Archive for the 'Uncategorized' category

Compliance City Blues: Dealing with the IACUC or IRB or OSHA

Aug 07 2017 Published by under Uncategorized

When I was a wee thing, compliance issues consisted of not blowing up the lab (too often). Or not using extension cords as clotheslines for hanging up wet X-rays to dry ("really, Dr. Theron, it wasn't like it was plugged in or anything"). I can't speak to what IRB's were like, as I wasn't doing any human research in those distant days. But we all have heard of the horrible excesses and unethical goings on of the times. If you haven't read Rebecca Skloot's excellent book The Immortal Life of Henrietta Lacks  you should.

For those of us that work with animals, we all know and love and work with, the Institutional Animal Care and Use Committees that govern our research lives. I lived through the no IACUC through ineffective IACUC through the regulated situation in which we do our work today. I have sat on my University's IACUC in the past, and been the stats person for the IACUC. It was in no sense fun. Even free lunch did not help.

My rule: do not offend the IACUC. Follow the rules. yes they will seem arbitrary. Yes you will be irritated and forced to compromise things that, in your perception, are Best for The Science.

I know plenty of people who bend the rules. But one of the things that I have learned is that by and large IACUC rules are not good ones to be bent.  I know people who live by "tis better to ask for forgiveness than permission". IME, this seldom works with IACUC's and their escalating scales of penalties.  Some Big Dogs I know are beyond rules. The worst, when caught, blame people under them, oblivious to the culture they have created. Some PI's are quite compulsive and follow everything. I had a colleague whose benchtop had outlines in masking tape, with a number, of where every piece of equipment needed to be, and a cross-indexed master list of places and equipment. In the days before personal computers, this was a hand-typed list.

In my lab, IACUC, IRB and compliance are unbendable, rules which cannot be bent. I've got two lines of justification for this: ethical and practical. Practical involves the level of problems that occur when one is caught breaking rules. These problems can grow into a moratorium on doing research with animals, a situation which can be devastating to all of the people in the lab. The decisions on which rules to bend are essentially ethical ones. None of us would do something that we perceived as "hurting the animals". And even if this instance of breaking the rules wouldn't hurt the animal, another instance might. The trouble with rules is that you can't plan for every instance.

I have found that the temptations to bend the rules usually stem from poor planning. Something MUST be done, or the experiments will fail, and the means to do so are not within the protocol (people, drugs, etc). The other category of bending comes from laziness or obliviousness, though it is seldom seen that way: I just don't want to get out of bed to go check on the animals. Or I am doing something else and plain forgot. These situations can be addressed with more planning, and taking working with animals more seriously.

Working with non-rodents, large animals, expensive animals tends to encourage the planning necessary to avoid these problems. It's harder to persuade people, trainees, collaborators, that mice deserve the same respect as dogs. This is part of the PI's job. The time a PI invests in laying down the no-nonsense, we are serious about protocol compliance, and I expect it from everyone, is well worth it.

The IACUC and animal facility at my new place is wonderful. They are reasonable about violations (yes, my lab had one, yes we, me and the trainee, learned from the experience). But I've been places where it's not quite that way. I assure you, finding out that your IACUC has a sadistic streak is not anything anyone wants to do.

 

 

 

 

 

 

 

5 responses so far

Quote of the Day: Miscellaneous thoughts on government

Aug 07 2017 Published by under Uncategorized

Ninety eight percent of the adults in this country are decent, hardworking, honest Americans. It's the other lousy two percent that get all the publicity. But then, we elected them. -Lily Tomlin
Loyalty to the Nation all the time, loyalty to the Government when it deserves it. -Mark Twain
Nationalism is an infantile disease. It is the measles of mankind. -Albert Einstein
And, as is true of measles, epidemics can be deadly.
It was once said that the moral test of government is how that government treats those who are in the dawn of life, the children; those who are in the twilight of life, the elderly; and those who are in the shadows of life, the sick, the needy and the handicapped. -Hubert H. Humphrey

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Writing paper reviews

Aug 04 2017 Published by under Uncategorized

I think the best advice I've ever given a trainee about writing reviews of other people's scientific papers is: don't take too much time on it. I know that will seem like heresy around here, and worse, feeding into reviewer 3 syndrome. BUT! if you start from the assumption of good-heart, open mind and commitment to helping others, then this advice makes sense.

My tendency and that of my bestest trainees is to spend too much time, to give too much, to bleed oneself dry. Indeed, we are more than committed, we are dedicated to helping others. And writing a good review, full of suggestions, showing where a paper works and where it doesn't is one of the best and most important ways of helping. I do not doubt that.

Nor am I suggesting that anyone should whip through a paper and pull from the folder of stock critiques ("methods are too detailed" "can't follow the discussion"). One needs to provide useful and thoughtful advice to the authors.

But one can piss one's life away helping others, writing out the details of what one would have done or said to make this better. As in all too many things there is a balance.

I just got back a paper to review for the third time. The first time I did not follow my advice. The topic and data were Important. The potential To Make A Difference was there. But, the paper was so opaque, so obscure, I could not follow what was going on. There writer was a relatively senior person and a physician and actually knows what research is. Although the reviews for this journal are double-blind, it was glaringly clear who wrote this (heck the acknowledgement of IRB approval had initials of PI attached to it).

What was wrong? New acronyms for existing things. Complex, convoluted statistics when simple ones would be appropriate. New meta-variables, for example calculating a measure of heart function based on rate and intensity and what you ate for breakfast when just testing heart-rate would have sufficed. Writing that read like it was originally in English, translated to German with Google and then back to English, so that the verbs at the end of sentences all piled up were. Figures that I coldn't see the points or determine what the variation intervals were, let alone whether the were SD, SE, IQR or something entierely different. I couldn't really tell what the conclusions were because all the other stuff got in the way. I also had problems with the scientific justification and context and, in NIH-speak, I could not figure out the premise of the work. It wasn't even that they only cited their own stuff, it was that there was no acknowledgement of other perspectives, other work that might impact on how they thought about these results.

The first review pointed out each thing, explaining why it kept me from understanding the paper. The review was too long and took too much of my time. But the letter that went out from the editor suggested that the comments were valid and that the authors needed to address them.

I got a revision back that was the height of absurdity. It said "thank you to reviewer #2 for the insightful comments. We have made the changes requested". Then it went through every comment and argued with me about it. Some of their replies made sense and some of them did not. But they changed nothing that I suggested, except redrafting the figures. That made my second review easier. I went through and pointed out the same problems. And said that since I had now read the paper several times, and was still unsure about what their specific results were, and what they thought it meant, that I had to respectfully suggest that reconsider my comments rather than just arguing with them.

The third version came back changed, with nearly everything much much better. One thing they did not do, though. My last review:

I appreciate the authors' continued engagement in my comments. The change in terminology facilitates the reading of the manuscript. The changes in analysis and presentation of results are acceptable and make the manuscript much easier to follow.

My only remaining concern concerns citations & interaction with the literature. The response to the review contains 12 citations all of which are from one group. There are MANY more perspectives as to what is a ____ and these authors seem reluctant to acknowledge the work of people outside of this one group, including the work in the [related] literature which is highly relevant to this paper, since the discussion claims implications to that field. This is not just a citation problem, it is an understanding of what other work is being done. Again, the problem is NOT so much the lack of other citations, it is the lack of understanding the literature outside a very small circle. The two groups cited here are not the only workers of ______ function.

However, this disagreement falls into the realm of scientific discourse, should not prevent publication.

I do not want to ever read this paper again.

 

2 responses so far

My heart, it dies a little bit with each of these stories

Aug 03 2017 Published by under Uncategorized

I just got this email from a wonderful friend (with a few edits to preserve anon-ity stuff and combine emails):

Hey Potnia!
I hope you are doing well!  I have an ulterior motive for emailing you.
So, I have a friend, Zeke, who is trans, and on the autism spectrum, and has various physical and mental disabilities. Xe is <...doing things to help xe-self...>  but that process can take anywhere from a few months to over a year. In the meantime, xe is only able to work part-time, and as such, is having trouble covering rent, food, and medical bills. Xyr family is not supportive, and xe is really struggling right now. 
That's why I'm reaching out to my queerfam and my honorary-queerfam, to ask if you would consider donating to help keep a roof over Zeke's head and food on xyr plate. If enough of us can spare a few bucks, we can keep a fellow queer safe and fed until xyr <stuff and options comes through>. I know money is tight all over so ZERO judgement if you can't chip in.
Xe is trying really hard to make everything work but like... just, can't. 
Thanks so much for considering it! <3I
-Avv
Avv is a good friend who has gone through much to be where xe is today. I've known too many people like this in my life. People who don't fit in, with mental and physical and gender challenges, rejected by nearly everyone. A few bucks? Of course.

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Some days people are just nice to you

Aug 02 2017 Published by under Uncategorized

I got a paper submitted yesterday. It felt good, like the relief right after you throw up. I've always felt that nausea is a great metaphor for many many things in life. You feel bad. You feel worse. You feel like you're going to die. You worry that you might not die. And then, behold: it is gone.

This paper had a new  co-author, involved in one part of the work. Here's what he wrote to me when I sent him the draft that was somewhere between "you feel worse" and "you feel like you're going to die":

                I have attached the manuscript with some very minor suggestions.  Very nice and I am honored to be a part.  You have a gift for writing. Be thankful.  That is something I lack, which was made even more apparent in a talk with a previous reviewer of our fluid flow paper.  She is a good friend for my sister at U Chicago and certainly helped to have her open up.  Her comments indicated her issues were not with the methods or data, or even the interpretations.  Instead, I/we had not adequately crafted a compelling story.  Creative writing (not to be confused with fiction) is not my forte. 

Ho ho ho. It did not feel like gift whilst I was in process. What I remember is the step between feeling like dying and feeling like you might not die.

This comment was from the person who wrote this letter. (note if you want to know about writing letters, I've got lots of posts, and you can go down this rabbit hole here and here). He writes beautifully, but can't see it. My job is to remind that he does. He is every bit as wonderful as a collaborator as his initial letter for my proposal suggested he might be.

New Co-Author's point is good. One crafts a compelling story. Writing creatively is one path to telling that story. If you write a paper, or give a talk, and overtly or implicitly say "this is another silly/stupid/trivial thing I did", no one will care. If your work is fun to you, exciting to you, something you love, let that come out. One needs the basics: a question or hypothesis or point, a solid design, data that answer the question/hypothesis/point in a paper or talk or grant proposal. But getting someone to care, getting someone to be the advocate for you, means getting their enthusiasm up and out of bed. Enthusiasm doesn't have to be loud, it can be quiet and strong. But its what will get you published, funded and invited to the fun parties.

So how does one get good at writing like this? The same way one gets to Carnegie Hall: practice, practice, practice.

3 responses so far

quote of the day: go outside today edition

Aug 02 2017 Published by under Uncategorized

The idea of wilderness needs no defense, it only needs defenders. 

and

May your trails be crooked, winding, lonesome, dangerous, leading to the most amazing view. May your mountains rise into and above the clouds. -- Edward Abbey

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When a trainee is ready to move on, also known as exceeding expectations

Aug 01 2017 Published by under Uncategorized

I have frequently written about problems with trainees and what to do about Problem Trainees.

But there is a flip side that may be discussed less: what to do with the Really Really Good trainees.

The temptation to hold on to a good trainee is large. I've seen it, and tried to be aware when I've got such inclinations. A good trainee moves your lab forward. A good trainee challenges your thinking. On good days you see it right away. On bad days you struggle not to shut them down when they challenge you.

I've had some incredible trainees. It doesn't take much of a push to remember ones from even 25 years ago: their names are on some of my favorite papers. Papers I love because they aren't in the standard journals. They're in other journals because they had a bit of this and a bit of that, and a context that made the work we did (and it was surely a we) interesting to more than the usual suspects.

So how do you know? It's not always an off/on lightbulb. There is probably a range of time that qualifies as "ready to go". If you're doing an IDP (also see here and here), it should be very clear that they have checked off boxes that are (and should be) more than boxes to be checked. They have 2, 3, 6 papers (number being a function of project, years-post-college, and how much they knew when they started with you).

But one of the things that really makes me know that a postdoc in particular, but can also be a grad student, is ready to go, is when they are doing the mentoring on their own. They are working with the college students or the med students or the beginning grad students in ways that you know are Good and Right. The mentoring may not be exactly what you would do, or what I would do. They are different people. It is a Good Sign when a trainee does something different from you. Neither you nor I want to turn out Mini-mes, the world certainly has enough of me's in it. But when your trainees have figured out how to do the job, whatever it is, science, mentoring, teaching, with their own skills and mindset, then you have succeeded. You want to teach the algorithm, the language, not the answer.

I am not just proud of my trainee's first authored papers. One of my current trainees, who is well ready to run their own lab, is last author on a fairly important paper (recently totally accepted, and coming out in e-version Very Soon). Last authored because not only did said trainee do the work the science to get the paper out, the trainee got the first-author-trainee to produce a beautiful paper. I am buried somewhere in the middle of the author list. And damn, it feels better than the last authorship would.

 

One response so far

Hard things I have to do

Jul 31 2017 Published by under Uncategorized

I know that some of the posts that you, my cherished readers, like best are those that tell stories. It's a human trait, we like our morality lessons (I almost said lesions, but that's what's on my mind) in palatable myths.

But this post is about things not said. And therefore not conveyed in a story with pseudonyms and hypotheticals.

It is a hard thing not to say things. There are a couple of points and people and incidents that right now, in my PI life, I want to address. There are a couple of specific people I'd like to sit down with and give them whatfor. But I know. I know from the painful lessons of past experience that It Will Do No, None, Nada, Bupkis good or utility, to actually talk to these people or address these issues. It will not move any goal forward. It will not make life easier for any third person involved. It will not change the direction of the University, College, Department or Interest Group. It will not be the first flag planted in the war. Talking would only make life harder.

So I keep my mouth shut. None of these things are a hill worth dying for. Some of these people are short-termers and won't be in my purview in the future. Some of these people I will have to work with tomorrow, next week, next month, over the next five years. So be it.

and ps. this is not a subtle message to those people or a passive-aggressive way of talking to them (they don't read this blog and probably don't know what a blog is). Because the flip side of not talking, is when you do need to talk, and do need to say something, you go up and say  it to the person. Directly.

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Skills a PI needs or a snowflake's chance in hell

Jul 28 2017 Published by under Uncategorized

H/T to Adam Kucharski

pointing to an article about training in management, titled "Not all PhD supervisors are natural mentors – some need training".

So let's look at a bunch of things.

Firstly, Adam is right. You may think you don't need that "leadership training", because you're not going to run for public office. But you do. There will be at least something worthwhile in terms of dealing with problematic students, techs, trainees and most likely Chairs-from-Hell. In the world of cost/benefit decisions, the immediate benefit may not seem so large, but it can be. It sure beats the school of hard knocks.

But secondly. Oye. This article was not going to convince me that I should get training, let alone work towards being a better human being. The sub-headline on the article is:

My supervisor’s high standards and cold manner made me feel inadequate. If only he had been taught how to encourage me.

WTF? Somehow the mentor is responsible for making someone feel inadequate? This is how legends of snowflakes rise. Reading on, the first part of the article is a litany of how bad the trainee felt. All the horrible and terrible and discouraging things that happened to her that were the mentor's fault. There was not one whit of self-introspection in the article.

Yes, it would be lovely if we all could be Mr. Rogers, Captain Kangeroo, or some wonderful grandmotherly figure (i.e., true, real life course evaluation: Dr. Theron is insufficiently nurturing to be a good teacher". That's not real life. But lots of us are Tony Stark, but without the money and nifty electronic things.

Yes, I do think its worthwhile shopping around for a good mentor. Let me put the list from that post here:

  • Look for individuals as mentors who enjoy their roles and responsibilities
  • Look for individuals as your mentors who are experienced yet willing to listen to your concerns and needs
  • Look for individual mentors with whom you can build a relationship on trust, mutual respect and confidentiality
  • Consider any personal and/or professional biases that they may bring to your mentoring relationship

But, in The Guardian article, the writer put the blame for failure on someone else's (lack of) people skills. Yeah, the mentor was a jerk. No, he wasn't encouraging, and perhaps did cross the line "between constructive criticism and cruelty". Yes, it would be great if every mentor was a psychiatrist and counselor and Buddhist spiritual guide. But they're not. They are human beings with the whole range of problems that human beings bring to the table that is human interactions.

The article concludes with the suggestion that

Academic institutions should develop and require mentorship training for staff at all levels, not just those who are early in their careers.

Let me suggest that this would have exactly no influence on the jerk who was so discouraging. Let me suggest that senior people are pretty damn resentful of being required to take training. Let me suggest that this is the suggestion of someone who is not mentoring or supervising or more importantly swimming as hard as they can to stay afloat in the competitive world of academia. This doesn't mean that such training wouldn't have the potential to help. Go see the first para of this post. But by and large, the BSD's of this world who might need this, if they went, which is unlikely to start with, would go with a phone or laptop full of Other Things To Do.  Required touchy feely seminars and workshops are not the way to change the system.

So grow up. If you want to do science, take some responsibility for finding the people who can help. The writer says she went looking for help and everyone turned her down. Really? She could not find a single person to help mentor her? A single friend, even outside of academia to help her with the confidence issues? I do not have much faith that this person will last long in any endevour. Find what you need. No one is going to hand it to you on a silver platter.

26 responses so far

My knee, or the slings and arrows of time

Jul 28 2017 Published by under Uncategorized

From the report on my knee:

Severe lateral and minimal medial femorotibial joint space narrowing with subchondral sclerosis and exuberant osteophyte formation.

Exuberant my ass.

Ah you runners, beware. Time flies like an arrow. Fruit flies like a banana.

One response so far

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