Archive for: February, 2015

Two takes on Leonard Nimoy Dying

Feb 27 2015 Published by under Uncategorized

and then, this interchange with me (millennial) tech.

me: Oh no!
Tech: what?
me: Leonard Nimoy died
tech: oh, I thought it was something important, like we got funded after all.

No responses yet

All life is a cost-benefit decision, even if you personally eschew capitalism

Feb 27 2015 Published by under life, time, Uncategorized

Forget the capitalism part, that's just trolling.

There is a convo on the tweets about paying for stuff that are "perks" or marginally necessary for what one does professionally.

As scientists, for the most part, there will never be anyone else to pay for many of the science things you wish to do. This ranges from going to meetings and staying somewhere other than a hostel with hordes of unwashed and stoned teenagers to journal subscriptions to page costs to duct tape with little animals on it.

I am not going to sit or stand or lie here and say "this is worth paying for and this is not". There are certainly extremes that are relatively easy to decide (forgo the duct tape and pay for your own coffee on the road). But whether something is "worth it" or not is a totally personal decision. Whether to dip into your shoe budget or cigs budget to buy that duct tape is not a decision anyone can make for you. The value you place on a Friday night beer vs a Monday morning fancy coffee vs flying or driving to a meeting is something everyone decides for themselves.

That of course, makes some of the decisions even harder. And many are not trivial at all. One example: people who are on a 9 month, academic year salary, do you teach in the summer? Depending on the university, the union and other factors one can earn 10-30% of ones academic year salary. That is not small potatoes. But, you still have to teach for that money. Sometimes the teaching is easy, and sometimes not. Sometimes even if its freshman bio, or remedial M1 physiology, and something you can do in your sleep, it will suck the life out of you. Even if its only in the mornings, you are too mind-fracked to do real science in the p.m. Sometimes the decision gets more complex. You add in the cost of daycare for little ones vs. salary in vs getting another paper out before tenure. These are tough decisions. And they are decisions that you weigh for yourself. They are based on your ability to parse time efficiently, stay on track and not run yourself into the ground.

The important thing is to understand that you are making a cost/benefit decision. Do I want to teach or write? The next most important thing is to be able to assess the costs and the benefits with some accuracy. What is a new car, better day care, a night out once in a while worth to me? The third most important thing is to remember that money is just a counter in your to translate those cost/benefit decisions. It is not anything more than that. Money means buying this or that. Money means my students don't pay me in sheep wool that I have to spin and then weave into a pair pants. I have always found it useful not to think "I need (to earn, to acquire, to beg) another $Xk", but to think about what that $Xk means to what I can and cannot do. Yes, this is the tedious "do a budget" thing, but it is important when you make these cost benefit decisions and comparisons. Just like time, money slips away. In fact, in organizing my younger academic life, I far more frequently that at any other time in my life thought money is time.

3 responses so far

Significance, p-values, and what to publish

Feb 26 2015 Published by under data analysis, ng, publishing, statistics, Uncategorized

I gave a Big Talk once on the difference between statistical significance and clinical significance. It was poorly received by the editor of the society's journal. He said to me that now he was going to be inundated with papers that say "Dr. Theron sez I don't need no stinkin' numbers". Actually he didn't quote The Treasure of Sierra Madre,  but the implication was there.

My simple point was that effect size is as important as significance. I've talked about this some, before. Something can be significant (because of pseudo-replication, over sampling, etc) but that the effect size is trivial, or less than your resolution of measurement. For (made-up) example, say you find a difference in a variable measuring "age at disease onset" between males and females, but that difference is on the order of days, i.e., males 60 years, 2 months and 3 days, females, 60 years, 2 months and 4 days. What does that mean in any kind of measure of effect size other than indicating there is probably some other bias lurking in your data. This one is obvious because we have an intuitive sense  of what the data mean. Other problems are often less obvious.

Now comes the journal Basic and Applied Social Psychology which is banning significance testing. In specific, they have banned  null hypothesis significance testing procedure (NHSTP). Steve Novella, who writes at the excellent Science-Based Medicine Blog, has a great discussion. He links to a video by Geoff Cumming that is similar to what I showed in the talk I gave.

All of this is well and good. Many Good Thinking People are cheering. But most of us publish in journals that require estimates of significance. My clinical society judges abstracts (which are severely limited in number of both talks and posters) based on some numskull criteria, which include "testable hypothesis" and "testing of hypothesis". They have not yet learned that horrible research comes in many flavors, and that one rule (must have p-value) does not a good piece of research make.

Another person who's view I respect is Andrew Gelman who has a good but short post on this. Here's the close of his post:

 Actually, I think standard errors, p-values, and confidence intervals can be very helpful in research when considered as convenient parts of a data analysis .... The problem comes when they’re considered as the culmination of the analysis, as if “p less than .05″ represents some kind of proof of something. I do like the idea of requiring that research claims stand on their own without requiring the (often spurious) support of p-values.

The bottom line always is: understand your data. Go back to what the effect size means. What are the data saying to you? What is the story? Use statistics to support what you do, but if they become the science of your research, you are in trouble.

3 responses so far

More on Meetings

Morgan Price's Comment that I blogged on the other day about going to meetings had the following parenthetical end bit:

(Do I not get it because I don’t like going to meetings?)

Lots of people have talked about why go to meetings, and what's hard about them. The upshot was, learn to like going to meetings. Lots of good stuff. DM (natch) had something important to say:

drugmonkey : I think it also takes some time in the field for meetings to become less uncomfortable. The longer you've been going to the meeting(s) with the same old crowd, the more likely to have old friends swing by your poster, to see people in the coffee line to chat up, to go out to eat with. You are more comfortable getting up to make a comment at the microphone, to grab the person in the hallway to discuss your / their data and folks from the platform call you out when they know you can answer a question better than they can.

It's a bit self-reinforcing. Here's the logic: I am uncomfortable at meetings. So I don't like going. But when I do I'm even more uncomfortable so I don't see that I get anything out of them but feeling inadequate in whatever way. So I don't like meetings even more than I didn't like meetings before, and I can now justify the unimportance of meetings because I get nothing out of them.

But this is also self-correcting. If you do go to meetings, and go to meetings purposefully, you will start to meet people and you will have new friends for the next time. It took me a while to realize that yes, I'm going to have lunch alone and that's not as much fun as lunch with friends. But, gird your loins and talk to someone and invite yourself along. You can do a little homework in advance. Find a new young asst prof whose work you admire. Go up to them. Ask about their work. Ask to have lunch or coffee or dinner with them.


One good point Qaz  makes is science is dialog. My PhD advisor (indubitably rolling in hell at this very moment) used to say that science is not an edifice built brick by brick, and if I am your advisor, your thesis will not be a stone in that edifice. It is a living breathing entity, he said, that if one is lucky, one can grow with science and into science. The implication, of course, is that we were all very lucky to be growing with him. "Under his care" would imply an involvement on his part that did not exist.
Qaz's point about good presentations is also important. Put your best self forward. Posters in particular open up those opportunities for dialog. If no one is talking to you, make friends with the posters on either side of you, or across the aisle. That is someone with whom you can go have coffee next year.
My answer to M. Price is could be. We may not love all parts of science, but meetings, for all their pain are totally worth it. Good meeting experiences are totally different from reading papers. Here's qaz again:
Too often people treat meetings as glorified reading sessions, where they sit in the back and let the text be talked at them. The whole point of a meeting is to engage the other individuals.
That's real science.

2 responses so far

So I didn't get a fundable score, either

Feb 24 2015 Published by under becoming an adult, grantsmanship

Here are things that I am grateful for, right now, when I didn't get a fundable score:

1. I am old enough not be totally incapacitated for 12 to 48 hours with grief and depression.

2. I am mature enough that I am not going to beat myself up and say that I'm stupid, that I'm incompetent, that my science sucks.

3. I have enough self control not to go out and get 3 gallons of expensive ice cream and eat it over a period of a few hours till I feel even more miserable about myself.

4. Nor am I going to take it out, in one form or another, on my current partner. I am not going to pick a fight, so I that can say that no one cares at all about me. No one in my life right now deserves that.

5. I am not going to blame: the molecular geneticists, Millennials, clinical idiots who don't like animal models, GenX, Sally Rockey, the study section chair, the reviewers, my mother, men, or anyone else. Not because they aren't at fault, but because it doesn't matter. Fault is irrelevant here. Getting funded is the goal.

These are all things I have done in the past.

It will be a while till I get pink sheets (reviews). I will read them. I will be unhappy. I will try & rewrite (as a new grant, of course).

Meanwhile, it's time to trot out ideas for proposals B and C and work on making them presentable, i.e., submittable.

My heart goes out to all the young people who are in the same boat, folks who haven't learned what I've learned about responding to being trashed by study section. Because it hurts a lot to be rejected.

If my thoughts help, great. That's why I write this blog. If they don't, well, my heart is still with you, whether you want it or not.



16 responses so far

More on why go to meetings

Feb 24 2015 Published by under Uncategorized

Comment from Morgan Price:

Why doesn’t reading broadly give the same boost to creativity as going to meetings? I don’t get it. (Do I not get it because I don’t like going to meetings?)

Two different things here: what and why and when you don't like going to meetings, and why meetings are different from reading broadly.

Firstly, why they're different? Because talking to people face to face is a way of getting messages tailored to you in particular. For example, Potnia going up to latest bunny hopping poster by young postdoc at Large National Meeting of Good Science

PT: Hi can you tell me about your poster?

YPD: Yes, the title of my poster is "the amygdala and bunny hopping" and I did all these things that no one has ever done before. I found that bunnies can't hop without their amygdala.

PT: That's interesting. I don't work on bunny hopping, but I do work on the amygdala and hissing and spitting in wombats. I think the amygdala is vastly under appreciated.

YPD: <getting visibly excited> Wow, you know, sometimes the bunnies would hiss and spit. I have some recordings of the amygdala when they did that. What did you find?

PT: Wombats can't hiss and spit without activating the amygdala. Its most active when they're upset, but also when they are shown a picture of a huge kangaroo about to kick their brains in. There's clearly a wombat memory issue here. I'm trying to figure out how to separate a memory from an event.

YPD: I actually had to do it too, and invented this new thingimibobbi that you just put on the brainstem and it sends memory and emotion separating signals to the amygdala.

PT: You did? That's in-fucking-credible... how do you feel about collaboration? You can have full credit and first authorship and an R01(except I don't give those out).

A tad hypothetical, but you get the idea. It can be a lot more specific about the things in which you are interested.

It's also a lot more wide reaching. A lot more opportunity for the serendipitous. When you read, you are often making decisions about what to read before you know a lot about the science or even read the abstract. How do you find the abstracts that you do read? At a meeting a lot more science stares you in the face. You are more likely to see something new and make a weird but wonderful connection. Its Chun the Unavoidable.

There is also the socialization aspect. I found this painful and horrible and awkward and painful in sixteen new ways each meeting. I'm finally old enough that there are no more shits to give about this. But you will find new ideas and new friends and new input by actually having a beer with people you don't know well. If you are worried about staying fresh, as opposed to being young and having so many ideas that they are dripping off the ends of your beard, these beers are times to Make You Think.

Finally, by talking with others you realize that your home institution is both unique and horribly the same as everywhere else. That idiot greybeard down the hall? He's just like the idiot greybeard down the hall at TheOtherMajor Uni. But, you also can see that you've got some neat and interesting people who are doing things that you didn't realize until you bumped into the Young and Bright-eyed Post Doc.

Tomorrow... I'll tackle why you don't like going to meetings and whether that doesn't help creativity.




3 responses so far

Fresh Eyes, Staying Young, and Pure Boys

Feb 23 2015 Published by under Uncategorized

When I was a young sprout ast prof, my best friends were the lady profs in chemistry. Its worth noting, for a long time, these were serial friends, as the chem dept only had one ladyprof at a time. Also at the time the physics dept (of 30-odd members) had no female faculty. The Dean took them to task, and their reply was "well, we keep trying, but there aren't any good females in the areas we need to hire". I didn't particularly like this dean, but damned if he didn't come through in this case, to wit: "well, even in this day and age of financial austerity, I will release two faculty positions, but they have to be women. no women, no hire". And damned if they didn't find two excellent female physicists, who, many years later, have out-performed their male counterparts.

At the time, one of my best friends (and Babz, wherever you are, whatever you are doing, you still have my heart), formulated a concept called "Pure Boys". The tag line was "they sleep in the forest with their manly spears". The concept is a bit worn these days (20-25-ish years later), but, in essence, content is more important than presentation, math is more important than qualitative science, that facts are more important than emotions, and the word "feel" does not belong in a laboratory. Pure boys were those who tattooed these on their manly biceps and took them to extremes.

One of the emergent concepts/ life style choices of the pure boys was "I do not go to scientific meetings because they are ego-fests and human peacocks strutting their research feathers. If people want to know what I am doing they can read my papers". I admit that I argued this one at length. I lost, mostly because pure boys never lose. But I thought of the pure boys when I read In Baby Attach Mode's latest post, When do fresh eyes expire?:

But to come back to the question in the title of this post: when do these fresh eyes expire, how do you notice they have expired and how do you keep them fresh? I guess it's difficult to realize that you've been somewhere so long that you don't realize you do the same trick every time. So how do you prevent this? How can you stay creative if you don't move to a new place every so many years?

And qaz has a great comment:

One can also stay fresh and creative by bringing new people to you. Say by mentoring new graduate students or postdocs. This is the advantage of teaching undergrads, and in developing new classes.

Going to meetings is one incredible way to stay fresh. The older I get (at the same rate as you, my little wiglets, one day per day), the less I like going to meetings. I am lazy, I like my life right now, and travel seems unpleasant. But, I do go, and sometimes something shakes up my head on the inside and one 20 minute interaction redeems the time and effort.

My goal when I go to meetings, now is to go to at least three talks that I would not necessarily chose. I used to do posters as a fly-by, finding the ones I like, etc. At the last SfN, I picked two related aisles and read every poster. Asked a question of every person. It was a small investment. It didn't change my science, but it made me think.

So, go over to IBAM and add your $.02 on staying fresh. I do not want to become an emotional raison or mummified guinea pig fetus. Neither do you.



9 responses so far

Evolutionary Idiots

Feb 23 2015 Published by under Uncategorized

In one of the clinical journals I follow, there is a monthly review of the literature from other journals. Sometimes I think the dudes who write it have blinders. Or worse. I'm trying for generous here.

The anatomy and physiology of the mouth and gut of snakes is a necessary evolutionary response to feeding demands. ... If you believe that ontogeny recapitulates phylogeny, this article is for you.

Sometimes you just get tired of educating the masses.


Cundall D, Brainerd EL, Constantino J, Deufel A, Grapski D, Kley NJ. 2012. Drinking in snakes: resolving a biomechanical puzzle. J. Exp. Zool. 317:152–172.


A Model of the Anterior Esophagus in Snakes with Functional and Developmental Implications Cundall D, Tuttman C. Close M Anat Rec 2014;297:586–98


No responses yet

Inspiration for making it through Friday afternoon: The Sun

Feb 20 2015 Published by under Uncategorized

From NASA Heliophysics

When we have dynamic pictures in our living rooms as a matter of course, this is what I want playing in mine

No responses yet

Cars as a Deadly Weapon

Feb 20 2015 Published by under Uncategorized

I'm sorry. This is A Thing for me. Cars and drinking. Cars and texting. The arrogance of not thinking about others.

Anthony DePalma wrote a short NYTimes op-ed called "Did a Text Kill My Brother". His piece is not only well-reasoned, it is reasonable. In the same place I would have been crying and screaming and wanting the head of a "young waitress at a Monmouth County country club" on a platter. Actually, I did.

In the end, this woman who quite likely killed someone walked away with "several traffic violations, including a $100 fine for texting while driving" and a 90 day suspension of her driver's license. For my family it was 9 years in jail for a chronic drunk driver.

The problem in DePalma's case was that the there was not an exact match between the time of texts and the time of the accident. 90 seconds difference.  There were eye witnesses, including a police detective, retrieved phone records and an admission that "I might have looked down".

DePalma's article is a calm call for more explicit laws about what constitutes texting while driving. I admire his reserve, his taking this tragedy and trying to make something better for people in the future.  I think this young woman who killed his brother was selfish, arrogant, and far too concerned about herself. We won't know whether she ever learned or grew from this. It would be nice to think that she did. But there are actions that make me think not: she tried to erase her texts. There was no data to suggest that she owned up to the consequences of her actions. Personal  responsibility is not necessarily a strong trait in the American public. OTH, finding hope were we can,  this story suggests that at least some people got the message.

Cars are 4000 pounds of unyielding metal. When they hit people, walking or on bicycles or even in other cars, they are moving and have significant momentum and force. We let children (and 16 year olds are children) and irresponsible adults (40 year olds with 5 DUI convictions are irresponsible) use these devices with impunity. We, as a society, argue about access to guns. We think, as in movie ratings, that sexuality is more detrimental than violence. We are only now getting to the point where car deaths are approaching gun deaths:


cars v guns


American society argues about morality in terms of letting two people in love marry because its not "Christian". But where the hell is morality of children who kill, our teaching to these children (aka driver's ed), and what we, as a society are doing about cars a lethal weapons?  Many things are very wrong in world.

5 responses so far

Older posts »