Archive for: May, 2017

Saying thank you

May 31 2017 Published by under Uncategorized

I went to see John, one of my oldest (in many senses of the word, his personal duration, our joint working duration) colleagues in Europe this week. John and other mentor and I (see here) have worked together for over 30 years. Nearly 40, depending on how you count "working together".

To say thank you to both of them, I dug up old pictures. Snapshots. Non-digital. Pictures of animals we worked with, and animals that were pets. Pictures of us in surgery, and laboring with equipment, and the blackboard planning of experiments.  We were all younger thinner and had more dark hair in those days. I scanned them in, and logged onto Shutterfly and made a book of what we've done.

The both loved it. One is Brit, one is South African, but trained in the UK, and stoic doesn't even begin to describe them. Very British Problems could have been written for them, by them., Needless to say, there were rough moments in the past, when I tended to lead with my emotions instead of my brain. But that was a long time ago, and perhaps they learned something from me, too.  They loved the book, and said so to me.

As good as it is to hear thank you, from one's students, one's trainees, and one's children, the reflection back I've gotten from my efforts to say thank you are far more gratifying.

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Ah the self-righteousness of people who have a death grip on the truth

May 30 2017 Published by under becoming an adult, Uncategorized, women

We have all read the stories about sexual predators in academia. Just those words "sexual predators" says it all. I do not dispute those. I do not even want to argue about the wisdom of getting drunk. Period. The wisdom of getting drunk, by anyone, in any situation that has remotely professional overtones is a very different kettle of fish. Nor am I remotely interested in defending or excusing these (largely) men, though I know of a distinctive case, years ago, in which a woman was the predator. There may or may not be cases of people wrongly accused, but those need to be considered on a case by case basis. We need to guard against both type I and type II errors, and recognize that controlling for one may impact on the other.

What interests me is that in one case one of the accusers is not a young person who experienced abuse but another, older, male professor not directly involved in the problem. This other professor went to great lengths to obtain evidence against the first prof, and has now written a number of editorials about how wrong the abuser was. This is a situation where someone, outside the course of events, someone not at all involved or in the line of authority for the particular abuses or alleged abuses, decides to take up finding evidence and prosecuting another, all in the name of "truth". The prosecution by Mr. A has been public, in the press, and certainly outside of anything resembling due process. It is relevant that one of the several cases did get due process, and the abuser was formally censured as guilty, though never admitting so. That particular case, as far as I can tell, had little to do with Mr. Accuser, but was considered on the merits of the individuals involved.

I laugh at this, but ironically, because I actually knew Mr. Accuser. Quite simply, he was a notorious bully in years gone by. It may not have been sexual, but he was aggressive and whether intentional or not, he did things to ruin other careers. I am sure he would argue that his actions and words were on principle, and it was the science he was attacking, not the person. But, that's not quite how the people on the receiving end saw it at the time.

Has Mr. A. done some good, any good? Possibly. Are the things he has found true? My instinct is to believe the young, or now not so young, women who have come forward. People are lauding him for "uncovering the truth". Yet, I cannot read his statements and op-eds without thinking of what I know. Mr. A is a bully. He may be cloaked in self-righteousness here, but he has done exactly this to others. All in the name of science.

Has he changed? I certainly admit the possibility that he has grown, and that he is trying to expiate his sins. But, is there any remorse in what he says, any acknowledgement of what he might have done? None that I can find in his writing. To me, it reads like Mr. A. has jumped on a bandwagon, seeing, if not glory, at least a lot of attention, his name in print, and glorified given the current political winds. In this case, he may have done some good. But what if he applied this to someone who is innocent?

To ask why someone does something is fraught with problems. We often don't know why we ourselves do something. Still, I am filled with sardonic? even caustic? mirth at watching Mr. A dance. I hope that deep down, somewhere, he knows why he has done what he has.





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Addiction isn't a moral failing

May 29 2017 Published by under Uncategorized

I have a good, nay, a great, friend who is a chemist. She does work that impacts/has relevance for the drug industry. We are argue about physiology and drug impact on physiology a lot, although neither of us exactly works in that field.

Part of what I know is from my own experience. A little less than 10 years ago I was very sick. In the hospital twice, once to figure out what was wrong (a massive rare infection in bone) and a second time to repair what the infection did (eat away significant parts of bone that were critical for my ability to... well, do anything). The pain, originally and then following surgery, was excruciating. 11 on the scale to 10. I was unable to do anything but lie there and moan.

The docs put me on Oxycodin/contin. In the hospital I had one of those button thingies, but at home I took pills. I was taking very large doses when I left the hospital the first time. The pain was under control,  so it became important to me to Get Off the Drugs before I had surgery, which was about 2 months later. I started gradually which was hard, but going ok.

One day,  about 2 weeks before the surgery, I decided to just stop. It was a mistake. My BP dropped to about 80/50 and I passed out. Luckily, my partner was there, took me to the ED, where I got an IV and a long lecture on going cold turkey. This lesson learned, after surgery, I set a schedule (I still have the little notebook where I kept track of times), and spent a few weeks watching the clock, several times each day, till I could take another pill.

The oxy did not give me a high. It did not make me feel like superperson, or anything like that. All it did was keep me from feeling the pain from the surgery, which involved significant metal implants, and transplant of bone to the metal and the place where the bone came from and the muscles that had to be cut to get to the place bone had been eaten away by infection. Yeah, I was a mess.

I remember sitting there, looking at my notebook, wanting a pill, hoping I got the time wrong, hoping that I could take another pill, realizing, no, I could not. I would go and walk for 2-3 minutes, which is all I could do, and sit back down. By my own, pre-illness standards, I would stop and think how pathetic I was. And then I'd look at the clock again.

But I was motivated. At the time, I had a job loved (albeit with the chair from hell), I had a partner who loved me. I did not have financial worries, or children to take care of.  I had great friends. I had lots of stuff that made life very worthwhile for me, and very little about which I was worried that was urgent. I was motivated. So I could wait, and stare down the clock, and took a pill with relief on the schedule of reduction. It did not bring me above baseline, but it erased the cravings, it erased the pain.

As time went on the pain receded, and the time between craving became longer. I could walk for 20 minutes, and get myself a glass of water without shaking like someone with late Parkinson's.  I rehabbed myself, and it is without question, one of the hardest things I have ever done.

How hard? Harder than writing a thesis, getting NIH funded, training for the swim leg of a triathalon, planning a wedding, planning a funeral, having a baby. But those things? They are all positive, improvement-things. They are things that when done, there is an accomplishment. Healing from surgery, from the drugs, etc? That only brought me back to baseline, and honestly, it was a baseline that hasn't ever been quite where I was before this happened.

(btw- no one ever  figured out how I got the infection. probably walking through the hospital. but it didn't really matter in the end)

So, when the self-righteous talk about "getting off drugs", especially with respect to the current pain-killer crisis, I want to ask if they've ever been there. Do you know what it feels like to look at a clock, waiting to take a pill to end the need? Have you ever had pain that keeps you from thinking, and then the drugs to make thinking possible again, knowing that those drugs are really not very good for you?

My wonderful friend talks about addiction to food, to sugar, to salt. And I say: that's not the same thing at all. Of course we are addicted to food: we die without it. But denying oneself sugar can be hard, and it can make you grumpy and you can feel the need, the desire, and the craving for it. But it is not the same thing at all as what Oxycontin feels like. And certainly, that craving and withdrawal are not the same for the rest of your (non-mind) body.

And for those people struggling with addiction: I had everything going for me when I stopped. I can imagine if one of those things wasn't in place: the partner, the job, the security of belief that my research was important (delusional as that may have been), let alone the security of knowing I could pay my bills, that I had good health insurance, a roof over my head. If any one of those things was not there, I might not have made it clean.

I had a big bottle of pills, that I kept for years, just in case the pain came back. I was never ever tempted to take. It's not because I object to feeling good. I drink wine, and beer, and a cocktail now and then. And it's not because I don't hurt. I do hurt, it's just not like it was then. The oxycontin didn't make me feel good. In the beginning it kept the pain at bay, and then it didn't just keep me from feeling bad, I took the pills because I had to.

The answer the "addiction crisis" right now may partly lie in restricting access to the drugs, more reasoned and thoughtful scrips to people in pain. It certainly does not lie in stricter prison sentences, which will only give us  very ill people going through withdrawal and possibly dying in jail. It lies in looking at the lives that people in pain live, and figuring out how to give them the reasons for getting off the medicine. It means figuring  how to deal with that craving that really has nothing to do with getting high, and everything to do with the cold hard reality of the physical legacy of pain medication.

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When students come seeking help

May 27 2017 Published by under Uncategorized

Yesterday a student from the medical class I teach came to me looking for advice. I think mine was the only open door on the hallway. She certainly had not sought me out before.

I knew her because she had failed first year Med School (M1), and squeaked by the in the class I teach 2nd year. As is true of many med school lab courses, its big (150 students, of which about 5 are PhDs, andthere are  7 or 8 people in lab, and a couple of us who lecture, etc), the grading is all computerized, pretty much, so there is almost no subjective assessment, and the bit of grading we do by hand, practical exams, is by IDnumber. So, its not like I have much say in pass or fail. And I don't sit on the committee that hears student appeals for grades. So there is nothing much I can do for a student with grade issues.

It seems this woman has failed her first year again. She had failed two basic science classes (Ithink it had been three the first time through). And she wanted advice. Except she really didn't. She wanted to complain. I kept my best sympathetic smile, plastered on my face, almost till the end.

Firstly, she said that she couldn't believe she failed because "she had really mastered the material. In my study group, you know, I always knew the answer". Secondly "this school is in the middle of nowhere and I had no support during the year, and there was nothing to do on the weekends". And, thirdly, "I was part of this program [one we have to help at risk students, in conjunction with a local college, because this university has no undergraduate programs at all] and it required me to drive to go to work there and I wasted time each week driving when I could have been studying".

Smile still plastered on my face. I didn't mention that two and three on her list seemed contradictory. I did say that failing the exams more than once suggested that perhaps she hadn't mastered the material. She insisted that she had, and that she "just couldn't take exams".

I don't want to debate, here, now, whether board exams for medicine are good or bad, whether we select the best people to be physicians, etc. Whether it is worth changing how we assess medical students, whether it is worth my time to work on changing that is another argument. Certainly this woman isn't going to be in a position to do anything about it.

I did ask her how she thought she could pass the boards (Step I, the exam med students take end year 2/ beginning year 3), if she couldn't pass class exams, no matter how much she had "mastered the material". She returned to point 2, "if I only had support I would have done better".

Then she said: I really believe that if someone wants something badly enough, and works at it hard enough, they can do it. I wanted to say: Then, not once, but twice, you either didn't want it enough, or you didn't work hard enough, since you didn't do it. I did say: You know, I was an athlete in high school and in college. But it was very clear to me, at the end of my 20s, early 30s, (and really much earlier) that no matter how hard I worked, I would never make it to the Olympics. (of course it was obvious much earlier than that).

She answered: Oh, that's different. I really want to be a physician. I know I can be a very good doctor. I am going to apply to go somewhere else.

Is it that different? I don't think so. I think part of what separates good amateurs from professional athletes is a kind of physical genius, which begs the whole question of the separation of physical and mental, since it is the brain that controls our motor systems (and I am perpetually irritated by the words "muscle memory". Muscles have no memory. They are stupid mechanical engines following signals from the nervous system). But its hard to acknowledge that your brain may not work in the right kind of way to pass medical school.

After about 20 minutes of this, I said (still trying to be gentle), is there anything I can do for you?

There was not.

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What does it mean to write "by the sentence"

May 24 2017 Published by under Uncategorized

Writing by the sentence is kinda like buying by the piece. You may need a whole lot of something, but you pick each individual one that you want.

Writing by the sentence means crafting each sentence. It means making sure it comes from the one before and leads to the one after. It means, for a grant proposal that each sentence works, does what it needs to, and not much more. It means there are No. Wasted. Words. If anything irritates me its having 2-3 sentences in a row that say the same thing.

This doesn't mean that the same information shouldn't show up in multiple places. When I had the consultant who got me funded on a proposal (here's the post based on his letter of support for me), I mentioned his collaboration in several places (the significance, at least two places in Research Design, and certainly in Vert Animals, as that was his expertise).

Writing by the sentence is one way to achieve making every sentence work hard for you. In fact, making every word work for you. The subject and the predicate need to convey information and not be place holders.

One of the problems of writing by the sentence is that you get bogged down. You get lost. You lose track of the forest, let alone the ecosystem. That's why Darwin discovered outlines. Do the outline first, and then fill in the sentences.

There is much more to say on this, especially examples. But! too many things happening this morning.

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Sometimes the words just find you: Advice edition

May 23 2017 Published by under Uncategorized

From this morning's tweets:

except for the typo:

"its ass" not "it's ass"

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What Trump doesn't know: Yad Vashem edition

May 23 2017 Published by under Uncategorized


President Donald Trump [was scheduled] briefly visit Yad Vashem

Image result for yad vashem children's memorial jerusalem

Children's memorial

For those who don't know,Yad Vashem is the Holocaust memorial in Jerusalem. It is a very powerful place.

Thematic and Chronological Narrative

Remembering the lost


I noticed this report from the Forward. Like is not the right word, but :

The Jerusalem Post took an uncharacteristic snarky approach and produced a video demonstrating what Trump will be able to cover in 15 minutes at the 45-acre complex. The paper quoted Israeli officials saying that an hour and a half is the “bare minimum” needed for a visit to the museum.

I visited in Yad Vashem. Recently. It shook me to my core. I could write about Auschwitz  and about my thoughts about Jews in Eastern Europe during the Shoah (search my blog for the tag "holocaust").

I could not write about Yad Vashem. Even now, one of things I remember is that my cousin came up to me and said something, and I thought or said "but we've only been here for an hour" and she said "we've been here for over four hours".

Yad Vashem was a place I did not, where one does not, know time. Evidently Trump is immune to not knowing time, no matter what pious and sanctimonious words he mouths.

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Moving lab

May 22 2017 Published by under Uncategorized

There are lots of issues with moving one's lab. I've done more than once, and each time I have sworn it will be The Last Time for This Kind of Nonsense.

I was reminded of one of the Big Issues by this post from ragamuffinphd about the problems she's had and is having as the postdoc in a moving lab. Her situation has been ugly, although she has found some support and help from other women at her current institution.

PI's move. Ambitious PI's often move a lot. I've moved more than most, it seems. I started to write a long discussion of the moves, which included to Australia, for a year's sabbatical. Then I realized it would be excruciatingly boring to anyone but me. And besides, its not the point of this post. What I do want to talk about is what happened to my trainees, and how I tried to work on that.

I tried to time each move so students were graduating, postdocs were ready to move on, or projects were coming to a close. Usually it was ok, but sometimes it just didn't work that well. Everyone is the hero of their own story. And I suspect there are trainees who paint me as very evil indeed for when I moved. I did my best, and there were times it just wasn't good enough in the eyes of some people. That is going to happen. But I did learn a few things, things that perhaps might be useful to others.

For PI's moving: do not underestimate the time you will lose due to the move. Even with the best of intentions, a superb team moving with you and great support at the other end, it will impact the flow of data collection, analysis, publication and grant submission. Factor this into your life. But, also, pay attention to the trainees. Talk to them as soon as you can, be honest, and give them as many options as you can. And understand that they may not do what you want. This is called life. Remember this will be true of your children, too. Your goal is not to be liked by your trainees, but to do the best you can by them and their professional growth.

For Trainees: understand that your PI has concerns besides you. Good PI's will do their best for you, but what motivates them, what pushes them may have very little to do with you. They may care about you, but their spouse, their children and most likely their career are all going to come before you in the world. This does not necessarily make them a bad PI or mentor. It might, but, it might not. Just recognize that this is the way of the world. This is akin to realizing that your parents have a life outside of you, and sometimes their priorities will not coincide with yours.

So what to do when your mentor or PI comes and says: "hey, I'm leaving".  Firstly, determine if they want you to go with them. Secondly determine if you want to go with them. The answers to these are not obvious. I suspect the most important piece of advice is DO NOT express an opinion in the immediate aftermath of the news. Sit down and think about what it means. Mentally follow the steps through the implications of the changes:  what does moving mean to you, to your family, to your expenses? One's first reaction may be emotional, but emotion is not going to serve you well in this situation.

Nextly, do not panic. It may feel like the end of the world, but it's not. As one of my oldest friends is fond of saying: it's an opportunity for growth, but it's time for someone else to have the opportunities. Seriously, figure out what do you want. What is important to you. And those are considerations that are really independent of what your mentor is doing. You will recover. You will find your path. Make a list of the important q's to ask your mentor. As with other interactions, going in to a meeting prepared, with a list, as opposed to going in emotionally charged, can make a huge difference to the ultimate outcome. Things to ask: when will this happen? if I move, does my (salary, position, title, responsibilities) change? Are there any resources ($$) to help me move? Will my lab/office stuff get moved with the larger lab/office stuff? If I don't go with you, what happens? How long can you support me? I am sure there are more, but this is off the top of my head.

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Reply to Ola: what does an ethical person do about the number of trainees?

May 17 2017 Published by under Uncategorized

Ola had a good comment, worthy of a good reply:

Personally I've worked with and come through labs that churned out 30, 40, 50 trainees in the career arc of the PI. I know for sure I don't want that - it's unsustainable, not to mention ethically problematic. However, at the other end of the scale, since becoming a PI 13 years ago I've trained 3 PhDs so far and have 2 more graduating in the next year. Should I stop at "replacing myself" those 5 times, and just not take any more students until I retire in 15 years? The question: what IS a good (ethical, sustainable) number of PhD trainees that a bioscience PI can reasonably expect to have in their lab' during a typical career? Is 5 too many? How about 25?

To Ola, I say: I don't have a good answer for you.

It's really a tragedy of the commons problem. You and I can limit who we train, but if the Big Labs keep churning them out, will our trainees get lost in the shuffle? Or can we argue that we are K-strategists (as opposed to r-) and that we give more to fewer trainees? (and if you know r/K theory, and want a good chortle, google it and "evolutionary psychology" and read some... well... bizarro interpretations)

For years, I've only taken clinical/PhD students, MDs/DMDs/PTs for whom there is more employment flexibility. But mostly I take only postdocs, with the idea that I can add some value to those people: not just marking time till the get job, but give them additional skills/background/credentials. But if a really good basic science type came along, interested in what I do? That would be a hard call.

People in the comments have complained that postdocs are too expensive. This is true if grad students are subsidized by your department, as many are. And if you have to pay your postdoc a reasonable wage, it will be more so. If students aren't subsidized or postdocs are subsidized, then it comes out closer to the same, throwing tuition in with salary for students.

It is worth remembering that training grants can support postdocs (I was the co-PI on one for years). Many also support residents to do a year of research or a fellowship in the middle of residency. This may align in clinical departments, and people working at the edge of basic/clinical research. If institutions realize that grad student stipend + tuition is in the same ballpark as a PD, then that might begin to change. This is part of the education of the "carpet-people" that needs to happen.

So the answer in part is: you need to do what that with which you are comfortable. You need to remember that your trainees are people, who require that you provide them with not just scientific training, but the professionalism necessary to succeed. You need to be able to sleep at night, knowing that you did what is right even when those around you have no trouble justifying dreadful behavior. And, you need to survive. Just be careful of justifying behavior on the basis of survival. On that path lies madness.


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More on not enough faculty positions

May 16 2017 Published by under Uncategorized

Let's do a little math, before I start preaching.

Firstly, let's think about new jobs. These are back of the envelope calculations. Order of magnitude of the problem. For the purposes of discussion.

There are ~180 medical schools in the US. As for biology departments, according to Wikipedia:

As of 2012, the latest figures available in 2015, the US has a total of 4,726 Title IV-eligible, degree-granting institutions: 3,026 4-year institutions and 1,700 2-year institutions.

Now some of these schools have more than one "biology" department. Certainly medical schools have multiple departments that hire PhD's. But let's just say 5000 departments? 10000?

How many PhDs in "life sciences"? Over 8000 a year. Other sources (NSF) have other, even higher numbers: ~12,000.

So the number of PhDs each year, in life sciences, is about equal or greater than the number of departments. This makes sense: most of those (non-SLAC, non-CC) departments have multiple faculty, churning out PhDs. Even if every single department hired one more faculty person, that would still have an excess of many, many  PhDs.

Let's say that again, there are, roughly, each year, as many PhDs generated as there are departments that could hire these faculty.

I know people are waiting for "Boomers to retire", but I want to remind you that, again, that the youngest boomers are only 52. People do not retire at 52. Or 55. Or even 60. I'm mid-boomer, 62. When I talked to my chair about being on a 4-6 year retirement trajectory, he was shocked. I was surprised he was shocked. (but for me, damn there are other things I want to do).

I know people argue all the time about "alternative careers". I wrote about this years ago, when I started blogging with Mama Isis (and can't find the post). But no one starts a PhD program thinking "Oh, this is a good path to an alternative career".

Back to the problem. There are many reasons we, the mentors of academia, train people. Some of them are what economists would call "market pressures". We need trainees to survive. We need trainees to generate data to finish projects, write papers, get grants, and, well, survive. Some of us (yes, we all know these dudes, although they are not always dudes) who need trainees because their egos can't stand a small lab. They are competing for new students.

So what to do?

I think senior people need to make a commitment to finding trainees/support/help that does not involve bringing more mouths to the trough. I think senior people need to make a commitment to supporting the existing junior faculty in ways that do not require them to have enormous labs to succeed. This, in fact, will require education at the decanal level and above. NIH is the cash cow of many schools. Everyone needs to commit to education about NIH and the need to support research in the US, let alone elsewhere in the world.

Yet, expanding NIH is only kicking the can down the road. Supporting more trainees now, giving jobs to all the PhDs now will just mean this crisis will come back either come back in 10 years, if money is jolted into the system now, and current PhDs get funded, get jobs,  and start training an even larger next generation. Or if money is dribbled in, there will just be the continual pain that we see now.

It is not the scheme is unsustainable: it's just a matter of where the selection and sorting (in the evolutionary sense) occur in the life history of a scientist. Although my GenX friends (and yes, I have one or two who do not perceive me as the devil incarnate) will be skeptical, this was an issue debated as I was finishing my PhD in the early-80s. There weren't a lot of jobs to go around then, even to people (and yes, you may laugh heartily here), who perceived themselves as the cream of the crop (I didn't, but that had more to do with my identity at the time). Academia had undergone an expansion in the 60s, and those people were the Boomers of the time. They were hanging on to jobs (in our view) and didn't care that they were training more people than there were jobs. Places weren't hiring (imagine that). I remember long discussion about whether it was better to restrict entry into grad school, and let selection occur earlier, or to expand postdocs (in ecology/evolution/organismic science PD's were relatively rare at the time) and push selection down the road.  In those days (and to some extent now), in those fields, grad students were PI's, and lab or mentor affiliation was a weak tie, and certainly not necessary for the faculty, except as ego-props. The numbers of grad student admissions was more fluid, and often based on teaching assistant needs. I don't remember what I thought, except that I was tremendously relieved to get a postdoc.

But back to what to do? Please do not think that retiring the boomers will change the situation. Do you not think that the GenXers who do get jobs will see their survival as justification for doing what they need to do to survive? Do you not think the millennials who make it will turn into the boomers of 30 years hence? The boomers I knew back then were good people who would never ever ever abuse trainees, or promise things, or even inadvertently be part of the problem. We are all destined to become our parents, our mentors, and partly what we despised when we were young.

The solution? For me, right now, is to be aware, and work towards a change. Commit yourself to things be different, better. Reach out that hand, dammit.


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