Archive for: November, 2014

Small Town Saturday

Nov 29 2014 Published by under Uncategorized

When I moved from MRU to almost-MRU, I also did some major changes in lifestyle.  I have always lived in Big Cities. Cities whose name everyone knows, and not because they are a suburb where something horrible happened. Often it was a "we" living, and compromises were made for schools and access to other  important things. I've also lived in the bush in Southeast Asia during the field work phase of my existence, which is another set of stories altogether. But until now, I've never lived in a small town.

When I got here I lived briefly in one small town, very close to my uni, in a house that a grad student had bought and not yet sold after she moved on to her postdoc elsewhere. It was depressing,  a dark house, small and cold.  The town was very white and cis-hetero. I couldn't connect with neighbors. And, I imagine that part was me and the slide down from the euphoria of change.

I moved again, to a nearby, but even smaller town. It is a college town, with the local state university (which will make it decidedly NOT a small town in some people's book), but not the med school where I work. It is nowhere near the size of someplace like Ann Arbor, but to me, used to living in the middle of the city, in a 13' wide rowhouse, where you can drive around looking for a parking place for 30 minutes  this place is SmallTownAmerica. Its still very white, but there is a crunchy aura of greying hippies and diligent Gen-X-ers raising their children to be good people. There is lots of parking, except when Leon Redbone plays the local stage.

In the past I/we never could afford to live in the either chique or cutting edge parts of time. But there was always a more fringy-place, inevitably more diverse, where couples of all sorts were welcome and you could walk the streets holding hands with someone of a different race or of the same gender and not get hassled. The new small town is sorta-kinda that (the first one was not). I have a hangout that is a jazz/wine bar, staffed by the arts students from Local U. Many are GLBT, and I love them to pieces, although its weird to be their Aunt (I refuse to be their Mom). Weird because they are so young, and so vulnerable and yet so much stronger and open and proud than I was at their age.

One of the things I love most is my new apartment. Its in a renovated old hotel. I'm on the fifth floor,  with lots of original windows (I can see all of the tiny downtown). I have hung all my art from various stages of my wandering life. I have my music. My science is going well. My once nascent, but still small, lab is kicking butt.

At SfN I saw many (former?) colleagues from the old MRU. Mostly Very Important Gen-X-ers, poised to take over the world. They are the ones who survived the reign of terror of the Chair from Hell. I am glad for them. But I am more glad for me.

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Rape and Rotherham and Abuse of Power

Nov 26 2014 Published by under Uncategorized

I am not a big fan of Ross Douthat. But he sometimes gets it right.  The word "right" doesn't take modifiers (as is true of the word "unique"), as in "very very right". But the urge to say so is strong. Here is the link  from a tweet from Dan McLaughlin

The article was about the rapes of over 1400 girls in Rotherham, England. Rapes that were largely ignored. Douthat's point is that the rapes were ignored because immigrant gangs were ignored because of commitments to diversity (I disagree on this point, but let's move on). He compares this to the Catholic Church abuses and says:

The point is that as a society changes, as what’s held sacred and who’s empowered shifts, so do the paths through which evil enters in, the prejudices and blind spots it exploits.

The money graf is:

So don’t expect tomorrow’s predators to look like yesterday’s. Don’t expect them to look like the figures your ideology or philosophy or faith would lead you to associate with exploitation.

Expect them, instead, to look like the people whom you yourself would be most likely to respect, most afraid to challenge publicly, or least eager to vilify and hate.

Because your assumptions and pieties are evil’s best opportunity, and your conventional wisdom is what’s most likely to condemn victims to their fate.

Just all priests and immigrants and football coaches are not predators, not all cops are, either. But policemen who can kill children do not deserve our respect or our support.

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The Importance and Neglect of Variation - part 1

Nov 25 2014 Published by under data analysis, statistics, Uncategorized

Within science, my old thesis advisor used to say, there are A-Sciences and B-Sciences. The names came from the Uni's classification of undergraduate requirements. Other than having the label "B", as opposed to "the more important science that gets neglected", he felt this was A Good Thing. In short, A-sciences depended on rules, laws, and invariants. Chemistry. If you take hydrogen and oxygen, and know the pressure and temperature, you will know the phase-state of the result. The stuff of the 17th century enlightenment.

On the other hand, evolution, ecology, astronomy, he said, were statistical sciences. It wasn't a matter of a single law or paradigm, it was a matter of which ones occurred most often. For the evolutionary biologists out there, there is old hat. Darwin depended on the existence of variation to drive evolution. Survival of the fittest implies a more fit and a less fit organism.

Of course, B-science was neglected. That was part of its glory. A-science with its bald white men in lab coats (back then), as compared to bearded white men in plaid flannel shirts with mountain climbing boots in the middle of the city (in case a mountain did appear in the middle of the city), was the dominant paradigm. We were the subversives. Current funding trends support that perspective, fueled by a justification for improving health.

So it is no big shock that an NPR story titled You might be surprised when you take your temperature maintains that the magic number of 98.6F is not so magic and that  "Baseline normal temperatures differ from person to person and from day to day". One of the two points in the article is a listing of temperatures that might mean something clinically (above 101.5 is a serious fever and multiple organ failures happen at 107F). The other of course is that normal is not a set number. Variation gets its due in a backhanded way.

I find the lack of attention to variation to range between irritating and bad science. I remember during my postdoc, a neuroscientist saying that something along the lines of "I measure single neurons" and that "variation is irrelevant as each neuron has an outcome". In my ill-equipped intellectual armamentarium at the time, I tried to point out there were many single neurons and how did he know that the one he measured was representative of all the neurons? And what about differences among neurons? I could not articulate the  value of concepts of variation vs. central location to all science, but that's where I was heading, even then. Sometimes what is important is not whether two things differ in central value (the mean, the median), but in how they vary around that value. Next post will look at that in some detail.

Meantime, an interesting book (technical) book on variation is: Variation: A Central Concept in Biology  2005 by  Benedikt Hallgrímsson (Editor), Brian K. Hall (Editor) ISBN-10: 0120887770 ISBN-13: 978-0120887774. Online ($$$) version here. Review here.




Summary:Darwins theory of evolution by natural selection was based on the observation that there is variation between individuals within the same species. This fundamental observation is a central concept in evolutionary biology. However, variation is only rarely treated directly. It has remained peripheral to the study of mechanisms of evolutionary change. The explosion of knowledge in genetics, developmental biology, and the ongoing synthesis of evolutionary and developmental biology has made it possible for us to study the factors that limit, enhance, or structure variation at the level of an animals physical appearance and behavior. Knowledge of the significance of variability is crucial to this emerging synthesis. This volume situates the role of variability within this broad framework, bringing variation back to the center of the evolutionary stage.      

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A few random-ish Blue Hair Thoughts on SfN and Meetings in General

Nov 18 2014 Published by under Uncategorized

As much as I hate to admit it, I'm bushed. I have to remind myself that after 6 days at meeting when I was 25, I was bushed.

Various bits from my SfN2014 experience:

  1. I walked 20K+ steps/day.
  2. Meeting tweeps/co-bloggers/FamousPseudos was high point for me.
  3. Closely followed by folks telling me "they love my blog/tweets/advice".
  4. Talked to many people, at many stages of career about science. I learned a lot. I have a new potential collaboration.
  5. I drank a lot of Saki with new  potential collaboration.
  6. I did the NIH walk. Got some support for moving institutes (I would like to very much).
  7. I ate way too much chocolate at exhibits.
  8. I acquired 57 pens for my tech who steals  mine all the time. This should pacify her for approximately 114 days. Maybe.
  9. Talked to various vendors who can't help me, and one (may Darwin shine his countaence on you, ADInstruments) who may solve a software problem for me.
  10. I am glad to be going home this evening, but have to get on a plane for personal issue tomorrow. Inbetween there is teaching.

This was first SfN since I moved from Major! Important! Highly-ranked MRU! to significantly less impressive not-quite-MRU. Found it not an issue for me, but did get a couple of "you;'re kidding, you really left a full prof position at MRU?". End perspecitve: life is too damn short to be unhappy.

One of my (Gen-X, natch) colleagues, the master of something or other (tight jeans?) told me that he had made his lab read two of my papers from mid-80's.  Then he said that the papers were not really rigorous and that he wished he could publish stuff like that now, and his h-index would be much higher.

<insert deep sigh of disbelief  here>

Try to imagine how little I care.

I'm sure there is more to process. But I'm meeting the husband of my late postdoc advisor, and he is very funny, very nice, and I don't get to see him enough (he lives in DC).





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At SfN

Nov 14 2014 Published by under Uncategorized

I walked into my hotel last night afgter dinner. In the lobby bar and saw a familiar scene - two small round tables pushed together with 10 people awkwardly arranged around them. Young people trying to listen intently, older people arguing. And one poor woman looking like she wanted to be somewhere else.

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What do about requests for collaboration

Nov 10 2014 Published by under Uncategorized

Dr Isis speaks the truth. Collaborators are a tricky thing, especially for newer/untenured scientists.

You do need to be careful. You do need to make sure that the BSD's or other malevolent life forms do not suck you dry and leave you covered with spots. When a senior person, where you are, asks to you "to collaborate",  first get the details. What are you being asked to do? Do not take their word that its just a "bagatelle" and "you can do this in your sleep". Think carefully and ask yourself: how much time? what if it doesn't work? who's paying for supplies, who's doing the stats, etc. Likely you have some marvelous skill (that's why they hired you). I was first trained in maths and stats, and was always getting asked to "just do this little bit". It took a while to sort through and figure out what I could do easily (ie 1-2 hours for a middle authorship) vs. things that were an on going quagmire.

Be equally leery of the "could your tech just run this sample?" request. Remember you are paying for that tech/asst/whatever out of your precious seed money, or starter grant. You need to be investing in yourself and your future. Do not be fooled that "helping" is going to make a difference at tenure time. If your tech has some spare time, maybe ok. But then, what's your tech doing with spare time anyway? Figure out something to keep 'em busy. Sometimes throwing a sample in a New Shiny Glittering piece of equipment is easy. The results come printed out nicely. Its very sexy and everyone is happy. That's great.

Also, ask about the outcome/product/final stuff. Who writes the paper? What's authorship going to look like. Remember, there is lots of time to do favors once you are tenured. This is very hard. It makes you sound ungrateful for the attention of the BSD. It makes you sound greedy, and grubbing and all sorts of nasty things. But! in the end it is your CV that is evaluated for tenure.

If you decide to say no, it can be tricky. You need to be honest, but not insulting to BSD. Things that you can say:

I'm sorry but I am just getting my lab going, and I am not sure about running that right now

I'm sorry, but I am so focused on analyzing my prelim data for my grant that I can't really do anything else.

I am writing my grant and its a struggle, would you look at my Specific Aims?

My dog eat the software, and the replacement is on backorder.

If you make the turn-down about you and not about their science, it will usually go OK. If it doesn't, go to your ally in the department (you do have one, don't you?) and lay it out. Do not say "you are a greedy micro-dick and I am not going to let your idiocy sink my career". Bad move.

The biggest problem you will have is saying no. Start practicing now.


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Best thing said on the internet in yonks

Nov 07 2014 Published by under Uncategorized

From Datahound's latest post:


DJMH: It makes me dream of a world in which the NIH kept track of this stuff.

Drugmonkey: It makes me sob for a world in which the NIH does not.


If you are NIH funded and not following Datahound, you need to. It's not just following, btw, its actually reading. His posts are hard, and reflect work on his part, and effort on ours.

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Things that happened when I went out for a glass of wine with an (albeit young) colleague

Nov 05 2014 Published by under Uncategorized

I have a marvelous colleague. She is a great scientist. She is an interesting human being. She is a Good Person. I enjoy her company and we try and get together once a week or so. Just to talk. No agenda. Let's call her Lucy so that I don't have to type out my friend too many times.

Lucy and I go to a quiet bar. A very quiet bar. It is a jazz and wine grown-up bar in our college town. The waitstaff are interesting arts students at the college. It is dark and brick-walled and decorated with old-tymey  photographs of Matt Dillinger and Al Capone. The wines are good, the beers very good, and the owner a lovely and warm person. Lucy and I are both east coast refugees, and this place is close.

We were early so it was extremely quiet, as in we were the only people there. There are three things from last night worth reporting on.

Seldom is there music on a Tues night, as it is slow. But there was an acoustic guitar player. With some kind of computer-rhythm/accompaniment electronics. He was a boomer. His music was covers of 70's and 80's quasi-blues/jazz/rock. Not our cup of tea (they have good live jazz on the weekends), but this guy was OK as background music. But, after his first few songs he walked up, with his guitar, playing and singing to our table. We were clearly discussing Serious Things (grant money on post-doc vs. technician). And started chatting. Kinda coming on to Lucy. (No one comes on to me in those situations, I've just cultivated a Too Damn Scary exterior). He said that he did requests, and oh by the way, here is a laminated, computer printed (dare I say Comic Sans)  list of songs he does on request. It was creepy. We said "Van Morrison" mostly to get rid of him  and I almost said "leave us alone" but he started singing there, and it was getting more creepy. We kept out humor the creep smiles in place and then he left (before I could tell him to fuck off). We discussed creepy and then returned to the topic at hand.

So, the topic:  post-doc vs. technician

Firstly, it is important to recognize that this decision, who to hire with  grant money or start-up is incredibly discipline dependent. I can talk about what Lucy and said, but it may not apply to you. Lucy is a neurophysiologist, and the range within neurophysiology is huge, too. She just got her first R01, after 3 years as jr. faculty. She has one postdoc, but money for another position. She needs to produce before tenure. There is a great candidate for PD, but he may not take it, and in any case he wouldn't  be here till mid-summer (ie 6-8 months). A tech could be here and right now, but would likely not be as committed to the research and move her work forward. She needs to generate data and papers. My advice was to start looking for a tech now. My second advice was something she already acted on - invite the potential PD to visit, and get that ball rolling. Judge by the people - if she finds an incredible tech who will be as good as a PD for a year or two, wrt generating data, hire them. If she finds a tech looking for only a year's employment, but is who great - hire them now, and figure out the 4-5 month overlap.  It is important to keep in mind that when hiring a PD or new tech, there is a more than one month (often) investment in training before the data payoff begins. She shouldn't wait for the potential PD to make up his mind, in case he decides otherwise. In this case, I would tend to say hire a tech, and if the postdoc turns out, then try & scramble for more money. Postdocs often look glittery and shiney as additions to the lab. They will Change Your Science. They will be A Junior Colleague. But if there are very specific goals, particularly for the run-up to tenure production, having a good tech, with explicit instructions can work much better to achieve the endpoint.

The third item of our evening was something Lucy told me that I found disturbing. She bumped into one of The High Ranking Administrators from our uni at the gym. Her first comment was that at least he was wearing enough clothes so it wasn't uncomfortable. He asked how things were going. She ran through what's going on in her lab, positive spin (do not unload on admin in this situation, it is always best to use it to reinforce the idea that you are marvelous and indispensable to the institution).  Then he said to her that she should take it easy. She works too hard. She should enjoy life. Lucy told me that she was totally flabbergasted at this point and could only nod. Does this admin who is on the tenure approval hierarchy, have, as my mother used to say to me, three brain cells to synapse together? This is the same person, who in 3 years will be telling her that while she is very good, she just isn't good enough. What a fucking, tone-deaf, smug, jackass. I am sure that he thought he was being "kind" and "in touch with young people". As long as we live with this broken tenure system (it destroys the youngers and the olders), the least that the power brokers can do is acknowledge the problems and not offer meaningless platitudes. He's forgotten what its like to be young and afraid.




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Post-election convo between my sister and my nephew

Nov 05 2014 Published by under Uncategorized

Nephew is freshman in college. Sister is later boomer (4 years younger than me).

Nephew: It's so depressing.

Sister: Yes

Nephew: what are we going to do if we loose the presidency, too?

Sister: Lived that. It was called the 80's.


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Pyramid Schemes, Mouths at the Trough, and the older you get the harder it is to remember anything (like your graduate experience)

Nov 04 2014 Published by under Uncategorized

A while ago Eve Marder's article on the number of PhD admissions stirred up the natives. It's been incubating or brining or gestating (pick your favorite metaphor) in my mind for a while.

I've read that it's a lot like r- and K- selection. To increase your fitness in an r-selection scheme, and the number of your genes in the next generation, do you produce lots of offspring, invest very little in any of them, but hope enough survive to make it (think insects, or fish). Or, as a K-selection type, do you produce a smaller number, invest heavily in them (think whales and elephants)? Of course the point of fitness is leaving your genes to the next generation and any concern/investment/strategy for the offspring beyond survival is still about leaving your genes and your fitness. Needless to say trainees are not genes, and improving one's academic fitness is not necessarily the goal of Good People (though as is true of BSD's, YMMV).

One perspective of the olders is that the youngers are actually living this, and therefore in the worst place to judge. If it was true that the youngers were saying "don't limit admissions", one would be tempted to argue that they perceive themselves as being at risk. If the youngers were saying "do it to Julia", then one would be tempted to accuse them of arrogance (yes, limit admissions, but not me). Instead what I am hearing is the rational concern that verges on anxiety about the future. Their future. Their hopes. And no K-selected parent can ignore that. And, no thinking scientist who cares about the future of the field.

Part of Marder's arguments that irritated me were:

Admissions committees are bad at predicting who will end up deciding to stay in science.  ....I f we knew how to spot the 25% of our applicant pool ... [who will] become an outstanding scientist, .... might make it sensible to decrease the size of our incoming cohort. But it would be counterproductive and sad to limit our numbers and then effectively lose the creative, determined and possibly unconventional individuals who might not make it through a more restricted gateway.

It's not that I disagree. Admissions committees are political entities with multiple pressures and goals, many of which are not about the candidates. The problem with Marder's logic is that we should then admit everyone who wants to be a grad student. Why limit it to what we have now? There might be some great future scientist that we are ignoring with the current standards. I am guessing Marder would say no to that scheme. The argument against admitting everyone who applies is that admissions committees can make some decisions, and there are some people obviously not suited for a career in science. But are admissions committees, right now, only dealing off the bottom of the deck, only excluding those we know won't make it. Of course not. We are making hard choices. We are drawing a line. The question becomes where do we draw that line?

Getting into grad school (even right now) is a classic supply/demand problem in economics. While the demand for seats in grad school are higher than the available supply of those seats, that supply is fairly elastic. The real supply/demand problem occurs for faculty positions. We've set the supply for grad school at an artificial, predetermined level. This level, the line we draw, is determined by a number of factors, mostly funding, that have little to do with the excellence of the candidates and their potential for being scientists. It certainly doesn't think about the future much (all my grad students get postdocs).

I  still think the real issues go back to what happens to those trainees. Marder can argue that we celebrate all those who don't make it. She can say that it takes grad school to figure out if you have what it takes to make it. But that's not really thinking about the people in those roles. I've said before that it is a bogus and somewhat condescending argument that "PhD programs in biomedical sciences train you for many careers".  No one enters a PhD program because they think its a good way to become a high school teacher.  The question remains: is there a better path to the "" endpoints?

Yet, there is still validity in the argument it is not obvious who will be a good scientist at the point of admission. Previous research experience, if it is real research experience, is a strong indicator. One of the advantages of the British/Aussie/Kiwi scheme of doing "honors" as the fourth year in a three year degree is that there is a condensed year where it is possible for the student to figure out what its like and what they want.

The discussion about where to draw the admissions line needs to be an ongoing one. It needs to involve people all along the career pathway, not just the Eve Marders of this world. And to those who say that blogs/twitter/social media are a waste of time, I say: feh. It is one way those other career-stage people get a voice.







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