30 November 2007

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.

29 November 2007

Disturbing news story in Texas

Chris ComerIn 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.

28 November 2007

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.

27 November 2007

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.

24 November 2007

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.

23 November 2007

"I don't want the broader picture"

RSS logoThis 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.

22 November 2007

Classic graphics #5: Brainbow

Blogging on Peer-Reviewed ResearchMotor end plates in Brainbow mouseIs 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.

GFP miceIt'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.

Livet et al. Figure 4The 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.


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.

21 November 2007

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!

20 November 2007

Getting to the bottom of things

Ph.D. comic for 20 November 2007Today'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.

19 November 2007

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

John Moschitta, Jr. in FedEx adWant 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.

18 November 2007

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.

16 November 2007

A new blog in town

Spot the babiesMy 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.

11 November 2007

We think you're clumsy

Watch your stepThey'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.



10 November 2007

Classic graphics #4: Cortical wiring

Blogging on Peer-Reviewed ResearchIn 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.


Felleman DJ, Van Essen DC. 1991. Distributed hierarchical processing in the primate cerebral cortex. Cerebral Cortex 1: 1-47.

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

Late SfN pics 2007

airport adWhen 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.

Slow SubwayFinding 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.

07 November 2007

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.

06 November 2007

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.

05 November 2007


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.