Archive for: July, 2014

Popular Press and What is a Random Sample

Jul 31 2014 Published by under Uncategorized

There are tons of examples of bad science getting good press and of good science getting exaggerated press that makes you think Cancer Has Been Cured or Disabled Children Can Not Only Walk but Walk on The Moon.

This morning on the tweets I engaged one Christian Jarrett @Psych_Writer  Editor of . Neuro blogger for ; writer on creativity/productivity . Next book: Great Myths of the Brain.

He tweeted about an article he wrote:

And was answered by

 My reply and his reply to me:

The original article is Differences in voice-hearing experiences of people with psychosis in the USA, India and Ghana: interview-based study by T. M. Luhrmann, R. Padmavati, H. Tharoor and A. Osei. The published study had a sample of 20 people from the USA, India and Ghana, who heard voices were diagnosed as schizophrenic, and were interviewed. The conclusions the authors reached was:

These observations suggest that the voice-hearing experiences of people with serious psychotic disorder are shaped by local culture. These differences may have clinical implications.

I've gone back and read both the original science and the report on it. Jarrett does say that more research is necessary to "replicate these findings". The point I picked up on from Keith Laws was that the sample may be so biased (because it was not controlled) as to make the results meaningless.

The real meaning of a random sample is that each and every member of the population has an equal chance of being picked for the sample. Of course, this is usually impossible, both practically and philosophically. If you are testing a new screening method for blood sugar, you want it not just to work for people right now, but for people who would need screening in the future. If your population is to extend into the future (i.e., the population is all people who have had diabetes, and all people who will have diabetes), then there is no way your sample can be truly random, because you can't include the future people. Practically what most people settle for is that there is no bias in your sample. That some particular group/characteristic is not more or less likely to get picked. Sometimes stratification can help with this (ie analyze the men differently from women, include age as a covariate).

This is not necessarily easy.

The worst bias is the stuff you don't know about. Or can't know about. Or haven't thought about it. This is one of the reasons that the NIH is asking animal researchers to include both sexes in their study. Bias is nasty, often insidious, and can wreck the best laid designs of mice and men and other non-exempt USDA species. Bias means that results you think are attributable to your main factor (sex, country, age) are in fact because there is another, unseen factor that is in your design. For example, if all the females were older, and all the males younger (animals, peoples, whatevers), and you found a sex effect, it might be due to age. That one's obvious. But there are other more subtle ones that creep in. Often in animal studies it's easier to control, things like uniform genetic backgrounds, controlled diets, controlled environments. My concern about the voice hearing study are some of the factors that were not controlled. Some of the other tweets raised concerns about the consistency of the diagnosis

So, the question is: are the remotely sampling for the same population?  A qualitative study can lay groundwork. But a biased qualitative study will only muddy the waters. Are people with SZ as likely to end up in the same place/facility in these countries? What about different socio-economic-religious groups? The point about "friendly" voices is very sexy. Very re-tweetable. But will anyone care when the study is repeated with an unbiased sample and finds no difference?

I do agree with the sentiment that cross-cultural research in mental health is to be encouraged. But not at the cost of publishing stuff that has a high potential to be wrong, and will then enter the greater knowledge-sphere of "true facts".*   * Of course this depends on what % of your brain you use.

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Writing a PhD thesis and thoughts from The Thesis Whisperer

Jul 29 2014 Published by under Uncategorized

I've just found the thesis whisper blog. The post I read first was about academic assholes, something that resonated deeply with me. I spend a lot of time on a subspecies of AA, the BSD.

I started reading other posts from TTW and came across this one on The Zombie Thesis. Her idea of a Zombie thesis was one that didn't live - it was ideas but no structure. One of her examples was a thesis with the comments:

he got his draft back from his supervisors with comments like “it is not a thesis yet”, “Where is your voice?” and “this is boring”.


A Zombie thesis can walk and talk, but it isn’t really alive.

A zombie thesis looks like a thesis – with title pages, chapters, graphs and charts – but the parts aren’t quite hanging together yet. This is largely because the apparatus we rely on to orient us in the text: introductions, transitions, topic sentences and so on, are not always in the right order, or they are missing in action.


Although the post was interesting, after reading it I can't give you a one sentence summary. I'm not sure why these problems make it a zombie thesis. But it did make me think about what makes a good thesis.

I think some, if not many, of the problems that TTW outlines in her blog can be / are easily avoided by science PhD's. If you think in terms of scientific papers. The best thesis, which I blogged about before, is one that you get published before you defend. This is not easy. I know. If you write your thesis as a series of publishable papers, then you are being held (by the journal) to a slightly different standard that a "normal/usual thesis". With respect to science, the standard is usually higher. With respect to clarity of presentation, it is almost always higher. With respect to filling in the little details, literature review, and a bunch of other stuff that I think unimportant, the standard in a journal will be lower. No one there cares about a lit review.

I have never understood people who say "you must write a classical thesis, with chapters, and a lit review". In The Olden Dayes, when scientists wrote Bookes, this made sense.  One was producing one's first piece of adult work. Now a days, many of the BSD's write books for their own greater glory, but seldom are they (the books, but possibly the BSD's) the cutting edge science that gets jobs, tenure and grants. Why make students do something that has little relationship to what their Growne-Uppe Job is going to be?

I often joke with my lab that we are a factory that is assessed on our widget production and our widgets are scientific papers. (I know this is a dreadful reductionism that leaches the joy and substance out of what we do. Please, its a joke). If you are going to go work in a widget factory, why insist that the student build a dishwashing machine, if they are never going to do that again (or at least not till they are an old fart)?

My PhD advisor occasionally had a good thing or two to say to his students. One of them was: doing science is not putting another brick in a large edifice. Doing science was part of a living organism that could grow, and contract, and remodel itself. The parts were interactive with other parts. But the bits we make that interact are the papers, the posters, the talks we give. I believe, strongly, that asking trainees to do something that has nothing to do with what they are being trained for is a waste of their time, my time, and an insult to the organism.




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I love A. O. Scott

Jul 27 2014 Published by under Uncategorized

From A.O. Scott's review of the new Woody Allen movie:

Stanley has a briefly seen, occasionally mentioned fiancée named Olivia (Catherine McCormack), who is a fellow skeptic and an intellectual peer, meaning that she has no chance with him.

It is too much to hope that less than plastic-beautiful women can be heroines or leads or loved in movies (the way that less than beautiful men are). But smart women? Probably not.


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The President

Jul 27 2014 Published by under Uncategorized

From Jezebel about Russia outlawing most of McDonald's menu.


* Sorry, Poot-Poot, you can kill as many pre-sedated tigers as you want, but you will never be remotely as badass as this picture. Or this picture. Or this picture. Or this one (ignore Grandpa Crankyjowls there). Holy crap does that guy looks badass in sunglasses, is my point here.


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Bleg (blog beg) on mentoring

Jul 22 2014 Published by under Uncategorized

I am facilitating (although that always makes me like a facility, or a large room, or perhaps a gym) a seminar thingie on mentoring for jr faculty. This is a bit different that what I normally do, as it is for another group outside my department &tc. So I don't/won't know any of the people, although it is supposed to be for about 10, so interaction will be high.

Any suggestions? I've got some standby organizing bits, about kinds of mentors, what mentors do etc. But, before I launch into it, I'd like to hear other thoughts. I'm totally open to major restructuring of this.


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Stealing Culture and Identity

Jul 21 2014 Published by under Uncategorized

John McWhorter (who has written extensively about language) has a post in the Daily Beast about stealing culture. Cultural appropriation. This is in response to a Time op-ed.

First, he makes the point that stealing for financial benefit (a la Elvis) when the originators receive nothing, but the thief gets rich is wrong. That is different, he says, from other situations.

But what began as a legitimate complaint has morphed into a handy way of being offended by something that should be taken as a compliment.

The meat of his point is in the next two para:

... editorial in Time, where a black woman tells white gay men to stop imitating them by taking on their gestures and expressions.... To her, these men are “stealing” black womanhood.

But what does it mean to “steal” someone’s culture when we’re not talking about money? With gay white men and black women, for example, it’s not as if the black women are being left without their culture after the “theft,” or as if gay white men are somehow out there “out-blacking” the women they “stole” from.

The argument goes somewhere interesting after this. Its starts with (this is McWhorter's argument):

  1. white gay men imitate black women out of admiration.
  2. some of that admiration is because black women are "fellow suffers of oppression"
  3. but that (as the Time op-ed claimed) white gay men suffer less oppression than black women is a slippery slope of an argument.

But the part I really liked is a bit more minor, and towards the end:

The claim that white gay men are wrong to imitate black women because they aren’t as oppressed implies that black women’s cultural traits are all a response to oppression.

He then includes a quote from Ralph Ellison (who I realize is quite out of style now, though he made a huge impact on me as a young adolescent):

“Can a people,” he [Ellison] asked, “live and develop for over three hundred years simply by reacting?”

and then McWhorter (who identifies as black) says:

So very much of what it is to be a black woman is simply being someone, being someone beautiful with a particular complex of cultural traits that simply are, for themselves. That isn’t something anyone can “steal.”

This takes me back to Deirde McCluskey's views on change. (if you have not read her book, you must. well written. insightful. etc)

My gender crossing was motivated by identity, not by a balance sheet of utility.

Who we are, what we are, what culture we embrace is both a response to oppression and  a response to the joy of what we are. I am neither a black woman nor a gay white man, and do not wish to evaluate the arguments about cultural theft in this case. But as in any good/interesting/valuably provocative debate, it has given me a new room in which to sit and think. The chairs in this room are not particularly comfortable.

On some axes (plural of axis, not plural of axe) I have privilege, on others I have struggled. For me, I refuse to let male academics define me as butch. or dyke. or hag.  I refuse to give into their expectations about older women. or quiet women. or respectful women. I am exactly what a woman in her late 50's looks like, neither young nor old for my age. I  behave exactly as a woman in her late 50's does. I am neither mature nor immature. My struggles have informed me, and helped shape me. But they are not me. I am a continuation of my parents and grandparents. Their struggles are stories that help me, but their struggles were not mine. I do not claim the oppressions against which they, my beloved ancestors, worked. I do not claim that my story, my experiences are even necessarily relevant to gay men or women of color or third world women children sold into slavery. But I read all of these stories to learn. And I share mine in the hope that will help or matter or provide a chair in which someone else can sit and learn.


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Just calm down, Potnia

Jul 18 2014 Published by under Uncategorized

I hate when people tell me to calm down. I want to punch them.

These are usually men people.

The best parts of me are those that are not calm.



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Vacation-style joke

Jul 18 2014 Published by under Uncategorized

Discussion about going to beach and august and what not on the tweets reminded me of this. I thought I had told this before, but can't find it. If you are hearing it again, laugh again or not. Today I don't give a shit (just my pigs do).

Grad student, Postdoc and PI are coming back from morning coffee, and find a magic bottle. Someone rubs it and out pups the Genii.

Genii: there are three of you so each gets one wish.

Grad Student: Ah, I want to go to Florida. Be on the beach. A beer in each hand, lots of semi-naked people that are appropriate to my sexual orientation and gender.

Poof. The grad student is gone.

Postdoc: I want to be on the beach in Hawaii, with my significant other, and a babysitter for the 1rst instar at home.

Poof. The Postdoc is gone.

PI: I want them both back in the lab by 2pm.



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Who needs to think about who they sleep with

Jul 16 2014 Published by under Uncategorized

A comment from  JustaTech:

The real quesiton for me is why is the advice “don’t sleep with your boss” and not “don’t sleep with your subordinates”? Isn’t that the way this power differential is going anyway?

Of course it is "don't sleep with your subordinates". Even more so. But anyone who needs that advice is 1) not going to be listening to me and 2) not listening to anyone, probably and mostly likely 3) thinks that they don't need it or it doesn't apply to them or that in this case it's true love.

Someone tweeted (blogged?) some wisdom that I can't find just now, hence an uncited paraphrase. If it was you, let me know, I'd love to give credit. Essentially ( I know this isn't quite right, and was even stronger) they said how can you trust someone to right by any of their trainees, if they can't do right by all of their trainees.


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How to find non-PhD student trainees/lab help

Jul 15 2014 Published by under Uncategorized

Drug Monkey has a great post on from whence does the over-glut of people looking for an academic job/grant come? It is an answer to a post from Thoughts for Breakfast about the morality of hiring postdocs. Needless to say, I come down on DM's side of this argument, which in a nutshell is:


One of the comments, from karassment, deserves more consideration (slightly edited for space):

I have been looking for a TT job for years, and now that it finally looks like it will happen, I think about this all the time. I am acutely, painfully aware of how hard the job market is. My current PI has flatly refused to take any students, .... I am not going to have the clout to do that, and even if I did, my start up will disappear really fast if I hire only high paid uber techs and staff scientists like you said. The students I'll be talking to about joining the lab will already be students, [more stuff on working with PhD students]. I'm not going to have much access to undergrads, and don't think I'll have the budget or fame to attract postdocs for a long time [my bold]...

Karassment's comments, the ones I redacted, about PhD students are heartfelt and admirable.

What I want to address is the point I bolded: places to look for lab-peeps without feeling you are being dishonorable and immoral for training people who can't ultimately get the jobs for which you are training them.

In my various past (often evil) lives, I did not have good access or opportunity to get grad students. There were no PhD programs in two of the departments to which I belong/belonged. Another dept had a tiny PhD program, where stealing of students from other labs was time honored, jolly old boys BSD tradition (which when this was brought up at a faculty meeting, the condescension would have done Lady Catherine de Bourgh proud). By the time I was senior enough to attract grad students, I saw the problem and didn't think it right to take any.

So what can be done in this situation?

First, do not overlook undergraduates wanting to do research. Many are pre-med, or other pre-clinical programs. I have found that these folks can be hard working. While not PhD students, they can be productive in ways that jr faculty need. They will undoubtedly need more supervision, but that doesn't mean that can't be productive. They can generate data, and write up a report that can be the basis of a paper. What is important is that they have a project that they can own, and that you talk to them minimally 2 times per week to keep them on track. Biggest mistake with such students is giving them too much rope, as they will always hang themselves.  And, even if you don't have access to UG's at your uni (as Karrasment suggested), its worthwhile reaching out to another nearby institution to see if you can forge a working relationship.

Do not necessarily assume you can't get a good postdoc. Keep your ears & eyes open. Maybe not the first year, but the second can work. People chose grad schools on The Name of The Uni basis, and sometimes on the program. People chose postdocs on the basis of the mentor. Attending meetings in one's subdiscipline, one can approach current grad students and say "your work is interesting, let me know if you're looking for a postdoc", and give them the 2-minute schpeil on your work. Keep in mind, at some private MRU's a student costs as much as a postdoc.

Another source are students in master's level or PhD clinical programs - SLP's, PT's, AuD's Dental students, Dental residents, some nursing programs, psych - folks that have do some kind of thesis. Often these schools don't have enough research faculty to supervise all the students they need. A friend of mine was responsible for 10  graduating MSc students a year, which in a 2-year program was hell. She was tremendously grateful that I took two of these into my lab. Again, they need tightly supervised projects. Part of the skill in working with these people is to craft contained projects that are useful to your greater vision/goals, but are interesting to them. You may not have these schools at your uni, but there might be some nearby. It's worth looking into.

Again one of the keys to this is to understand how these students are different from you (the former PhD student). They are not living and breathing and excreting science they way you did. They are doing something that they perceive needs to be done to finish their degree. But, they can also perceive that working in your lab maybe doing it in a more interesting way than the alternatives. You don't have to entertain them, but you do have to treat them like human beings. More work on organization and supervising is critical to getting what you need from the interaction.

Finally, if one of these doesn't work, end it quickly. A student not showing up, doing something bad with the animals, screwing around with the data, etc, is not worth saving. Learning to move on is also important.

I don't think that Karassment's situation is dire. You don't have to give into the soul-sucking strategies for success. I also think that having one grad student at a time, someone with whom you work to ensure a higher probability of ultimate success is defensible for younger scientists.






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