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.

Ignorance

A cashier in a store said to me today, "College professors have the cushiest jobs." Or maybe it was, "easy jobs."

I didn't clench my teeth physically, but I did the mental equivalent. I was really ticked. I replied, "You don't know anything about my job." It took a lot of willpower not to say more.

Life imitating art scaring the pants off of life

I watch and read science fiction. Have done as long as I can remember.

Last night, I watched Episode 2 of Torchwood, about the havoc wrecked after a meteorite hits.

War of the Worlds movie adaptation. People thought the Martian spaceships were meteors.

It Came From Outer Space. In a meteorite.

And there was the "Lonesome Death of Jordy Verrill" segment of Creepshow.

This scares me.

Classic graphics #3: The somatosensory cortex

When I lived in Montreal, I had the unusual experience of living in a city where a scientist was not just known (unusual enough), but frankly, revered. That scientist was Wilder Penfield.

I worked at McGill University, I worked on Dr. Wilder Penfield Avenue. And when I went to some talks at the Montreal Neurological Institute, I heard a speaker talk about having the chance to meet with "the great man," with no hint of irony.

Although it was probably Penfield's reputation as a surgeon that cemented him in the minds of Montrealers as a great individual, one of his most lasting scientific contributions is the map of the somatosensory cortex. This is truly a classic figure, that has been reproduced many times, and is virtually a standard in any textbook that even mentions brains.

Indeed, this picture has been used to study how textbooks copy from one another. In one redrawing of this diagram, a right hand got drawn onto the left side of a body (or vice versa). The error was then propagated in textbook after textbook.

I think this diagram comes from The Cerebral Cortex of Man: A Clinical Study of Localization of Function, co-authored with Ted Rasmussen and published in 1950.

The one up top shows half the story, namely the motor cortex. An equivalent diagram is available showing the sensory side.

What makes this figure a classic is that it uses images so successfully to tell the story. Wrapping the images of the highly distorted body takes something that is actually very abstract and makes it much more easy to relate to. If I am not mistaken, Penfield made these maps during open brain surgery, often with the patient awake. He would stimulate these regions, and observed what the patient did in response to the stimulation (on the motor side), or what the patient reported.

The diagram compiles all those observations of various body movements and miscellaneous reports of sensations.

This edited version of the figure has all the same information as the top one, only using text labels. Indeed, the text labels on the top diagram are almost redundant. But it is clearly nowhere near as compelling as the one showing all the bits of body, with some regions enlarged and some shrunk.

Some people have gone the other way, and created representations of a body sized proportionately to the area of the brain that represents them. In my estimation, these are not as powerful, either.

The distorted body (sometimes called a homunculus, which means little man) is now isolated from the brain. You lose that sense that this is something tied to how the brain works. Such representations have a certain interest, but I don't think they make the scientific point about how our body is represented in the brain anywhere near as well as the original.

Additional, 15 February 2015: Ran across this academic article describing how this diagram changed over time. The first effort, in 1937, was confusing compared to the famous 1950 version.

Schott GD. 1993. Penfield’s homunculus: a note on cerebral cartography. Journal of Neurology, Neurosurgery, and Psychiatry 56 329-333. http://jnnp.bmj.com/content/56/4/329.full.pdf

Villainy II

Take the Villain quiz.

Villainy I

Your results: You are Riddler

Riddle me that, riddle me this, who is obsessed with having a battle of wits??

Riddler		75%
Dark Phoenix		69%
Apocalypse		68%
The Joker		65%
Poison Ivy		65%
Magneto		64%
Mr. Freeze		61%
Dr. Doom		61%
Venom		55%
Catwoman		54%
Juggernaut		53%
Lex Luthor		51%
Mystique		45%
Green Goblin		33%
Kingpin		33%
Two-Face		29%

Click here to take the "Which Super Villain am I?" quiz...

And it's The Riddler, thank you.

Did I miss my calling?

Careers I would apparently like...

1. Taxidermist (What?!)
2. Desktop Publisher (Kind of did that)
3. Veterinary Technician
4. Industrial Designer
5. Cartoonist / Comic Illustrator (Done a bit of that)
6. Animator
7. Fashion Designer
8. Costume Designer
9. Set Designer
10. Botanist (Getting close)
11. Artist
12. Graphic Designer
13. Paleontologist
14. Critic (Sort of did that)
15. Writer (Does blogging count?)
16. Computer Animator
17. Biologist
18. Political Aide
19. Activist
20. Communications Specialist
21. Market Research Analyst
22. Public Policy Analyst
23. Print Journalist
24. Website Designer
25. Interior Designer (Could you picture me on Trading Spaces?)
26. Translator
27. Medical Illustrator
28. Technical Writer
29. Animal Breeder
30. Craftsperson
31. Potter
32. Marine Biologist
33. Public Relations Specialist
34. Veterinarian
35. Zoologist
36. Criminologist
37. Anthropologist
38. Professor
39. Biological Tech
40. Optometrist

This meme courtesy of John Wick.

Lights out

A few minutes before five o'clock, the power went out in my office. My building. And I soon learned the power was off on the entire campus. It took a while to find out a transformer had gone out, and power wasn't coming back on in a few minutes.

At least this was at the end of the day. If it had been earlier, it would have been very disruptive to the site visit of the regional director for Beta Beta Beta. Students are trying to establish a chapter – they need a faculty advisor – and I said, “Okay.” So part of establishing a chapter is the visit, and I think that went well.

In other emergencies...

Our president had to go through major heart surgery unexpectedly. And we also just found out that one of our scheduled Science Symposium speakers for HESTEC has to cancel because he has to go in for major heart surgery (triple bypass). And our Beta Beta Beta visitor was the recipient of quadruple bypass surgery not too long ago.

Another sad day

Some become so famous that one one name is needed. Elvis. Madonna.

In the field of animal behaviour and psychology, most people knew about Alex.

Poor Alex died unexpectedly last week. When I saw a new story about a "famous parrot" dying, my heart sunk, because I knew there was only one parrot that it could be.

Alex was the African grey parrot that Irene Pepperberg had worked with for 30 years in her classic studies of comparative cognition. People had always known parrots were clever, but started to show just how clever. Categorization, counting, concepts... Work with Alex really started to undo a lot of the thinking that had permeated animal behaviour since the Clever Hans affair and the radical behaviourism of American psychology in the mid-20^th century. For decades, anything that remotely smelled of "thinking" was exiled from scientific study in animals, and sometimes even humans.

Irene Pepperberg's work can be seen at the Alex Foundation.

Classic graphics #2: Crayfish tailflips

This particular picture is not famous outside of my own field. But it has been reproduced many times, and as such, I think warrants the classic designation.

Crayfish tailflipping was one of the first natural animal behaviours that neuroethology really cracked. It was one of the first cases where we could explain how the connections between the neurons explained a lot about how the behaviour of the animal worked.

One of the little oddities in the story of understanding the escape response of crayfish was that the major neurons involved were recognized back in the 1920s. These huge neurons became known as the lateral giant (LG) and medial giant (MG) neurons, but even in the flapper era, there was pretty strong evidence then these giant neurons were involved in tailflipping.

But it took over 40 years for people to explain why there were two sets of neurons involved in tailflipping. And they can be forgiven for not figuring this out quickly, because this behaviour is so blindingly fast, you can't make it out with the naked eye.

When people finally got around to using high speed film, the answer became clear. There wasn't one behaviour. There were two. There were two different kinds of tailflips, each triggered by a different set of neurons. (Actually, it turned out that there were three kinds of tailflips, but that's another story.)

What fascinates me about this particular figure (from Wine and Krasne, 1972) is that it was not the first to make this point. Priority is huge in science. Normally, the first to show anything gets priority, and hold a very strong sway on our imaginations. Ask someone who was the second person to climb Mount Everest, or the second person to fly solo across the Atlantic. Heck, I don't know.

Just a few months earlier, in the same journal, another group of researchers led by Jim Larimer (which included my intellectual predecessor, Don Kennedy) published a picture that shows the same thing: that stimulating the different neurons generates different movements.

In this case, I think it's pretty clear why the later picture became the canonical representation of crayfish escape behaviour: context. You see the stick tapping animal, and you see the whole animal, moving through space, rather than an isolated part of an animal being held static. The advantages of this are huge.

The top diagram makes it forcefully clear what advantage there is to having two tailflips: both tailflips take the animal away from the source of the offending stimulus, but do so by throwing the animal in different directions. The crayfish jackknifes into the water when the LGs fire, but heads straight back when the MGs fire. You can sort of extrapolate that from what's shown in the earlier figure, but since you can't see where the stimulus would be, you don't have that immediate "Aha!" insight.

Sometimes, it isn't better to be first. It's better to be better.

References

Larimer, J. L., Eggleston, A. C., Masukawa, L. M. and Kennedy, D. (1971). The different connections and motor outputs of lateral and medial giant fibres in the crayfish. The Journal of Experimental Biology 54, 391-404.

Wine, J. J. and Krasne, F. B. (1972). The organization of escape behaviour in the crayfish. The Journal of Experimental Biology 56, 1-18.

Classic graphics#1: The Cartesian reflex

One of my side interests is in graphics. And I'm curious about what makes an image famous. Particularly scientific images. So I'm going to try exploring that from time to time, focusing on my own field of interest, neurobiology.

Over at the left is an image that I've seen reproduced many times. So often, in fact, that I'm having a hard time finding exactly the original source, to my embarrassment. It's from the work of René Descartes, 17^th century French intellectual. I think it's from Treatise on Man, published around 1662 after Descartes' death.

I do not know if Descartes drew his own figures. I doubt it, because preparing woodcuts is a pretty specialized talent. And Descartes, I've heard, loved a life of luxury. I don't think he was the sort to handle woodcutting tools. Be that as it may...

What the figure is showing is Descartes' conception of how behaviour worked. It looks fairly modern. Even if you understand only a bit of modern biology, you might think, "You have a sensory stimulus, impulses travel up the spinal cord to the brain, are processed, and you get a withdrawal from the painful stimulus."

I think that's one reason why this particular diagram is famous: because it is almost eerily prescient.

And indeed, in broad strokes, that's what this is showing. Descartes was the first to develop a reflexive theory of behaviour, although I don't think he used the term "reflex." Because Descartes is so famous for his ideas on the soul, his arguments that much of behaviour -- even in humans -- is purely "push pull" sorts of automatic, reflexive responses is often overlooked.

That the picture looks quite modern in some ways actually sort of overshadows some important problems. Descartes had what I consider to be a pre-scientific concept of behaviour. The discovery of biological electricity was centuries away, so Descartes followed the ancients in thinking that behaviour was controlled through the movements of "animal spirits."

Is the picture at top famous because of the idea that it shows? I don't think it's just that. Over to the left is another picture showing the same basic idea, again from Descartes, and I think even from the same book. Regardless, you see the same basic elements: a fire, an outstretched limb, and "animal spirit vessels" leading to the brain.

Yet this one I have not reproduced seen over and over again like the top one. I would say the top one is a classic, but the bottom one not. And here, the actual rendering of the diagram might be important in why this one isn't reproduced that often.

I find the second one is kind of disturbing. The figure has sort of babyish proportions. The torso sort of floats out of a cloak, which no obvious indications of a bottom half. Plus, the "animal spirit vessels" don't go right out to the fingers, making the idea that there's a connection between the stimulus and the person's brain harder to understand.

Or maybe the reason the top one is more famous is that editors are always looking for excuses to put in more nudes in their books.

Oh, no.

I was just looking for something for another post I was writing, and boom, learned Barry Beyerstein was dead.

Geez.

I can't say I knew him well, but he was someone who did me some favours. When I was a grad student, he invited me over from UVic to SFU to give a talk to the BC Skeptics after reading an article I published in The Skeptical Inquirer. It was my first invited talk. Later, he was a special science guest at I-Con 2, a SF convention I helped organize in Victoria.

He was wonderfully friendly guy. I'm sorry I'll never get a chance to run into him again.

Additional, 20 March 2014: Here’s someone who heard Barry Beyerstein at I-Con 2, which, as I said, I was involved in organizing and inviting Barry to. He calls hearing Beyerstein speak, “a life-altering shock to me, a road to Damascus moment.”