28 February 2013

“Neuroscience! Because Alzheimer’s!”

Europe has a big brain modelling project, and now the United States is talking about a big brain project. Attention exploded when “mapping the brain” was mentioned in the American State of the Union speech. This prompted a lot of talk about this proposal, as you can see in the long list of external links below.

Let’s see what was said about the project in the American State of the Union speech.

Today, our scientists are mapping the human brain to unlock the answers to Alzheimer’s(.)

The justification is why I am unable to conjure up anything other than a weary sigh about this project.

“Neuroscience! Because Alzheimer’s!”

I’m surprised Parkinson’s didn’t get mentioned, too. It usually is in these sort of speeches.

The brain mapping is being pitched politically as worth doing because it will lead to cures. If you go digging through the long list of external links below, you will find basic neuroscientists who are talking about what is technically feasible, whether this is better done as one big project of funding lots of small ones. But neuroscientists are not talking about curing neural diseases as a reason to do this project. Mainly, they are seeing this as a chance to get a lot of fancy new toys to record activity from a lot of neurons at once.

If you go back to the 1980s and 1990s, you would hear promises like this:

“Human genome! Because disease!”

That has not happened, at least not in the way that people talked about at the time. People have memories, and they will wonder why we don’t have all that great personalized medicine that they were promised.

I am not saying the human genome project should not have happened. By most accounts, it was a good investment and generated a lot of economic returns. This was mentioned in the State of the Union address, too (although the exact number is contentious):

Every dollar we invested to map the human genome returned $140 dollars to our economy.

I wish there were more people trying to build trust in the research enterprise rather than making promises.

Additional: Speaking of personalized medicine, here’s a long read on the current state of the art.

When I tell my parents the results, I can’t help sounding disappointed. “It’s reassuring,” I say when we gather around the kitchen table. “But I expected to find out more that seemed relevant to our family.”

Hat tip to Ed Yong.

Additional, 12 March 2013: Having grumbled about genomics and medicine above, I would be remiss if I didn’t link to a more promising story, again courtesy of Ed Yong.

Related posts

Overselling the connectome
Brainbrawl! The Connectome review
Promises versus trust

External links

Obama seeking to boost study of human brain
US government to back massive effort to understand the brain
Why Some Scientists Aren't Happy About Obama's $3 Billion Brain Research Plan
Brain Project Draws Presidential Interest
BAM! My Thoughts on Big Bucks for Big Brain Science
Here’s how Obama’s brain mapping project will actually work
A 3 billion dollar mistake: Why the American government should think twice about a Brain Activity Map (BAM)
Connecting the Neural Dots
How Smart is Proposed Brain Activity Mapping Project?
A Manhattan Project to map the brain
Finding the treasure: A practical view on where the Brain Activity Map project will lead us
Brain Activity Map: boondoggle or bonanza?

Image from here.

27 February 2013

Pushing away talent

On The Science Show, William Press, the president of the American Association for the Advancement of Science (AAAS) said:

Among young people, science is cool again. Science was cool after Sputnik a whole generation-and-a-half ago, maybe that's two generations by now ago. But we are again at a time where there are TV shows, at least in the United States, which hinge on the scientists figuring things out, the profile of the nerdy intellectual, whether male or female, is often the one in these stories that saves the day. The sad part would be if this resurgence of interest in science among young people coincides with an age of austerity where we’re not able to give them the career opportunities to let their creativity come into play and make these important new discoveries.

Press is right to be concerned. He was speaking at his society’s recent annual meeting in Boston. As it happens, in conversation with individuals who went to Boston to that meeting, the lessons they learned from being at the meeting were:

  • Do not, under any circumstances, do a Ph.D.
  • Nobody in the grad school or post-doc stage is happy with their supervisor.

To add one more anecdote, I’ve seen another student who got involved in research early in her undergraduate career... and is already prepared to get out. This is someone who is super excited, superb in the lab, loves the research. She is getting rewarded by being worked like a dog (because she’s good at what she does). She’s seeing up close the stress of labs chasing biomedical research funding.

I see all the effort that is going into telling students, “Go into STEM!” Yeah. The brightest and most engaged students are going to be the one who figure out how much craziness and stress is going into chasing money to keep labs afloat. And they’ll leave.

This sucks.

External link

Obama promises more funds for research

26 February 2013

Tuesday Crustie: The crab as enzyme


The caption to this recent Cell cover (volume 153, number 3) leaves me baffled.

The cover image depicts RNA polymerase as a crab, with the small crab (upper right) symbolizing an elongating RNA polymerase moving along a string (i.e., DNA) and its claw, representing the clamp domain, closed. The central crab represents a paused polymerase. It is in a meditative state with its claws open, yet it keeps a grip on the string. Art by Oliver Hoeller.

Um. What?

25 February 2013

Mentoring Venn

Last Friday, I attended a very interesting workshop with Marcos Pizarro from San Jose State University. One of the things he presented was a diagram of what a good mentoring relationship looks like.


This is a situation where you can get good things happening. The student knows what it is that she has to learn, and the professor knows how to articulate those professional skills to the student.

On the other hand...


This is the danger zone. And this situation is common.

The student is completely ignorant of the need to do something, or an opportunity that exists. The student doesn’t even know to ask the question.

For instance, I remember back as an undergraduate student, one of my professors took me into her office, and asked me, “Would you like an enserk?”

“Great! Um... what’s an enserk?”

It turned out not to be enserk, but NSERC, the acronym for the Natural Sciences and Engineering Research Council (sort of the Canadian equivalent to the NSF). This was the first time I’d ever heard of this agency. I later learned there were three science agencies: enserk, murk, and shirk, or to use the acronyms, NSERC, MRC (Medical Research Council), and SSHRC (Social Sciences and Humanities Research Council).

The professor was asking me if I would be interested in an NSERC supported summer job, which I ultimately did land. But I was solidly in the land of the “unknown unknowns” in the diagram above.

What about on the mentor’s side? This one is trickier. This is usually cases where the professor genuinely knows stuff that the student actually needs. The problem is that she doesn’t think to provide the information to the student because she has gained so many skills that have become reflexive, and is so steeped in and socialized to the academic culture that she forgets what it is like not to know something.

For instance, I recently had someone ask me, “How do you read a scientific paper? What do you look for to figure out if it’s any good?” That was tough to try to articulate, because as you become a scientists, there are so many individual little pieces that you learn to look for. I was momentarily at a loss in trying to describe my process for tackling a paper. How deeply you need to read it? What are the signposts you look for? I never developed an explicit checklist for it.

At some point, you don’t easily remember what it was like not knowing the stuff you know.

Sketchnote from session:


If you’d like me to explain anything in the sketchnote, please let me know in the comments!

23 February 2013

47

47 is 42, corrected for inflation.
Rick Berman


The number 47 is interesting. It’s a prime number, for one. And it has ties to one of the shows that helped shape my mental landscape... A partial list in Wikipedia:

  • In Star Trek: Generations, Scotty manages to beam up 47 El-Aurians before their ship is destroyed by the energy ribbon.
  • In the Star Trek: The Next Generation episode “Darmok”, the computer of the Enterprise reports to have found 47 occurrences of the word "Darmok" in its database.
  • In the Star Trek: Voyager episode “Parallax”, the Emergency Medical Holographic Channel is 47 and that the EMH has the experience of 47 individual medical officers.
  • In the Star Trek: Voyager episode “Before And After”, the phase shift is 1.47.
  • In the 2009 film Star Trek, the Enterprise was built in Sector 47 of the Riverside Shipyards, and 47 Klingon ships are said to have been destroyed by Nero’s ship, the Narada.

And today, it’s the number of times this little planet has circled around the sun while I’ve been on it.

External links

The Star Trek Connection
47
The 47 conspiracy

22 February 2013

Dreaming of Mars

On today’s #scistuchat, Adam Taylor asked

Should we dream to go to Mars?

I have mixed feelings about this now.


A couple of years ago, I went to Hawaii for the annual meeting of The Crustacean Society. And I did get to walk around in Honolulu a little while I was there. And it’s beautiful there.

I started trying to imagine what would it have been like to be the very first person to arrive on Waikiki beach. Or maybe take a trip in the TARDIS back to a time before human settlement. No people, no hotels, no tide walls... just the waves hitting the beach, and the trees covering the land going up the hills and mountains.

Oh, but the first people on Hawaii were lucky, lucky people.

I couldn’t help feeling we kind of spoiled it. Not entirely. But I would liked Waikiki more if it had much less of a human presence on it.

I was talking to a friend about parks in my old stomping grounds, Alberta. Everyone knows Banff National Park. It is beautiful, but I don’t think has been well served by the amount of development there. I used to love Waterton Lakes National Park, because it had remained true to the spirit of being a park, with much less development.

So images of these holes drilled on Mars by Curiosity give me pause:



As we have explored, we have not always done a great job of thinking about preservation. There may be some places that humans should only go rarely. Mars, or at least some parts of Mars, might be among those places.

Curiosity picture from here.

19 February 2013

Tuesday Crustie: Two first names

Her name is Laurie Teresa:


Or, if you insist on Latin, Lauriea teresae. This lovely little squat lobster is one of several new species found in the Pacific and Indian Oceans that was just published last month.

Reference

Macpherson E, Robainas-Barcia A. 2013. A new genus and some new species of the genus Lauriea Baba, 1971 (Crustacea, Decapoda, Galatheidae) from the Pacific and Indian Oceans, using molecular and morphological characters. Zootaxa 3599(2): 2. http://dx.doi.org/10.11646/zootaxa.3599.2.2

18 February 2013

Decision making: “No one knows what you know inside”

I’ve been enjoying Victoria LaBalme’s blog a lot. Although it is ostensibly about what acting can teaching us about presentations, it’s much richer than that. I particularly enjoyed her post today.


This bit resonated with me. Maybe it’s because between search committees,grad school applications, fellowship applications, research applications, I’m often acutely aware that I have to make decisions on very little information.

So really, when you hit that “Y”, that divide, you have to go with the inside. Because on the outside, no one knows what you know. No one knows what you know inside, no one has the design that you’ve been dreaming with in your mind and in your heart. You have that. And even though the path may not be a hundred percent clear, you have to learn to trust your uncertain convictions.

When you’re seeking advice, it can be very helpful to get outside opinions. And in academia, there are no shortage of people who are willing to offer us opinions: our colleagues, our PIs, our fellow students, what have you. Their pressure to take a certain path in your career can be intense. You hear a lot of stories of people pressuring their students and post-docs into a lab, a program, or something that the boss thinks will be great.

But as Victoria reminds us, no matter how much experience and expertise someone has, opinions from someone on the outside is always going to be imperfect. They can never have all the information. They don’t know what you know.

Related posts

You do not know the end of your story

External links

Are you about to take the path you don’t really want?

Incompetence Theory

The other day, my colleague Mike said to me:

You’re an Incompetence Theorist.

He was contrasting me to conspiracy theorists, you see: the people for whom everything is explained by invoking vast, shadowy organizations. I frequently invoke some version of “Hanlon’s razor.” Roughly, “Don’t invoke conspiracy when incompetence will do.”

Maybe we need more incompetence theorists out there, reminding people that everyone makes mistakes.

15 February 2013

Sea cucumbers, the original “buttchuggers”?

A while ago, there were some reports of young men at universities who came up with an interesting way of imbibing alcohol. It was nicknamed “buttchugging.”

Yeah.

This method of alcohol delivery is, from a certain very twisted point of view, quite clever. The gut is a tube. This means that regardless of which orifice alcohol enters your gut,you can still uptake the alcohol into your system and enjoy the intoxicating effects.

Now, a new paper from Jaeckle and Strathmann looks whether sea cucumbers might be able to ingest food via the back door. It turns out that sea cucumbers have an odd system for taking up oxygen. They have respiratory trees that connect to the anus, shown below:


Consequently, the anus isn’t just an exit point for undigested waste in sea cucumbers. There is much more activity than simple expulsion, with water being moved to and fro to allow for respiration. Given this, there would seem to be much more opportunity for nutrition to enter the digestive system through the anus.

To test this, they performed two experiments. In the first, they put giant California sea cucumbers (Parastichopus californicus) in tanks with algae that contained a heavy carbon isotope (14C). Let’s look at Figure 2.


What the authors are trying to show is that the closer you are to the respiratory tree, the proposed entry for the food, the more of the heavy carbon isotope you find. After 24 hours, though, the level is nearly as high in the digestive system as the respiratory tree. But a close look at the figure starts to see some significant shortcomings.

First, the more disturbing thing about this graph is the error bars. There aren’t any. There is no indication of sample size anywhere in the paper. There are no statistical analyses, either. I suspect that each data point was pulled from one individual. If so, that is a huge problem that makes it difficult to conclude much of anything.

Then, notice the time collection intervals. You get a lot of measurements in the first 8 hours, then nothing until 25 hours. I am betting the #OverlyHonestMethods version of this would read, “We did most of the work in one day, went home to eat and sleep, and came back the next morning.” That day long cycle might matter for the results, depending on the behaviour of the sea cucumbers. Are they nocturnal? Do they feed differently in the day that the night? Those sort of questions are not answered. They also don’t appear to take any steps to try controlling for ingestion through the mouth.

In the second experiment, they exposed the animals to large molecules containing a lot of iron. The iron allowed them to stain it later to see if it had been taken into the tissues.

I don’t like this experiment as much as the first one, because it seems unlikely that sea cucumbers are hanging out in regions that are rich in large nutritional molecules. The previous experiment seems to better represent actual ingestion of food in cells: the sort that a sea cucumber might encounter in the wild.

Again, there are some shortcomings in how they present their results. In their figures 4 and 5, Jaeckle and Strathmann show that there are bits of respiratory tree tissue that have stained blur for iron, indicating that those molecules were incorporated into the animal. But... the authors show only the positive experimental stains. While they say in the text:

In the respiratory trees of control animals, there was no equivalent presence of the blue reaction product.

It would be much better if they also showed the negative control in the pictures.

And another weird thing that you can see in the acknowledgements is that this work was done in 1996. While this is not a record for delay between the experiment and publication, over 15 years in the waiting has to be in the top one percent of waits.

The authors note that even if the sea cucumbers were able to retain all the food in the water, the amount of food they would be getting would probably not be that large. The authors do raise the possibility that this unusual way of feeding might allow sea cucumbers to get different kinds of food than they would get by ingesting it through the mouth. But this is speculative, and it seems likely that anal feeding would contribute at best only a small amount of the animal’s nutrition.

This paper makes a plausible case for this sea cucumber species to be able to get some nutrition via the anus, but it is very limited in what you can conclude from it.

P.S.—And if all that didn’t make sea cucumber anus remarkable enough, it can also provides a home for fish.

Reference

Jaeckle WB, Strathmann RR. 2013. The anus as a second mouth: anal suspension feeding by an oral deposit-feeding sea cucumber. Invertebrate Biology: in press. DOI:

Giant California sea cucumber photo by Ken-ichi; sea cucumber diagram from here.

Comments for first half of February 2013

I make a cameo at The Dragonfly Woman. I’m part of point number 4.

So God made Doc Becca because he needed someone to make “So God Made a Scientist.

I make a cameo appearance in Brian Switek’s article on seafofod pain.

Erin McKiernan wants opinions on the goal of simulating a human brain.

Basic Space covers the “Blogging for the long haul” session that I co-moderated at Science Online 2013.

InBabyAttachMode considers what starting a new lab is like.

Dr. Doyenne takes up an idea that crops up every three years or so: making credit for scientific contributions more like movie credits.


14 February 2013

Using advantages


Johnny Blaze is a man with absolutely everything to fear.

In the movie Ghost Rider, Johnny Blaze sells his soul to the devil. You don’t get out of deals with the devil. He knows that he is damned.

With everything to fear, do he run and hide? Absolutely not.


Instead, he becomes a daredevil. johnny Blaze, world’s greatest stuntman, out there performing for the crowd and doing crazy stuff. Before each performance, each stunt, he looks in the mirror, plays Karen Carpenter, and says to himself:

“You can’t live in fear.”

I quoted the Ghost Rider movie when I was talking at the identity session at Science Online 2013. I have always blogged under my real name (even though people sometimes think it is a pseudonym). And I mentioned the kilt story here, too:

@DoctorZen wears the kilt to remind himself to BE FEARLESS. #scio13ID #scio13


Yes, I’ve mentioned this anecdote before. But what I haven’t told you is some of the things I’ve done that I considered to be part of my efforts to “not live in fear.” For me, when I’ve talked about “being fearless,” I’m mostly thought of things I’ve done in a professional capacity. I think about things like trying crowdfunding, self-publishing a book on Amazon, and publishing a paper on my blog.

In a way, this kind of fits with the Ghost Rider. Ghost Rider was not, like many other superheroes, a character who helped others out of selflessness. Blaze is possessed by a spirit of vengeance. Whether or not the Rider helps anyone is almost incidental to the things he does.


In the “Identity” session, I mentioned I have advantages in being online as my known, professional self:

@DoctorZen : as white tenured guy easier to be brave public intellectual online. Kilt = reminder to be fearless #scio13ID #scio13

Danielle Lee responded to that:

@DNLee5 calls @DoctorZen a Tony Stark - and we need that she says - people to use their advantage to call things out #scio13ID #scio13

Tony Stark has some of the same advantages I have (middle aged white man) and some that I don’t (wealth and genius). Danielle’s point was that when you have all those advantages, first, you don’t have to hide behind any sort of secret identity (the movie got to this point much, much faster than the comics, though). And the second thing she pointed out was, indeed, that Stark at his best doesn’t just leave things as he finds them.


I said then being compared to Iron Man was one of the nicest things that had been said to me in a while. Later that night, I had a great chat with Dr. Rubidium in the bar where we discussed related issues: how you can help people, and when. And again, it surprised me that anyone would consider me in those sorts of terms.

Following that conference, I decided I needed another reminder to myself. I needed a reminder not just to be fearless in things I try for myself, but to try to leverage some of the advantages I have in aid of others. So I bought this shirt:


While I may not have learned a lot of new information at Science Online, I did get some reminders that went deep with me. And one was a reminder about the power of a compliment, and the power of discovering that others might see you in more positive terms than you might think. For some, maybe this feed imposter syndrome, and they sit there and think, “I’ve fooled them all”... but maybe you can push yourself yourself and try to meet some of those perceptions.

Additional, 11 March 2013: The Identity session from Science Online 2013 is now up for viewing! The bit between Danielle Lee and I starts about the 9:00 mark.

13 February 2013

Sasquatch DNA: new journal or vanity press?

The sasquatch DNA story I was watching back in November has moved forward. The promised paper has now appeared.

In the first issue of a brand new journal that has no other articles in it.

You may recall that a couple of weeks ago, I co-moderated a session at Science Online that talked about how anyone can start a new open access journal on the web, and issues of credibility arising from that. Well, remove the “open access” part of the equation (they want $30 to read the single available paper), and you still have a lot of the same issues, and they are all in full view and writ large with the launch of the journal DeNovo.

Now, I am a scientist who is on the record as people should sometimes submit papers to new journals. I have occasionally taken a shot and submitted articles for new journals. Indeed, became one of my fastest papers to accumulate citations. I like to support new publishing ventures. Would I submit to DeNovo?

Nope.

  • There is no editor listed.
  • There is no editorial board listed.
  • There are no people who are identifiable by name anywhere on the website that I can see.
  • There is no physical address.
  • There is no phone number.
  • A section requesting people perform “Open peer review” has no manuscripts ready for anyone to review.
  • The bottom of some pages lists “denovoscientificpublishing.com”, which goes to a placeholder.
  • The journal was created with a service that “helps you easily design & create gorgeous websites with just a few clicks.”

This whole thing looks completely dodgy, with the lack of any identifiable names being the one screaming warning to stay away from this journal. Far, far away.

I’m predicting this journal will never have a second issue. Meet me here in one year, and we’ll see if there has been any progress. Or if the journal is even still online.

Update: Carl Zimmer just paid $30 for a copy of the paper. I said I would happily donate to help pay the cost of the reprint, and he said I could buy a book of his instead.

Support science journalism. Go buy one of Carl Zimmer’s books.

Oh, I cannot wait for the critiques. Carl has already written on Twitter:

The phylogeny in this #sasquatchgenome paper is incomprehensibly illegible & doesn't seem to use any method I can recognize.

How... interesting.

Yet more additional: Cryptomundo reports that Ketchum says she had nothing to do with the “acquisition” of the journal or its editorial process. Melba Ketchum is reported to write:

One thing I want to make ABUNDANTLY clear. I did not self publish, but acquired the other journal. I have had and still have NOTHING to do with any publishing, editing or peer reviewing for Denovo. That was all completed prior to the acquisition of Denovo.

But this raises more questions. If this was an “acquired” journal, what name was it previously know by? Are there any existing archives of past issues from before the acquisition and re-branding? Since we have no actual names of the publishers or editors, how can we confirm Ketchum’ claim of non-involvement?

Oh, and there’s this video:


I remain unconvinced, but still hoping there is more evidence.

Additional, 14 February 2013: Houston Chronicle blogger SciGuy is collecting reactions to the paper from some scientists who have read it. One thing I will point out is this from Leonid Kruglyak:

There’s also the strange statement they couldn’t deposit sequences in GenBank because it’s a new/unknown taxon — GenBank does that no problem.

I’ll second that. Marmorkrebs, the unusual clone crayfish I work work, had sequences in GenBank well before it had a proposed species name.

Related posts

Sasquatch DNA?

External links

Ketchum Bigfoot DNA paper released: Problems with questionable publication
Like OMG! Bigfoot DNA paper is published!
Ketchum Sasquatch DNA Study Update: Questions Answered…

12 February 2013

This Darwin Day, please stop using quotes that Darwin never wrote

Charles Darwin was a good writer, albeit one who suffers a bit from the wordiness typical of the Victorian era he lived in. He gave us many lovely passages and metaphors. This makes it all the more irritating that I saw multiple cases of people posting quotes from Darwin that weren’t actually Darwin, from folks who should know better.

First, the science show Nova blew it on their Twitter feed.


This quote actually comes from management professor Leon C. Megginson from Louisiana State University.

Then, Sigma Xi blew it on their Facebook page.


The original source of this quote has not been tracked down, but it is definitely not found in any of Darwin’s writings.

I’ll leave with a personal favourite quote of mine from Charles Darwin. Unfortunately, this one requires a bit of context; it’s not a pithy self-contained quote. It appears in the sixth edition of On the Origin of Species, as the last line of chapter VII. Darwin has spent much of the chapter answering objections from critics, particularly  Mivart, who argued for sudden appearance of new features; “momentous and abrupt transformations,” as Darwin calls them.

I just love, love, love the last line, which I’ve bolded:

He who believes that some ancient form was transformed suddenly through an internal force or tendency... will be almost compelled to assume... that many individuals varied simultaneously. ... He will further be compelled to believe that many structures beautifully adapted to all the other parts of the same creature and to the surrounding conditions, have been suddenly produced; and of such complex and wonderful co-adaptations, he will not be able to assign a shadow of an explanation. He will be forced to admit that these great and sudden transformations have left no trace of their action on the embryo. To admit all this is, as it seems to me, to enter into the realms of miracle, and to leave those of Science.

It is one of the most effective dismissals for special pleading that I’ve read.

Tuesday Crustie: Satan Smells A Rat


This is Lobster Johnson, Mike Mignola’s homage to pulp. This cover will grace a one issue story with the awesome title, Satan Smells A Rat.

Cover spotted here.

11 February 2013

Becoming Batman (Academic edition)

We like to think about the events and people that changed people’s lives. When we talk about “life changing events,” it’s often a positive thing. It doesn’t have to be, though. Bruce Wayne had an event that changed his life.


Bruce Wayne’s parents were killed in front of him.

Whether the event that starts you on a path is positive or negative doesn’t matter to the story of Batman, or the story of an academic. The point is that these thing can happen when people are powerless to do anything about it.

This is many students, maybe at the high school or beginning undergraduate days. They have something they want to do, but... they realize they have to wait.

Eventually, they start to train. And they train hard. Often to the exclusion of everything else.


For some people, this is their university education. For others, this might be grad school.

After all that training, there’s that chance – finally – swing into action. To put all that training to use. His first time out as a crime-fighter, Bruce Wayne put on a ski mask and hits the mean streets of Gotham City. And he gets his ass kicked.


This is a lot of academics at the post doc or assistant professor stage. You have the theory and the training, but not the experience. You’re not yet Batman.

Bruce Wayne had a very definite point that demarcated when he became Batman.


You reach that where you have the training and the seasoning pay off. Bruce Wayne becomes Batman.


For academics, this can be a very drawn out process. Imposter syndrome, for instance, is something many successful academics struggle with. They’re still think they’re Bruce Wayne in the ski mask, not Batman. For some, tenure might be a point where some might think they have “made it.” At some point, you realize that you can do this.

You can’t do everything, but you realize that in some domains, you can do a lot. And people can marvel at how it is you can do all the things you can do. They don’t quite know how you manage all those things.


But here’s the turn in the story. And the reason for this post.

Batman has always had a drive, a confidence, and was always a man with many, many advantages. Very few people seriously challenge him. And those two things combined can turn nasty.


Bruce Wayne is, ultimately, a regular human being, not a Kryptonian or someone imbued with mystic energies. He is a person who, like everyone, is going to get older. And age will take its toll. There are different versions of what happens to Bruce Wayne as he gets older.

In The Dark Knight Returns mini-series, we meet Wayne who has tried to give it up, but is so completely driven that he returns to being Batman.


The Batman who returns is not the Batman most of us are familiar with. This is a relentless, ruthless Batman. He still doesn’t carry a gun. His supporters in the media keep reminding the television audience, “Batman hasn’t killed anyone.”

But you’d be surprised what you can live through.


Batman doesn’t seek out companionship, but through a series of events, a girl named Carrie Kelley comes to his aid.


In this story, you never get the sense that Batman cares deeply about Robin. He’s glad to have her a resource, and he tries to keep her alive. I think Batman even calls her a “soldier” at a few points.

This Batman is the academic who is charitably called “effective.” This is the primary investigator who brings in a lot of money, and has often unreasonable expectations of people working with him or her. This person is often brilliant, and fascinating, but... harsh. This is the academic who can make life hell for students and postdocs and colleagues.

But there’s another story of what happens to Bruce Wayne.

In Batman Beyond television series, we again meet a much older Bruce Wayne. He’s quit being Batman, and he has to live with a the choices he’s made, and they weren’t always good ones. Particularly at the outset of the show, he’s not a warm character.


But in this story, Bruce meets Terry McGinnis. Terry has his own score to settle with criminals, and enlists Bruce’s aid.


Bruce decides to help Terry, and work with him. He gives him a job as an assistant. He is the voice of experience in Terry’s ear when he is on missions, providing Terry with insights earned from Bruce’s years on the street. Sometimes the relationship is strained, sometimes both are frustrated, but both work through it because there is an common understanding of what they’re trying to achieve. In short, Bruce becomes Terry’s mentor.



This is my question for those who make it to the point of becoming a senior academic.

Are you going to be the Batman who is driven to complete his own mission, come hell or high water, and see those who follow you as chess pieces on the board?

Or are you going be the Batman who passes on the mantle?


09 February 2013

“All sides of scientific information” is not “Anything goes”

Ars Technica reports that Barbara Cargill, chair of the Texas State Board of Education, is unhappy with proposed materials for the K-12 schools on biology.

Cargill’s complaint is that the material overwhelmingly supports the theory of evolution, which was clearly not what she intended when she voted for the “all sides” language in the standards. Of course, evolution would have never reached the status of theory if it weren’t overwhelmingly supported, so it’s not clear what Cargill was expecting.

The testimony suggests that the confused language of the recently approved science standards was intentionally chosen to allow the board to exert pressure on publishers to undercut accurate science education. Which is precisely what many people warned at the time (the title of the Texas Freedom Network’s announcement for the video starts with “Told You So”).

When the standards were approved, I wrote:

The good news, such as it is, is that the wording specifically says “scientific explanations,” which should cut out the worst possible offenders.

08 February 2013

Science Online 2013: I’m not going back

At some point during this conference, someone asked me, “What are you going to do about the demand for people to attend this conference?” And I replied without a pause, “I’m not coming back.”

There are some mundane reasons for me not to return. This year was unusual in my course scheduling, and I didn’t have to cancel any classes because I was out of town. Normally, classes will be in session during Science Online. This is the main reason I haven't gone before. And the financial cost gives me pause about going back. I paid for this trip entirely out of my own pocket.

It was quickly clear to me that I didn’t feel the same way about Science Online that a lot of other people did. I enjoyed it. But I didn’t feel like I had boarded the Mothership. I didn’t feel exceptionally energized. Or that my head was exploding with new ideas. Or that the experience was life changing.

A couple of people asked a standard conversation starter: “What session were you in, and what did you learn?” I had problems answering the second part. The pure information part of the conference didn’t hold a lot of breakthroughs for me in my thinking. And I’m not sure the information I did get penetrated more deeply for having been physically present compared to following along online as I had previous years.

That said, I was glad that I went, but not because of what I got out of the conference.

Lilly, one of the students who participates in #scistuchat, tweeted that she felt “honoured” to meet me. This made me furrow my brows, because, well, from my point of view, I’m just this guy, you know? It’s not hard to contact me or interact with me. But it got me thinking more about other people’s perspectives.

I also had a chat with Rene, a librarian, about my experiment in self-publishing a paper on my blog. I gave her some ideas about how and why I went about it, and what the reaction was. I had a great chat with Nick about the state of science funding and how to read a paper.

I told a lot of people the kilt anecdote, and about trying to be fearless. This seemed to resonate with people. In the identity session, I talked a bit about why I’ve always blogged under my real name: “You can’t live in fear.” I mentioned that I realized I had certain advantages that made it easier for me to do so.

After I sat down, Danielle Lee compared some of the stuff I said to Tony Stark, a character who has lots of advantages. I was caught completely off guard by that. It hadn’t occurred to me that I was probably one of the older people at this conference, and one of the few jobbing scientists. Maybe it helped other people having someone there to say that you have to work at not being complacent or timid.

I was glad I went because I think I contributed things that some people found useful.

Nevertheless, when all was said and done, while I was glad to have contributed, I thought this experience is going to be more valuable to someone else. I’m not going to Science Online 2014 because someone will be able to make better use of that slot, and experience the “life changing brain energizing explosion of bloggy love” that apparently other people get, but that I didn’t.

I’m not saying I’ll never go back. I’m just saying that I’m not planning on it immediately.

Besides, while many faiths require a pilgrimage, they typically only require the faithful to complete the journey once in their life. Not every year.

07 February 2013

Science Online 2013: days 3 and 4

The thing I remember most about day 3 of Science Online was getting green around the gills. I got a headache – possibly a caffeine withdrawal headache – and felt ill and queasy much of the day. Those of you who were there may ask, “Zen, how could you have a caffeine withdrawal headache when attendees were averaging 15 gallons of coffee an hour?” I don’t drink coffee. I drink soft drinks, and there wasn’t a vending machine in sight, in stark contrast to my own campus. I recovered by mid-afternoon, but it definitely took much of the fun out of the day.

Headache or no, I saw the Beyond Text session. This could have been two sessions: one for video, one for podcasts. The level of thinking about multimedia seemed very basic to me.

Because of the headache, though, I thank Morgan at BioInFocus for doing an interview with me. (Will let you know when it’s available.) We talked a bit about things I do online, particularly #SciFund. Focusing on the interview took me out of my head long enough to give me some relief from the pain.

Speaking of #SciFund, we managed to get this picture of most of the #SciFund participants at Science Online 2013:


(L to R: Jai Ranganathan, Diane Kelly, me, Jarrett Byrnes, Alex Warneke. Absent: Anthony Salvagno.)

In contrast to the previous group dinner and open mic night, day 3 was dinner on our own. I ended up at The Busy Bee with a big whack of people. They were out of table space, but they let a few of us sit down on their stage floor. It was a little bit of a picnic atmosphere, and their food was good.

On day 3, I switched it up and went back to wearing jeans, but a lot of people were asking me where my kilt was. I couldn’t disappoint the fans, so I went back to wearing the kilt on day 4.

Day 4, Saturday, was the most fun for me. The night before, I got an email from the Office of Graduate Studies using they were looking for the next speaker for the STEM lecture series this spring. I thought, “If I cannot get a speaker for a STEM lecture at this conference, I. Am. A. Failure.” This gave me the chance to have lots of great conversations, because I was able to tell people, “I have a speaking opportunity, an all expenses paid trip, and a budget. Pitch me!” I will be going back to UTPA with a list of about a dozen prospective speakers.

The ebook session started with Carl Zimmer providing some perspective on how the market has changed from even over a few years that it’s been discussed at Science Online. Ebooks have gone from being resisted and marginalized to being sold routinely. I think we are now just at the cusp of a technological leap in ebook reader capabilities. Much discussion was influenced by Snow Fall, a New York Times branded ebook that was much praised, but had a budget of a million dollars.

Perhaps the session that was the most unexpectedly fun was the identity session. When I read the warm-up post from Scicurious, I had a suspicion that she had plans... And my hunch was right. She was wearing a full Batwoman costume.* I told my kilt story again. This prompted a rather astonishing compliment from Danielle Lee, who compared me to Tony Stark (Iron Man). Blush. (I have more to say on Ghost Rider, fear, and Iron Man later.)

I went to the science writing for kids, and want to plug Elizabeth Preston’s (a.k.a. Inkfish) magazine, Muse. Matt Shipman recently wrote about a feature in the magazine called Bo’s Page. Bo’s page has six stories, and the kids have to figure out which one is fake. Preston said it can be tricky to think of fake stories, and she said she would welcome suggestions and contributions for Bo’s Page! Bloggers hear enough crazy science ideas; how hard can it be?

I went to Beasley’s, a restaurant that served fried chicken with Eve. Not only was the food excellent, we had a very fun conversion about her cat ears. She wear cat ears because her friend wears bunny ears because that friend has a friend who wears cat ears... At this point I interrupted, “Is this like turtles under the Earth? It’s animal ears all the way down?”

The restaurant gave us a postcard with our bill, and Eve and I signed it and took it to Karyn Traphagen as the “lucky last” postcard for the Science Online postcard project. I had no idea Karyn would be so excited by postcards, especially ones from a couple of blocks from the hotel. She reacted like I’d brought a limited first edition book from overseas.

I had a lot of very good conversations in the bar that night, and stayed up very late, taking advantage of the afternoon plane flight home to sleep in in the morning! I spent a few minutes looking around the downtown core in the daylight.

But after the wretched trip to the meeting, I almost got screwed by United again on my trip back. Like my flight to Raleigh, United changed my flight without notifying me. his caused me a few minutes of panic as I wondered, “Did I book my planet tickets for the wrong day?” I eventually found it, but was pissed when I saw that unlike the previous trip, however, this flight time moved forward by about an hour. Someone in the lobby said, “You have to opt in for notifications.” I said, “No, when your flight moves earlier, they should notify you no matter what.” Arriving too early and getting a delayed flight is annoying, but arriving to late and missing a flight is a disaster.

I was lucky to save on cab fare by hitching a ride to the airport from Cyrus Radfar, where we talked about why Instagram was free, and with Melanie Tannenbaum about why we need more social scientists at this conference.

Unlike my flight to Science Online, my flight back home was uneventful. Maybe Raleigh was glad to see the back of me.

In any case, I’m not going back to Science Online next year. Tomorrow, I’ll talk about why.

* Tangent: Let me tell you what it’s like interacting with Scicurious face to face. To paraphrase something Billy Crystal said on Inside the Actor’s Studio about Robin Williams:

No matter how fast you are, she’ll be faster.

No matter how funny you are, she’ll be funnier.

No matter how geeky you are, she’ll be geekier.

Being in the room with her always pushed me to raise my game. It was great sharing mod duty with her.

06 February 2013

Science Online 2013: day 2, open mic

I’d forgotten that open mic night was at the end of my first day of the conference. As I mentioned earlier, I was wearing a kilt that day. And online, I’d said I would rap at open mic night. It was kind of a joke (I said I’d either rap or heckle, giving me an out), but kind of not.

I wanted to cover Buck 65’s “Indestructible Sam” for a couple of reasons. It’s about a man digging all day. I dig to collect sand crabs. It’s about someone who keeps going and can’t be stopped. That also seemed apropos, given that Scicurious and I were co moderating the “Blogging for the long haul” session.

Rapping on stage was nerve wracking enough. I get even more nervous because partway through the night, I could feel my throat getting sore from talking through a good chunk of the day. (Co-moderating two sessions will do that.)

Adding the kilt to the rapping mix made it... Well, Tara Smith tweeted:

...and now @DoctorZen rapping in a kilt. Not something I thought I'd ever type. #scio13

When open mic started, David Shiffman and Jacquelyn Gill set up an order the acts were supposed to appear. However, because there was a lot of (somewhat inebriated) improvisation, the line-up kept changing. I was never quite sure when I would be called upon to be next.

This led to terrifying moment when Baba Brinkman got up on stage.

Baba Brinkman had been the Converge speaker that morning. I was already familiar with Baba's work: I'd heard him on The Science Show years ago. Baba has had several rap shows related to science, including the Rap Guide to Evolution.

Baba knows what he’s doing when it comes to rap.

Baba freestyles a birthday wish, rocks the house, and all the while, I’m watching, thinking, “I might be next, and I’ve got to follow that? And my throat is about to give out? Oh crap...”

Fortunately, a few other acts went up before me. And when I did get up and start telling the story of Samuel Dombay... people got into it. I did it a capella, but people were able to pick out the beat and started clapping along. Thank you, all who felt the flow.

Of course, a recording can never capture the feel of a live performance, but for what it’s worth, here’s what I did.



And as I said on stage, that is a true story that was wrote on account of ol’ Sam workin’ so hard... and that’s how I reckon it oughta be.

Here’s the original artist (ignore strange sounds in for 25 seconds or so of first video):



And later that night, I danced onstage with a lemur. Because I do like to move it move it.

05 February 2013

Tuesday Crustie: Armored ghost


The person who took this picture was unsure of what kind of crustacean it was, whether it was even a crab or lobster. I am fairly sure it is some sort of ghost shrimp or mud shrimp (Thalassinidea), although it is an unusual looking one. It seems to have a much heavier, thicker exoskeleton than I’ve seen in other thalassinideans I’m familiar with. But the tail and claws are very reminiscent of burrowing beasties.

Photo by Mountain/\Ash on Flickr; used under a Creative Commons license.

04 February 2013

Science Online and Google Plus: a plan and a test

At Science Online 2013, Fraser Cain talked about using Google Plus to host virtual star parties. It was an excellent talk that showcased something that Google Plus can do that no other platform does well yet (as far as I know).

The other thing that happened today was that people at the meeting started whinging about not to have to wait until next year. Seelix tweeted:

Would anyone want to #scio13 session Hangouts On Air? Looking at the planning wiki, there are many I don't want to wait for #scio14 to see.

Taking my own advice to be fearless, I’m plowing ahead and I’m inviting you all to a Google Plus hangout this Saturday, 9 February, at 12:00 noon Eastern Time (11:00 am Central Time, where I am). The subject for discussion is to talk about what kinds of research projects social media can help solve. This is inspired by “Social media as a scientific research tool” on the Science Online 2014 planning wiki, suggested by David Shiffman.

If this somehow works, what I would like to see is for later hangouts to move around. No regular time will be good for everyone. And let’s have different people host, and let them pick the topics.

If you have Gmail, you basically have a Google Plus account. You don’t need a camera to participate; you can just use the chat function and type if you want. Or just use audio.

Let’s see what happens.

External links

Converge: ScienceOnline Announcements; Fraser Cain; Baba Brinkman

When to pack it in


Between the Science Online panel about long haul blogging, and Kate Clancy’s “I’m this close to quitting academia,” and my own annoyance with travelling so high that I was wondering of conferences are still worth it, I’ve been thinking a lot about the dynamics of quitting.

When should you stop?

As part of my preparation for my panel, I read Seth Godin’s The Dip. One of the recommendations is that you should never quit something because you’re frustrated now. You’re too likely to let the pain of the moment play too big a role in your decision making.

Instead, when you are about to embark on something, realize that it will get hard, and make a plan very early, even before you start, about when you will quit. Decide what circumstances seem so bad to you, as you look forward, that you think you should not continue.

This does a couple of things. Not only does it help you avoid the “heat of the moment” snap walkout I mentioned above, it helps you avoid the Concorde fallacy (too much invested to quit). It can help you distinguish between “the dip” (expected hardship) and the cul-de-sac (dead end, made classy by giving it a French name).

This is hard advice, but probably good advice. This may something that students and academics should have at every stage of their career. I think my “I’m out of science once and for all” criterion was “employment.” If I couldn’t find a post-doc, I'll do something else. But in retrospect, maybe that was the wrong bar. There have been moments since in my current job where I’ve held my head in my hands, saying, “I want to leave.” But... I also have moments where I’m glad I’m here instead of someone else.

Figure out when you’re going to pop the escape hatch before the moment of crisis.

Photo by fuzzcat on Flickr; used under a Creative Commons license.

01 February 2013

Science Online 2013, day 2: In which sartorial choices are explained

I was wearing one of my kilts at Science Online yesterday. This is still unusual enough for a guy to wear that you get questions about it. Questions like, "Are you Scottish?" (No.)

I told a few people the story of why I got myself a kilt.  I decided that I was going to get one as a present to myself for getting tenure. The first time I wore it was my first full day as a tenured associate professor. I’d told one of my students that this was my plan a week or two in advance. She showed up in my office on the first of the month saying, “Let’s see it.’ I stood up, and she said, ‘... I didn’t think you’d actually do it.’

Getting tenure is supposed to afford you a certain amount of protection to make unpopular or unusual decisions. I got myself a kilt to remind myself to be fearless.

Because a man in a kilt fears nothing.

External links

Utilikilts

Comments for second half of January 2013

Odyssey asks why people write reviews.

I make a cameo on Haute Science as part of the lead-in to Science Online 2013.

BenchFly has rules for a scientist’s life.

Drugmonkey looks at an argument over whether researchers have the right to publish where ever they want. Expect a lively comment thread!

Advice on deciding where to publish a research paper from Jabberwocky Ecology.

Alexander Brown examined Open Access.

Miriam Goldstein quits blogging... for while, at least.

Mike the Mad Biologist looks at the stability of NIH funding. When you say, “We want this to happen,” how do you know how much people will jump to do it?