Scientopia http://scientopia.org Fri, 22 Jul 2016 23:13:54 +0000 en-US hourly 1 I oppose H8 http://drugmonkey.scientopia.org/2016/07/22/h8/ Fri, 22 Jul 2016 23:13:54 +0000 http://drugmonkey.scientopia.org/?p=9191 Sometimes just shaking your head isn't enough.

One of the things that I've believed is the very essence of the American Dream is the aspiration to own your own little home, live in a nice neighborhood, raise your kids as best you can and live happily ever after with your spouse.

NBC Philadelphia reported on the American Dream of one couple as it is right now in 2016.

The couple said they bought the house in 2014 and moved there for a fresh start — a place where their boys, now ages 8 and 13, could play in the yard with the four family dogs and leave behind the hurt of their biological parents’ struggles with drugs and crime.

But, the pair said, they found only discrimination and hate. First, they said, in the form of the frivolous lawsuit, and later during a months-long campaign of repeated vandalism to their home that included someone using the cover of night to scrawl the slur onto their garage, breaking their security sensors on numerous occasions and twice taking a hacksaw to the white fence that supposedly sparked it all.

There's a gofundme set up to pay this family's legal bills.

I'm going to suggest that this is a great opportunity to give even as little as $5 just to register a vote of protest against hatred and in support of decency. Or as the lighting of a candle in the darkness.

Or maybe, as I do, you think that this could easily be you, your family or the family of people that are really close to you. The specifics may vary. Maybe it is not your sexual orientation but the color of your skin. Maybe it is your religion or the clothes you choose to wear. Maybe it is your chosen profession or perhaps a health or ability condition. Whatever it may be, you might be unlucky enough to end up in a neighborhood with people who hate you for what you are, not for who you are. And some of these sick individuals may be feel it is perfectly acceptable to persecute you because of their hatred.

And if so perhaps you hope, as I do, that if you had uncharitable neighbors like these poor people do, that the rest of the country would rise up and register a small vote of support for you.

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Personal jihads and distinguishing better/worse science from wrong science http://drugmonkey.scientopia.org/2016/07/22/personal-jihads-and-distinguishing-betterworse-science-from-wrong-science/ Fri, 22 Jul 2016 20:33:56 +0000 http://drugmonkey.scientopia.org/?p=9185 This is relevant to posts by a Russ Poldrack flagellating himself for apparent methodological lapses in fMRI analysis.

The fun issue is as summarized in the recent post:

Student [commenter on original post] is exactly right that I have been a coauthor on papers using methods or reporting standards that I now publicly claim to be inappropriate. S/he is also right that my career has benefited substantially from papers published in high profile journals prior using these methods that I now claim to inappropriate. ... I am in agreement that some of my papers in the past used methods or standards that we would now find problematic...I also appreciate Student's frustration with the fact that someone like myself can become prominent doing studies that are seemingly lacking according to today's standards, but then criticize the field for doing the same thing.

I made a few comments on the Twitts to the effect that this is starting to smell of odious ladder pulling behavior.

One key point from the original post:

I would note that points 2-4 were basically standard practice in fMRI analysis 10 years ago (and still crop up fairly often today).

And now let us review the original critiques to which he is referring:

  • There was no dyslexic control group; thus, we don't know whether any improvements over time were specific to the treatment, or would have occurred with a control treatment or even without any treatment.
  • The brain imaging data were thresholded using an uncorrected threshold.
  • One of the main conclusions (the "normalization" of activation following training") is not supported by the necessary interaction statistic, but rather by a visual comparison of maps.
  • The correlation between changes in language scores and activation was reported for only one of the many measures, and it appeared to have been driven by outliers.

As I have mentioned on more than one occasion I am one that finds value in the humblest papers and in the single reported experiment. Often times it is such tiny, tiny threads of evidence that helps our science and the absence of any information on something whatever that hinders us.

I find myself mostly able to determine whether the proper controls were used. More importantly, I find myself more swayed by the strength of the data and the experiment presented than I am by the claims made in the Abstract or Discussion about the meaning of the reported work. I'd rather be in a state of "huh, maybe this thing might be true (or false), pending these additional controls that need to be done" then a state of "dammit, why is there no information whatsoever on this thing I want to know about right now".

Yes, absolutely, I think that there are scientific standards that should be generally adhered to. I think the PSY105: Experimental Design (or similar) principles regarding the perfect experiment should be taken seriously....as aspirations.

But I think the notion that you "can't publish that" because of some failure to attain the Gold Plated Aspiration of experimental design is stupid and harmful to science as a hard and fast rule. Everything, but everything, should be reviewed by the peers considering a manuscript for publication intelligently and thoughtfully. In essence, taken on it's merits. This is much as I take any published data on their own merits when deciding what I think they mean.

This is particularly the case when we start to think about the implications for career arcs and the limited resources that affect our business.

It is axiomatic that not everyone has the same interests, approaches and contingencies that affect their publication practices. This is a good thing, btw. In diversity there is strength. We've talked most recently around these parts about LPU incrementalism versus complete stories. We've talked about rapid vertical ascent versus riff-raff. Open Science Eleventy versus normal people. The GlamHounds versus small town grocers. ...and we almost invariably start in on how subfields differ in any of these discussions. etc.

Threaded through many of these conversations is the notion of gate keeping. Of defining who gets to play in the sandbox on the basis of certain standards for how they conduct their science. What tools they use. What problems they address. What journals are likely to take their work for publication.

The gates control the entry to paper publication, job appointment and grant funding, among other things. You know, really frickin important stuff.

Which means, in my not at all humble opinion, that we should think pretty hard about our behavior when it touches on this gate keeping.

We need to be very clear on when our jihadist "rules" for how science needs to be done affect right from wrong versus mere personal preference.

I do agree that we want to keep the flagrantly wrong out of the scientific record. Perhaps this is the issue with the triggering post on fMRI but the admission that these practices still continue casts some doubt in my mind. It seems more like a personal preference. Or a jihad.

I do not agree that we need to put in strong controls so that all of science adheres to our personal preferences. Particularly when our personal preferences are for laziness and refelect our unwillingness to synthesize multiple papers or to think hard about the nature of the evidence behind the Abstract's claim. Even more so when our personal preferences really are coming from a desire to winnow a competitive field and make our own lives easier by keeping out the riff raff.

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Using spiffy WordPress themes in an IE environment http://christinaslisrant.scientopia.org/2016/07/22/using-spiffy-wordpress-themes-in-an-ie-environment/ Fri, 22 Jul 2016 19:07:58 +0000 http://christinaslisrant.scientopia.org/?p=1212 At MPOW we apparently have "compatibility mode" on by default by group policy. So this disables all the cool HTML5 and does weird things in general with a lot of web pages. If you go to the WordPress plugins, there are a few to show nasty messages to visitors that they have to change or update but that's just super unhelpful for those many visitors who don't actually have a choice.

Anyhoo... I pieced this together from a few different sites... If you go into network dashboard to themes to edit the theme and find the header.php file (back it up first just in case).

Then under <head> make the next line:

<meta http-equiv="X-UA-Compatible" content="IE=Edge,chrome=1">

and update... works. This tells IE not to show compatibility view.

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Group effects. or "effects". http://drugmonkey.scientopia.org/2016/07/22/group-effects-or-effects/ Fri, 22 Jul 2016 17:56:18 +0000 http://drugmonkey.scientopia.org/?p=9182 How many times do we see the publication of a group effect in an animal model that is really just a failure to replicate? Or a failure to completely replicate?

How many of those sex-differences, age-differences or strain-differences have been subjected to replication?

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Words I never thought I would say http://mistressoftheanimals.scientopia.org/2016/07/21/words-i-never-thought-i-would-say/ Thu, 21 Jul 2016 13:15:42 +0000 http://mistressoftheanimals.scientopia.org/?p=2617

I'm so relieved that they are only taking 19% out of the budget. I can cut that much.

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Book Club – Lab Girl http://portraitofthescientist.scientopia.org/2016/07/20/book-club-lab-girl/ Wed, 20 Jul 2016 23:06:28 +0000 http://portraitofthescientist.wordpress.com/?p=1160 Continue reading ]]> We recently read Lab Girl, the nationally bestselling memoir by Hope Jahren, PhD. Dr. Jahren is a Professor at the University of Hawai’i Manoa where she runs a Geobiology Laboratory. She also blogs about interactions between women and men in academia at https://hopejahrensurecanwrite.com. The book is mostly about her life and career path, but it also weaves in interesting vignettes about plant life that appear as metaphors related to aspects of her experiences.

Lab Girl image

What was the most relatable part of the story for you?

fishprint: I read this book, in part, to find a relatable female scientist. I probably wouldn’t have admitted this at the time, but I like her writing, I love her Twitter presence, and I really wanted to relate to her. So, I spent the first half of the book hating it. Until finally I recognized I’d brought all these expectations to the book. Then I could let all that go and read it.  Do not read this book if you want a relatable female scientist role model to compare yourself to. Read this book for a well written, complicated personal story. You may relate more to the grad student who quits, “sneering on her way out that she didn’t want a life like mine”, but that’s OK. No one, probably not even that student, was really being asked to have a life like Jahren’s. But the proximity of the book (and worse if you work for her, I imagine) makes you compare and question.

peírama: One thing the book relies on and yet only briefly touches on directly is how Jahren’s relationship with Bill is important to her success in science. There are the straightforward ways, that he works for almost nothing yet works harder than most employees would and that he is a consistent presence in her lab from before she even starts her lab throughout her career (a trait which can make someone invaluable if they are competent, which Bill seems more than). Then there is the personal aspect of it. As Jahren readily admits, doing science is hard. There are setbacks from the natural world and from the world of people. Having someone interested in the same things as you, thinking about the same questions as you, who you get along with, who is there to support you when things get tough, makes things so much easier. I think the way our scientific society is set up to put people out on their own without a built in network and constantly ripping scientists away from people they know is counterproductive. Jahren lucked into a situation that should be more common in science – scientists with common interests working closely together, supporting each other, and working toward the same scientific goals.

Curiouser&Curiouser: Unlike fishprint, I had not heard of Dr. Jahren before reading this book, but I think I initially expected to find a role model in Lab Girl.  I did not.  I found very few specifics in her story relatable, but these 3 themes resonated with me.  

  1. In science you do not act alone.  I felt like the second half of the story was basically a platonic love letter to her best friend/lab manager.  While at times I felt awkward when it seemed to me that she was writing for/to Bill, (even though he said he would never read the book) I appreciated the sentiment that led her to want to say thank you and make sure credit is appropriately shared.   
  2. Being a scientist is hard work. ‘Nuf said
  3. Your personal struggles impact your career both positively and negatively.  It’s not always possible to check your personal baggage at the door.  

SweetScience: Dr. Jahren has clearly worked hard throughout her education and career, but it seemed like many major elements (i.e. certain jobs, her work partner Bill) just fell into place for her. This is not to say that she didn’t earn and work to keep those things, but I can relate to feeling like some things just come to you, even while things you try so hard for remain elusive.

 

Here are a few quotes that resonated with us. (Pages refer to original hard-cover edition)

  • “…my true potential had more to do with my willingness to struggle than with my past and present circumstances.” P. 18
  • “As much as I have loved being a scientist, I am ready to admit that I am tired of all the hard things that should be easy by now.” P. 25 (stated in the context of funding, but widely applicable)
    • C&C: This was one of my favorite quotes from the book.  I feel discouraged at least weekly by how much of a struggle it can, and will continue to be.  
  • “…there are only two kinds of people in the world: the sick and the not sick. If you are not sick, shut up and help.” P. 44
  • “On some deep level, the realization that I could do good science was accompanied by the knowledge that I had formally and terminally missed my chance to become like any of the women that I had ever known.” P 71
  • “…because I am a female scientist, nobody knows what the hell I am, and it has given me the delicious freedom to make it up as I go along.” P 277
    • SS: I can’t directly relate to this because I feel that female scientists are common in my field/generation, but I do think it’s interesting and important to understand that someone has felt this way in very recent history. Further, I can relate to the idea of ‘making it up as I go along’ as it feels like everyone is struggling through the decisions that need to be made early in one’s career in a way that is probably different than previous decades, given the overabundance of PhDs, lower relative number of traditional academic research jobs, and wide array of other science-related careers open to us. There’s no clear path, and no history of scientists having to navigate these conditions.

 

What surprised you about the book?

SS: I was surprised that there was virtually nothing relating to the interactions between women and men in academia that are the focus of Dr. Jahren’s blog, and a talk I saw her give to a Women In Science group. Given that she’s had plenty of experiences relevant for the subject and is clearly passionate about the topic and changing the state of academia’s treatment of women, I wonder why she didn’t draw attention to those issues in this book. Maybe it will be the focus of book number two?

f: She still doesn’t sleep. She still goes to the lab every night.

P: I was also surprised about how she talked about working all night like it was normal and how her family seems like afterthought.

C&C: I didn’t pick up on her struggle with mental health issues early on in the book, and so I found her description of her interactions and environment unnerving and often depressing.  Once she made it clear that there was more going on than a selectively empathetic, extremely driven person I was able to let go of the idea that an “ideal scientist” should follow her model, and I was surprised to find that I enjoyed the second half of the book.  

I also was shocked by Bill’s living conditions until they get to hawaii, what a loyal friend to stick it through!

 

Are there any messages in the book you disagree with for yourself or as a role model for young scientists?

SS: I don’t love the propagation of ‘the absent-minded professor’ stereotype, particularly the scientist who is so passionate and caught up in their work that they are up all night excited about a potential discovery at the expense of their personal lives; it is possible and indeed common for a career in research to be ‘just a job’ and that’s something I feel is a valuable message for young scientists.

f: Many of the pronouncements in this book are things that have worked for Jahren, and are not broadly true (or good) for other people. She is in lab all day and then hits the lab again every night starting around 10:30pm. I doubt she sleeps more than a few hours a night. And that’s OK for her, it makes her happy, and it works for her team (Bill). But seen as a message, it is a damaging one. My first PI bragged about sleeping 3 hours a night. In fact, every boss I’ve ever had has tedious glory days stories about being in the lab all night. They are not all successful, but they all want to cast themselves as passionate, committed night owls. Why? Is that really when they do their best work? That’s when I start breaking things and deleting files. Not sleeping and not caring for your health can look like a thing that interesting and successful people do, but it’s not going to work for everyone. In defense of Jahren, she’s just telling her story. It’s messy, it’s literally manic, and her life would only work for her.

Oh, and that part about trying to weed out the students who value their time. Sigh.

P: She paints a picture of a world where a certain type of man is what the world sees as a scientist, and thus she and her best friend/lab tech who is a man but doesn’t fit that description are science outsiders who have to work twice as hard as everyone else to gain scientific acceptance.

I do not argue with that, as that is clearly true. However, she paints an alternate picture of a stereotypical scientist. The scientist that can’t stop until they’ve answered all the questions. The scientist who works until their knuckles bleed and needs no other sustenance but a good question. I think a lot of people, including myself and my fellow bloggers, love science and consider ourselves scientists but also do not fit that stereotype of a scientist.

One sentence that caught my eye in the very first chapter was “I glanced at the clock and noted that my son had gone to bed several hours ago.” She makes clear that her priority is science over everything else. That is not how I want to live my life. Yes, my husband is perfectly capable of putting my children to bed and does on many occasions, but I like to put my children to bed. My children and my husband bring me joy and I knew a life with a husband and children was something I wanted as surely as I knew I loved science. Hope Jahren has written a memoir, so perhaps it is unfair to criticize what is only her own story. Her way is one way to be a scientist. Perhaps the problem is not that she has told her story without any acknowledgment of other alternative ways to be a scientist but that there are not more stories that make it to the mainstream of those other alternative ways to be a scientist.

C&C: From the description in the book I don’t think Jahren can be considered a viable role model for most young scientists.  She has a unique set of challenges and gifts (she has found the most loyal employee ever and neither of the seem to need to sleep?!) that make her career and life choices reasonable to her, but I can not see them leading to happiness or scientific success for most people.  

 

Who would you recommend this book to?

SS: I would recommend this book to anyone interested in learning about what it means to be an academic scientist, or who likes different memoirs.

f: People who enjoy memoirs and science. I would not pitch it as an “inspirational female scientist”.

P: On the whole, I enjoyed this book as a book. That is to say, I enjoyed reading it when not thinking critically about what message it was sending and whether I agreed with that. I think it tells a compelling story of a woman finding her way in the world. It flows well and drew me in.

I also think this book is good for anyone interested in the natural world. I learned a lot about seeds and trees.

C&C: I think people who feel marginalized and/or struggle with mental health issues may enjoy the book.

 

All in all, most of us enjoyed reading most of the book, and we’d love to hear what you think too – tell us in the comments!


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I'm tired of being an old lady http://mistressoftheanimals.scientopia.org/2016/07/20/im-tired-of-being-an-old-lady/ Wed, 20 Jul 2016 14:17:39 +0000 http://mistressoftheanimals.scientopia.org/?p=2613 I am not tired of being me, of being over 60, of being where I am in life. I am not tired of how I look (though, of course, I could stand to lose a few pounds, but that has been true of me for the last 40 years, really). I would not trade where I am now for youth.

What I am tired of is the condescension and patronizing attitudes of younger people, particularly younger men. My almost-MRU has put in a new "wellness center", including a state-of-the-art gym. With a Pool!. I have been using it. They have a "wellness portal" that we are encouraged to use, with the usual information, misinformation and buzz words for fitness. I did sports in high school and college, when it wasn't easy for girls/women. Up until an injury, I ran 10-30 miles a week. I was a lifeguard, and did local Master's Swimming (but not well). When I logged on to The Portal, I found my account tagged with a note:

Your personal data indicate that you are a high risk individual. We will need a doctor's clearance before you can use our facility.

WTF? What is the data? That I am old, and "slightly overweight for your height". (I hate BMI, because I am (slightly) muscular and have always been high, but that's another rant). Really? Fucking really?

There is a form to fill out for a health insurance co-payment reduction. It requires a doctors signature, and you guessed it, available through the Wellness Portal. I couldn't find the form online, the contact info was out of date, so I emailed the Wellness Portal Liason (I kidd thee not, that's the title). I explained that the only form was out of date (ie contact info), couldn't be read (a bad scan of a bad scan), and not particularly useful to give to my physician (too many irrelevant pages for her). The email I got back was awful. The email was full of implications that I couldn't use the website (everyone agrees its beautiful, but useless, kinda like the people who work there), that perhaps if I looked harder, or worked harder, it wouldn't be such a problem for me. Oh, and I should stop complaining and just use the damn form that they provide (which is buried in six layers of menus). All this said, of course, in the most business/polite language. If I spoke that way to students, I would be having a meeting with my chair and dean to answer a myriad of student complaints.

I am not in a good place to be told to work harder. I'm in the middle of challenging experiments (live large animals), and everybody, EVERYBODY in my group is exhausted.  It's a new version of our model, we've learned a lot. This is the first day in about 10 that I've been able to sleep past 5:30 am.  I (and others in the group) have come in to care for animals at 4:30a more than one day, and stayed till afternoon to work on the problems we're having. Let me add, though, that the group is incredible, working hard, and I am totally thankful for the marvelous people on this project. I'm not complaining about the work. It is my choice. But, I'm not in a good place to be told to work harder by anyone.

Older, not-glossy-magazine-pretty, women are invisible in our society. There are studies that show the intersection between age and gender (let alone race) is enough to sink course evaluations. The most frequent comment is that I am not sufficiently nurturing to be a good teacher. Indeed, I'm not nurturing. I'm pissed off and angry.

 

 

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The words we all want to hear http://mistressoftheanimals.scientopia.org/2016/07/20/the-words-we-all-want-to-hear/ Wed, 20 Jul 2016 13:15:01 +0000 http://mistressoftheanimals.scientopia.org/?p=2609

We project that the award will be issued later this week with an August 1 start date.

Let's try not to look a gift horse in the mouth, but what is the cut going to be?

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Quote of the Day: how to be a wise faculty member http://mistressoftheanimals.scientopia.org/2016/07/19/quote-of-the-day-how-to-be-a-wise-faculty-member/ Tue, 19 Jul 2016 19:14:50 +0000 http://mistressoftheanimals.scientopia.org/?p=2519

When there are two conflicting versions of a story, the wise course is to believe the one in which people appear at their worst. --H. Allen Smith

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Thought of the day  http://drugmonkey.scientopia.org/2016/07/15/thought-of-the-day-46/ Fri, 15 Jul 2016 21:30:19 +0000 http://drugmonkey.scientopia.org/2016/07/15/thought-of-the-day-46/ I was joshing with the spouse about coups, Trump and the ready availability of pseudo-combat firearms today and a thought later occurred to me.

I'm actually pretty confident in the trigger pullers in my household.

Don't get me wrong, we're not a gun nut family- very likely I'm the only one who has so much as touched a firearm. But if they had to..... 

I was thinking about their respective ages and peers and what not and I'd pick them every time. 

I didn't know I had that particular confidence in my spouse and kids. 

Funny thought to occur. 

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