Category Archives: opinion

Meeting in the Aisle

Lab meetings: love them or loathe them, they’re an important part of lab-life. There’s many different formats and ways to do a lab meeting. Sometimes it feels like we’ve tried them all! I’m going to describe our current format and then discuss some other things to try.

Our current lab meeting format is:

  • Weekly. For one hour (Wednesdays at 9am)
  • One person each week talks about their progress. It rotates around.
  • At the start, we talk about general lab issues.
  • Then, last week’s data presenter does a 5 minute, one slide Journal club on a paper of their choice.
  • We organise the rota and table any issues using our general lab Trello board.

Currently, we meet in one of the pods in our building. A pod is a sound-proofed booth that seats 8 people on two sofa style seats. It has a table and an additional 2 people can cram in if needed. Previously we used a meeting room, with the presenter stood at the front using PowerPoint with a projector. One week the meeting room was unavailable and so we used a pod instead. It is a lot more informal and the suggestions and discussions flowed as a result. So we have kept the meeting in the pod, using a laptop to present data.

In addition to this, each person in my lab meets with me for 30 min on a Monday morning to go through raw data and troubleshooting. They also present a more formal talk to the centre once every 6-9 months. I mention this to give some context. Our lab meetings are something between “my cloning hasn’t worked” and a polished presentation.

I’m happy with the current arrangement, but we’ve tried many alternatives. Here is a brief list of things you can consider.

 

Two presenters

In my opinion this is a bad idea. We went through a period of doing this so that lab presentations were more frequent, or because we were also doing journal clubs too (I forget which). What happens is that one person has a lot of data and gets lots of discussion and then we either run out of time or the other person feels bad if they don’t have as much stuff to talk about. Accidentally you have made unnecessary competition amongst lab members which is not good. Just go for one presenter. The presenter feels like it is their day to get as much as they can out of the meeting and then next week the focus will move to someone else.

Round-the-table

This is where you go round and people say what they have done since the last meeting. Depending on the size of the group, this probably takes 2 hours or “as long as it takes” which cuts further into the working day. If the meeting is too frequent, lab members can soon get into a groove of saying “nothing worked” each time and it’s difficult to keep track of who is struggling. Not only is it easy for people to hide, the meeting can also become dominated by someone with interesting data. The format also doesn’t develop any presentation/explanation skills. My preference is to keep the focus on one person.

Rotating data talk and journal clubs

It is really common, especially if you have a small group to do data presentation one week and then journal club the next week. My feelings on Journal Clubs are: if they are done properly, they can be really useful and constructive. Too often they regress into the complete trashing of a paper. As fun as this is, it doesn’t teach trainees the right skills. I’d love it if people in the lab were on top of the literature, but forcing people to delve deeply into one paper is not very effective in promoting this behaviour. I think that it’s more important to use the lab meeting time to go through lab data rather than talk about someone else’s work. Some labs have it set up where the presenter can pick data or paper, which means people who are struggling with their project can hide behind presenting papers. I’m not a fan. We currently do a 5-minute journal club to briefly cover a paper and say why they thought it was good. This takes up minimal time and people can read more deeply if they want. I got this tip from another lab. I recently heard of a lab who spend one meeting a month going through one paper per lab member. We might try this in the future. We also have a list on our General lab Trello board for suggesting cool papers that people think others should read.

Banning powerpoint, western films on the table

At some point I got fed up with seeing a full-on talk from lab members each week, with an introduction and summary (and even acknowledgements!). Partly because it was very repetitive, partly because it inhibited discussions and also I felt people were spending too much time preparing their talk. Moving to the pod (see above) kind of solved this naturally. In the past, we did a total back-to-basics: “PowerPoint is now banned bring your lab book and let’s see the raw data”. This was a good shock to the system. However, people started printing out diagrams… these were made in PowerPoint … and before I knew it, PowerPoint was back! Now, there is value in lab members giving a proper talk in lab meeting. Everyone needs to learn to do it and it can quickly get people used to presenting. Not everyone is great at it though and what lab members need from a lab meeting – I believe – is feedback on their project and injection of new ideas. A formal talk from someone struggling to do a good job or overcome with nervousness doesn’t help anyone. I prefer to keep things informal. Lots of interruptions, questions and enthusiasm from the audience.

Joint lab meetings

When my group was starting and I just had two people we joined in with another lab in their lab meetings.   This worked well until my group was too large to make it work well. What was good was that the other PI was more experienced and liked to do a “blood on the floor” style of lab meeting. This is not really my style, but we had a “good cop, bad cop” thing going on which was useful. For a while. If the lab ethos is too different it can cause friction and if the other PI has any bad habits, things can quickly unravel. There’s also issues around collaboration and projects overlapping which can make joint lab meetings difficult. So, this can be useful if you can find the right lab to partner with, but proceed with caution.

Themed lab meetings 

No, not turning up dressed as someone from The Rocky Horror Picture Show… In my lab we work in two different areas. For a few years we segregated the lab meetings by theme. This seemed like a great idea initially, but in the end I changed from this because I worried it set up an artificial divide. People from the other theme started to ask if they could work in the lab instead. There was also different numbers of people working on the two themes. I tried to rotate the presenters fairly, but there was resentment that people presented more often on one theme than the other.  I know some dual-PI labs who do this successfully, but they have far more people. This is not recommended for a regular one PI lab with less than 10 people. Anyway, most labs just work in one area anyway.

Skype and remote lab meetings

For about one year, we had a student join our lab meetings via skype. She was working at another university and it was important for her to be involved in these meetings. It worked OK and she could even present her data when it was her turn. We used the lab dropbox folder for sharing slides, papers and data with her. We still use this folder now for that purpose. I know PIs who skype in to lab meetings when they are away, so that the lab meeting always goes ahead at the same time each week. I have never done this and don’t think it would work for our lab.

Fun stuff – breaking the routine

OK. Depending on your definition of fun… to check on the state of people’s lab books. I ask lab members to bring along their lab books without warning to the lab meeting and then get them to swap with a random person and then ask them to explain what that person did in the lab on a random date. It gets the message across and also brings up issues people are having with recording their data. We also occasionally do fun stuff such as quizzes but tend to do these outside of the lab meeting. I’ve also used the lab meeting to teach people how to do things in a software package or some other demo. This breaks things up a bit and can freshen up the lab meeting routine. Something else to consider to keep it fun: a cookie schedule. We don’t have one, but people randomly bring in some food if they have been away somewhere or they have cooked a delicacy from their home country.

State of the lab address

Once a year, normally in January when no-one wants to do the first lab meeting of the New Year, I do a state of the lab address. I go through the goals and objectives of the lab. Things that I feel are going well, areas where we could have done better. Successes from last year. The aim is to set the scene for the year ahead.

People in the lab can get a bit deep into their project and having some kind of overview is actually really helpful for them (or so they tell me!). Invite them along if you are giving a seminar or use a lab meeting to try out a seminar you are going to give so that they can see the big picture.

Ideas session

It doesn’t happen often that a presenter has nothing to present. The gaps between presenters are long enough to ensure this doesn’t happen. However, sometimes it can be that the person scheduled to talk has just given a bigger talk to the whole centre (and I forgot to check). When this has happened, we have switched to a forward-looking lab meeting to plan out ideas. Again this can break up the routine.

Time

I think 1 hour is enough. Any longer and it can start to drag out. I try to make it every week. Occasionally it gets cancelled when my schedule doesn’t allow it. But if the schedule gets too ad hoc, it sends the wrong message to the lab members.

Wednesday morning works well for us, but we’ve tried Tuesday mornings, Wednesday afternoons etc. I’m happy to set this by the demands from experiments etc. For example, most people in my lab like to image cells Thursday and Friday so those days are off limits. I also ask that everyone comes on time, and try to lead by example. I know a lab where they instigated a 1 Euro fine for lateness, including the PI. This is used as a cookie fund.

No lab meeting at all!

During my PhD we never had a regular lab meeting. Well, I can remember a few occassions where we tried to get it going but it didn’t stick. In my postdoc lab we also similarly failed to do it regularly. I didn’t mind at the time and was happy to spend the time instead working in the lab. However, I can see that many issues in the lab would’ve probably been solved by regular meetings. So I’m pro-lab meeting.

And finally…

Maybe this should have been at the beginning… but what exactly is the point of a lab meeting?

Presenter – Feedback on their project, injection of new ideas, is this the right route to go down? etc. Improve presentation skills, explain their project to others can help understanding.

Other lab people – Update on the presenter’s project, a feeling for what is expected, ideas for their own project. Have your say and learn to ask questions constructively.

PI – Update on project, give feedback, oversee the tone and standard.

Everyone – lab cohesion, a chance to address issues around the lab, catch up on the latest papers and data.

If none of the above suggestions sound good to you, maybe think about what you are trying to get out of your lab meetings and design a format that helps you achieve this.

The post title is taken from Meeting in the Aisle by Radiohead, B-side on the Karma Police single.

Reaching Out

Outreach means trying to engage the public with what we are doing in our research group. For me, this mainly means talking to non-specialists about our work and showing them around the lab. These non-specialists are typically interested members of the public and mainly supporters of the charity that funds work in my lab (Cancer Research UK). The most recent batch of activities have prompted this post on doing outreach.

The challenge

Outreach is challenging. Taking part in these events made me realise what a tough job it is to do science communication, and how good the best the communicators are.

There are many ways that an outreach talk is tougher to give than a research seminar. Not least because explaining what we do in the lab can quickly spiral down into a full-on Cell Biology 101 lecture.

A statement like “we work on process x and we are studying a protein called y”, needs to be followed by “jobs in cells are done by proteins”, then maybe “proteins are encoded by genes”, in our DNA, which is a bunch of letters, oh there’s mRNA, ahhh stop! Pretty soon, it can get too confusing for the audience. In a seminar, the level of knowledge is already there, so protein x can be mentioned without worrying about why or how it got there.

On the other hand, giving an outreach talk is much easier than giving a seminar because the audience is already warm to you and they don’t want you to stuff it up. It’s a bit like giving a speech at a wedding.

The challenge is exciting because it means that our work needs to be explained plainly and placed in a bigger context. If you get the chance to explain your work to a lay audience, I recommend you try.

Disarming questions

The big difference between doing a scientific talk for scientists and talking to non-specialists is in the questions. They can be disarming, for various reasons. Here are a few that I have had on recent visits. How would you answer?

Can you tell the difference [down the microscope] between cells from a black person versus those from a white person!?

For context, we had just looked at some HeLa cells down the microscope and I had explained a little bit about Henrietta Lacks and the ethical issues surrounding this cell line.

You mentioned evolution but I think you’ll find that the human cell is just too intricate. How do you think cells are really made?

Hint: it doesn’t matter what you reply. You will be unlikely to change their mind.

Do you dream of being famous? What will be your big discovery?

I’ve also been asked “are we close to a cure for cancer?”. It’s important to temper people’s enthusiasm here I think.

Are you anything to do with [The Crick]? No? Good! It’s a waste of money and it shouldn’t have been built in London!

I had wondered if lay people knew about The Crick, which is now the biggest research institute in the UK. Clearly they have! I tried to explain that The Crick is a chance to merge several institutes that already existed in London and so it would save money on running these places.

Aren’t you just being exploited by the pharmaceutical industry?

This person was concerned that academics generate knowledge which is then commercialised by companies.

My friend took a herbal remedy and it cured his cancer. Why aren’t you working on that?

Like the question rejecting evolution, it is difficult for people to abandon their N-of-one/anecdotal knowledge.

Does X cause cancer?

This is a problem of the media in our country I think. Who seem to be on a mission to categorise everything (red meat, wine, tin foil) into either cancer-causing or cancer-preventing.

As you can see, the questions are wide-ranging, which is unsettling in itself. It’s very different to “have you tried mutating serine 552 to test if the effect is one of general negative charge on the protein?” that you get in a research seminar.

The charity that organises some of the events I’ve been involved in are really supportive and give a list of good ways to answer “typical questions”. However, most questions I get are atypical, and the anticipated questions about animal research or embryo cloning do not arise.

I find it difficult to give a succinct answer to these lay questions. I try to give an accurate reply, but this leads to  long and complicated answer that probably confuses the person even more. I have the same problem with children’s questions, which often get me scurrying to Wikipedia to find the exact answer for “why the sky is blue”. I should learn to just give a vaguely correct answer and not worry about the details so much.

Amazing questions

The best questions are those where you can tell that the person has really got into it. In the last talk I gave, I described “stop” and “go” signals for cell division. One person asked

How does a cell suddenly know that it has to divide? It must get a signal from somewhere… what is that signal?

My initial reply was that asking these sorts of questions is what doing science is all about!

Two more amazing questions:

Is it true that scientists are secretive with their results and think more about advancing their careers than publicising their findings openly to give us value for money?

This was from a supporter of the charity who had read a piece in The Guardian about scientific publishing. She followed up by asking why do scientists put their research behind paywalls. I found this tough to answer because I suddenly felt responsible for the behaviour of the entire scientific community.

You mentioned taxol and the side effects. I was taking that for my breast cancer and it is true what you said. It was very painful and I had to stop treatment.

This was the first time a patient had talked to me about their experience of things that were actually in my talk. This was a stark reminder that the research I am doing is not as abstract as I think. It also made me more cautious about the way I talk about current treatments, since people in the room may be actually taking them!

Good support

With the charity I’ve been to Polo Clubs, hotels, country houses, Bishop’s houses, relay events in public parks. The best part is welcoming people to our lab. These might be a Mayor or people connected wth the city football team, but mainly they are interested supporters of the charity. It’s nice to be able to explain where their money goes and what a life in cancer research is really like.

To do these events, there is a team of people doing all the organisation: inviting participants, sorting out parking, tea and coffee etc. The team are super-enthusiastic and they are really skilled at talking to the public. The events could not go ahead without them. So, a big thank you to them. I’ve also been helped by the folks in the lab and colleagues in my building who have helped to show visitors around and let them see cells down the microscope etc.

Give it a try

Of course there are many other ways to engage the public in our research. This is just focussed on talking to non-scientists and the issues that arise. As I’ve tried to outline here, it’s a fun challenge. If you get the opportunity to do this, give it a try.

The post title comes from “Reaching Out” by Matthew Sweet from his Altered Beast LP. Lovely use of diminished seventh in a pop song and of course the drums are by none other than Mick Fleetwood.

Ten Years Gone

Ten years ago today I became a PI. Well, that’s not quite true. On that day, I took up my appointment as a Lecturer at University of Liverpool, but technically I was not a PI. I had no lab space (it was under construction), I had no people, and I also had no money for research. I arrived for work. I was shown to a windowless office that I would share with another recent recruit, and told to get on with it. With what I should be getting on with, I was not quite sure.

So is this a cause for celebration?

By Rob Irgendwer (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)], via Wikimedia Commons

By Rob Irgendwer (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)%5D, via Wikimedia Commons

The slow start to my career as an independent scientist makes it a bit difficult to know when I should throw the party. I could mark the occasion of my lab finally becoming ready for habitation. This happened sometime in March 2007. Perhaps it should be when I did the first experiment in my new lab (April 2007). Or it could be when I received notification of my first grant award (Summer 2007), or when I hired the first person, a technician, in October 2007. It wasn’t until December of 2007 when my first postdoc arrived that the lab really got up-and-running. This was when I felt like I was actually a PI.

Looking back

In retrospect, I am amazed I survived this cold start to my independent career: effectively taking a year-long involuntary break from research. But I was one of the fortunate ones. I was hired at the same time as 6 other PIs-to-be. Over time it was clear that without good support some of us were going to fail. Sure enough, after 18 months, one switched to a career in grant administration in another country. Another left for a less independent position. One more effectively gave up on the PI dream and switched to full-time teaching. But there was success. Two of the other recruits landed grants early and were in business as soon as our labs were renovated. I also managed to get some money. The other person didn’t get a grant until years later, but somehow survived and is still running a group. So of 7 potential group leaders, only 4 ended up running a research group and the success of our groups has been mixed: problems with personnel, renewing funding…

Having a Plan B is probably a good idea. It’s well publicised that the conversion rate from PhD student to Professor is cited as 0.45% (from a 2010 report in the UK). It’s important to make new students aware of this. Maybe a one-in-200 chance sounds reasonable if they are full of confidence… but they need to realise that even they persevere down the academic route, they might indeed get a “group leader job” yet it still might not work out.

I had no Plan B.

I think there were many things that the University could have done differently to ensure more success among us new starters. The obvious thing would be to give a decent startup package. Recruiting as many people as possible with the money available gets lots of people, but gives them no resources. This isn’t a recipe for success.

Also, hiring seven people with completely unconnected research interests was not a smart thing to do. With nothing in common, any help we could give each other was limited. Moreover, only a few of us had genuine research links to established faculty. This made life even more difficult. Going over this in more detail is probably not appropriate here… I am grateful that I got hired, even if things were not ideal. Anyway, I survived this early phase and my lab began to grow…

Reasons to be cheerful

I have been very fortunate to have had some great people working in my group. The best thing about being a group leader is working with smart people. Seeing each develop as a scientist and progress in their careers… this is undoubtedly the highlight.

With talented people onboard, the group really got going and we began making discoveries. My top three papers which gave me most pleasure were not necessarily our biggest hitters. These are, in chronological order:

  1. Our first paper from the lab is special because it signified that we were “open for business”. This came in 2009. Fiona Hood and I showed (somewhat controversially) that two clathrin isoforms behaved similarly in cells depleted of endogenous clathrin.
  2. Dan Booth and Fiona worked together to find the spindle clathrin complex and show that it was a microtubule crosslinker. This paper was the main thing I was aiming to do when I setup my group.
  3. Anna Willox and I worked on one of my favourite papers showing that there are four interaction sites on the clathrin N-terminal domain. I love this paper because it was a side project for Anna. We made a prediction based on symmetry, and a large dollop of guesswork, which turned out to be right. Very satisfying.

Of course there were many more papers and I’m proud of them all. But these three stand out.

I’m also thankful that I’ve been able to keep the lab afloat financially. Thanks to Cancer Research UK, who funded my lab right at the start and still do today. Also thanks to Wellcome, BBSRC, MRC, North West Cancer Research who all funded important projects in my lab.

The other highlight has been interacting with other groups. There have been some great collaborations; most productively with Ian Prior in Liverpool and Richard Bayliss in Leeds, as well as other stuff which didn’t generate any papers but was still a lot of fun. Moving from Liverpool to Warwick in 2013 opened up so many new possibilities which I am continuing to enjoy immensely.

“The move” was the most significant event in the history of the Royle Lab. Many circumstances precipitated it, many of which are not appropriate to discuss here. However, the main driver was “being told to get on with it” right at the start. Feeling completely free to do whatever I wanted to do was absolutely fantastic and was one of the best things about my former University. Sometimes though, the best things are also the worst. I gradually began to realise that this freedom came because nobody really cared what I was doing or if my career was a success or not. I also needed more interactions with more cell biologists and this meant moving. Ironically, after I left, the University recruited a number of promising early career cell biologists all of whom I would have enjoyed working alongside.

If you have read this far, I am impressed!

Posts like this should probably end with some pithy advice. Except there’s none I have to offer to people just starting out. Ten years is a long time and a lot has changed. What worked back then probably doesn’t work now. Many of the mistakes I made, maybe you could dodge some of those, but you will make others. That’s OK, we’re all just making it up as we go along.

So, ten years of the Royle Lab (sort of). It’s been fun. I have the best job in the world and there’s lots to celebrate. But this post explains why I won’t be celebrating today.

The post title comes from “Ten Years Gone” by Led Zeppelin from their Double LP “Physical Graffiti”.

The Digital Cell: Workflow

The future of cell biology, even for small labs, is quantitative and computational. What does this mean and what should it look like?

My group is not there yet, but in this post I’ll describe where we are heading. The graphic below shows my current view of the ideal workflow for my lab.

Workflow

The graphic is pretty self-explanatory, but to walk you through:

  • A lab member sets up a microscopy experiment. We have standardised procedures/protocols in a lab manual and systems are in place so that reagents are catalogued to minimise error.
  • Data goes straight from the microscope to the server (and backed-up). Images and metadata are held in a database and object identifiers are used for referencing in electronic lab notebooks (and for auditing).
  • Analysis of the data happens with varying degrees of human intervention. The outputs of all analyses are processed automatically. Code for doing these steps in under version control using git (github).
  • Post-analysis the processed outputs contain markers for QC and error checking. We can also trace back to the original data and check the analysis. Development of code happens here too, speeding up slow procedures via “software engineering”.
  • Figures are generated using scripts which are linked to the original data with an auditable record of any modification to the image.
  • Project management, particularly of paper writing is via trello. Writing papers is done using collaborative tools. Everything is synchronised to enable working from any location.
  • This is just an overview and some details are missing, e.g. backup of analyses is done locally and via the server.

Just to reiterate, that my team are not at this point yet, but we are reasonably close. We have not yet implemented three of these things properly in my group, but in our latest project (via collaboration) the workflow has worked as described above.

The output is a manuscript! In the future I can see that publication of a paper as a condensed report will give way to making the data, scripts and analysis available, together with a written summary. This workflow is designed to allow this to happen easily, but this is the topic for another post.

Part of a series on the future of cell biology in quantitative terms.

Voice Your Opinion: Editors shopping for preprints is the future

Today I saw a tweet from Manuel Théry (an Associate Ed at Mol Biol Cell). Which said that he heard that the Editor-in-Chief of MBoC, David Drubin shops for interesting preprints on bioRxiv to encourage the authors to submit to MBoC. This is not a surprise to me. I’ve read that authors of preprints on bioRxiv have been approached by journal Editors previously (here and here, there are many more). I’m pleased that David is forward-thinking and that MBoC are doing this actively.

I think this is the future.

Why? If we ignore for a moment the “far future” which may involve the destruction of most journals, leaving a preprint server and a handful of subject-specific websites which hunt down and feature content from the server and co-ordinate discussions and overviews of current trends… I actually think this is a good idea for the “immediate future” of science and science publishing. Two reasons spring to mind.

  1. Journals would be crazy to miss out: The manuscripts that I am seeing on bioRxiv are not stuff that’s been dumped there with no chance of “real publication”. This stuff is high profile. I mean that in the following sense: the work in my field that has been posted is generally interesting, it is from labs that do great science, and it is as good as work in any journal (obviously). For some reason I have found myself following what is being deposited here more closely than at any real journal. Journals would be crazy to miss out on this stuff.
  2. Levelling the playing field: For better-or-worse papers are judged on where they are published. The thing that bothers me most about this is that manuscripts are only submitted to 1 or more journals before “finding their home”. This process is highly noisy and it means that if we accept that there is a journal hierarchy, your paper may or may not be deserving of the kudos it receives in its resting place. If all journals actively scour the preprint server(s), the authors can then pick the “highest bidder”. This would make things fairer in the sense that all journals in the hierarchy had a chance to consider the paper and its resting place may actually reflect its true quality.

I don’t often post opinions here, but I thought this would take more than 140 characters to explain. If you agree or disagree, feel free to leave a comment!

Edit @ 11:46 16-05-26 Pedro Beltrao pointed out that this idea is not new, a post of his from 2007.

Edit 16-05-26 Misattributed the track to Extreme Noise Terror (corrected). Also added some links thanks to Alexis Verger.

The post title comes from “Voice Your Opinion” by Unseen Terror. The version I have is from a Peel sessions compilation “Hardcore Holocaust”.