Texas Education Agency and Chris Comer, Part 13

There's a local prediction that "south Texas is the new Florida." The idea is that retirees looking for a warm place to move to will start moving to south Texas, because Florida is full. But here's another interesting comparison to make between Florida and Texas. Someone from a state education agency emails people about upcoming reviews to the state K-12 science curriculum.

In Florida, an email that says:

(I)work for the Florida Department of Education as the Director of the Office of Instructional Materials... I say all of this, obviously, to give this e-mail credibility. ...

Districts will not have a choice in teaching evolution as a theory... Whose agenda is this and will the Christians in Florida care enough to do something about it? ...

The least we can do is make sure evolution is presented to our children and grandchildren as a theory as it has been in the past. Hopefully, though, we can do better than that.

gets a reprimand.

In Texas, a forwarded email with "FYI" gets a forced resignation.

The Florida situation appears to have occurred after news of Chris Comer's resignation broke, so perhaps those in the Florida Department of Education took note at how much attention the Comer situation has received nationally.

Meanwhile, let's see what the Texas Education Agency's education commissioner, Robert Scott, has to say in Dallas News interview:

I'm aware of the reports and a bit disturbed by them because they're not based in reality or fact.

If that's the case, it might have been handy for the Agency to have been communicative. Mr. Scott goes on to say:

The really frustrating part about this is, if I start talking about activities and things that happened, I get sued.

Nevertheless, since the Austin American-Statesman published a TEA memo on proposed disciplinary action, it seems a little coy to say that he can't talk about things that happened. Indeed, the memo absolutely supports Mr. Scott's contention that Ms. Comer was not forced to resign over one thing (i.e., the forwarded email about Barbara Forrest's presentation).

Nevertheless, I think that many reasonable people have looked at that memo. I admit that memos like that don't give the whole story and don't capture workplace dynamics. Unless there was something else really major that was not written down in print there, a lot of people have concluded that the matters in question are not something you normally fire someone over. Ooops... I mean, "not something you normally ask for someone's resignation over."

Regarding whether Ms. Comer advocated evolution, Mr. Scott says:

But she may have given the impression that ... we were taking a position as an agency – not as an individual but as an agency – on a matter.

"May have." So the problem is, as I've said before, is just the possibility of the appearance of a conflict of interest.

You know, the memo published by the Austin American-Statesman has been read by a lot of people. The vast majority (I am being measured here, because I am tempted to say "all") who've looked at this don't see Ms. Comer advocating any position on the subject, much less one that could be confused as a Texas Education Agency position. This is simply not how reasonable people are viewing the situation.

And when the paper calls the bluff of neutrality directly and asks, "Why shouldn't the agency advocate the science of evolution?", you get a very telling remark:

But you can be in favor of a science without bashing people's faith, too.

When did anyone's faith get "bashed"? What kind of "bashing" is he worried will occur?

I'm having a hard time finding sympathy for the TEA at this point. A lot of statements that have been made by people associated with the Agency give the impression that it is run by a lot of people who are very thin-skinned and very, very worried about what one particular group of religious people might say.

Another editorial over the weekend, this one from the San Antonio Express-News.

The Organization for Economic Cooperation and Development recently released the results of a test that assesses science and math skills of students in 30 industrialized countries. The results showed American students scored in the bottom half — worse than their peers from 16 other countries, and better than only those from Italy, Portugal, Greece, Turkey and Mexico. ...

Do Texans truly want their educators to be neutral on the teaching of religious faith versus science in schools? If so, then the State Board of Education and the Texas Education Agency are well on their way to making students in Italy, Portugal, Greece, Turkey and Mexico feel proud.

Outside of the state of Texas, the Atlanta Journal-Constitution is also concerned about America's standing in science education rankings:

Some politicians don't seem to grasp the difference between science and faith, so it's no wonder scientific theory befuddles U.S. high school students.

Over in Utah, Salt Lake Tribune writer Robyn Blumner says:

Really folks, in this information age, when scientific innovation is the key to our nation's future, we don't have the time to be mucking around in this tired debate. You don't produce doctors and scientists by teaching science from the Bible. Period.

He talks a little about Comer, but is more concerned with George W. Bush's track record in science and prospects for the next presidency.

Texas Education Agency and Chris Comer, Part 12

The Austin American-Statesman has just published its second editorial on the Chris Comer resignation.

The firing of Comer already has done real damage to Texas’ reputation as it competes with California and New York for research and development projects, grants, biomedical industries and the nation’s best scientists.

Yup. They got it. You can't expect to benefit from knowledge while promoting ignorance.

Blogs by researchers have cast Texas as a backwater state that puts religious ideology on par with science.

You're welcome. Go me.

Something that has been missing in the editorials, though, is that Texas has a plan in place called "Closing the Gaps," which aims to increase university participation and student success across the state. Biology is a very popular major, and many non-science majors take some biology to fulfill biology requirements.

Weaken teaching on evolution, put in any language that waffles or sows doubt, and students are going to be in for a shock. They'll be left playing catch-up as they find that, say, intelligent design is not taught in science classes (except, perhaps, in a historical context under its original name of natural theology, or as an example of how to do science wrong). They'll be in for a rude awakening that all those alleged "weaknesses" probably have solutions that have been known for decades.

Students would be less ready for a university education, and less likely to succeed.

Texas Education Agency and Chris Comer, Part 11

Even some of the major intelligent design guys are stepping back from the Texas Education Agency's treatment of Chris Comer. William Dembski, on the Uncommon Descent blog (which I earlier characterized as "strangely quiet") wrote:

I’m still not clear about the details of the case, but if Comer’s firing were solely for supporting Forrest, this ought not to be.

Dembski seems very reserved in saying he doesn't know the details. They've been up for a week (including PDF from the Texas Education Agency) and there has not yet been any factual challenge as to what happened -- only why.

Anyway. Chris Comer's interview on Science Friday was only about 20 minutes, and largely consisted of a narrative of the events leading to her resignation. Not a lot of the information is new, although a few things are worth emphasizing. She did not send the email in question through her work account. The person who pushed for her resignation was not a recipient of the email, but found out about it and lodged a complaint within hours. And the ultimatum of resign or be fired was rather abrupt.

Texas Eduation Agency and Chris Comer, Part 10

In addition to speaking on Science Friday, Chris Comer is interviewed by an Austin TV station, News 8 Austin. The video link is incorrect, but may be fixed in the future. An accompanying text article says:

Unemployable is how Castillo-Comer describes herself now.

Castillo-Comer has not decided whether she will file a lawsuit against the state.

Frankly, if she does, I think she would have a lot of people behind her. Not least of which is the American Institute of Biological Sciences, who have issued a position paper:

Biologists and evolution education advocates across the United States are outraged that the TEA requires, as agency policy, neutrality when talking about evolution and creationism.

As much as I try to be a level-headed guy, yeah, I would have to agree that I'm stepping towards outrage on this.

Update: The video link in the News 8 Austin page now works and actually shows Comer and not sports.

Texas Education Agency and Chris Comer, Part 9

Today (Friday, 7 December), Chris Comer is scheduled to appear on Science Friday on America's National Public Radio (NPR). It's slated for 1:00 pm Central Standard Time. If this is as usual for the show, they will have a "Listen again" feature on the Internet for those outside the county.

Meanwhile, I've been looking in blogs for anyone who is willing to defend the Texas Education Agency on this.

About the only one I can find is an argument that certain people have double standards, drawing parallels between Comer and one Guillermo Gonzalez, an astronomer who supported intelligent design, and was recently denied tenure. As these are unrelated cases, each case has to be looked at upon its own merits. I'm not getting into the Gonzalez case, as others are doing that. Much is getting written on Panda's Thumb.

Even Uncommon Descent, arguably the most famous intelligent design blog, is strangely quiet, asking if Texas can or should remain neutral. It posts several questions, mentions the Gonzalez situation, and posts two news stories from the Austin American-Statesman.

I also found this piece, which affirms that many Christians also smell something rotten in the TEA's actions. And even a post that starts "I'm a creationist," admits:

How can the Texas Education Agency justify her firing her for endorsing a view which is taught at every Texas public school? ... I’m still confused as to why Comer was let go.

Finally, a more personal perspective is taken by someone who is familiar with one of the key players involved, Lizette Reynolds, and is boggled. "But she seemed so smart..."

More newspaper editorials today. In keeping with my quest for alternative views, the University of Texas at Austin Daily Texas is more forgiving than most to intelligent design:

Darwin's theory of evolution may be just that - a theory, and as much of one as intelligent design - but scientifically, a theory is a call for questioning and synthesis, and a path toward tangible fact.

But that's as far as they'll go, still not supporting TEA's actions:

There are facts and there are suppositions, and as the TEA has proven, the former does not belong in the realm of political politesse. But the latter does not belong in our schools.

One in the International Herald-Tribune:

Surely the agency should not remain neutral on the central struggle between science and religion in the public schools. It should take a stand in favor of evolution as a central theory in modern biology.

Another in the Dallas Morning News:

Professional educators need assurance that no one aims to impose a religious agenda on students and require the teaching of creationism alongside evolution in science classes.

If Ms. Comer was incompetent, it's certainly not reflected by her 27-year career as a teacher and nine years of service as director of science. The impression we get is that her bosses were gunning for her, and the forwarded e-mail was the most expedient excuse they could find.

This action could not have sent a worse message to our state's educators, when we should be doing everything possible to encourage people to choose teaching as a career, not frightening or bullying them into leaving.

Incidentally, since all of this was set off by a presentation by Barbara Forrest, the website for Creationism's Trojan Horse, the book she co-authored has lots of resources and may be of interest.

Texas Education Agency and Chris Comer, Part 8

The Austin American-Statesman, the paper that broke the story on Chris Comer's resignation from the Texas Education agency, has an important follow-up story:

"We were actually told in a meeting in September that if creationism is the party line, we have to abide by it," Comer said(.)

Holy shit.

If true, we (Texas, biologists, educators) are in much, much more trouble that I thought.

More importantly, the paper has finally got comment from an agency spokesperson, Debbie Ratcliffe:

She said charges of misconduct against Comer were prompted by a lack of professionalism(.)

"An employee shouldn't say something that's contrary to the curriculum, and they shouldn't look like they are siding with one camp over another," Ratcliffe said. "It's no secret that there are political differences on the State Board of Education. ... And employees have to be able to work with all the members in a fair way without the perception that they are siding with one group or another. That's why it's important for us to be neutral on issues and just to say what the policy is and not to create it ourselves."

This seems to me to be a 100% admission that the Texas Education Agency wanted Comer to resign for political reasons.

By the sounds of it, it would not be "neutral" to point out that there are mountains of peer-reviewed papers on evolution, and rather fewer on intelligent design. It would not be "neutral" to point out the outcome of the Kitzmiller v. Dover case. In other words, according to the Texas Education Agency, correct and factual information is not "neutral" when evolution is involved.

"Obviously, there was a concern about the forwarding of that e-mail ... that she was supporting that particular speaker and (how) that could be construed ... as taking a position that could be misinterpreted by some people," Ratcliffe said.

So Comer was getting pressured for the mere possibility of the appearance of bias.

Board Chairman Don McLeroy said that he does expect evolution to be a hot topic during the upcoming review(.)

Well, yeah, it sure as heck is going to be now, given the provocative actions the agency has taken, and the clear alignment with the point of view that evolution, alone among scientific disciplines, should be singled out for criticism.

McLeroy said he would support changes that further spell out what evolution's strengths and weaknesses are.

You're not fooling anyone, Mr. McLeroy. You'd support spelling out alleged weaknesses because it's an opportunity to attack evolution and thereby make religious views look better by making evolution look bad.

Meanwhile, there are more editorials in the Waco Tribune-Herald, which notes:

Texas parents, teachers and lawmakers should be on guard that the state avoids the mistakes that led to the 2005 Dover, Pa., lawsuit.

And in Kansas, on the idea that Comer should remain neutral on intelligent design, the Wichita Eagle asks:

Why should she be?

Indeed.

The Eugene, Oregon Register-Guard says:

Comer’s ouster already is a tragedy.

Texas Education Agency and Chris Comer, Part 7

One of the triggers for the resignation of Chris Comer from the Texas Education Agency was that she forwarded an email about a presentation by Barbara Forrest. Now, Barbara Forrest comments on the situation she was tangentially involved in:

If anyone had any doubts about how mean-spirited ID politics is, this episode should erase them.

War on fools

An anonymous author at Slant Six Creative argues:

Always let a fool have the last word.

I was reminded of the first rule of arguing with a fanatic: Don't.

I left a comment, upon which I will expound slightly further.

Unfortunately, fools are often numerous, persistent, and influential. Worse, errors left unchallenged gain the perception of truth. So it’s often the case one must continually confront fools, because the consequences of not doing so are grave.

The sad fact is, not all fools drool. Many fools have expensive watches, large incomes, stable home lives, and can be excellent conversationalists at social functions. But they can be badly, badly wrong. They can hold strong beliefs about impossible things.

To paraphrase an expression written on some buildings in Washington, D.C., "Eternal vigilance is the price of intelligence."

Last lecture of semester

...is now done.

Hooray.

Now, to catch up on proposals, marking, manuscripts, grant management...

Research is hard

Errol Morris investigates what appears to be a simple question: Which of those two photos was taken first?

Finding the answer is long and hard, and is an excellent demonstration of how even simple propositions require major efforts to yield a definitive answer.

Texas Education Agency and Chris Comer, Part 6

More editorials today. Houston State Chronicle:

It will be more than sad if the Texas Education Agency is leaning toward taking an anti-evolutionary stance and allowing religious doctrine to be taught side by side with valid science in the state's classrooms.

Rick Casey, also writing in the Houston State Chronicle:

The doctrine of separation of church and state is not found in the Constitution. It evolved through the courts and through public consensus based on painful experience.

Casey lists several egregious examples of religious intolerance, several between Catholics and Protestants.

Outside of Texas, Bill Wineke writes in the Wisconsin State Journal is blunt:

I suppose you don 't really need another reason to be happy you live in Wisconsin and don 't live in Texas.

Ouch.

If proponents of this scientific quackery can terrorize a state education agency and force the resignation of a veteran science teacher, they will establish a precedent that will cripple serious science education not only in Texas but around the country. That's the last thing this country needs.

One wonders if any amount of negative press and criticism would make the Texas Education Agency do something like apologize. Admit a mistake. Ask Comer back.

Texas Education Agency and Chris Comer, Part 5

The Comer situation continues to attract attention since the story broke at the end of last week. Today sees multiple newspaper editorials about the situation, both nationally and within Texas.

The New York Times has an editorial on the resignation of Chris Comer. In part:

Ms. Comer’s dismissal and comments in favor of intelligent design by the chairman of the state board of education do not augur well for that review. We can only hope that adherents of a sound science education can save Texas from a retreat into the darker ages.

Today also brings an editorial in the Waco Tribune. In part:

We can only hope that the state school board is not so inclined as to turn discussions of evolution, as with the greenhouse effect, into the picking of nits that completely undermines and ignores the immense science backing both biological facts.

Then there's the Corpus Christi Caller-Times editorial, which might have the best title: "Official forced out for telling the truth on intelligent design." It reads in part:

Education officials say that Comer should have been neutral on evolution. What a shame. Instead of supporting teachers as defenders of truth and scientific inquiry, apparently state education officials want educators to perpetuate an academic scam on the state's schoolchildren in service to special interests.

And I would be remiss if I didn't mention the paper that broke the story, the Austin American-Statesman, was the first to have an opinion:

Whether one accepts the theory of intelligent design or not, discussion encourages scientific exploration, which is what a science curriculum director should do. Forcing Comer out of her job because she passed on an e-mail about the critic’s presentation is egregiously wrong.

I've been hard-pressed to find anyone who is seeing anything in this situation besides dodgy politics meddling in education for religious reasons.

Oh, now this is a great news story to start the week with.

A mummified dinosaur with skin and maybe some soft tissue preserved. Wonderful!

I can't wait to see some pictures.

Texas Education Agency and Chris Comer, Part 4

Chris Comer has now given the first interviews since the story broke about her resignation from the Texas Education Agency. Of particular note:

Ms. Comer said state education officials seemed uneasy lately over the required evolution curriculum. It had always been part of her job to answer letter-writers inquiring about evolution instruction, she said, and she always replied that the State Board of Education supported the teaching of evolution in Texas schools.

But several months ago, in response to an inquiry letter, Ms. Comer said she was instructed to strike her usual statement about the board’s support for teaching evolution and to quote instead the exact language of the high school biology standards as formulated for the Texas Essential Knowledge and Skills test.

My worries are not being assuaged here. The Texas Education Agency better speak up. Not about Chris Comer, since they've consistently said it's a personnel issue, which I can live with. They'd better speak up about the state standards on evolution and what we can really expect in the revisions.

Texas Education Agency and Chris Comer, Part 3

The Texas Freedom Network has a clear political bent. Their logo on their webpage announces, "A mainstream voice to counter the religious right." Nevertheless, there seems no reason to think that their transcript of Don McLeroy's talk is at all suspect, particularly as there's also an audio file of Mr. McLeroy speaking.

Don McLeroy is the chair of the Texas State Board of Education, an agency that has supervisory ties to the Texas Education Agency, which is under scrutiny for its treatment of Chris Comer.

McLeroy's talk makes it perfectly clear that he favors teaching intelligent design because it is in line with religious views:

Why is intelligent design the big tent? It’s because we’re all lined up against the fact that naturalism, that nature is all there is. Whether you’re a progressive creationist, recent creationist, young earth, old earth, it’s all in the tent of intelligent design. And intelligent design here at Grace Bible Church actually is a smaller, uh, tent than you would have in the intelligent design movement as a whole. Because we are all Biblical literalists, we all believe the Bible to be inerrant, and it’s good to remember, though, that the entire intelligent design movement as a whole is a bigger tent. So because it’s a bigger tent, just don’t waste our time arguing with each other about some of the, all of the side issues.

Perhaps McLeroy's views have changed in the last two years. After all, he probably said that before Judge John Jones emphatically ruled in the Kitzmiller v. Dover case that teaching intelligent design was illegal.

Perhaps McLeroy's views have changed since 2005. But this seems unlikely.

While there is no evidence I'm aware of that links McLeroy to Comer's situation, it speaks to the some of the ideas circulating among those in charge of K-12 education in Texas.

Abbreviations

Some of colleagues might know what JEB is.^* Many would not.

Many publishers, to save space, abbreviate journal titles in scientific articles. I've ranted about this before. Earlier this week, I read this bon mot:

Unlike women's skirts, the more abbreviated a journal citation, the less it reveals.

- C.W. Hart, Jr. & Betty Ursomarso, 1964.

^* It's short for The Journal of Experimental Biology.

Sesame Street ruined my life

It must have. Because I watched it a lot as a kid,learning the alphabet and numbers. And some of those early episodes of Sesame Street are now out on DVD.

With an "Adults Only" label.

I kid you not.

These early Sesame Street episodes are intended for grown-ups and may not suit the needs of today's preschool child.

First, they came for Bugs Bunny. And I said nothing, because I was not a bunny.

Next, they came for Big Bird. And I said nothing, because I was not a bird.

When they come for Biology Boy, will there be anyone to say anything for me?

The Texas Education Agency and Chris Comer, continued

Political narratives become established quickly.

I mentioned yesterday's worrying new story about Chris Comer, a member of the Texas Education Agency.

Here's how it's being pitched elsewhere.

• "Evolution Debate Led to Ouster, Official Says" - Associated Press
  
• "McCarthyist-like witch hunt" - Email from Tom Johnson, Texas Faculty Association
  
• "I did assume that the Texas Education Agency would support science education. I guess I was wrong. The situation is really bad, though, if learning about science is a subject that gets the Texas Legislature upset." - PZ Myers on Pharyngula
  
• "Apparently, not being a team player in the The Republican War on Science is a firing offense at the TEA." - Wesley R. Elsberry on Panda's Thumb
  

The narrative being told by many is real clear: This is an attempt by religious people to get rid of someone who would oppose the weakening of biology teaching so that concepts friendly to biblical literalism can be introduced into the public school curriculum.

Now, just because such shenanigans have happened before -- repeatedly -- doesn't mean they happened this time.

Good for the Austin American-Statesman to have the actual copy of the memo in question (PDF format). I looked at this and tried read it as objectively as I could.

My impression was that this was perhaps not as clear cut as many would like it to be. This whole thing isn't about one forwarded email. There's a series of events, and it looks like there had been warnings delivered before about how her employers wanted things done.

But I have to say these do not look like the sort of issues that people lose their job over. I wouldn't quite call them trumped up charges yet. The whole things reeks of a bad (maybe hostile) working relationship. But the situation may be more complex than a one-note summary termination that some are saying this is.

And yes, there's enough there that I still have the nagging suspicion that this could be part of a bigger trend to reduce opposition to introducing pointless language about evolution into the Texas education standards.

The Texas Education Agency should expect a lot of very careful scrutiny in the next little while. Because if there is any further hints of "criticism" of evolution, they can expect a huge fight on their hands.

Disturbing news story in Texas

In today's Austin American-Statesman, "State science curriculum director resigns -- Move comes months before comprehensive curriculum review."

Forwarding an email about a presentation is communicating about a science curriculum review? And you can be fired for that? Watch this story closely.

(Spotted at Panda's Thumb)

The Zen of Presentations, Part 12: Being a good audience

When scientists give talks, we usually do it in flocks. Conferences. Where you’re one of several talks in a row. A few conferences can yield huge audiences (like the recent Neuroscience meeting)... but most do not. And in those small audiences, you have a chance to be noticed. Not to the degree as when you’re up front talking, but noticed nevertheless.

If you one of several presenters, you have responsibilities when you are not talking.

Nominally, you’re supposed to stay quiet. Make sure your mobile phone is off. Maybe clap politely at the end.

But if a speaker is good, he is looking out at the audience. And there is a big difference between looking out and seeing someone who is smiling, nodding, tracking you as you move around the room... and seeing someone with their eyes closed. Scribbling a note. Or, heaven forbid, with a laptop in front of them looking at the screen.

I once went to a play, and in a reception afterwards, one of the actors said, “You were on the edge of your seat!” In a darkened theatre, with lots of audience members, I got noticed. People take it as a huge compliment when you’re actively listening.

If you don’t want to sit through a bad presentation, for goodness sake, give the speaker some encouragement to do better.

Seth Godin puts it well in a recent post, and I've talked a little about this before.

Abandoning evidence

The National Center for Science Education links to Hanna Rosin's article on creation geology. This quote on page 4 by young Earth creationist Kurt Wise is very revealing:

If all the evidence in the universe turned against creationism, I would be the first to admit it, but I would still be a creationist because that is what the Word of God seems to indicate.

Now there is a prime example of the different degrees of faith I wrote about yesterday. All the evidence in the universe – not just the world, the universe – isn’t enough to change someone's mind. That’s faith with a capital F – and capital A, I, T, and H, underlined, in a gold box, and flashing neon lights. That's not the small f faith that scientists operate with.

Degrees of faith

Paul Davies wrote in an editorial for the New York Times over the weekend:

But until science comes up with a testable theory of the laws of the universe, its claim to be free of faith is manifestly bogus.

Putting aside the question of how a method for understanding the natural world "claims" anything...

The piece leans towards a very well-worn argument: Science is just like religion. It's particularly threadbare in the U.S. because it's a common ploy used to argue that creationism should get equal time in classrooms as evolution.

But to say science operates on faith is a little bit like claiming that lighting a match is an explosion. There's a difference.

The faith that you're required to have in science is roughly, "The natural world is lawful and understandable." That it a fairly sparse set of assumptions that you're asked to take on "faith," first of all, and second of all, it's the same kind of "faith" that your car will start in the morning. Why do you expect that? Because it did the almost all previous mornings and the car is in good working order. It's really inductive reasoning, not faith.

In contrast, when faith is used outside of a scientific context, it is usually referring to a long litany of very specific propositions that are backed by less evidence than a inductive reasoning. A list of propositions like the time and manner of the creation of the universe, the nature of the creator, a specific long set of historical events, that a particular collection of writings are true by definition, and so on.

I'm not saying that's bad... just pointing out a difference. A difference between a minimal set of assumptions backed by induction versus a long, long set of assumptions that are often held to be true despite large amounts on contradictory evidence.

Those are not the same thing, and to say they are is pure sophistry.

There ought to be a parade

In Carolyn Porco's Ted talk (below), she talks about the landing of the space probe Huygens probe on Saturn's moon Titan. I recommend watching it, because her delivery is so much more powerful than reading the quote I took from it.



About 9 minutes in, she says:

And I just want to emphasize how significant an event this is. This is a device of human making and it landed in the outer solar system for the first time in human history. It is so significant, that in my mind, this was an event should have been celebrated with ticker tape parades in every city across the U.S. and Europe, and sadly, this wasn't the case.

I was also thinking over the weekend about the recent publication that two research teams had created human pluripotent stem cells from adult tissue. (Here's one and here's the other.) I heard about this, and thought nothing much more than, "That's good news" or some such.

But I got wondering why every biologist in the department wasn't high fiving each other. I haven't had a single conversation about this research since the announcement.

Is it because it hasn't yet impacted us?

Is it because, being in the field, we sort of knew this would be possible and that it would probably happen sooner or later?

Or are we just so accustomed to change that the wondrous has become mundane?

Because make no mistake: We are living in a wonderful time of scientific achievement and discovery.

"I don't want the broader picture"

This article in The Age is about youth and new media, but I sure as heck don't think the issues being raised are confined to youth. In particular:

The promise of creating your own news world — "The Daily Me" — reduces the likelihood of encountering "unexpected ideas and unpopular opinions, a necessary ingredient in any democracy". ...

At the 2006 Online News Association conference in the US a panel of young people was asked by a journalist in the audience whether "reading RSS (Really Simple Syndication) feeds exclusively would stifle discovery of the broader picture". One 15-year-old panellist replied, "I'm not trying to get a broader picture, I'm trying to get what I want."

The difficulty of listening to views contrary to your own seems to be the theme for today. As I was walking over to work, I was listening to a fascinating interview (streaming audio) with William Rees (who coined the term "ecological footprint") on Sounds Like Canada, who argued we are neurologically predisposed to filter out bad news and ideas that don't agree with our own.

I've talked about this phenomenon at least once before, if not more often (just can't find the posts). It worries me terribly. From home schooling to higher education, it becomes possible to spend your entire educational career with people who agree with you.

I'm wondering a lot if scientists are better at making these serendipitous discoveries and compiling the broader picture or not. My initial expectation is not as much as it used to be, since more and more research is being guided by directed searches through Google Scholar and PubMed rather than thumbing through printed journals in library stacks, as I did through most of my undergraduate career.

On the other hand, I suspect that researchers, by the nature of their training to seek out alternative explanations and to look at evidence, may have slightly -- ever so slightly -- wider filters than the general population. A scientist should be less likely to discount an idea because of its source. But there's no doubt it's a hard task to do.

Classic graphics #5: Brainbow

Is it presumptuous to award "classic" status to something that's less than a month old? Normally, yes. But sometimes, something is just so stunning that you strongly suspect it will be shown for years to come.

This essay is different from the previous ones, which each focused on a single image. This one pans out to review a veritable gallery of images that will surely just be the first of many galleries.

At the start of this month, Livet and colleagues published a paper in Nature that has arguably the most beautiful pictures of neurons ever taken. And that's a tall order, because most neurons are really beautiful in their own right, particularly when you get a good stain, and you're really able to see their structure in detail under a microscope. But these leave you open mouthed, gaping "The colours, man, check out the colouuuuurs..." like a hippie on an LSD trip in the Summer of Love.

The authors have created mice whose neurons glow a variety of colours. Hence, brain + rainbow = Brainbow.

Unfortunately, in contrast to the beauty of the pictures, the prose of the actual article is not accessible to anyone but real specialists. By specialist, I don't mean, "biologist" or "neurobiologist," I mean, "transgenic mouse neuroscientists." The paper is loaded with cryptic abbreviations ("XFP" means "fluorescent proteins" -- I get the FP, but the X?) and hinges on what the authors call the "widely used Cre/lox recombination system," which I had never heard of, and got sent to a 22 page review when I tried to make heads or tails of it. And even though the word that will probably stick in most peoples' heads when they sit down to search Google Scholar is the neologism "Brainbow," the word "Brainbow" is not in the title.

As far as I can tell, here's what they've done.

It's been a reasonably common trick in biology for some years now to be able to take a gene from one organism and put it into another. These are transgenic organisms, and when they're plants, they're also known as genetically modified (GM) crops. A fairly well known example is to take a gene from a jellyfish that makes then glow called green fluorescent protein (GFP) and introduce that into other animals (like mice), so now that other animal gains the ability to fluoresce, just like the jellyfish.

Now, how were Livet and colleagues able to get neurons to glow a bunch of different colours?

After people were able to put GFP into new organisms, people started tweaking the sequence and found they could make other colours -- like red fluorescent proteins. Other people took genes from other animals that glowed different colours. By doing so, researchers developed a palette of different colours. But as an artist knows, the trick is in combining the colours on the palette.

The authors introduced several of these fluorescent genes (up to four different ones) into mice, and found a way to get each neuron to activate a random selection of these genes using this Cre/lox system. If you remember colour theory, you can mix two colours together to create a third. If you mix three colours, the range of possible new colours is very large indeed. By having these multiple genes activating in unpredictable combinations, each cell glows a particular colour that is shared by few of its neighbours. The authors estimate there are at least 89 distinct colours that they can see.

Now, there is some more genetic trickery involved here that I don't pretend to understand fully. One is that the expression is not automatic in all cases -- it can be turned on in specific regions of the nervous system (Figure 3e in the paper shows neurons "lit" only in the retina of the eye). There's also some jiggery-pokery involving crossbreeding some of these genetically modified mice. Sometimes, the mice gave only the single "primary colours," indicating that only one protein was ever expressed. Some others showed the mixtures, giving many different colours.

The paper goes on to show that the colour of a neuron appears to be consistent throughout its length, an important consideration given that neurons have such long projecting branches. They also show the colours stay stable over time by tracking some neurons for 50 days.

As far as I can tell, this paper is a real technical tour de force. There are a lot of experiments compiled here, that appear to be very thorough. The authors did not just stop and publish when they had a few pretty pictures. ... Okay, make that breathtaking pictures.

It will be very interesting to see how this technology develops, and what it will reveal about neuronal wiring. Because so much research is driven by what we can see.

Meanwhile, here are some more pictures.

References

Livet, J., Weissman, T., Kang, H., Draft, R., Lu, J., Bennis, R., Sanes, J., & Lichtman, J. (2007). Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system Nature, 450 (7166), 56-62 DOI: 10.1038/nature06293

Supplemental info: http://www.nature.com/nature/journal/v450/n7166/suppinfo/nature06293.html

When "annual" means nine months

I walked into the building today, and haven't seen a single person since. Ahhhhhhhhhhhhhhhhhhhhhhhh. Bliss.

I spent the morning chunking away on the first annual report of the REU program. This is the first time I've had to submit an annual report to the NSF, and it's a bit weird on a few counts. First, the annual report is due 90 days before the end of the award year. So I'm not actually reporting on a full year's worth of work. Plus, the reporting system is very structured and slightly finicky, about what kind of information you have to present in what order. Still, I think that now that I've gone through it once, it'll be much easier the second time around.

I'm also doing another kind of report -- on student short essays. I'm also grading today, and hope to finish that up before I go home today.

Also on the agenda during this break before classes start again next Monday: animal care, recommendation letters, student research project planning, and maybe some science blogging.

That was last month

Thanksgiving is in October! Why can't Americans understand this and stop wishing me "Happy Thanksgiving" in November?

They could wish me a happy Grey Cup weekend instead. Go Blue Bombers!

Getting to the bottom of things

Today's Ph.D. comic captures something that's not fashionable for practicing scientists to talk about, in this age of restricted and competitive funding. Any comment by me might spoil the punchline, so just check it out.

The Zen of Presentations, Part 11: The Chinese Run-Through

Want to test that you really know your talk?
This is a trick I learned from actors, where it is often called a Chinese run-though. Or Italian run-through. Or [Insert name of language other than the one you speak] run-through. It's typically one of the last stages of rehearsal.

Do the entire talk out loud as fast as you possibly can.

You should sound like one of those frantic radio ads for demolition derby Sunday or the old FedEx ad.

It becomes incredibly obvious where you don't know your stuff, where the transitions are weak. And talking as fast as you can really gets your energy levels up. So do the Chinese run through it as near to the actual presentation as you actually can.

The embarrasment of networking riches

I've spent the last couple of days adding in sharing / social networking / bookmarking tools to this blog. I don't think the process is complete. Compare the list of option currently added on the "Share and subscribe" list (about 9) to the little patchwork quilt of sharing icons that I found on another website (pictured).

While any one of these may be all someone needs as a reader, it's very frustrating as a writer. You want to provide useful tools, but there are so many competing services that it's very hard to stay on top of them all.

A new blog in town

My latest venture is to launch Marmorkrebs.org, and an associated Marmorkrebs blog. The reason why should be fairly obvious: it’s a new animal I’m gearing up to work with, and I’m excited about it and want to evangelize it.

They are more technical websites and blogs than this one, which is meant to be loosey-goosey. (And I like it that way!) So if there’s nothing of note over there, you can click on the picture here and try to count the baby crayfish.

A new icon in town

If you look back through some of my old posts, you may start seeing something new. You may see a little icon with a paper and a check mark, and it says, "Blogging on Peer Reviewed Research." The icon and the idea behind it can be traced back to BPR3 – itself a blog, naturally.

Although reviewing papers isn't the main thrust of this particular blog, it does crop up occasionally (and maybe more often now that I have a cool icon to use). Some recent examples include the "Classic graphics" entries I've been writing. Perhaps a little different than the majority of blog posts that cover recent papers, but they're still peer reviewed. Those are the first I've tagged with the new icon.

We think you're clumsy

They've stuck these signs up around my campus at various places. At first, I thought it was just near some of the places they're doing construction, but no, it's all around.

That's right, we cannot be trust to walk safely without warnings. I'm sure there's a pithy comment about standing on your own two feet in there somewhere.

It's absolutely emblematic of the mania for safety that has gripped our current society. Everyone must be safe. Everyone must be appraised of every possible risk, so that nobody is culpable if you get hurt.

I'm surprised they don't have these next to every stairwell.

11/11

Classic graphics #4: Cortical wiring

In the last installment of this series, I talked about cortex. And here we are again at the cortex.

I got the idea for looking at this graphic from the recent Neuroscience meeting, where I saw this diagram in at least two of the featured late afternoon talks. So I reckoned that qualified it as a classic. Of course, it probably didn't hurt that one of the authors of the paper that featured this diagram was the current president of the Society, David Van Essen. I was able to track it down, and it's freely available online in the original paper (it's figure 4, on page 30).

It also didn't hurt the fame of this diagram that it was printed in the very first article of a brand new journal, I imagine.

And I'm pretty sure I saw this picture prominently featured in a commentary by Nobel laureate and DNA structure describer Francis Crick in Nature. He used it as an example of something we know in monkey, but we should know in humans. We discussed the Crick paper when I was a grad student at our weekly "neurolunch" seminar. (Checking this now, it was Crick and Jones, actually.)

This figure shows the wiring diagram of the part of the brain responsible for visual processing in macaques -- which, because primates are visual animals, and because it's easy to control visual stimuli, is one of the best understood regions of the brain. 32 areas, 10 hierarchical, levels, and 187 linkages, most two-way between connected areas.

I should say, though, that the original was published in colour, based on comments in the text. That the PDF online now is in black and white is probably an oversight.

This diagram is clearly not famous because of its elegance. It's very hard to interpret and looks like the electrical wiring from the Chilton's manual of the car you hope you never own. Heck, even the authors write, "The sheer complexity of Figure 4 makes it difficult in many places to trace the lines representing specific pathways." (They go on to describe a computer representation that allows you to highlight specific connections. Sadly, that diagram does not appear to have made its way online, though I haven't looked hard).

But then, that's the point. It's considered a classic, not despite its complexity and difficulty in interpretation, but because of it. It emphasizes the tremendous complexity of the cortex and how different areas are connected to others.

And make no mistake: this diagram certainly represents a nearly heroic compilation of experimental results. And perhaps that admirable feature has helped people view it favourably over time.

Looking at the text, though, I'm struck by the several qualifiers, provisions, caveats, and tentative interpretations about the information that went into making this figure. The diagram, in a way, is often shown as factual, but is in fact somewhat hypothetical. Something which is not often mentioned when this picture is shown. It's possible, I suppose, that all the hypothesis have been shown correct in the following 16 years of research -- though I doubt that.

Next in this series, I will probably be looking at some graphics by Jerison on brain size.

References

Felleman DJ, Van Essen DC. 1991. Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex 1: 1-47.
http://cercor.oxfordjournals.org/cgi/content/abstract/1/1/1-a

Crick F, Jones E. 1993. Backwardness of human neuroanatomy. Nature 361: 109-110. http://dx.doi.org/10.1038/361109a0

Late SfN pics 2007

When was the last time you saw an ad directed specifically at scientists in an airport? Science journals, sure. Science websites, sure. Airports?

The view from my far too nice hotel room, overlooking the San Diego convention center.

The main, overwhelming fact about the Society for Neuroscience meeting is that it is big. You can't really grasp the vast number of people in a single picture, but some give you hints.

And more people...

I was listening to the Nature podcast for 1 November, and they estimated 25,000 attendees. A substantial underestimate of the actual attendance of 31,000 plus.

A featured lecture; Jeff Hawkins prepares to give a talk. It's pretty rare that to need a big screen at a scientific conference to determine that the speaker does, in fact, have a face.

Again, an attempt to convey the airplane hanger-like size of the poster sessions / vendors area.

Note that the exhibitors row numbers (top) here is in the low hundreds; the other end is up in the thousands.

Finding lunch can be a challenge. Especially if you make the mistake of going to the world's slowest Subway... :(

And of course, there's the enticement to attend next year.

The flight home

Has been made much more pleasant because I had the good fortune to be seated in the first row behind first class. Extra leg room - yes!

Also got seated next to a very nice neuroscientist from Baylor University who works on development of the cortex in mice. Whisker barrels, in particular. Had a very nice talk to her.

And we even got some food, which is an unpredictable rarity these days on planes. Not getting food on the plane would not be such a problem if airport restaurants stayed open longer. Flights come in from around the world, at odd times, with people coming from different time zones... but the restaurants close at 9 or so. C'mon -- if Wendy's drive through can stay open late or even 24 hours on some odd highway somewhere, why not in an airport? I'm just saying.

How connected are we?

There are two people on the shuttle back to the airport: myself and another neuroscientist. I mentioned I had been at J.B Johnston Club. She asked if Joe Ayers was a participant.

Two people out of 31,000. 1 degree of separation.

Joe Ayers was the external examiner on my Ph.D. defense.

SfN, last day

Insanity: Doing the same thing and expecting different results.

It pays to be insane, I guess, sometimes, since I kept trying to get wireless in the convention center for days before it worked. And I seem to have finally found one -- and seemingly only one -- room where it works with my Pocket PC. Strange.

FUN social last night was packed. Very much busier than previous years, I hear.

Last morning for me here, partly spent revisiting the world of cricket hearing. I have an afternoon flight back, and will be home late tonight.

SfN, Monday

Good thing there weren't many posters I wanted to see this afternoon - not much chance to see after the symposium.

Celebrity spotted: Daniel Dennett (author of Breaking the Spell and philosopher of science), seen near the lectern after the evolution symposium. He's taller than I expected!

Speaking of evolution, the FUN committee meeting on evolution was good. Went perhaps a little long, because the topics lend themselves to wide ranging conversation and it can be tricky to stay task oriented. If you're in San Diego, the --

31,731 (attendance value just announced)

Dussini Mediterranean Bistro is worth visiting just for the menus alone. Heavy, metal bound, coppery-looking things in a trapezoid shape.

Wireless!

The SfN wireless is finally working!

The Evolution of Nervous Systems symposium is FULL.

31,300 and change

That's the attendance total for Society for Neuroscience.

Lots of cool posters today. Crayfish sleep, katydid attention, and found some good stuff in the vendors.

Problem remains finding lunch and dinner company. Because you really feel like such a loser to be eating alone at a meeting over over 31,000 people.

SfN, Days 1 & 2

So the hotel wants $$$ for wireless, and the free wireless at the convention center isn't working for me, for some unknown reason.

Cool posters from yesterday: nociception in fruit flies helps them escape parisitoid flies, and a cool neuron in the STG with multiple spike initiation zones.

Not cool: featured lecture in the evening with barely legible slides in a huge hall with a speaker who rarely looked at his audience. Cool topic spoiled by not tailoring the talk to the huge venue.

Today the vendors open up.

SfN, Day X

Yep, it's reaching the point where it's all a big blur.

And why is even freaking Starbucks wanting people to pay for wireless?

On today's agenda:

FUN evolution committee lunch meeting.

Paul Katz's evolution of nervous systems symposium. Which is the main reason I'm still at this meeting.

SfN, Pre-day 1

I'm in the San Diego conference center, sitting on the hallway floor, after finally getting wireless to work. First lecture in 75 minutes.

JB Johnston Club meeting was good. The talk went well on many fronts. I had some good discussions with some cool new people I hadn't met before (Hi Kara! Hi Sarah!).

I am completely kicking myself now, though, over a purchase several months back. My PDA has two expansion slots -- one for a Compact Flash (CF) car, and one for an SD card, both of which are also used in digital cameras. I could just take pictures with the camera then swap them over to my PDA directly to email and such. But no... I had to go and buy a Sony with its silly memory stick.

Neuroscience food

Things I like about SfN meetings in San Diego:

CineCafe, across from the convention center, is the only place I've found in North America that keeps Violet Crumble in stock. (An Australian chocolate bar.)

The conference center sells these soft pretzels, and the cinnamon one is very nice.

JBJC Day -1

According to some of my intel, I should have 'Net access for much of this trip. So I'll be trying a little reportage on this meeting.

Currently in the McAllen airport waiting to fly to Houston. McAllen has free internet; :)Houston makes you pay. :(

The talk is as ready as it's going to be. Fortunately, I can practice on the long flight to San Diego on my Pocket PC. I remembered to copy the talk over to it... Whew!

California dreamin'... I wish

Didn't sleep well last night. Don't expect to sleep well tonight. I'm getting on a plane later today and going to San Diego for the annual meetings of the J.B. Johnston Club and the Society for Neuroscience.

I'm giving a talk at the J.B. Johnston Club, and the talk was not at the point I wanted it to be last night. So I was having a bit of a freak-out trying to get it to where I wanted it to be. I'm almost there, but a couple of practice runs are needed to be sure.

And there are so many things I wanted to do before I left that are not done.

On the plus side... someone read one of my papers! And cited it!

One of the nice things about living in the digital age is that lots of things can be done automatically. Many journals offer "Citation alerts" that send you an email when a particular paper has been referenced in another journal. Yesterday, I got my very first one! And the best part was.. it was by someone that I personally do not know. It's very easy in this business sometimes to think that the only people who have looked at your stuff are people that you have actually met, so small is this community.

And even better was that the paper was actually relevant to some other projects I'm currently doing.

Right. Time to continue panicking for conference trip.

And the suck factor goes up again

Damnit damnit damnit damnit!

I just discovered that an abstract I submitted for an upcoming meeting has a typo in it. In the title. In the species name.

Once, this probably wouldn't have mattered so much. But now, since this is being published, it means that people who are searching for papers on that species through Google or something won't find it.

This alone does not prove that I suck. What proves that I suck is that this is the second frickin' time I've done this.

Mad at myself now.

Denied!

Forgot to mention something from Monday.

Various funding agencies have limited submission programs: they only accept a set number of proposals from an institution. So, when more people want to submit proposals than there are slots available, there has to be some mechanism to sort out who will submit.

So I had submitted an internal preproposal for one of these limited submission grants. Previously, we had our Dean review these and decide. This year, for the first time, for reasons I don't entirely understand, instead of just reading the preproposal (which was about 5 pages, if I remember right), they formed this little committee to review the preproposals, and asked the authors (like me) to come in and give a presentation justifying our preproposal.

I spent several hours working on a little song and dance for this.

Since you read the title for this entry, you know I got turned down.

At this point, I am not convinced that this new review mechanism adds any value to the submission process. It just seems to eat up more time.

Weather watching

The fires around San Diego are really scary. But according to the Society for Neuroscience, the show is going on. I expect the air quality to be atrocious, but if that the biggest problem I personally have, I reckon I have nothing to complain about and a lot to be thankful for. I've been putting a fair amount of time tweaking my talk for the J.B. Johnston Club over the last couple of days, which I'll be attending right before the Neuroscience meeting. Unfortunately, a few other things are going way on the back burner.

Ugh. No pun intended.

Fire

I'm supposed to got to San Diego in 8 days for the Society for Neuroscience meeting.

Today, I start seeing headlines like this:

Half a million flee California wildfires

President declares emergency as wildfires continue to rage unchecked across drought-struck region.

It's going to be an interesting week.

Time tricks

I was gone to Texas A&M for less than 48 hours, but I feel like I've been gone the better part of a week. Weird.

I really enjoyed the trip. A&M is very, very different than any other uni I've visited in some ways. I haven't been on another campus where I've seen people standing around handing out bibles in the middle of campus, or any place with so many cadets with crew cuts and knee high boots.

Met several very nice scientists, and I think my talk went well. Had lunch at the Dixie Chicken, which has atmosphere to spare and good pub grub. Dinner was at The Republic, which had excellent steak and what I called "the schizophrenic desert" – a key line cheesecake / creme brule combo, that worked unexpectedly well.

Mike Smotherman, you rock! Thanks for the invite!

Aggieland

I'm in College Station tonight. Tomorrow, I'm giving a guest seminar at Texas A&M University. A&M was just named best university in the U.S. by The Washington Monthly and which has a football stadium that may be visible from low Earth orbit.

Last night, my talk was not in a state I was happy with, and I did not sleep well because of it. Tonight, I'm still terrified / intimidated, but the talk is in much better shape. And I've had a hot bath to help me relax. So I hope for a good night's sleep.

Just a snapshot from walking home

Learning curves

I was thinking about something this morning, and I thought of the saying that something has "a steep learning curve." I started thinking about graphs showing learning.

And realized what a stupid expression that was.

The term "learning curve" comes from psychology. Typically, you plot time on the X axis on the bottom and proficiency (or accuracy, performance, percent correct, or what have you) on the Y axis on the right.

The typical learning pattern is much different from the graph I sketched up for this blog post. Usually, people improve quickly with very little practice, and then it gets harder to get better. The graph I drew goes in the reverse pattern, but it doesn't matter to the point at hand.

When you're getting better at something quickly, the graph shoots up at a steep incline. The closer to vertical, the faster you're learning.

So when you say something is hard to learn, you should really say that thing has a shallow learning curve, not a steep one.

It's strange that I've studied learning and behaviour and such for years, and have used the cliché "steep learning curve" meaning hard for years, but never put the two together until this morning.

Of course, other people have beat me to this realization. But at least I arrived at the insight through my own independent thinking.