Archive for: March, 2012

Thanks for reading Neuropolarbear!

Mar 31 2012 Published by under Uncategorized

Dear Scientopians,

Thank you for reading my posts over the last two weeks, and thanks for all the comments. Now that my guest posting period is over, I will be returning to my wordpress account, from whence I came. Over there, I post less frequently, spend less time writing, and use more dog photos. In conclusion:

7. This filing cabinet is so full of pubs it must way 500 pounds.
8. With your application, make sure to send a photocopies of the 5 pubs you are most proud of.
9. For $700, we will allow you to colorize your pubs
10. In my experience, anatomists don't have a lot of pubs, but the ones they have are really long.

One response so far

I don’t think there’s a replication crisis

Mar 30 2012 Published by under Uncategorized

Everyone seems to be abuzz with the crisis in replicability, which feels like a new thing. I don't think it’s new or a crisis. In my small corners of the research world, problems with replication have been common since, let’s say, the mid 1980’s, and the field is still doing fine.

When I became interested in the replication problem, 10 years ago, it was not a theoretical issue, it was a practical one. Two close friends of mine in grad school left and began post-docs, brimming with hope and optimism. They first took on the chore of extending their new labs’ recent S/N-worthy discoveries, and then proceeded to waste years not being able to even replicate the original result. Who wants to waste even one year of their life for anything? When I was a youngish grad student, these were my ghost stories, fascinating and horrible. I began to collect these stories in my head. And there were lots of them. I at one point decided that failure to replicate motivating studies was the leading cause of post-doc burnout. I began to trace out a map of what was true and untrue in my field, and which labs were publishing solid stuff, and which labs were producing flashy soft stuff.

I decided that trusting a paper just because it was published was naive. I learned that few people would ever give an unbiased opinion of their own paper. I decided that, as a consumer of scientific data, it was my responsibility to judge for myself. I developed a credo, which was, "If it's in Science or Nature, it's probably wrong." I did not take publication as proof of correctness. This skepticism had practical benefits: when I started my post-doc, I was asked to follow up a project that seemed slightly fishy, so I passed on it. [I still don’t know for sure whether my hunch was right, but I still think it was.]

When I tell people this, many don’t want to hear it. I think a lot of people are attracted to science for the promise of hard solid truth. I think some of those people would be happier teaching the stuff we understand well, and not on the front lines, doing research, dealing with erroneous crap all the time. Other people, when I tell them that I don’t trust a lot of what it published, act like I just told them the sky is blue. I think that one of my biggest responsibilities as a PI is to encourage my students to doubt everything they read, including papers I wrote.

How can you be expected to know if data is legit? It’s not easy, but I think that gaining this sense if one of the most important skills for a scientist to cultivate. Not just reading papers, but critically evaluating them. It’s what a good journal club teaches you. Also, this is one place where networking is really helpful, especially for young scientists, who have more to lose by making the wrong decisions. A lot of people aren't shy about sharing papers they hate! Also if you learn to read between the lines on a paper, you can often see where it's calling bullshit on other ones, then you can judge for yourself. I love the review journals, especially when the authors are subtly catty. [Sometimes, not so subtle.] With practice, I think you just develop a spider sense, especially when you have experience with the method, and have collected that kind of data yourself.

Im not sure it's a crisis. Certainly it doesnt only apply to Stapel/Hauser style psychology, and certainly it goes back at least to the mid 1980's, the period when the papers I carefully read in grad school started to come out. I think that bad results it just what happens when you are out on the front lines, and not symptomatic of some gigantic crisis that's soon to explode when the whole scientific method dies. These things generally get caught as the field advances, inch by inch, over the years. People doing good work eventually get rewarded, but sloppy people often get away with bad work. Sometimes even fraudsters do. That’s just a sucky fact of life.

For the record, I think the reason people are so worked up over cognitive psychology is twofold: (1) Because the normal process of advancement doesn’t shake out bad results on its own very quickly. (2) Because the findings are remarkably non-robust to small deviations in method. As a consequence, it's hard for practitioners to tell bad data based on the spider sense test. And the loop doesn’t close very quickly, and things get stuck out there and believed for years and years. I have no opinion on whether Bargh is right or not, but I do think it's worrisome that he is claiming that tiny deviations in method are so critical. As for Hauser+Stepel, I wonder if these factors make it easier for people to do large amounts of fraudulent work without getting caught. As for the neuroimagers, and the geneticists, I think the fields are in their adolescence, and are actively creating new and better standards. And as for the psychologists, I am incredibly optimistic about the PsychFileDrawer, and I hope it makes truth win out a lot faster. I'm looking forward to seeing the tide go out over the next 10 years, and we can see who is secretly swimming naked.

3 responses so far

We need a word for this concept

Mar 30 2012 Published by under Uncategorized

I spend a lot of time thinking about causes of the gender disparities in science. Partly this is because my mother-in-law's research is principally about this question, so every time I see her, we discuss it. One of the less well-known factors is that PI's, who are disproportionately male, often organize fun activities that are more appealing for male lab members than female ones. Fun activities are fun, and don't in principle involve direct scientific mentorship. But they probably lead to greater bonds among the attendees, etc, etc. Everyone knows this, but as far as I know, there is no term for these activities. It's a thing, and it deserves a term. Also, I want there to be a term so that I can ask the Twitterverse whether my favorite medieval/fantasy card game, Dominion, is in this category.

5 responses so far

The horizontal PDF and other suggestions re:papers

Mar 29 2012 Published by under Uncategorized

8 1/2 x 11 paper can be oriented in two directions, portrait and landscape. As best as I can tell, all papers in all journals are published in the portrait orientation. This made sense in 2000, when the PDF was just a brief waystation between the journal's website and the printer.

But now, I read papers on the computer most of the time. So do you, I bet, web-savvy blog reader. Most computer monitors are in the landscape direction. Don't you want to see papers oriented 90 degrees offset?

I still do read printouts, so papers should come published in both directions. Preview and (ugh) Adobe Reader, and the other viewing programs should bring up a paper, as a default, in landscape mode and then, if you hit "print" ask if you want it in portrait.

I doubt this can be done without doing all the fancy-pants type-setting stuff twice. You'd have to rearrange the text into 3 or 4 columns, move the figures around, probably resize them a little bit. All that hassle will need to be done twice. It may double the size of the document. It's worth it.

While I am on the topic, it's time to get rid of numbered citations forever. It's time to replace them with real in-text citations. It's seriously ungainly to shift back and forth between page 2 and page 17 to find out that [6] means Smith et al. 2004. I often literally ⌘C-⌘V a paper I am reading and open both copies, one to where I am reading and one to the ref list. If logic were king, you should be able to hover the mouse over the citation and your PDF reader will bring up a box with the full citation, including full article title. I can think of how to do this with a very little intelligence in the PDF reader and two bytes per citation, so it's cheap, space-wise.

When you download a PDF, the name should be "Neuropolarbear_etal_JON_2010.pdf." This naming scheme makes them obvious for someone looking at the title, and also compatible with the search engine on my computer. Instead papers are usually called "science.pdf", "1-s2.0-S0006322310010103-main.pdf", and "3726.full.pdf" to name 3 papers currently on my desktop. I realize commenters will point out the beauty of Mendeley right here, and I agree, but there is no reason to not also give your PDF a reasonable name. This can be solved by the journal in less than a minute per paper!

Authors submitting a paper for review should be pasting the text for each section (Methods, Results, Discussion, etc) into a box on the website and at no point should upload a word document. Then the website would create a PDF. Think of the numerous advantages:
(1) Reviewers could request a single- or a double-spaced version of the paper, depending on their preference.
(2) No need to for authors count words in each section. The server does it for you. No need to reviewers to estimate words when authors don't provide this info. Why does Frontiers ask its reviewers whether the paper violates word length policies? Computers can do that.
(3) When the server creates the PDF, it inserts line numbers. As a reviewer, I love line numbers. Of course, if for some reason, you dislike them, you can request the server to make version without line numbers.
(4) No need to submitters as PNAS to insert weird markups into their paper anymore. In fact, doing it this way would make it much easier for editors to guess at page length at all journals. And I take it that page length is something editors care a lot about.
(5) Figures could be placed in-line. Much easier to read that way.
(6) Reviewer wouldn't have to pedantically point out that Neuron has a Summary instead of an Abstract and an Experimental Procedures instead of Materials and Methods. The program would take care of it.
(7) The program could provide rudimentary typesetting to make the review copy look a little nicer.
(8) Spell checking!
(9) No more realizing that track changes was on, but not visible on the screen, and you accidentally inserted comments into your review manuscript saying "reviewer 2 is a fucking asshole. change this so that you cite their latest stupid paper."

Neuropolardog, in portrait mode

19 responses so far

Why are we so close to going broke?

Mar 27 2012 Published by under Uncategorized

Recently I had one of those moments where something you have lived with about for >10 years all realigns and you see it differently. In all my previous labs, incl undergrad, my PI's always seemed to be near the edge of running out of all their money. Grants were obtained in the nick of time, things looked bad and then got worse, post-docs were hired despite the dire straits, etc. Then I started to manage a lab, and started to have people ask me for things that cost money, and I realized the value of telling everyone how close to the brink the lab is. That there is a never-ending strong pressure to tell the underlings that the money situation is parlous. I'm not saying it's a lie. Things ARE pretty much always dire, if you look at it from the right pessimistic perspective. And, running a lab, there is an incentive to take that perspective.

Telling people you are close to broke makes them less likely to ask for things, makes them likelier to think first before asking for inessential luxuries, puts them in the frugal frame of mind. It provides an incentive for people to apply for F and K and NSF awards, and to not just phone it in. It gives you a no-hurt-feelings excuse to reject lab applicants at all levels, and even provides some help in ushering out bad students + post-docs if it comes to that. It's a flexible control system: if you have to spend, you can just say, "oh we found a small pile of money", or you can blame the department accountants for misleading you, and then say, "but now we really are broke."

This deceit is helped along by the fact that it's really hard to know exactly how much money one has. Grants are unpredictable, money is budgeted into different accounts with weird rules, and money gets allocated without appearing on the budget until later, etc. As far as I can tell, it's basically impossible for lab members to guess how much money there is. I had no idea what a start-up was when I was in grad school, and it was embarrassingly late when I realized that an R01 is 249 per year not for a lump sum to be spread over 5 years. I also wasn't sure whether overhead came out of that 249 or not. And so on. It wasn't too relevant to me at the time - back then I was focused on learning the science. Now, I worry about the money. And I try to spread that worry around, in overly pessimistic bunches.

11 responses so far

Back Issues of Mad Men

Mar 27 2012 Published by under Uncategorized

When I was about 9-13 years old, I was obsessed with Mad Magazine. I subscribed, but mostly I read old issues. My mother would often go to antique stores and I would quickly locate the one guy selling back issues of Mad for a quarter or 50 cents. And then I would spend my whole allowance ($2/week) on Mad, both the magazine and the trade paperbacks that often had new content. In doing so, I acquired a detailed knowledge of the social, political, and cultural world of the 1960’s and 1970’s. I knew more about Watergate than pretty much anyone else born in 1978, and I understood the election of 1964, for example, better than I understood the election of 1988. I knew more about the Saturday Night Massacre than I knew about Tianenmen.

The thing about Mad is that it was produced on Madison Avenue, by people who lived next door to the real world Mad Men (and, I assume, worked in advertising). These pages were dense with allusions to the world of 3-drink lunches, office smoking, trains to Greenwich, crazy parties with nubile secretaries, and the occasional hippie, civil rights protester, experimentation with pot, and lots and lots of advertising. It was a weird world, and I was deeply immersed in it. Mad Magazine was well written, and skillful in making it seem real. But my immersion was private; no one else I knew read Mad. I stopped reading Mad in about 1992, and now, 20 years later, everyone is suddenly fascinated by this world, via Mad Men.

I feel an intense sense of recognition when I watch Mad Men. It’s the same Madison Avenue I grew up with - in back issues of Mad. And most interestingly, it’s portrayed from the same cynical perspective. Mad Men sees it through the cynical eyes of the 21st century, Mad saw it through the cynical eyes of astute social criticism. Much of the criticism is stinging, and much of it is identical. In fact, it’s so similar, that I have wondered whether Matthew Weiner grew up reading Dave Berg, Al Jaffe, and ‘the usual gang of idiots’. I wonder if the name of the show is a tacit admission of this fact – Mad Men was the term that Mad writers used to refer to themselves back in the day. In any case, I love the TV show, and I’m certain a large part of it is nostalgia for my own childhood, technically in the late 1980’s and early 90’s, but spiritually in a Madison Avenue ad firm.

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We found a significant effect in subjects A through Thnad

Mar 24 2012 Published by under Uncategorized

Dr. Seuss has given us so much. He taught many people to read. He opposed racism, anti-semitism back in the 1940's. He possibly coined the word Nerd. Half the items in the Dartmouth gift shop bear his drawings. But one thing he offered has not been taken up, his extension to our alphabet.

After Ten Apples Up On Top, my favorite Dr. Seuss book has always been On Beyond Zebra. I first read it a long time ago, a little after I learned the normal alphabet, which had, to be candid, started to bore me. I disappointed that things stopped at Z. Talk about wish fulfillment. OBZ introduced 20 extra letters, with pronunciations, illustrations, and words that could be used with them. I never understood why those letters didn't make it out of the book. Now's the time.

I am currently doing a small behavioral project in which I hypothesize the existence of a new variable. Unfortunately, all the Roman and Greek letters, both capital and lowercase have other meanings, and I want to avoid confusion. For example, pi means 3.14159 and theta means angle. And also, the same letters are kind of boring. Sure you could put a little diacritic on top of them but la dee da. And I guess there are cool alternative greek letters like koppa and pamphylian digamma. But... well, when Kurt Gödel Georg Cantor was in this position of needing a new variable, he adopted a totally new, previously unused alphabet. Of course, the various infinities he described are ALL named after aleph, and math+science have never even gotten to beth.

What's wrong with shin? In Hebrew, it stands for "add one m+m to the pile." Which is appropriate, since my equation is designed to measure devaluation of a reinforcer.

But why stop with phoenecian-derived alphabets like Roman, Greek, Hebrew, and Arabic? Why not use Japanese, Korean, Ethiopian, Inuktitut or even Mayan?

This mayan letter is pronounced "kin" and it means, "The world will end in a few months!!," which is also somewhat relevant to the theme of my paper, which involves limited time horizons for reward-seeking decision-makers.

Or maybe we can use undeciphered alphabets, like Rongorongo, the putative writing system of Easter Island. No one knows how this letter is pronounced or what the words mean, but that air of mystery is good, since my effects are somewhat mysterious. And perhaps using it in more equations will turn up the pressure on linguists to get off their butts and decipher the language.

For the meantime, I am pronouncing this particular letter "shark".

But in the end, I am leaning towards Seuss. I am thinking of submitting my paper with Wum in the denominator. For the record, wum can be used to spell wumbus, which is the name of a whale who lives on a hill. It can also be used to spell wum-tiddle-um, which refers to a statistical effect that is publishable, and deserves a mild review process.

11 responses so far

Some examples of places where it would be bad to type "pube" when you mean "pub"

Mar 23 2012 Published by under Uncategorized

1." Sorry you weren't chosen. I bet you'll have a better shot next year when you get more pubs."

2. "Last night I was working late and ran across some interesting pubs. I left them on your desk."

3. "In this department, your dissertation committee is going to want you to examine your pubs before they let you defend."

4. "I found some of Edward Tolman's pubs from the 1930's in bound volume in the library. I scanned them if you want to see a copy."

5. "I strongly believe the government should require everyone's pubs be free for everyone to look at whenever they want."

6. "I love that lab's pubs except that they are just too long. They just need to learn how to trim."

4 responses so far

The quick and dirty dissertation

Mar 23 2012 Published by under Uncategorized

As the longer and longer post-doc becomes more and more standard for us, I would argue that there's more of a reason to do a quick and dirty dissertation. Because as the standards for post-doc TT applicants rise, (I feel like) there's less and less benefit to doing something impressive as a graduate student. Getting high profile publications is essential for a post-doc, but beyond some low threshold, doesn't matter as much for a grad student. Not as much as it did 25 years ago, I would imagine. I've heard people who have votes in faculty hiring say that they discount grad student C/N/S publications, since they are thought to reflect mostly the PI. And even if this is wrong, who cares, since the grad student isn't going to be applying for a faculty position for several years, and it's the most recent papers that matter most (the "what have you done for me lately?" principle).

When you apply for a post-doc, it mostly comes down more to whether you seem smart, and give a good talk, and have good letters. When you apply for a F32, my impression is that the reviewers discount impact factor in favor of just having a few reasonable pubs.

My hunch is that a job applicant with big papers as a post-doc and nothing as a grad student has a much better shot at that faculty position than someone with the reverse record.

Maybe the dissertation is becoming more of a pre-post-doc. The goals are to learn the skills, and to begin to form the friendships, that will serve one as a post-doc. What's the incentive not to just get through it as quickly as possible? [And I realize many people don't want to stay in acedemia - but I think these arguments apply equally well to them: why wait to get started on the preferred life path?]

These are the thoughts I had near the end of grad school. Due to various reasons, I was faced with only two options: graduate in 5 or in 6. Had I gone with 6, I would have likely had another pub, but I reasoned, that pub was not in the field I wanted to pursue, and wouldn't mean much for me professionally. I left in 5 and tried to get the pub out from long distance, but it's still in limbo, 7 years later. And here's the thing: I don't regret it at all. I was sick of grad school, I was eager to go do more interesting stuff, and I did. And as a post-doc I got paid more.

So I wrote a crummy dissertation at top speed (still ~3 months, I'm a slow writer), and one of my committee members (who I adored) told me I would never succeed in science if I continued to write like that. "But," I thought "I can write better, I'm just doing a poor job because no one cares what I write in my dissertation." And as far as I know, he was the last person to ever glance at my dissertation.

I realize that everyone is in a slightly different situations and there are going to be large numbers of exceptions to my generalizations here. And I realize that I am overgeneralizing from my own experiences. But I have several friends who are reaching the same decision point I was at in my 4th year of grad school. And many of them, unlike me, have perfectionistic tendencies, and desires to write an A+ dissertation. And in most cases, I am gently nudging them in the direction of just getting it done and moving on. I think that would make them happier, and would most benefit them professionally.

16 responses so far

Future retractions from This American Life *

Mar 21 2012 Published by under Uncategorized

Following the unfortunate Mike Daisey embarassment last week, This American Life has decided it need to emphasize the importance of journalistic integrity to all its guests. So serious are they that Ira Glass has sent a letter to all former contributors emphasizing journalistic standards, and asking for any admissions of factual error. I have obtained the internal memo detailing the upcoming retractions the show will make, and am publishing it here, in the interest of openness in the media.

Episode 74 ("Funny Things Kids Say"): The intro to the episode interviews several 6 year olds on their feelings about watching their parents kiss. Little Susie claimed that it make her want to barf. Actually, this was originally said 5 minutes earlier by her brother Danny, but he was too shy to come to the microphone, so Susie repeated it. They were not her words and we can neither confirm nor deny that thinking about her parents kissing made her want to barf. Also, Susie was 7 and a half at the time, not 6. TAL regrets the inaccuracy.

Episode 103 ("Valentine's Day Special: Love at First Sight"): In this episode Ira claimed that Duncan and Edith kissed the first time they met, at a canteen in Luzon in 1945. Edith now admits that Duncan awkwardly hit on her three weeks earlier at a WAC/WAVE dance, but that he was so drunk he forgot. It was not, in fact, love at first sight. TAL apologizes for the error, and regretfully admits this weakens the episode's broader claim that love at first sight is real.

Episode 256 ("Poultry Slam 2005"): One of the stories involved a graduate student at the University of Idaho who kept a pet eagle. According to USDA guidelines, eagles are not considered to be poultry, and the story should therefore have not been broadcast in an episode called "Poultry Slam." TAL regrets the error and retroactively retitles the episode "Words about Birds".

Episode 381 ("Road Trip"): It is stated that Dishwasher Pete hopes to wash dishes in all 50 states. Even before this episode was broadcast, Dishwasher Pete was had admitted to Ira that, like Sufjan Stevens, he had no hope of achieving his 50-state goal, and now has the more modest goal of washing dishes in all the 8 states of the upper midwest, and, if he has time, Kansas and Oklahoma.

Episode 411 ("Driving Lessons"): In Act 3 of this episode, Ira teaches Sarah Vowell to drive. Although never explicitly stated, the recording of their conversation implies that they would have great romantic chemistry. Unfortunately, subsequent meetings have demonstrated that Ira and Sarah have no chemistry, but are both happy to be platonic friends. The episode has been re-edited to introduce more awkward pauses, and to make it at least 20% less flirty overall.

Episode 442 ("Animals in Love"): In Act 4, David Sedaris tells the charming story of mixed signals and barnyard romacne between a talking squirrel and a sulky pig. In the events the story was based on, the squirrel was actually a chipmunk, and the pig was actually a different chipmunk. TAL regrets the error, and promises to just skip all animal love stories in the future.

Episode 460 ("Retraction"): In Act 1, it was implied by guest Mike Daisey himself the he is not a mendaacious con-artist, and that he had some legitimate defenses to Ira's questions. TAL regrets the misleading impression.

* Note: this post is not literally true, in the journalistic sense. Neuropolarbear is unfamiliar with Daisey's Rules of the Theater, but they seem to match the rules of the internet. Meaning, when people read the internet, they expect everything to be made up facts with no basis in reality. Neuropolarbear apologizes most of all his loyal audience.

3 responses so far

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