How to get hold of your growing supplies (for rice) in North Cal

After all the seriousness in our recent blog posts we want to share a rather entertaining Northern California story. It is about getting growing supplies in a state where medical marijuana is legal.

The background to the story is… I am working on the rice immune system and growing rice of the same high quality the whole year round is difficult even in California. So because our new assays require constant and fully reproducible growth conditions we recently switched to grow our experimental plants in semi-hydroponic system in the growth chamber. For this purpose we adopted so-called ‘plugs’, a kind of pressed soil mimic that can equally retain moisture, and we use a separate plug for each plant.

How to get these plugs!?! From your local hydroponic (a.k.a. weed grow) shop

One colleague of mine started using the plugs and we aimed to extend our rice plant growing empire. So we went to our local Davis weed grow, mmm… I mean hydroponic, shop in order to get more supplies for our scientific operations. Funny enough, the manager wasn’t always available and our orders were not always processed in time. I guess he was busy doing other business. Because we did not want to wait forever as time is money and we in the science community are mostly short of both I extended our supply search operation to Oakland, my main hometown.

//Oakland is a beautiful city in the East Bay. The second city I lived in, after Glasgow, where advertisement asks the community not to flush their controlled substances down the toilet but to dispose them appropriately.//

After having looked up some distributors on the plugs producers’ webpage I get into my car on a Monday morning with my little four-month-old son in the backseat. The first stop is just a couple of blocks away from my home and a short drive through industrial pretty West Oakland. After a couple of turns Google tells me the shop is just to my right but all I can see is a run-down townhouse with silver foil in the windows and a barking dog in the front yard. Well…the producer might have sold plugs to these guys but for sure not for resale. So I take off to the next distributor on the list. The shop is supposed to be near the harbor and after circling the block twice I even see the name on a hand-painted sign. I park the car, get my little son, still sleeping in his car seat, out of the back and try to find the entrance. Thanks to my street credit earned by my plenty-full tattoos a white guy with gold chains smiles out of the SUV and says: “Yes dude, you are right here. This hole in the wall is the entrance”. So I drag my son and myself through this hole inside a debilitated warehouse with a small very messy room, which is suppose to be the showroom. People are talking over the ‘counter’ about some sort of growing… and become a lot quieter as soon as they see my kid and me. A kind of tweaked out white thin lady asked me what I am looking for. I with my foreign accent and mumbling try to tell her I am looking for these plugs. After several back and forth she says she finally gets what I am after but is out of the supplies and her shipment would come in at 3 p.m. I simply reply I would come back later and call before to confirm. She nods and shows me out of the door in a brisk fashion.

Just around three I look up their phone-number on the web. The website gives the number and states in bold letters DO NOT MENTION MEDICAL MARIJUANA ON THE PHONE OR WE WILL NOT SERVE YOU. Well no problem I think I only grow rice. The voice mail box is full… and I just take a ride there hoping to finally complete my mission… bad luck though the shop is closed and also these guys are also clearly not interested in selling plugs (but maybe other stuff though).

I don’t want to postpone my whole next week of work that I already planned out so I continue my quest. The next shop turns out to be a money laundry hydroponics shop. It looks all fancy from outside, yet the door is locked and I have to ring the bell to enter. The shelves are full to the brim but there are no plugs and no one interested to sell really anything. I slowly get disillusioned with the East Bay grow shops and decided to have one last go. This time I call the shop beforehand again. Wow! Someone picks up the phone, speaks clearly and promptly confirms their actual will and ability to sell these plugs. So off for my final ride of the day. When I arrive I enter a pretty looking small old factory building with loads of plants and greenery inside. Loud hip-hop music fills the air. In the corner stands a nice 80’s looking pinball machine and a pin-pong table occupies the middle of the room. A mid-twenty trendy looking guy with a baseball hat smiles at me from behind the counter and a young woman appears from one of the side rooms. Both greet me warmly and offer their kind assistance. I ask them for my plugs and get 500. Just in case so I don’t have to go treasure plug hunting in Oakland again. Both just smile knowingly. Well if they only knew that I am a rice grower… Luckily, getting a receipt for my purchase is no problem with these guys. So I am finally happy and shove the plugs into the trunk of the car for the ride to UC Davis the following day.

Happy hydroponic plant growing in North Cal everyone.

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DO mind the scientific skeletons in the closet

Yet another Science paper retracted today. Nothing much new unfortunately (sting!).           Except that for me and my colleagues this was not just another example of non-reproducible work. We planned our research projects around it. So here are my thoughts about this: just in time for Halloween.

There has been much talk about the problem of reproducibility of data and the rise in retractions. The discourse is mostly centered around the perpetrators and the negative impact this sloppy or knowingly flawed science has on the industry and the perception of scientific endeavor in society. Who did this awful study? What reviewer did not catch this missing control and the missing/sloppy stats? Why did they do it? Why don’t they admit their mistake? What’s wrong with peer-review? Well….much is wrong with the industry and many people have great ideas how to tackle some of these issues.

What is usually missed from the discussion is the impact such dubious science can have on young, early career scientists if they are at the receiving end of non-reproducibility. What do you do if you come to a famous (or not so famous) lab, you get a project, which is based on fantastic data and high impact publications, BUT you cannot reproduce it? How do you approach this issue? What does it mean for you and your career if your project just goes to shreds because it’s simply based on bad data? Do you get another chance? Will you be forever associated with this flawed data and your reputation damaged? Are you going to be so disillusioned with science to the point that you want to leave academia? Do you try to fix the problem or silently move on? Do you try to make it work? Do you tell the boss and explain your situation? Or is it you? Can you just not get it to work? Can it really be that this is all wrong? Why cannot I reproduce this data? Can this BE???

I think everyone can appreciate the complexity of the issue. Many people I talked to had their own experience to share. Here is what’s frightening:  sloppy science and misconduct, I thought, is something you read about in journals and not something I would experience myself. This would never affect me or close friends in other labs, who are all great scientists in my eyes. I was wrong.

We young, early career scientists in our lab went through something very serious and exemplary recently. In mid 2011 to beginning 2012 we just joined the lab of Pamela Ronald during a huge turnover of people. Everyone of the “old crew” of many years, sometimes more than 8, left or were about to leave around the time we came in. We were all super excited to get going and to push the borders and boundaries of science /// Thanks Saul for this awesome expression./// However, no matter how hard we tried, our own data did not add up and we could not make much sense of it in the view of the lab’s recent  immunity-related publications, which appeared in Science and Plos One. /// Here is a three sentence summary: The lab cloned an amazing immune receptor XA21 in rice that confers resistance to the most important pathogenic bacteria on rice (Xanthomonas oryzae pv. oryzae) in 1995. In 2009 they published the identification of the bacterial protein Ax21 as ligand of this immune receptor. In 2011 they reported the function of this bacterial protein Ax21 as a novel cell-cell communication factor (also referred to as quorum sensing factor) in the bacteria./// We, a group of concerned early career scientists in the lab, brought this discrepancy  regarding the 2009 and 2011 studies to the attention of the PI and explained to her what we thought was wrong. A long, intense, careful, multifaceted, repetitive and diligent truth-searching endeavor started. I won’t bore you with the details. In short, we were not able to reproduce the core findings of both Ax21-related papers.  Of course, this was very distressful for everyone involved especially as other people published similar work in relation to the bacterial protein Ax21. /// I am not sure what this says about the current state of science. I find it very concerning./// Kudos to Pamela Ronald, who reached the only scientifically correct decision and retracted both papers. She obtained much praise for this brave step. For sure, not every PI would have followed through in a similar situation. Pamela Ronald’s decision became the topic of the inaugural post in the new category “Doing the right thing” on the famous “retraction watch” blog. You can also read her perspective on how this whole story unfolded in her guest post on the Scientific American blog. I can only agree and applaud Pamela Ronald on making the right decision and retracting these two papers. For sure, it was not easy.

What I would like to highlight is the importance to clear the scientific record once mistakes in publications are discovered. Mistakes will always happen yet they need to be corrected. People should not fear to clear their scientific record but rather be rewarded for doing so. I am sure every reader of this blog knows of multiple scientific skeletons in people’s closets. It takes much courage from the PI’s perspective to bring these mistakes out in the open. They potentially have much to lose….BUT the PI will have the time to correct the situation. On the other side what’s going to happen with early career scientists, who got into one of these situations without their own wrong doing? Who is routing for them? What happens if the PI does not retract the paper(s) and simply disregards the concerns? I know of least of one situation in which a good friend of mine had exactly this happening to her. Finally she simply left academia, because there was no support for her and no way out. Young, early career scientists can be treated like a dispensable commodity if they don’t play along. Of course, this is the worst-case scenario, yet once you are trapped in the non-reproducibility hole you will lose a lot of time no matter what. You might be asked to repeat experiments multiple times, generate the same material anew, and, in general, spend a lot of time on research that is hardly publishable ///Ha!! no impact factor for retractions///. No one can give you this time back in your career and many people might not understand why you are not moving forward. Well, you simply cannot build skyscrapers on swampland. Only once everything is cleared up will you be able to move on with your career without losing too much. This is the only way out for the early career scientists, and PIs should be aware that they are not only dealing with their own careers. ///In this regard again thanks to Pamela Ronald for taking the courage.///

It is not only the PI’s but also the early career scientists’ significant efforts and courage that leads to the clean-up of the scientific record. Be diligent in these situations. Talk critically with your co-workers in the lab. Verify your own stock and everything given to you. Perform the right controls. Ask for advise from other senior colleagues. Follow your understanding of science as a truth-finding endeavor. This journey won’t always be linear and sometimes mistakes happen. Deconstruct them, correct them, learn from them and build something new. In my opinion, this is what truly makes a reputable scientist.

P.S.: So let’s figure out what’s really going on with this amazing rice immune receptor XA21. /// For the “love of wisdom”///.

Inspirational supervisor: a portrait drawn by trainees

Much has been written of how to be a desirable student or post-doc. We thought it would be helpful to turn the tables around and write a short manifesto of what we think a great academic supervisor is all about. The inspiration for our views comes from many printed and living sources. This insightful piece on what to expect from your adviser in Science Careers is refreshingly frank and clear. Several other good articles make very helpful guides for mentors such as this one in Nature, Science or ESA bulletin and references therein. Much of the advice and guidelines written for the mentors are of course applicable to supervisors too. Let us clarify: your supervisors do not need not to be your mentors, but ideally they are. Irrespectively, they should propel you forward and fulfill the highest standards of supervision.

So what are the goals of outstanding supervision?

Overall, it’s pretty simple really!?! An excellent supervisor gets the best out of each and every apprentice he or she takes on. Be it the odd undergraduate student, the hard-working PhD student or the aspiring post-doctoral scholar. An excellent supervisor is able to guide their apprentices according to their specific needs, character and future career goals. Of course, there is not one type of supervisor that fits each and everyone’s needs. Some people need very close guidance; others cannot stand it and flourish only with the ‘hands-off’ approach. Some people want to be networked and others seek technical expertise. However, each and everyone will benefit from supervision that has been thought through and aspires to the highest standards.

Of course, this is an idealistic view, yet we think it is always best to start with the highest aspirations. It is easier to lower the bar later on than to correct already muddled standards. So let us paint you a portrait of an idealistic supervisor, a ‘rara avis’ that may not exist and that we have never been ourselves. Nonetheless, getting as close as possible to it is our ultimate goal.

1. Truly care about your people

It is obvious that something is wrong with science as an industry. We are producing too many disposable and interchangeable PhDs and post-docs. We offer too little career opportunities for the masses of aspiring scholars. Some call it The Life Science Bubble. For many trainees, understanding this can lead to a sense of isolation, low self esteem and even depression. It will make a difference if you truly care about your people. Most people have only one shoot at a successful PhD. It’s success can make all the difference in peoples’ lives in the current economic climate. So treat your trainees as persons and not as minions. Support them and show that you care.

2. Lead from the front and by example

A boss is not always a leader, but a great supervisor is.

3. Build scientific integrity in the wake of your own scrutiny

Now, this is very important. It is a fundamental role of a great supervisor to foster scientific integrity. This is one place where you need to be inflexible with your trainees even at the price of appearing ‘not nice’. Many of us, who are still in the game at a later stage of their career, choose to stay in academia for the joy of performing science. So nurture it in others and show how it’s done for real. Teach your folks proper statistical analyses, logic, experimental design, repetition and controls. Science is nothing without it. Show that you care about good record keeping and organization. For your graduate students (and post-docs) the training in scientific rigor and scrutiny you provide will coin their future approach to science.

4. Be human and stay humane

Life is not only about science. It is so much bigger and so much more diverse. So let your people have a life outside the lab, even though you might not have much of one on your own. This was your choice and not theirs. Supporting your folks during family hardships, pregnancies and the first months of a newborn is simply the right thing to do. It makes your lab a more relaxed and appreciated environment. In addition, treating every member equally independent of their religion, race, gender, desire, ethnicity and social status is simply the ultimate goal of a fair civilized society.

5. Network and support your folks

If you ever going to make it in science you need to be connected. Politics is a huge part of science. That is one point in which science and Bavaria countryside politics, now and 25 years ago, are pretty much the same. People trust you more if you had a drink or two with them and know your face. Also the simple recommendation by an influential figure in your field can be very far reaching. So sending your folks to conference where they can give poster presentations and talks will only help them. Well-written and supportive reference letters are an absolute plus for everyone’s career no matter if you apply for a tenure track position or a job in industry.

6. Teach with transparency the skills of becoming a successful group leader

It is hard to learn a skill if no one ever showed you how it’s done, or at least everything is easier once a great teacher instructed you. This is particularly true when it comes to writing a successful grant, submitting a cover letter for a paper or serving on a review panel. Leading your lab with transparency and involving people in writing grants, reviewing papers and mentoring will only do them good. They not only will feel involved and being a part of a team, they will also learn how it’s done and what they might want to do differently.

7. Guide and foster ideas and careers

What is a professional success in academia? Have you ever thought what constitutes your own ‘Impact Factor’ as a scientist? One can measure it in papers written, grants received and the titles acquired. But there is another ruler: you can measure your success by the number of people whose careers you fostered. These would be former students and post-docs who are now prominent figures in your field or in industry. These would be the people who gather around you at conferences to take a ‘lab alumni’ group picture. A great supervisor is not only the one who can attract best students and post-docs but also the one who can guide their careers, give credit for their ideas and eventually let them go.

The zen of addressing reviewers’ comments

Here is the main trick: always respect your reviewers.

Yes, this can be tough – respecting even the arrogant referees or those who clearly did not spend much time reading the paper, did not understand a thing about your research. Often, this means taking some time to cool down after reading and re-reading the reviews. Do not fixate on bad reviews. Do not start responding emotionally.  By all means, it is most advisable to go and vent about “the third reviewer” to your friends over beers (two or three Indian Pale Ales coupled to a wild mushroom oven-roasted pizza work particularly well). Then – sleep it off and be sincerely polite and respectful while taking part in scientific discussion of your data. At the end, each reviewer is your colleague, at some point in life you can be – or appear to be – one of them. So, get the patience to “respectfully disagree”, clarify with both words and reasonable amount of experiments. At the end of the day, these two or three people actually took the time to read your paper and respond to it.

Here is another thing to remember: it is called a ‘peer review’ because a reviewer is your peer. You do not need to be submissive to every single request simply out of fear. It is important to evaluate each comment carefully.  Imagine your response as if you are in front of the audience of your prospective readers. Does or does not a particular reviewer’s concern shatter your interpretation of the data? Now… be honest with yourself. If you are hesitant – may be you do need to re-phrase your conclusions or do this one extra experiment to reject an alternative. If reviewers’ concern does not change what you think – spell out your logic.

In practice, I respond to reviews similar to how I used to go through short-answer questions on a take-home exam. I start by copying and pasting reviews to new file. If the review is written in a free-flow format, I divide it into smaller bullet-point sections. Then, I start writing the responses to each and every section. Sometimes, it is less demoralizing to answer easy points first, then come back to the tough ones. In my opinion, every comment deserves an answer, even something simple as “missing a comma on p.7” can be answered with a single word “fixed” or “addressed”. Avoid unnecessary battles: if there are two ways to spell or phrase something, go with reviewer’s suggestions, unless you are 100% sure that only your phrasing can truly convey what you meant to say. If there is an easy control experiment you can run – do it even if it seems redundant.

Ones everything is addressed, identify the meat of your dialog with a referee and write a short two-three sentence summary placing it in the beginning of your response. If the whole response turned out to be worth of Leo Tolstoy’s novel – you can also write a one-two sentence summary at the end. This would remind both you and your unknown discussion opponent that you are in fact on the same page.

Lastly, take a second to re-read your paper one more time after resubmission. With all the pitfalls of peer review, more often than not I sincerely found that my papers improved a lot due to the review process.

Other blogs on peer review:

Moving across the atlantic to do science. What for?

I have repeatedly discussed this with friends and colleagues, even before I left Europe for the United States. Sometimes, we touched on specific details about the States, other times we had more broad musings concerning leaving your home turf for a far away country “simply” to work there. Well, it is hopefully not only work what you are planing on doing while living in a far away land but rather immersing yourself in the culture and becoming part of a community. In this snipped I am trying to address several of the issues that come hand in hand with a big move across oceans and landmasses. It’s gonna be a mix of self-lived experiences and advices gathered along the way. One of those I got early on, when I was still an undergrad at Glasgow University. It boiled down to not to cross the Atlantic in order to get a PhD in the States. The reasoning be that it simply takes b…. ages to graduate compared to most European countries. Another point being that with several more years of science and life experience I would be professionally and personally better equipped to be proactively involved in one of these “big” American labs that can be for sure overwhelming without adequate skill set.  I am glad about this advice as I stayed for grad-school in the UK and had a splendid time. That said, I also meet several friends that had a amazing time during grad-school in the States. So here we go.

Most importantly know why you want to be, live and work in a new place far away from home. Don’t just leave because you have nothing else to do. Or it is the thing you ought to do. You won’t enjoy your stay. Also one place is not like any other and this holds true abroad as well. What I mean is that it will be a totally different experience of where you gonna end up within one country. For me it was pretty clear that I wanted to leave Europe to live in the States for some time. Yet the only place I really wanted to move to (within the States) was sunny California. Having seen several other states by now I absolutely don’t regret living here in northern California. It was similar when I went to Japan: only being in Tokyo, and not somewhere in Okinawa, made it such an impressive experience.

My next point might sound like a no-brainier, yet personally I  consider it one of the main reasons why I enjoyed all my moves to different countries. I always aim to be open, relaxed and content before departure. This is even more important when moving across an ocean and several time zones.  It involves taking all your belongings you can manage to get across and leaving much of your previous life behind. \\\ In case you had the experience of moving within a country or continent, for the purpose of Europe, just multiple the distance you feel between your friends and family back home now by the multiple of hours you need to spend on a plane reaching your next destination. This might provide you with a glimpse of the distance you going to cover.\\\ It sounds dramatic and it definitely can be. Moving to another continent implies adapting your life to a different society with distinct rules of engagement and social codes. Whereas at the same time you will be without most of your accustomed social backdrop and comfort network. So be prepared for your move. Practically, this means arrange everything for the first month or so before you arrive. Have a bucket of cash you can spare on the side. Take a break between your old job and your next assignment. Spend as much time as you think you need with friends and family. Get yourself in this space where you absolutely enjoy your life and feel good about yourself. Be open! Be ready! So bring it on 🙂 This smile was brought on my face by taking off three months before I left from good old Europe to the States. Within this time (and even before) I meet most (if not all) of my plenty great friends I made over all these years. This involved traveling all over western Europe seeing lots of places I’ve (never) seen before and some I always wanted to see. Milan, Bern, the Alps, Barcelona, Berlin, Tel Aviv, Jerusalem…just to mention a few and to give me some time to reminisce….Yes, everything is close together in Europe and yes sometimes I really miss the magical views and sunsets on-top of old-grown European cities. With all this energy and amazing memories on board it was much easier to stick to my rule of thumb. For moves to give myself at least a year for arrival and settlement. Because each and every time before I move I think I am pretty clear about all those facts. I give in to the delusion of having a solid idea about what I getting myself into. Well…that’s before and totally contrary to what I always experience when submerged in these moves. \\\ At a recent EMBO meeting of European post-doctoral fellows working in the States a fellow and me came to a similar conclusion about our experience of moving to the States—“…but it is really different from what I expected it to be.”—“Well didn’t we all think so!”—\\\

This gulf between expectations and reality of course can also easily be experienced within your new lab and towards your new boss. At the end of the day these two components might be the main reasons why you came all across the world. Accordingly you might feel entitled to be rewarded for all your efforts and personal ‘losses’. This sounds logic, at least somewhat, yet in fact it might come totally different. This whole move of yours is for sure a huge step and game-changer for you but your colleagues might just don’t give a s… and simply see you as another competitor. Similarly your boss might perceive you as just another of multiple minions, never have time, no real interested in your project and actually not really be a scientist at all anymore. He or she might have slowly morphed into a politician or sales(wo)man without you realizing from afar. These and many more horror stories have reached me via the grapevine or first hand from other colleagues. Thankfully I haven’t experienced such an horrific situation myself. Though at first I struggled with having to start from scratch; again being no-one at all. In this sense most of your new colleagues likely have not read your papers, do not know your reputation or in fact that you might have any at all and are rather concerned with their own projects (yet sometimes offer to help with bits). Overall it boils down to you starting at a similar position as at the beginning of your PhD (just at a higher level). You have to prove yourself all over again and reclaim your turf just as you have done before with the one you just left behind. Of course, as you can imagine this can be at times a rather arduous exercise and upward struggle. Being just another reason to start your new assignment with energy and full-heartedly…..and ah yes the approach to science might be as different as the banking system. So don’t bank on what you are used to in this respect either.

In a nutshell you not going to know what you get yourself into and it might go all wrong. You ending up unsatisfied and ready to leave after your first year starting a new post-doc somewhere else in the States or back home. This won’t be the end of your life or career. You still gonna have had this experience and you most likely will have grown and learned a lot scientifically and personally. Alternatively, it might be also simply the start of an amazing new part of your life. You getting to know the love of your life, making the discoveries of your lifetime and ending up with your dream position in the place you wanted to be.