Archive for the ‘Editorials’ Category

So, you’re thinking about graduate school?

November 4, 2014 Leave a comment

Your interest in this piece might be to get an idea of how my graduate school experience has been at UC Davis. Perhaps you are thinking about attending or applying to grad school, or maybe you just want to compare your experiences in grad school with mine. If you are the former, congratulations on asking a few questions before you make a life-changing decision. If you are the latter, please leave a comment to affirm my experience or contrast my perspective with your own different experiences. I want to share these words for the people who are trying to find out about the graduate experience, what one may expect in this new environment, and how the first year will be like no other.

For me, I had no question in my mind. I was a non-traditional student returning to school for the best education I could get. I joined an undergrad science program at 24 and never turned back. Fully committed, I applied to a few schools in the Bay Area and went to all of my interviews. The choice I made was based on a number of things, but UC Davis was ultimately the best “fit” for me. Simply based on the feeling I got in the town, from the people and with the academic community, I knew there was something about the environment that just made sense. I arrived in the Summer of 2013 and began my first rotation early. Now, I have joined a lab, I am beginning my second year in BMCDB and I am learning more everyday. Experiments, mentors, seminars, and classes are all a part of this new stage in my development, and for the first time in my life, a text book is the least important source of information for my daily progress and learning.

The first year was designated for a core curriculum and finding a lab to join through research rotations. From my experience, I might suggest a few priorities and considerations for anyone in their first year of grad school. Funding, intellectual stimulus, and social competence are three things I was advised to consider before joining a lab. I feel lucky to have received the advice, and so, I share it with you. Above all, you must secure funding. This could be through a scholarship, fellowship or through a lab that is willing to support you for 5 years, but you must know where your support will come from. If you are not secure, you could face some dire challenges by working or teaching the entire time you’re in grad school or worse, you may not find a supporting lab = you’re out of grad school. They say we’re paid to go to school, but that doesn’t mean that anyone can foot the bill. If the University wants you, that’s great! But you have to find a lab that wants you for the following years. That’s both a personal and financial consideration. So, apply to every source of funding you can. Consider it one of your many jobs as you enter the world of scientific research. It also means you may need to limit your rotations to funded labs. Next thing to consider is your intellectual stimulation, and don’t be fooled by what you thought your interests were during undergrad research. Now is not the time to pursuit the same type of research all over again. Not that there’s anything wrong with that, but rotations are fantastic! Now is the time to explore other options and learn about new types of science and research. If you make it this far, you should think about meeting with as many professors as you can for one-on-one meetings to learn about up-to-date research topics and how different labs operate. Don’t make the mistake of weighing your decisions to rotate in a lab based on internet resources or lab home pages. Plus, if you are flexible, you will find that rotating in almost any lab can be incredibly stimulating. Then, you will only have one remaining task: find the best fit. Social competence can mean different things in different environments. Everyone fits in differently. It is important to find a lab where you feel competent to communicate with the professor and everyone else in lab. This also means you can get along with your potential future colleagues.

So many things that I have not mentioned might include keeping up your grades (yes, you still have to earn your grades), maintaining and building connections to people who can write letters of recommendation, devising research proposals, getting familiar with your new environments, managing your income taxes and living expenses, keeping a sliver of work/life balance, etc. This list can be different for everyone. There are a lot of things that may happen to fall into place, but everyone has a different experience and a different knack for getting things done. I wish everyone the best of luck! I’ll recount my 2nd year in 2015 when it has come to an end. From what I hear, I can expect another year of important grades, vigorous preparations for my Qualifying Exams, and some challenging days with variable rates of success in my research progress. I am looking forward to it! If you feel like you’ve had drastically different experiences, please let me know by leaving a comment. The world of undergraduates in STEM fields deserves to hear your opinion – especially if you disagree with me!

A final thought. I once believed that getting a PhD would be 5 years of my life lost, a delay towards starting my real life. In hindsight, I find this idea to be absurd. I do not feel stagnant. I do not feel restrained. I do not feel like I am missing anything or losing any time. I feel like the education and network I have and will continue to develop during this time is something for which there is no substitute. I was fortunate to have a life structure that allowed me to continue my education. However, graduate school is not for everyone for many different reasons other than life structure. Research requires exhaustive patience, meticulous focus, and perseverance through trial and error. Despite inevitable failures one faces during research, your desire to learn must be greater than ever now. I encourage anyone who is still considering grad school to fully commit and pursuit a program that is right for you. You will gain more than you ever could have imagined.

Adam Contreras

2nd Year Graduate Student

BMCDB Graduate Group, UC Davis

Chiu Lab, Department of Entomology

Editorial – A Tenured Professor: an Academic Sportsperson successfully gone Professional

December 9, 2012 Leave a comment

by Daniël P. Melters

Imagine, you just looked through the lens of a microscope. You see only five chromosomes. Not ten, but five. At first you think this must be a mistake, but your postdoc assures you that it is real. There really are only five chromosomes. Your post-doc re-did the experiment and found the same ‘errors’ again. More interestingly, the mutant phenotype your postdoc expected to see was absent. The plants looked normal. As if all of the chromosomes were from a single parent. It daunted on both your postdoc and you that you are looking at a haploid genome. You made a haploid plant. Even better, every now and then one of the offspring will be a homozygous diploid plant. The potential for plant breeding are ridiculous. Now it is theoretically possible to create a mutant of your likings and with a single cross you can have a ‘pure’ mutant plant containing only your phenotype of interest. No need to do a dozens of back-crosses to clean up the background mutations. You have a plant breeding revolution in your hands. Of course this work was published in the top-tier journal Nature. This observation was like winning a gold medal at the olympics.

This is what a success story of a young scientist could look like. Indeed, this is the success story of Simon Chan. His plant breeding revolution in progress was rewarded with a Howard Hughes Medical Institute / Gordon and Betty Moore Foundation (HHMI/GBMF) fellowship at age 37. A success story which would have had many more chapters if he had not died on August 22nd, 2012.

The road Simon took to get to where he ended was a regular one; one almost every professor has taken. After college in New Zealand he went to graduate school (UCSF). He joined a well established lab of Elisabeth Blackburn (would later receive the Nobel Price, the equivalent of being inducted into the Hall of (Science) Fame). After completing his PhD, he moved on to a post-doc position in Steve Jacobsen’s lab at UCLA. After four years of post-doc-ing, Simon applied to and was offered a faculty position at UC Davis. Whereas Simon did one post-doc, many of his pears have taken two or three post-docs before becoming tenured faculty. There are some rare occasions, such as Joe DeRisi at UCSF, where someone becomes a professor directly out of graduate school, skipping the postdoc step all together.

Just about every graduate student today is being trained/mentored by a professor who took this very same route.

[College -> Grad school -> post-doc (-> post-doc (-> post-doc …)) -> faculty]

This is not the case for your average professional football player, as they are often represented by a manager. Yet their professional mentors are almost always former professional football players.

Does this mean that these rather different people don’t experience very similar problems, such as the potential for great personal gain or in both cases understudied mental health challenges [sport | science].

Life for the average graduate student (or postdoc or professor) is not that straightforward. First of all, doing research can be very expensive. Of course scientists cannot pay for their experiments out of their own pockets. To fund your research you enter the rat race of grant applications, where the odds for getting funded keep dwindling. Getting a fellowship, scholarships, or grant is like being recognized by scouts. It proofs that you are considered a talent worth investing in.

The analogy with professional sports persons is not that far-fetched. Allow me to elaborate. Say you would like to become a professional football player (or soccer if you prefer that term). You start playing football with your friends on the street and once you are between four and six years old, your parents will bring you to the local football club (or FC). Here you will receive your first formal football training and here you will play your first official football matches. It like you are taking science classes and you are partaking in your first science fair. This would hopefully spark your interest in majoring in science and subsequently apply for graduate school.

Once you succeeded at your local football club, you will move to a bigger club that will further your official football training. Many of the biggest clubs in the world have a player development program. For example, Lionel Messi was recruited by River Plate at age 11 and before he was able to start at River Plate, he was picked up by FC Barcelona. Most of us know that today he broke Müller’s record of 85 goals in one season.

Just like Messi, every aspiring young football player dreams of playing at the biggest stages and be part of the biggest league in the world. In science the biggest league is the United States. At this moment, more money is pored in basic research in the US than anywhere else. This means that it would benefit an individual scientist career to do part of its training in the US, as did Simon.

In football, a single event can make or break you career. Being recognized by scouts at an early age can pave your way to Camp Nou, as it did for Messi. Being recognized by an early career award makes you a more attractive up-and-coming scientist. On the other end of the spectrum, a career of a great talent in football can be broken in a single moment, as in literally broken, as it happened to David Busst. Similarly, in science this can happen. One of the most notorious examples is Hwang Woo Suk who claimed to be able to clone embryonic stem cells. Scientific misconduct is the worst possible offense in science. Although it is not known how common this is, most scientists do not quit the rat race because of it. A scientific career tends to end when you try to move up on the academic ladder of success. (This is also the most common reason for prospective professional football-players quite their dreams.)

In both football and science, a fair amount of leeway exists to make ‘errors’. L’enfant terribles such as Eric Cantona or Nigel de Jong are notorious for their antics, yet they both had and have successful careers. In science a retraction could be seen as an ‘error’. Recently, PLoS Pathogens retracted a paper from the DeRisi lab at UCSF. Although I am not familiar what the effects were for the lead author of the retracted paper, Joe DeRisi didn’t suffer from this ‘error’. The value a particular player or scientist is perceived to have in their respective fields helps them maintain their respective edge, as does their legacy. Established players and scientists simply have more leeway for ‘errors’.

This brings us down to luck. Success in either football (or any other sport) or science depend on luck. Without a well established scout defining you as a future star, your odds of playing for AC Milan or Real Madrid, greatly decreases. The same is true for scientists who made a well-talked about scientific discovery. Of course, you need to be talented and you need to work hard, very hard. Luck is the one factor that no football player or scientist can control. For a scientist just to keep up with the literature, you have to read at least one article per day. That would be the equivalent of say 350 articles per year or 1750 articles at the end of a 5 year PhD. Add to this three-to-five years of post-doc, you could have read roughly between 2080 to 3500 articles before you start your faculty position you aimed to reach. Devoting many hours to your trait helps increase the odds of becoming lucky, but that comes at a cost: less time for non-football or non-science related things.

To be a successful professional football player of scientist, you need to show great perseverance and resilience. Do you have the perseverance and resilience to become the next top scientist?

Stay Calm and Carry On.

P.S. Advised reading: Chapters 2, 7 and 10 from How Economics Shapes Science by Paula Stephan. In Chapter 2, Stephan compares tenured faculty with professional sports persons.

Categories: Editorials

Top 10 Best Things To Know As An Incoming Graduate Student

September 21, 2012 1 comment

Top 10 Best Things To Know As An Incoming Graduate Student
1. Cite EVERYTHING, especially if it was written by your PI.  And make sure you read all those papers as well.
2. Remember that it’s better to be called “roton” than rotten.
3. Establish study groups early, and ask questions if you’re confused.
4. Don’t forget to eat, sleep, and occasionally have some fun (outside of lab)
5. Become friends with the lab technician- they know where everything is and how to operate it.
6. Liquid nitrogen is cold, very cold.  Likewise, Bunsen burners are hot, very hot.
7. Go out to lunch with your fellow first years- they understand best what you are going through, and 20 years from now they might be reviewing your papers.
8. Don’t be afraid of cockroaches, dead mice, or Drosophila.  They’ll turn up in the most unlikely places.
9. If you don’t like a lab after 5 weeks, you are definitely not going to like it after 5 years.
10. Get organized- keep a calendar and a list of things to do.  5 years feels like all the time in the world, but goes by incredibly fast.

Good luck first years

-BMCDB Bloggers


Tips for riding your bike around UC Davis

September 19, 2012 2 comments

This first week of all the students being back in Davis is an exciting time but, also a hazardous time. The main danger being, riding your bike in a sea of inexperienced freshmen who are unfamiliar with the rules of the road and the responsibilities of riding a bike in Davis. Here are some tips to help avoid an embarrassing, costly and potentially harmful situation on your bike.

First tip: Get familiar with the laws/rules for riding a bike. Cops in Davis will pull you over and ticket you on your bike for: running a stop sign or red light, not using your hand to signal, riding with both headphones in (one is alright), riding inebriated (can lead to losing your drivers license) or otherwise irresponsibly/dangerously, and I think most importantly – for not having a bike light at night. A strong front light, back light, and ideally white or reflective clothing are strongly recommended while biking at night. Also, be familiar with the signs and be careful not to ride your bike in certain areas where it is forbidden (the MU and in certain sections of the Arboretum).

Second Tip: Pay attention while entering/exiting rotaries on campus! Most sensible people are familiar with the rotaries, but unfortunately most freshman are not very sensible. Technically the riders in the rotary have the right of way. Bikes entering the rotary must yield to bikes already in the rotary however, do not count on other riders to adhere to this rule. Many people will just bike right into a rotary without looking, so just be aware of this. When exiting the rotary it is never a bad idea to signal, and check over your shoulder that you will not hit another rider as you turn out of the rotary. Also be wary of actual traffic in the rotaries, buses, trucks, and cops can cause mass confusion when a high volume of bike traffic is present. Rotaries mishaps account for the majority of collisions and injuries on campus, so just be careful!

Third tip: Don’t be afraid to speak up! While riding around campus, especially around lunch of in between classes you will run into groups of slow moving bikes or people walking in the bike lane. Occasionally you can easily pass them by, but it is often necessary to alert those blocking the way of your presence. Just a quick “On your left/right” can save you from getting nailed by a swerving bike or errant pedestrian. Also very helpful with riders who are unable to ride in a straight line or are completely unaware of their surroundings (be especially aware of Cruiser bikes as they tend to be harder to control).

Davis is a great place to ride a bike, just make sure you do it safely and responsibly. If anyone has any other recommendations or stories please feel free to chime in!

Updates: When walking in a bike lane, remember to walk on the left side so you can see oncoming traffic. It is also a good idea to buy a U-lock, almost any other kind of lock can be easily cut (and there is nothing worse than finishing a long day in lab, and finding out that your bike has been stolen). Also a good idea to register your bike with the campus police for a variety of reasons.

Pro tip: As we transition from Summer/Fall into winter remember that the weather changes dramatically. Equipping yourself with splash guards on your front and rear bike tires can save you from getting an impromtu mud facial next time it rains. Riding your bike in the rain is not that bad, as long as you have the right equipment. Getting a solid rain jacket, rain pants, and a pair of water resistant gloves will make you much happier when you arrive at your destination.

Happy Riding!


Fairy wands and hypothesis slides; reflections on teaching MCB220L

August 7, 2012 Leave a comment

By Dan Starr

The past three years I had the opportunity to teach the incoming BMCDB students in the rotation course. I was lucky to have great partners in this endeavor, Ted Powers for the first year, and Jodi Nunnari the past two years. The following are some of the highlights from my experience.

Far and away the best thing about teaching this course is the way I got to know the whole class, and watch them as they work hard to constantly improve their skills! I now know the students of these three classes better than any faculty member in BMCDB, and I can say with confidence, we have an awesome group of students!

We made some significant changes to the curriculum of MCB220L. I think the most important change was the requirement of writing an NSF-style grant proposal at the end of each rotation. This not only teaches the students how to write grants, but more importantly, gets them to think about the big picture before joining a lab. I feel this exercise was very successful. Especially to Amy, Nadia, and Alex, who turned their assignments into NSF fellowships—congrats you three! For all the other students, I think the assignment made you better scientists.

The second addition to the curriculum was the chalk talk. This is an important means of scientific communication that was completely new to the students. I hope that with the experience (and stress) of the chalk talks, now any of my students can give you a 5-10 minute version of their research at a chalkboard in a chance encounter in the hallway.

There were of course humorous moments to teaching the class—Ralph’s “pointer” comes immediately to mind. The other occurred at the MCB NIH training grant retreat at Fallen Leaf Lake when all the then second years cornered me after my talk. I still can’t believe I forgot the hypothesis slide!

In all, teaching MCB220L was one of the most rewarding things I have done as a professor! Watching my former students give a talk or hearing about them get a grant fills me with pride. We have an awesome group of students! I’m sure Bob, Elva, and Enoch will continue the high quality experiences of the class. Have fun!

In the boiler room of the Titanic

July 26, 2012 Leave a comment

In today’s Science Dr. Henry Bourne and Dr. Mark Lively write an editorial arguing that the current state of biomedical research funding is like the Titanic heading for a collision with an iceberg.  If the biomedical enterprise is the Titanic, then current graduate students are like workers in the boiler room.  We have a repetitive job to do in a windowless room that smells funny and is full of toxins.  Putting the metaphor aside, graduate students should pay special attention to the issues in the editorial- what is the state of future funding? who will provide funding? for what will funding agencies pay?  I find it easy to focus on the immediate goals- what controls do I need to run? will this get published? will I ever graduate?  However, the issues facing the field are important because graduate school should be training for the next step, and the best way to train is to know what that next step will look like.  Some might point out- if we are in the boiler room of the Titanic our job is to make sure that the engines are powered enough that the ship can turn when needed to avoid the next iceberg.

Happy Independence Day (4th of July): Scientific Grilling Tips

July 4, 2012 Leave a comment

As you get ready for a day of celebration and revelry, you will no doubt come across a grill sizzling with some tasty morsels. However, chances are that the guy standing there in flip flops holding a beer and poking at everything on grill doesn’t actually know what he is doing! The biggest mistake made in grilling is people messing with their meat too much, for steaks and burgers put them on and leave them alone until juice pool on the top and they are ready to flip. If you want nice criss cross grill marks on your steak just turn 90 degrees after 2-3 minutes, wait another 2-3 minutes and then flip and repeat (most steaks should take 4-5 minutes per side to achieve medium rare). When grilling chicken the best way to do it is by splitting your coals, have a hot area with most of the coals underneath, and a cooler area without lots of coals underneath. Start the chicken skin side down on the hot side, get a good sear all the way around and then move it over to the cooler side to finish cooking. Thighs and wings will take longer to cook than the breast so start them before putting the breast on the grill. Also extremely important to grilling any piece of meats is to let it rest for 5-10 minutes under tin-foil to let all the juices redistribute in the meat.

Happy Grilling from the BMCDB Bloggers

Here are some more tips and explanations of the science behind them.

Excerpts from

Grill Science: How to Make This July 4th The Tastiest Ever” By Stephanie Pappas, LiveScience Senior Writer

What happens to meat as it cooks?

Meat goes through a few stages when you put it over heat. At about 110 degrees F (43 degrees C) internal temperature, muscles fibers begin to coagulate and toughen, Joachim said. At around 115 degrees F (46 C), fats start to melt.

When the internal temperature of the meat hits 130 F (54 C), the proteins in the muscle fibers denature, meaning that long, convoluted strands of protein lose their shape and unravel. Then they coagulate back together. That’s when meat starts to take on an opaque look. At 160 F (71 C), the connective tissues that hold together the muscle fibers start to melt and turn into gelatin. That’s the jelly-like yellowish-white stuff you see at the bottom of a roasting pan that you’ve cooked meat in, Joachim said. [7 Foods Your Heart Will Hate]

When you barbecue, Joachim said, the goal is to use those long, not-so-hot cooking times to melt the connective tissues and create barbecue’s trademark tender mouthful. Grilled cuts of meat usually contain less connective tissue, so they don’t need hours of heat to taste delicious.

Does it matter if I cook on gas, charcoal or a wood grill?

Absolutely, Joachim said.

“The big difference is the temperature and the moisture,” he said. “Charcoal and wood burn hotter and drier than gas.”

That’s because propane contains moisture, Joachim said. For every hour of grilling on gas, you release a half-cup to a cup of water vapor into your grill. That keeps the temperature down and prevents the formation of a seared, browned crust on your meat.

Some gas grills now come with a sear burner, Joachim said, which is a ceramic block that holds heat better than the grill grates. Because the burner can build up more heat, home grillers can use it to brown the outside of a steak or pork chop to get that dark crust.

Okay, but why does a seared crust taste so good?

Time for a chemistry lesson: When you apply heat to meat, you get something called a Maillard reaction. The amino acids that make up the meat’s proteins react with sugars in the meat, creating hundreds of flavor compounds.

Maillard reactions make pretty much everything taste awesome, including roasted coffee, grilled vegetables and even your morning toast.

“Any browned food tastes so good because it’s something new added to the food,” Joachim said. Browning doesn’t just lock in flavors; it creates new ones.

What’s the key to the perfect Fourth of July burger?

“The trick with ground meat is once you grind up meat, you’re grinding up the muscle fibers, and these are what hold the moisture in,” Joachim said. “What I recommend doing is adding moisture back in.”

That added moisture can take many different forms, Joachim said. He uses apple butter in turkey burgers and steak sauce in hamburgers. Simplest of all, he said, you can just mix ice water into the ground meat, along with whatever seasonings you want to use to spice up your burger. The ice water adds in moisture while keeping the inside of the burger cool so it doesn’t overcook. [Grilled to Perfection: Joachim’s Recipe for Bison Cheeseburgers with Horseradish Mustard]

Fat is another important component of a good burger, Joachim said. He recommends a ground beef that’s 80 percent protein and 20 percent fat. Contrary to popular belief, though, extra fatdoesn’t make a burger juicier. Instead, fat stimulates saliva production, moistening your mouth.

When you add fat to a burger, Joachim said, it’s not getting juicier: “You’re getting juicier.”