31 March 2009

Neurochemicals and Superman villains

Patsy Dickinson, I always like talking to you at meetings. But couldn’t you and your team have given the new peptide a name that a human being might actually have a prayer of remembering? Or, you know, pronouncing?

SYWKQCAFNAVSCFamide?!

It’s the Mr. Mxyzptlk of neurochemicals.

I wonder what will happen if I say the name of the chemical backwards...

Reference

Dickinson PS, Wiwatpanit T, Gabranski ER, Ackerman RJ, Stevens JS, Cashman CR, Stemmler EA, Christie AE. 2009. Identification of SYWKQCAFNAVSCFamide: a broadly conserved crustacean C-type allatostatin-like peptide with both neuromodulatory and cardioactive properties. The Journal of Experimental Biology 212: 1140-1152. doi: 10.1242/jeb.028621

In which claims are verified

Some time ago, I bemoaned that about one in three Americans don't know where food comes from. Recently, I found some photographic evidence of that fact.

Yes, even more Texas science standards voting aftermath

Christopher Hitchens writes about the new Texas K-12 science standards in Newsweek here. Hitchens has a talent for finding devastating turns of phrase and unusual angles of attack, and this isn't an exception.

The Texas anti-Darwin stalwarts also might want to beware of what they wish for. The last times that evangelical Protestantism won cultural/ political victories – by banning the sale of alcohol, prohibiting the teaching of evolution and restricting immigration from Catholic countries – the triumphs all turned out to be Pyrrhic. There are some successes that are simply not survivable. ... There are days when I almost wish the fundamentalists could get their own way, just so that they would find out what would happen to them.

Also, an editorial from last week in the Dallas News that I missed.

There's also this comment from the Minneapolis Church and State Examiner.

Something there is about the Texas mentality that discounts the life of the mind.

Here’s a snippet of some quite good analysis in
  • Ars Technica:

    (T)his focus on multiple theories makes frequent appearances when elected bodies, like school boards and state legislatures, attempt to modify science education. It suggests that, when faced with the fact that science has adopted a theory that the officials dislike, they assume there must be another, competing theory that is more amenable to their beliefs.

  • Popular Science (?!) and USA Today, the latter saying:

    The issue is so complicated and controversial, however, that we thought we’d give you a flavor of the issue by showing you how various news organizations reported the final vote: [snip]


    Newswise provides a quote one-liner to summarize:

    NCSE’s Josh Rosenau summed up the frustration of scientists and educators alike: “This is a hell of a way to make education policy.”
  • 30 March 2009

    Can Master’s degrees make a comeback?

    Professional Science Masters logoThe frequently asked questions regarding the National Science Foundation and the Recovery Act mentions a Science Masters program. Intriguing.

    I’ve commented to NSF staffer multiple times about Master’s degrees. The NSF have lots of programs for undergraduate research (I run one), and how they have programs for doctoral research, but Master’s are almost completely ignored. For department like mine, which has a Master’s program but no doctoral program, this is a real issue.

    The problem is that in many institutions with doctoral programs, Master’s degrees are viewed as a consolation prize. It’s lovely parting gift for those who can’t
    hack it in the Ph.D. program. And that point of view seems to have permeated the funding agencies.

    But in an institution like ours, a Master’s degree for our students, can be an important stepping stone to a doctoral program at another institution, or the key to a higher entry level in a job. It’s not an “also ran.”

    Perhaps not coincidentally, Science magazine featured a policy forum on Master's degrees this week. The model it explores is something called a professional science Master’s degree. At a glance, it seems to be a degree for industry technicians (and, just to be clear, I am not disparaging that). Students take academic courses in their scientific discipline as well as in business.

    The NSF will have $15 million to fund new professional science Master’s programs. My concern is that this doesn’t address – or justify – continuing to ignore the more traditional academic Master’s programs.

    29 March 2009

    More aftermath roundup on Texas K-12 science standards

    The image is from the Bad Astronomy blog, which comments (original emphasis):

    Do I sound unhappy? Yeah, damn straight I am. These creationists are trying to destroy science in Texas. And they’re succeeding. They are imposing their narrow religious and ideological views on reality, and it’s the schoolchildren in the state who will suffer. ...

    It seems incredible that here we are, in the 21st century, and a group of less than a dozen religious zealots has the kind of power to affect millions of children across the country, but there you have it. One problem with a democracy — and it’s a doozy — is that it’s possible to game the system, and give far too much power to people who are far too unqualified for it.

    And it’s brought us here.

    A warp-up on Thoughts From Kansas reminds us:

    Texas has new science standards. Those standards are better than the old ones, but those old standards really did suck.

    I referenced a New Scientist article before that described the standards as containing “loopoholes.” But I wanted to call out one point (emphasis added):

    Experts suspect that strategically, the Discovery Institute actually wants teachers to be prosecuted in a Dover-style court case, and that they are using the proposed Texas academic freedom bill to lure teachers into a legal trap by encouraging them to bring religious ideas into the classroom. ...

    “The Discovery Institute is pushing the legal envelope and inviting litigation because they have been shopping around for years for the right judicial district in which they could win this kind of case,” (Barbara Forrest, a philosophy professor at Southeastern Louisiana University) told New Scientist. “They need a district where they can control the people on the ground, as they do in Texas. They want a ruling that conflicts with Dover in a different judicial district, because that would be the most likely scenario in which the Supreme Court would hear a case. That is exactly what they want.”

    Elves and hidden people

    Houses of hidden peopleOne of the things I do to try to challenge myself and expose myself to things I would not normally encounter is to listen to the CBC podcast of The Current. Yesterday was another one of those time when I learned something new.

    A majority of Icelanders believe in elves and hidden people. Companies pay real money to hire people with psychic powers to determine if their buildings and constructions would interfere with the domains of elves and hidden people – which live in another dimension. Apparently the Icelandic term for this is “Huldufólk.”

    Of course, I’m one to talk.

    28 March 2009

    Aftermath roundup on Texas science standards

    Don McLeroy and Gail LoweThere will probably be more articles early next week reacting to the votes on the Texas science standards. For today...

    This Salon article described how excited the Discovery Institute is over the new standards. And provides yet more quotes by Don McLeroy that make me wonder why what he says isn’t being criticized by more scientists.

    “Scientific consensus means nothing,” he tells Salon. “All it takes is one fact to overthrow consensus. Evolution has a status that it simply doesn’t deserve. People say it’s vital to understanding biology. But it’s genetics that’s the foundation for biology. A biologist once said that nothing in biology makes sense without evolution. Well, that’s not true. You go into the top biology labs, and it makes no difference if evolution is true or false to what they’re doing and studying. It makes no difference."

    I’d love to know what “top biology lab” McLeroy has ever gone into.

    Why Evolution is True has a good summary about the two worst additions to the standards. The good news, such as it is, is that the wording specifically says “scientific explanations,” which should cut out the worst possible offenders.

    The Houston Chronicle features an AP wire story. They have another story here.

    The Austin American-Statesman, naturally, had is own reporters there for this article. And what I read makes me proud of the representative whose district our university sits in, Mary Helen Berlanga:

    Mary Helen Berlanga, D-Corpus Christi, was one of two board members who consistently voted against the rewrites proposed by members critical of evolution today. She also voted against accepting the document in its entirety.

    New Scientist has an article here.

    Pharygula also has some analysis, including a comment on one of the Chronicle stories:

    (T)he Houston Chronicle blandly reports that "Scientists from throughout Texas helped shape the new science curriculum standards." What they don't bother to mention is that these insertions into the standards were generated in opposition to the input of scientists, in defiance of what the scientific position would propose.

    And, lest I leave you thinking that only biologists are targets of contempt, the Marshall News Messenger notes that the new standards also attack climate science. In particular, it is official educational policy to cast doubt on global warming.

    Language that instructed students to “analyze and evaluate different views on the existence of global warming,” which had been offered as an amendment and was adopted unanimously in an initial vote Thursday, led to outrage among environmental groups.

    Texas has been oil country for a long time. Old habits die hard, I guess.

    Additional: ScienceInsider policy blog calls it a win for creationists.

    27 March 2009

    See you in two years for the textbook fight

    Damning with faint praise: “It could have been so much worse.”

    The final votes on Texas K-12 science standards are done. “Strengths and weaknesses” didn’t make it in (yesterday), and neither did a lot of other non-scientific amendments. But things got watered down.

    I must remember to write an email to Rick Agosto, the Republican who voted against arguably the most non-scientific language and who must have received incredible pressure not to do so. Interestingly, he represents the northern half of the county our university is in, although the university resides in Mary Helen Berlanga’s district.

    And here, perhaps, is a good summary of the entire anti-intellectual, unprofessional, disrespectful nature of these events... Don McLeroy, quoted on the Texas Freedom Network and Thoughts From Kansas blog:

    I disagree with all these experts. Somebody has to stand up to these experts.

    ...wow.

    A man charged with an important supervisory role of a massive education system says he doesn’t value expertise. Experts are the enemy.

    Isn’t one of the points of education to create experts?

    How can we make expertise and skills and professionalism respected again?

    Textbook adoption in two years. But it looks like there won't be too many more posts with the “Texas science standards” label in the near future.

    Festiba!

    Our university has an arts festival called Festiba. This year, a group of students, who taking two courses that have been joined at the hip – one on evolution and one on linguistics – put together several displays relating to evolution in some way, but with an artistic bent. This is not all of the coolness that was there on Thursday, but some pictures came out better than others for blogging purposes. And several have to be seen close up to really be appreciated.









    Very cool.

    Photos by Deborah Cole (but with a camera supplied by yours truly!).

    26 March 2009

    Roundup of Texas science standards articles



    25 March 2009

    Am I a far left academic or a secular elite opinion maker?

    On the first day that the final hearings on the Texas K-12 science standards begin in Austin (covered in blog form at Evo.Sphere and Thoughts from Kansas; the link goes to the first in a series of posts), Don McLeroy offers an insulting essay in the Austin American-Statesman.

    (T)he greatest difficulty in writing these standards is the culture war over evolution.

    The controversy exists because evolutionists, led by academia’s far-left, along with the secular elite opinion-makers, have decreed that questioning of evolution is not allowed, that it is only an attempt to inject religion or creationism into the classroom.

    Having already hit the gutter, McLeroy somehow manages to actually go downhill from there.

    He redefines science.

    He distorts the ideas of Stephen Jay Gould.

    I want to fisk it, but I’m really too angry to do it now.

    What am I going to write about after this?

    The final debate among the Texas State Board of Education about the K-12 science standards starts today.

    I’ve been thinking over the last couple of weeks: “What am I going to write about after this?” I’ve been blogging about the Texas science standards so much over the last year, and it’s been such a rich vein to mine... After this week, the science standards won’t be reviewed again for years.

    I’m going to have to work harder to come up with more substantive blog posts.

    While I’m here, I might as well mine the vein a little longer and point out an editorial in the Washington Post on the subject:

    It’s disturbing enough that the Texas board of education might seek to impose its religious views on public school students in that sizable state. It’s even more alarming that the Lone Star State's textbook market is so large that many publishers write books to meet its standards and then sell them across the country.

    Explanation and evangelism

    I was reading a review of Jerry Coyne’s Why Evolution is True in the new issue of Current Biology. Reviewer Tom Tregenza writes:

    Like many biologists, I occasionally panic that if the appeal of religious dogma can prevail over such a well-supported and rigorously tested theory as Darwin’s, then it can only be a matter of weeks before we’re all wearing sandals and the next breakthrough in oncology is expected to come from making offerings to a parsnip with a resemblance to the Virgin Mary. At such times, I vow that I will drag myself out of my ivory tower and try to explain what I do to the (surely fairly rational?) man in the street. Similarly, reading the manifestos of those seeking election to offices of the European and American Evolution Societies, there is universal agreement that evolutionary biologists need to do more to explain their work to the public. The fact is, however, that we’re still not very good at delivering on these good intentions.

    This reveals a lot about why good intentions don’t deliver. People think the problem is that people outside of science don’t know. That’s not the problem. The problem is that they don’t care.

    To use a wacky Zen metaphor...

    I enjoy Australian Rules Football, for a lot of reasons. Those around me... don’t.

    I might think that this is just due to their lack of information about the game. So I should go around and explain to them the rules and how it’s played. Then they will automatically become more interested, right?

    Not necessarily. They may understand the game on an intellectual level, but that doesn’t mean they’re going to start bugging me to set up a footy tipping competition, start checking the AFL website on weekends, adopt a team and learn the club song. In short, they won’t care.

    Getting someone to care is complicated. Marketers spend all day and all night trying to work it out. It isn’t just about explanation. It requires evangelism – not in the religious sense, but in the general sense that Guy Kawasaki talks about is always talking about. The sort of evangelism that sales and marketing people talk about. Going out there and connecting with people and demonstrating passion, solving peoples’ problems, engaging with them.

    A lot of scientists are out there explaining Aussie rules football and wondering why people don’t show up for the games. The people who don’t show up for the game are not necessarily ignorant or uneducated about how the game is played. It takes more than explanation to create a fan.

    We might be better off if we ditched phrases like “public outreach” and thought about “building a fan base.” We should create science fans.

    (I’ll bet this post didn’t head in the direction you thought it would from reading the title.)

    23 March 2009

    This is the week for Texas science standards

    The final vote on the Texas K-12 science standards is this week. It’s going to be... intense.

    The Wall Street Journal reports:

    All members of the board have come under enormous pressure in recent months, especially three Republicans who support teaching evolution without references to “weaknesses.” The state Republican Party passed a resolution urging the three to back Dr. McLeroy’s preferred curriculum. A conservative activist group put out a news release suggesting all three were in the pocket of “militant Darwinists.”

    It’s time to put the word “militant” away and save it for people who actually carry guns and bombs.

    Meanwhile, the Evo.Sphere blog is collecting letters from national scientific agencies who have written letters to the Texas State Board of Education that more or less ask them to adopt the standards the experts originally submitted, and take out some of the amendments that McLeroy and other got in. The big one is the letter from the American Association for the Advancement of Science, who got signatures from an impressive number of big university mucky-mucks, including the chancellor of the University of Texas system to which my institution belongs.

    I feel sad for those State Board of Education members who are generally characterized as “swing voters.” I don’t even want to think about what kind of politicking they must be getting subjected to.

    Prediction: I’m betting that all of this won’t change much. I think there will be a lot of 8-7 votes. I think they’ll be in favour of the original expert recommendations, but I’m not counting on it.

    Fisking an editorial

    Don McDonald has an opinion editorial in the San Angelo Times with the misleading title, “Teach evolution in classroom.” In fact, Dr. McDonald (who does not live in Texas and is not a biologist; he instructs in human resources) he teaches argues quite the opposite, as obvious from his first sentence:

    As a doctoral candidate in sociology in the 1990s, I found my dissertation process derailed until I feigned allegiance to Darwinism.

    I must admit, it’s a fairly gutsy opening gambit to admit lying to get a doctorate. And then we’re off with a typical stack of creationist objections.

    Objectors to the proposed language in the science standards commonly express fear of “Creationism creeping into the classrooms.” But the amendments to the indicators say nothing of creationism, and they do not mention intelligent design.

    First, the proposed language implies a debate where none exists. Second, it doesn’t matter much if the exact words “creationism” or “intelligent design” are in there or not. People can interpret generalities in ways that people never intended. Remember, the law is a club, not a scalpel. The law is a blunt instrument that does not make fine distinctions or easily take into account whether consequences are intentional or not.

    And since he’s admitted to having little use for evolution, I can’t help but wonder if phrases “creationism” or “intelligent design” were in the proposed standards if Dr. McDonald would be okay with that.

    If we tell students that they must have one certain conclusion before peering into a microscope or turning over a rock, is that science?

    By McDonald’s argument, if students do experiments that shows that heavy objects fall faster than light ones, we shouldn’t tell them that they’ve likely made a mistake or not measured accurately enough. For some things, there is a solid body of evidence that K-12 students are extremely unlikely to revise or overturn. To say that teachers should ignore that established science and let students’ own conclusions reign supreme is not good teaching practice.

    19 March 2009

    Where scientific progress occurs

    The Dallas Fort Worth Star-Telegram has a story concerning Representative Christian’s house bill to re-introduce “strengths and weaknesses” back into Texas K-12 science standards.

    The bill says that neither student nor teacher could be penalized for subscribing to any particular position on any scientific theories or hypotheses. ... Rep. Wayne Christian, R-Center, who filed the bill, said it is not an out for students, because they must still be evaluated on course materials taught.

    Emphasis added. It seems to me that Representative Christian just admitted that teachers could not be held accountable for teaching just about any fringe idea and calling it “science.” In which case, ooooh, there would be a world of bad teaching and probably many lawsuits to follow.

    “The state is successful and will continue to be so,” said Jonathan Saenz, a lobbyist for the Plano-based Free Market Foundation, which promotes Judeo-Christian values. “It’s important that we fix the curriculum to allow for scientific progress and debate.”

    Real scientific progress and debate doesn’t occur in K-12 schools. They happen in universities and research institutions. And I’m saying this as someone who has published research co-authored by someone who was a high school student when she was working in my lab (Flores and Faulkes 2008). The overwhelming majority of scientific papers are from universities.

    See also an editorial in the same paper. I feel bad for students in Kansas... they’ve got a reputation through not fault of their own.

    18 March 2009

    Open Laboratory 2009 candidate logo design

    Open Lab 2009 design
    A Blog Around the Clock asked for graphics for buttons to encourage people to submit nominations for the next Open Laboratory anthology of science blogging. The one above is my take.

    The goal here is not to get people to vote for me, just to explain a little bit of the thought process behind the design. For comparison, here is last year’s logo:

    Open Lab 2008
    Basically, I wanted to make my design to be 180° away from last year’s. So I started with the idea of a greenish hue for the background. Similarly, I looked for a font that was distinct from the heavy font used in last year’s logo. I wanted to play with the idea of expressing the feeling of “openness” in the type, so the letters are set very far apart.

    The space at the top is deliberately unfilled here. The idea is that this space can be used to put in different things like “Nominate for,” “Judge for,” “Featured in,” and so on.

    Win, lose, or draw, it was worth the bit of time I put in, because I learned a few new tricks in Corel Photo-Paint doing this.

    Check out the other fine button designs by Daniel Brown (who blogs at Biochemical Soul) at A Blog Around the Clock, and leave a vote in the comments.

    Why tweet?

    Twitter logoI was listening to CBC Radio’s The Current coming in yesterday morning. They were talking about Twitter, and in particular, its use in political circles. Stephen Marche may have had the best one-liner when he said something like, “I’m not a fan on instant thinking.”

    I agree with that. I’m not a fan of instant thinking, either. Since I’m on Twitter now, this raises the question: Why?

    The original reason I started Twittering was to provide an easy way for students to figure out where I was. But as I’ve used it more, it’s become more like mini-blogging. I try to put out more substantial stuff on Twitter than I did at first. Pointing out a cool article might have got a short blog post before, but now it gets a tweet.

    But in both blogging and twittering, the reason I do it is, in my mind, that I want to take on the responsibility of being a public intellectual. Not always easy, especially considering that “intellectual” is an insult to some people’s thinking.

    Plus, I would add that for some people, writing is a way of thinking. I’m not arguing that I’m working on my next research paper through Twitter, but there is something to be said for practicing being concise. Saying the most you can in the least space requires discipline.

    Now that I think about it, a lot of scientists should twitter more, because it might help them write things like “now” instead of “at this point in time,” or “can” instead of “has been shown to be capable of,” and so on.

    Additional: A good post on “Why should scientists blog?”

    Incidentally, I think I am the only active blogger out of my entire department. Maybe several science departments in our university.

    17 March 2009

    Use your laptop, lose a letter grade

    laptopsI’ve noted that I don’t allow laptops in my classes. So far, I haven’t heard any students grumbling about this.

    Now, Diane Sieber at Colorado University has given students another reason to put away computers: enlightened self-interest. She found those using computers in class did 11% worse on average than those who didn’t (my emphasis). (See also here.)

    Last fall, Sieber had 96 students in one of her courses and she took note of which ones were frequently using their laptops. After the first test, she alerted the 17 students who used their laptops intensely that, on average, they performed 11 percent worse than their peers who weren’t glued to computer screens. The number of students on laptops eventually dwindled to a half dozen, and the test scores of students who stopped using their computers during class shot up, according to Sieber.

    “These are grown-ups,” she said. “They need to identify what keeps them from learning, and then act on it because they aren’t going to have me for the rest of their lives telling them ‘No, no, no. Focus.’”

    Now, how can I get them to put away their smart phones?

    External links

    Profs grapple with laptop rules as campuses go wireless
    Students Stop Surfing After Being Shown How In-Class Laptop Use Lowers Test Scores

    Science publishers are agents

    A while back, I talked about how science publishing is undergoing a Marxist revolution. Today, Seth Godin notes:

    Travel agents... gone.
    Stock brokers... gone.
    Real estate brokers... in trouble. Photographer’s agents, too.
    Literary agents?

    The problem with being a helpful, efficient but largely anonymous middleman is pretty obvious. Someone can come along who is cheaper, faster and more efficient. And that someone might be the customer aided by a computer.

    If specialized scientific publishers want to survive, Godin points out a way:

    Middlemen add value when they bring taste or judgment or trust to bear on a transaction that isn’t transparent. ... To thrive in a world of self-service, agents have to hyperspecialize, have to stand for something, have to have the guts to say no far more than they say yes.

    Right now, there are still research journals that do this. Science, Nature, and Cell, although sometimes derided as “glamour mags,” do this: they make judgments about what constitutes cutting edge science. They say “No” a lot.

    So the real pressure of open access, and that everyone can have a printing press and distribution channel, is going to weigh upon, not the top journals, but the many other journals that publish most of the bread and butter, meat and potatoes scientific research. What can a journal do that’s going to add value for either the authors or their readers that’s above and beyond what an author can do herself? Here are a few thoughts:

    • Develop a review system that checks for scientific fraud as well as scientific rigour.
    • Become more active in revising manuscripts for clarity.
    • Offer more assistance revising graphics.
    • Create long-term archival materials, perhaps more than just the published text.
    • Retain scientific reviewers to ensure fast turnaround on review times. Days, not weeks or months.

    Any other suggestions? What could a journal do that would be “a dream come true” for the authors?