any place that required publication before defense. Yet apparently many do.

I wonder if this is a question of different practices in different disciplines, or whether it's just institutional variation.

A personal review of 2008

Despite a fair amount of good news professionally, it's been a long, tiring year.

Two papers finally came out, after way too many months of me not finishing revision. One is a quite substantial review article on the evolution of crustacean tailflipping that I'm quite happy about, from a writer's point of view. I think the explanations are clear, with good turns of phrase. Figure 1 was a bear that went through many revisions, but I'm pleased with how it finally turned out.

The second paper, on larval ascidian settlement, I'm pleased with because it came from work I did with my former high school intern, Amanda. And it's just cool to have a high school student as an author on a peer-reviewed journal article.

I got a small grant for my Marmorkrebs research. I got good feedback on the Marmorkrebs blog, and the Marmorkrebs research is chugging along well.

I had a set of damn fine research students, and my first Master's student, Sandra, successfully defended her thesis. Working with them has probably been the best thing about the year.

I blogged a lot here, on Marmorkrebs, and for my REU program.

I got tenure. In a year of economic meltdown, the prospect of a little security is welcome. But I still have mixed emotions about it.

And I taught non-stop. I taught in spring, I taught both summer sessions, and I taught through a fall semester that forced me into hiding.

So yet again, I can't wait to see the back end of this year. Roll on 2009.

No limitations in Texas science standards

Just before Christmas, the National Center for Science Education reported that the latest draft of K-12 science standards for Texas has removed the "strengths and limitations" wording found in an earlier draft.

This is a pleasant surprise. Maybe the turnout at the public hearings actually accomplished the change. Hard to say.

Blog in review 2008

Late in 2007, I decided to try to ramp up my blogging. I wanted to do more substantive posts more frequently. While others will have to judge whether I was more substantive, this was certainly the most active this blog has been by far, pushing close to 300 posts.

Of course, it was helped by the amount of stuff going on in Texas concerning the forced resignation of Chris Comer, the efforts of the Institution for Creation Research to offer Master's degrees in science education, and the ongoing review of the Texas K-12 science standards. All three stories focused attention on the relationship between science and creationism. I could have written much more about this, but I wanted to keep focused on those that were occurring here in the place I live.

Some favourite posts of mine from this year follow. Following convention, I've cut it to 10 examples.

January

The point of doubt

February

Deep research
Lecturing doesn't matter

March

Why am I blogging about buying a car?

June

Making mimetics scientific (The one I nominated for the Open Laboratory 2008)
The big four questions

July

Anniversaries: One even number, one odd
A word is needed for an inability to think graphically

August

Tools of the trade

October

Don't hate beauty

Cityscapes and recession

Over at Ockham's Razor, Peter Newman makes a case for urban sprawl being a contributing factor to the current financial recession. Really interesting, one of my favourites on this show for a while.

Briefly, he argues that people will only spend about an hour commuting to work on a daily basis, regardless of whether they walk, take trains, drive, or what have you. The current city design -- expanding circles around a core central business distract -- was made possible by cheap fossil fuels. The far edges of cities were all about cheap housing, so people who moved there were often more economically vulnerable to start with. Now, combine people with mortgages (especially those sub-primes we hear about) with increases in fuel costs. The rise of fuel prices disproportionately squeezed on people who were already struggling to make ends meet, and suddenly a lot of mortgages don't get paid. And that may have helped collapse the whole thing...

Did earthrise change us?

A lot of posts are commenting on the anniversary of the famous picture of Earth from space (here's one, two, and three). Many people claim this picture changed how we view the world. Admittedly, I was only 2 when this picture was taken, but I don't know if it changed things as much as we would like to think.

I think there was sense in the few years of the Apollo missions that this was just the start. But it hasn't worked out that way. True, we have a lot of fantastic robots exploring the solar system. True, India and China have started to pick up the slack left by the U.S. and the Soviet Union. But that's a far cry from what we were expecting. People were expecting us to have a permanent presence on the moon and be well on the way to a manned mission to Mars in the first decade of the 21^st century.

People also talk about this picture being the start of the environmental movement. But it's been 40 years, and I only have to say "climate change" to point out that people's goodwill towards the environment hasn't exactly resulted in great outcomes.

Maybe I am just too young to fully appreciate the differences in mindset that occurred 40 years ago. Or maybe this is just my "Bah, humbug" post for the year.

Heroes! Villains!

This article is worth checking out for the title alone: "Science heroes and villains of 2008."

I didn't make either list. Hmmmm. That may be my first New Year's resolution.

Envy

Jennifer Mather gets to speak at TED 2009.

Jennifer is my former boss, from way back in my undergraduate days^*. She helped get me rolling on this research thing.

Words cannot describe how incredibly jealous I am.

Congratulations, Jennifer! I can't wait to see your talk on the TED website!

^* My student Sakshi gleefully reminded me recently this was 20 years ago.

The Zen of Presentations, Part 23: Bad presenter thought

The opposite of a great presenter is a bored presenter, not a scared presenter.

Advent days

Last week was busy. Two students are prepping papers for the SICB meeting in Boston in January. A third student was gathering data that will go onto an abstract for the Texas Academy of Science meeting in March. I try to help...



Yes, that's a heater at right. I know you're thinking, "Why do you need a space heater in southern Texas?" Because the first time it got chilly this month, the building heating didn't work right, and the temperature dropped in the lab quite substantially. And while uncomfortable for us, that's not as important as the animals -- which really don't do well when they're cold.


These crabs don't measure themselves, you know...

Photos by Kevin Faulkes. Thanks Dad.

Teaching rubbish doesn't help students think

Arnold Loewy has an opinion piece in the Lubbock Avalanche-Journal (which may well be the coolest name for a newspaper I have yet heard).

Although the name of the newspaper may be cool, the column is not.

Currently, a national debate is raging over whether or not to teach intelligent design in public schools.

I haven't seen much debate on that front since the Kitzmiller v. Dover trial. I see a lot of people who want to attack the teaching of evolution, though.

To begin with, it is important to disabuse ourselves of the notion intelligent design is an alternative to, or the opposite of, evolution. The opposite of evolution is creationism, the theory that the Earth was created in six days, less than 6,000 years ago.

This is a peculiar opening gambit: to claim that some complex scientific idea has a necessary logical opposite. What's the opposite of germ theory? The opposite of atomic theory?

Be that as it may, there's a strange backhanded effort to claim that intelligent design is not an alternative to evolution. But that is expressly what it is meant to be.

The opposite of intelligent design is no intelligent design, or atheism. It is possible to believe that an intelligent designer designed evolution as many (I have been told, including Darwin) believe.

And here we have the classic wedge strategy: it's any religious belief you might happen to have, or evolution and godlessness. As always, this does a huge disservice to the wonderful variety of human beliefs.

Most of the objection to teaching intelligent design is predicated on the ground that the subject matter is religious, and should be taught only in church. I disagree. The characteristics of the intelligent designer are most assuredly a matter for religious training and belief. On the other hand, most religions posit the existence of an intelligent designer (usually denominated God), but do not seek to examine all of the scientific/philosophic evidence for or against that supposition. In short, they accept it on faith.

It's like he's destroying his own case. So... I think he's arguing that ID is religious... but that somehow that doesn't matter because...? I really don't understand the argument here.

While faith is everything in religion, it is not everything in schools. Every proposition has to be empirically examined to determine its validity. Thus, when intelligent design is examined in school, there is no a priori assumption of its correctness, or incorrectness. The evidence is examined and the chips can fall where they may.

But why teach discredited ideas in a school setting? Should we teach phlogiston theory?

The reason that I am so supportive of teaching intelligent design in public schools is because I studied essentially the intelligent design/no intelligent design debate in an English literature course at Boston University.

Stop! There is a huge difference between teaching something at a K-12 level and at the university level. What is perfectly appropriate for one level does not export well to all levels. Plus, the rules for universities are totally different than they are for K-12 public classrooms.

Frankly, this course of action is not risk-free for fundamentalists. Although I concluded that it was more likely than not that there was an intelligent designer, I suspect some of my classmates were not similarly persuaded. Consequently, if we do adopt the "teach the controversy" perspective that many fundamentalists are advocating in regard to intelligent design, there is a real risk that some percentage of the students will conclude that there is no intelligent designer, and hence no God.

For me, this is a risk worth taking.

That he characterizes this as a "risk" shows a lot going on here. Being religious is good. Not being religious is bad. So this clearly shows that proposing to teach intelligent design cannot be taught in K-12 public classrooms, for the same reason creationism can't be taught in classrooms: it is about using a public government institution to promote particular religious views.

Science teachers who don't understand science

The San Antonio Express News has an opinion piece by a public school teacher, one Scott Lane, about the "strengths and weaknesses" -- oops, "strengths and limitations" -- language that the Texas State Board of Education wants to put into the K-12 Texas science standards.

Mr. Lane is a science teacher, but he shows effectively no understanding of the state of modern science.

We... can present several hours of scientific evidence which supports creation. Included in these will be the fact that evolution violates the 1st and 2nd Laws of Thermodynamics, as well as the Law of Biogenesis. We can show you creation evidence in the fields of microbiology, genetics, probability, biochemistry, biology, geology and physics which support creation and undermine evolution.

Just... wow. This is one of those points where you don't even know where to begin.

Ups and down in teaching

Watching Ben Zander in his Pop!Tech talk the day after submitting final grades for my classes is a humbling experience.

@ Yahoo! Video

This week, I have worried a lot about teaching. Am I being fair and consistent in my grading? (That's a big one for me, as I know unfairness drives students absolutely nuts.) Did I ask reasonable amounts of work? Was I too soft?

Zander makes me think those are not the first questions I should ask. The first one I should ask might be, "Did I lift students up, or did I grind them down?"

I may have done more grinding than lifting this semester.

How interesting.

Missing the point of Science Commons

I've watched the Science Commons video (below) and visited the Science Commons website.

And I don't get it.



The video talks about knowledge in "silos," that highly overused business term. I think the "silos" they're talking about are for-profit journals that are protected behind password-protected subscriptions and pay per view deals. But it's maddeningly vague about this. If you mean you want open access publishing, say open access publishing.

The video talks about sharing data. For me, the big problem is still generating data. It feels like this is talking about automated, high throughput molecular data, not those who do any other kind of science.

U shaped

Why does it always seem that when marking assignment, you get a couple of really good papers right off the bat, followed by lots of utter dreck, before a few people near the end restore some semblance of hope that someone was paying attention?

Michael Rennie was ill...

The Day the Earth Stood Still – the original – was made at a critical point in Earth’s history.

Humans had split the atom, but hadn’t gone into space.

What a wonderful combination of terror and optimism. We saw the potential for complete destruction, yet I think there was really a sense of incredible potential then. People could almost taste space travel. And really, isn’t there a hint of pride that other civilizations could actually perceive us as a threat?

Today, I think we feel the threat, but not the sort of hope the early 1950s had. I don’t think we think of ourselves going into space, expanding ever out, they way we did then. Space travel has proved difficult.

It’ll be very interesting to see what zeitgeist the remake opening today tries to tap into.

This quiz must be faulty

D'oh!

Which College Major Should You Be?
	Your major should be Engineering. Logic is your friend. With enough work, you can find a solution to anything... Unless it involves dating or parties.
Find Your Character @ BrainFall.com

Well, too late now...

Make me laugh

In one of my classes, I had my students blogging throughout the semester. Last week, since it was the end of semester and I reckoned everyone could use a break and do something different, I threw down the gauntlet and issued a challenge.

"Make me laugh."

Oh, that was fun.

I got Canadian cartoons and signs.

I got profane Muppets.





And I got a couple of posts mentioning this picture, which I used in during lecture twice (only twice, really).


So that's what they're referring to here and, my personal favourite, this post.

Fail, 8 December 2008 edition

One of my students is trying to share some work with me through Google Docs. I try to login, and can't. I contact the specified email address. I am told, "You have to share the documents with their @gmail.com email addresses."

He apparently hasn't looked at the login screen.



Fail.

Even the might of Google is no match for institutional cluelessness.

On the fence

One of my earlier articles concerned the evolution of intelligence on other planets. This lengthy blog post picks up on some of those ideas.

Farewell, Forry

Forrest ("Forry") J. Ackerman has died at 92 (reported many places, including here and here).

If you knew Forry Ackerman, you were one degree of separation from everything connected to science fiction and fantasy in the 20^th century. He was an architect of today's society. George Lucas, Steven Spielberg, and thousands more like them learned about movies through Forry's Famous Monsters of Filmland, for decades the only SF magazine about film and TV until Starlog came on the scene.

I can't say I knew him, but had the honor of seeing and meeting him a couple of times.

The first, at Norwescon, he brought the voice of H.G. Wells to the fans. Ackerman had seen a talk by Wells when he was young, and decided that he would try to memorize the way Wells spoke and some of his words. he had been inspired by one child who was so moved by Lincoln's Gettysburg address that he memorized it and would recite it in Lincoln's style to preserve it. Ackerman relayed his surprise that Wells had a thin, high voice, almost like one of old ladies in Monty Python skits. And the phrase was something like, "I am going to talk to you about the war. [Not certain if it was "war," actually.] East is east. West is west. And the two are coming together with a bang."

Additional: A better recounting of Ackerman's anecdote is here.

RYAN: MR. ACKERMAN, YOU HAD THE OPPORTUNITY TO HEAR [AUTHOR H.G. WELLS) SPEAK. WHAT DO REMEMBER ABOUT THAT?

Ackerman: It was 1938. It was predicted that 100 years into the future that on top of Mt. Everest, a statue would be erected in his memory, 'First of Civilized Men.' When he spoke, because he had given us WAR OF THE WORLDS and TIME MACHINE and so on, I thought he'd have this deep, sonorous, Orson Welles personality. I was very surprised to hear he had this squeaky little voice. He had this small rolly-polly, bloody complexion and said [in a high accented voice], 'I am going to talk to you for about an hour. Today, East is West, and West is East, and they're coming together with a bang.' He was very prophetic, because unfortunately we went to war with Japan.

The second time, at Con*Cept, I had more opportunity to hear him. He was in Montréal tracking down a rare edition of Mary Shelley's Frankenstein. He gave an hour long panel talking about some of his many experiences. He talked about his love of Esperanto, and complimenting a beautiful woman in the audience in Esperanto. He expressed how disappointed he was with Tim Burton's movie Ed Wood, a depiction Forry said was terrible. (Forry had been Wood's agent.)

I asked him if, in building his renowned collection of sci-fi memorabilia, there were any pieces that he had tried to get for his collection that "got away," as I phrased it. His reply was not what I had expected, and he talk about items that had literally got away because someone had stolen them from his house.

At the end of his panel, I was able to get an autograph from him on -- of all things -- a Vampirella trading card. (Vampirella was a character Ackerman named that was undergoing a resurgence of popularity at the time.)

Robert J. Sawyer's post on meeting Forry gives a good sense of the well known generosity of the man.

I have to disagree with the reports that say he died from heart failure. A heart like his would never fail -- only stop.

No more waking from a dream

Arguably anyone who has studied psychology or neuroscience has probably heard of HM, a patient who lost the ability for form new memories. He died Tuesday, 2 December 2008, at the age of 82.

His real name was Henry G. Molaison.

See here, here, and here.

Here is a famous quote from him, speaking on his own condition:

Right now, I’m wondering, have I done or said anything amiss? You see, at this moment everything looks clear to me, but what happened just before? That’s what worries me. It’s like waking from a dream. I just don’t remember.

Help the National Academies of Science

The National Academies are running a short and sweet poll on current science issues to find out what resources they should be focused on developing.

One of the interesting things is that when you reach the end, they should you how people have voted so far. I won't spoil the surprise.

Check it out and vote.

Lectures are over!

Just gave the "dead dog" lecture to my last class. I still have a huge amount of marking to do (about three major assignments), but at least there's no more prepartion to do, and the end is now in sight.