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December (3)

The first step is the most important
Thursday, December 30, 2010

Have we really found a stem cell cure for HIV?
Wednesday, December 15, 2010

This paper saved my graduate career
Tuesday, December 14, 2010
November (3)

Valium or Sex: How do you like your science promotion
Tuesday, November 23, 2010

A wedding pic.
Tuesday, November 16, 2010

To rule by terror
Tuesday, November 9, 2010
October (2)September (5)

Hiccupping Hubris
Wednesday, September 22, 2010

A death in the family :(
Monday, September 20, 2010

The new lab fish!
Friday, September 10, 2010

What I wish I knew...Before applying to graduate school
Tuesday, September 7, 2010

Stopping viruses by targeting human proteins
Tuesday, September 7, 2010
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Brian Krueger, PhD
Columbia University Medical Center
New York NY USA

Brian Krueger is the owner, creator and coder of LabSpaces by night and Next Generation Sequencer by day. He is currently the Director of Genomic Analysis and Technical Operations for the Institute for Genomic Medicine at Columbia University Medical Center. In his blog you will find articles about technology, molecular biology, and editorial comments on the current state of science on the internet.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Recent Comments

Jaeson, that's not true at most places.  Top tier, sure, but 1100+ should get you past the first filter of most PhD programs in the sciences. . . .Read More
Jun 24, 2013, 8:39am

All I can say is that GRE's really do matter at the University of California....I had amazing grades, as well as a Master's degree with stellar grades, government scholarships, publication, confere. . .Read More
Jun 19, 2013, 11:00pm

Hi Brian, I am certainly interested in both continuity and accuracy of PacBio sequencing. However, I no longer fear the 15% error rate like I first did, because we have more-or-less worked . . .Read More
Feb 26, 2013, 12:13am

Great stuff Jeremy!  You bring up good points about gaps and bioinformatics.  Despite the advances in technology, there is a lot of extra work that goes into assembling a de novo genome on the ba. . .Read More
Feb 25, 2013, 10:20am

Brian,I don't know why shatz doesn't appear to be concerned about the accuracy of Pacbio for plant applications. You would have to ask him. We operate in different spaces- shatz is concerned a. . .Read More
Feb 25, 2013, 8:01am
Tuesday, November 9, 2010

When I started graduate school at Iowa, I went in there with a chip on my shoulder.  They didn’t choose me, I chose them.  They weren’t a highly ranked “elite” institution, so to make my mark I had to work for the biggest and the best that Iowa had to offer, or so I thought.  I sought out the highest profile researchers at Iowa and picked the one that best aligned with my interests.  No matter what school you look at, there’s always, “That Professor.”  You know who I’m talking about.  The professor who publishes the most papers, who has the most respect.

I did my homework on my mentor.  I read a bunch of old papers, I understood the direction and the goals of the lab.  I remember our first lab meeting vividly, well, I remember how I felt after the lab meeting.  I was exhausted.  My brain physically hurt.  I thought I knew it all going into that meeting and I realized I didn’t know anything.  It was a wake up call, but I think I liked that feeling.  It was fresh and challenging.

During my rotation, I put in ungodly long hours, not because I thought it was expected of me, but because I wanted to.  At this point in time I was enamored with the science.  It’s funny how this changed for me as I look back on my four and a half years in that lab.  I wish I had that same vigor throughout the entire process.  Somewhere in the middle I started to hate the long hours and hard work.


There were warning signs.  Almost from the beginning I heard and saw them but they didn’t register, or I chose to ignore them.

“Who is your first rotation with?”

“Really? I heard that guy is a slave driving asshole.”

My mentor could be both. He also was the best researcher there, that’s why I chose to work in his lab.

Another warning sign came during my rotation.  One of the current graduate students was finishing up a western blot.  Something had gone wrong, and it didn’t turn out.  The lab erupted with a shout from my mentor, “Why didn’t you do it the RIGHT WAY?”  The berating went on, but everyone seemed unphased.  Afterward, a different graduate student came up to me and said, “I usually try to hide those from him.  Don’t save the pictures of bad gels on the computer, he checks the logs.”

I didn’t experience any negativity directly during my rotation, so maybe I sub-consciously  summed up the warnings and experiences as hearsay.   Maybe that graduate student was terrible and deserved the treatment, or maybe the other graduate students and faculty members were just jealous.  I decided I’d form my own opinion through learned experiences.

I joined the lab and picked up a new project that no one wanted.  In the end, the first 6 months of my work in the lab ultimately were a failure.  I could find no connection between our protein of interest and a cancer associated protein, despite the fact that our collaborator said they were linked.

I eventually stumbled on another project that turned out to be the shining star of my thesis.  Through a collaboration, we discovered a new protein in our favorite protein’s regulatory complex.  My thesis went on to characterize this protein both in human cells and in fruit flies.  It was a great project.  I worked really hard on it, although I can only remember two occasions where my mentor told me I had done a good job. 1) When I discovered that our new protein was a bona fide member of the regulatory complex.  And 2) the day of my thesis presentation.

The time in between my rotation and thesis presentation can be characterized, from my perspective, as hell.  And I’m not sure that I’m being overly dramatic.  Conversations with other lab members seemed to verify this sentiment.  It was almost as if we were united by our mutual discontent.  It also didn’t help that our mentor outright, word for word, said he was an asshole, this was just his style and if you didn’t like it you knew where the door was.  I guess this is a good policy, at least he was upfront about it.

After joining the lab, I didn’t fully realize the situation I was in until I had presented at my first lab meeting.  I was still really green, things weren’t working 100%, my westerns looked dirty, my gels were smeary, and my slide titles poked fun at all of these problems.  When I finished the presentation, I thought I had done a great job for a first time presentation, but that all changed when I was packing up my laptop and my mentor said, “We need to talk.”

The next hour was spent with the door closed in my mentor’s office.  We went over my slides.  He told me how terrible the fonts were, how the colors were all wrong, and that the presentation itself was wholly unprofessional.  This science stuff we did was serious business and my presentations should reflect that.  “Ok, Ok,” I thought, “I get it, can I get back to work now?”

This type of meeting happened often in my PhD lab.  I wasn’t the only one to experience them.  We lovingly referred to them as anti-pep talks because the point of the meeting was obvious.  Good things were rarely said.  The highlight was always how little you’d done over the last 6 months, how distracted you appeared, or your lack of a drive for success.

My mentor’s demeanor never scared me or made me overly fearful, though.  And I think that may be part of the reason why he was so hard on me.  The problem with this approach to motivating me is that I try to find humor in everything, because it does you no good to get stressed out about problems and cloud your mind with irrational thoughts.  This is just the way I do things.  If something isn’t working, I know I’ll eventually find a way to make it work, so I have no worries.  I know now that after reflection that this really angered my mentor.  He wanted me to be fearful, he wanted me to be stressed, he TOLD me this in one of our meetings halfway through my stay in his lab. “I’ve tried everything,” he said, “I’ve tried to be mean, I’ve tried to make you fear me, nothing works with you.  It’s not good to be a scientist and be so laid back.”  I disagreed.

I worked tirelessly in that lab, I’m talking 7am to 7pm six to seven days a week.  I worked really hard to do the best possible science I could.  My tolerance for the situation definitely waned somewhere around year 4 though, and it all came to a head during a lab meeting.  We were just getting started in next generation sequencing, and we were discussing all of the new technologies.  I had been reading up on the field, because it really interested me.  Around this time, we started having joint lab meetings with another professor who did similar research. My mentor was having a discussion with him and for some reason I just snapped.  My boss said something about how X system was worse than Y and the analysis of X system is much more esoteric than Z and people haven’t even thought about what strands these sequences are coming from, and blah blah blah.  I knew most of this was untrue, the analyses had been worked out, I read the papers on it, there were already two papers out looking at the analysis of strandedness.  All of this stuff had been thought about already, but we were having a discussion about it as if we were on the cusp of pioneering these things.  It just seemed ridiculous to me and a waste of my time.  So I told them that. I asked my boss if he’d ever directly used these machines or done the analyses.  Knowing he hadn’t, he didn’t have much to say and I know I totally embarrassed him in front of his colleague.  I admit it was a really poor play on my part.  It was stupid and not my place, but I think both my mentor and I can agree that it was possibly the best thing I ever did.  It lit a fire under both of us.

After the meeting I handed my boss a couple of the papers I mentioned in the discussion.  I went back to work only to be greeted 10 minutes later with the all too familiar mechanical crunch of the lab door, and my boss yelling about my terrible attitude.  All I could do was laugh.  To which he said, “Oh, you think this is funny?  Well I’m talking about you not finishing up your PhD in my lab, I’m done with you.”

This was the only time I was ever truly fearful.  I knew I had done something really stupid and it was because I resented everything my boss stood for.  Essentially it came down to an issue of respect.  He made it clear in lab that we were not his equals.  We were employees.

I walked into my mentor’s office.  I forgot to close the door.  The fight that followed could probably be characterized as a Chernobyl of disrespect.  The gloves were off in this match.  My boss called me lazy, he called me weird, he said that the stupid website that I work on was a waste of time, he called into question my drive, my purpose, he said that I was given my first paper and that I hadn’t really done anything, he said I was dirty, he said I was disrespectful and selfish.  I’m pretty sure he exhausted the thesaurus of negative terms you could ever apply to a human being.  The meeting ended with my boss telling me I had a week to improve and a letter of discontent was going to be put into my personal record.  The shit had hit the fan.  I now hypothesize that this tactic was two fold, he really was mad and this was his last ditch effort, for whatever reason, to put the fear of God into me.

It took a few weeks for the dust to settle.  A letter never went into my personal record.  I had meetings with my committee members, my department chair, and my friends (who all asked me what the hell that insanely loud argument was about).  Everyone was actually very supportive.  I really do suggest being careful on your committee member selections.  The side mentorship I received from them was invaluable in dealing with this situation.  Everyone said the same thing.  It was put up or shut up time.  I was only 4 years in, but I was also 4 years in.  If I got kicked out now, I’d have to start over new.  This wasn’t a project that could be carried over.

Fortunately, I had a plan, and because I essentially had 2 chapters worth of data in the books, I only needed a third to graduate (no drive and nothing accomplished, indeed).  I drew up a list of experiments to do and my mentor and I agreed that if I successfully completed them, I could defend.  I set a tentative date of 6 months.

During the next six months I pulled out all of the stops.  I threw everything I could at my complex to figure out how it was regulated.  Nothing seemed to work!  As a final swing for the fences, I embarked on another no-no.  I went behind my mentor’s back and expressed and purified a protein he had sworn off.  It was one of our competitor’s favorite proteins and I thought that it was possible that it was a regulator of the complex.  If this failed, I’d surely be chastised for wasting time and reagents.  I made a wildtype and a mutant peptide in E. coli (with the help of our absolutely fantastic technicians) and surprisingly, they had the desired effect!  I did a bunch of confirmatory experiments to show that the effect could be replicated.  I then successfully defended my thesis.

I think that, in the end, I did earn my mentor’s respect, and that’s really what the four and a half years in his lab was leading up to.  During our final fight, I asked him, “Do you think that maybe my attitude is reflected in your disrespect for me?” To which he replied, “Respect? Respect?! You’re just a graduate student, you don’t deserve my respect.”


As you can imagine, I don’t agree at all with my mentor’s approach to mentoring out of fear.  After our battle, I think he caved.  He actually started being nice to me, even friendly.  Maybe it was because everything I did finally worked the first time around.  I’m not sure, but by the time I presented my thesis, he introduced my talk in uncannily positive light.  He said he had never seen anyone work so hard in the last six months of their graduate career and that he was proud of my accomplishments.  I was stunned.

I really do wonder how things could have gone differently.  Would I have been more successful if the environment were centered on positive reinforcement rather than negative?  I guess I can’t really argue with his tactics.  On a certain level, they work.  He gets a ton of publications every year, but I don’t think the graduate students are better for it.  Dealing with that kind of pressure takes a special kind of person.  And certainly not everyone who came through the lab left it with glowing praise, or even a degree.

Now that I’ve graduated and moved on, I can look back at the experience from a different perspective.  My PhD mentor is an amazing scientist.  He has genius level intelligence.  He asks the right questions at the right times and publishes high impact research.  I have the utmost of respect for my mentor.  My scientific pedigree certainly is better for having done my PhD with him, and I don’t think I would have been a better scientist having gone through the circus with anyone but him.  But that doesn’t mean I’m going to run my lab the same way.

With this lab, I’ve taken a half and half approach.  I like to be really hands off.  I show my mentees how to do things a couple of times and then set them free.  If they’re still having problems after a few weeks, I sit down with them and we work it out.  I rarely get angry.  I’ve only had one or two violent outbursts, which I think were deserved.  It shouldn’t take someone 30 minutes to calculate how to do a 3x dilution of a 10ug/mL solution and people shouldn’t be talking on their cell phone while working with infectious virus in the hood.

I’ve only been at this leadership game for 6 months, so time will only tell if I’m taking the right approach.  For me, everyone has my respect until they lose it.  If you’re in the sciences, you’re here for a reason and it shouldn’t be my job to stress you to the absolute breaking point.  If I see deficiencies, we’ll sit down and talk about the problems.  We’ll work through them in the most respectful way possible.  Mentoring has responsibilities well beyond a boss-employee relationship, and I think that it is absolutely important to make that distinction.

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Dub C Med School
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Wow.  You're definitely much more good natured and controlled than I am.  Had I had that guy as a mentor at any point, punches would definitely have been thrown.  Still, you came through it with a perspective that keeps you from raining hell upon your own mentees.  And that's definitely commendable and admirable.

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Great story, Brian. I don’t get why people choose that approach, I suppose it does work sometimes, but it certainly is not the only way, or best way. I have been around far too many people who match that description, I still don’t see a need to be so unpleasant and condescending. I would also argue that science would be much more appreciated and respected in the public eye, if more scientists were more respectful of non-science folks, and of not-yet-proven-science folks.


Guest Comment

Why is this culture so prevalent in science, especially in older scientists?  Perhaps the biases and beliefs they are based on influence the choice on who to punish.  Some think that if they do not act as constant monitors anarchy is soon to follow.  Somehow they must think the behavior is worth the effort, regardless if it is motivated by a primitive craving to dominate at any cost, or fear of the consequences of proteges intellectual and physical freedom.


When they are rewarded for extreme coersion in mentoring their students such as threatening your job and getting the most efficient work immediately afterward (not blaming here i would have done the same), sadly they react positively to that.  Because these bad managers have little insight into their own contribution to the problem, they over-inflate what they believe works, and because it is so rewarding for a narcissistic immature bully to see submission in everyone around them a vicious cycle is maintained.  One other possibility is if a high turnover in the lab occurs and they can get a series of new ppl to repeatedly run their experiments reliably and work the bugs out for them, then they consider it to be more easily reproducable- ruthless but it does not surprise me.


I have had personal experiences with this rule-by-terror phenomenon as well...quote from PI "It's time now for the choosing of a resident- you know deciding people's lives-but why should i care, they are just some of many that will come and go, kids are a dime a dozen."

Brian Krueger, PhD
Columbia University Medical Center
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@jay, Sometimes I wonder if that was the goal.  It certainly would have been an easy way for him to get rid of me :P  But I think it was just his motivational style.

@Evie, the attitude is pretty prevalent and I don't think it has a place.  Unfortunately, it works, and it was enough of a deterrent to make me think twice about wanting to go into academics.

@Beth, In this case, I think it boils down to his experiences and how he was mentored.  He had a very rough couple of years as a post-doc and one of his mentors was even more of a tyrant.  Like I said, I haven't been mentoring long, and maybe after enough people walk all over you and take advantage of you, this sort of style develops as a defense mechanism to help weed those people out.  But you have to think of it from a different perspective.  Where would Jorge Cham of PHD comics be if we didn't have these personalities in the sciences?

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Unfortunately I have seen that attitude WAY too many times when it comes to leadership.

I think you are taking a brilliant approach though to your leadership position. I think the best results I see in labs is that approach. The hands off one lets people feel more in control of their own destinys and more likely to put in more effort in the long run. (Just as long as you don't have any people that will take advantage of you.)

Prabodh Kandala
Texas Tech University Health Science Center
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Brian, You not only survived, you proved what you are.

Many interesting lines in this post.

I always wonder, whether scaring people can ever get best out of them.


Guest Comment

it looks like your advisor's approach worked.


Guest Comment

I wonder how long it’s been since you graduated, Brian. You’ve heard of Stockholm Syndrome, no? When you say things like:

I have the utmost of respect for my mentor.  My scientific pedigree certainly is better for having done my PhD with him, and I don’t think I would have been a better scientist having gone through the circus with anyone but him.

I just want to shout, “Noooooo!” I can understand why you respect him as a scientist – for his output and brilliance. But as a human being? As a mentor? Sorry, what he did was not “mentoring” any more than someone who throws a child into the middle of a pool is “teaching” that child to swim. You may have the benefit of his pedigree, but I’m pretty sure you would have learned a lot more—and enjoyed your life more, too—had you actually encountered an equally brilliant but real mentor in grad school.

The fact that some people survive abusive relationships and become stronger for what they had to overcome doesn’t justify the abuse, and it doesn’t mean that those people needed to be in an abusive relationship to become strong. That kind of thinking only perpetuates the circumstances that make the abuse possible. Think about it this way: if a prospective grad student contacted you about joining your former advisor's lab, would you tell them to do it?

Brian Krueger, PhD
Columbia University Medical Center
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I totally agree with you, Hope.  I do, however, think that going through a lab like that certainly made me stronger.  It's sad that labs like that exist, the problem is that science is full of them and making it through that trial by fire made me be on top of my game.  I don't think that type of environment is good for everyone though, and I was nothing but honest when people asked about the lab or how I was treated.

Southern Fried Scientist

Guest Comment

People seem toforget that leadership is a completely separate set of skills from expertise in any field. Just because someone is a fantastic scientist doesn't mean they're a good leader, teacher, or mentor, and it looks like your experience reflects that.

If you are really serious about developing the skills that will make you an outstanding mentor, teacher, and leader, you need to go outside of the scientific community to find them. It's simply a matter of experimental design - your success, failure, and the morale of your lab group is too tighly confounded by the progress of the lab. Even a poor mentor will have hard-working, positive mentees if all the science is going great.

Which means that you have to seek out leadership rolls in your community where success and failure is dependent not on your expertise, but on your skills as a leader and mentor.

Brian Krueger, PhD
Columbia University Medical Center
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That's some great advice, Andrew!

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