dissertation acknowledgments

March 19, 2015 at 2:27 pm | | everyday science, grad life, history

Paul and ChemJobber posted about acknowledgements in theses and dissertations. Paul has a nice one here. It made me reread mine:


Most importantly, I thank my advisor, W.E. Moerner. It is difficult to explain how wonderful it has been to study under him. W.E. is a real scientist’s scientist: he fundamentally cares about good science and presenting results in a clear and honest manner. He always impressed me with his understanding of sciences outside his field and his scholarship, as I doubt that there is any paper I have read that he has not. W.E. always knows where some obscure piece of equipment is in the lab, and what type of power cable it requires. W.E.’s humor and generosity have been invaluable during my time in his lab, not to mention his scientific guidance. I could not have asked for a better Ph.D. advisor.

I joined the Moerner lab because W.E. seemed to run a fun and exciting research program, and I have not been disappointed. Other members of the Moerner Lab have been instrumental in my education and research. Kallie Willets mentored me when I first arrived at Stanford. Kallie was fun to work with and I am very grateful for the time and energy she dedicated to helping me get a solid footing in the lab by teaching me the right way to do things (and clean up afterwards).

After Kallie graduated, it was entertaining (to say the least) to get to know my officemate Dave Fromm. Dave was always willing to discuss problems I was facing in my experiments, and often suggested perfect solutions. (He was also always willing to discuss his adventures and funny stuff he found on the internet.) Dave and Jim Schuck regularly played darts over my head … literally. In general, this was entertaining and helpful to my overall spirit, and I appreciate the fun times with Jim and Dave. In those early years, I also enjoyed the company of (and scientific input from) Nick Conley, Anika Kinkhabwala, Adam Cohen, Stefanie Nishimura, Jaesuk Hwang, Kit Werley, So Yeon Kim, Andrea Kurtz, Marcelle Koenig, and Jian Cui.

In the later years of my tenure in the Moerner Lab, I have benefited from another batch of amazing people. Nick is one of the most motivating collaborators I have had the pleasure of working with; he is always excited about results, and his mind wanders to great places (not to mention that his skills as an organic chemist were very helpful to me)! I also had the opportunity to work with Hsiao-lu Lee, who was always generous with her time and expertise in cell culture. I am thankful to have those two wonderful coauthors. Alex Fürstenberg has been a fun (and very tolerant) officemate, and is always a great person to ask about anything photophysical. Mike Thompson is hard working and smart, but most importantly he laughs at more than 83% of my jokes. Julie Biteen is opinionated and usually right, and has been fun to bounce ideas off. All the other members of the Moerner Lab (Shigeki, Randy, Majid, Steve, Jianwei, Whitney, Lana, Yan, Sam B, Quan, Matt, etc.) are exceptional people and have made Stanford a wonderful place.

Marissa Lee started joined the lab in 2008, joining my project. I have enjoyed mentoring her and passing on as much as possible of what Kallie, Dave, Jim, Stefanie, Nick, Hsiao-lu, So Yeon, Jaesuk, Adam, and Anika taught me over the years. I wish her luck in her time at Stanford. Several summer students worked with me to get a taste of research. I thank Jennifer Alyono, Daniel Lau, Nathan Hobbs, and John Servanda for their help taking spectra.

Of course, I must also acknowledge Bob Twieg and his students at Kent State University. As a physical chemist, there is nothing better than an excellent collaboration with a group of top-notch synthetic chemists. W.E. and Bob have worked together since their IBM days in the 1980s and 1990s, and I had the fortune to benefit immensely from that bond between labs. Nearly every compound mentioned in this Dissertation was synthesized by the Twieg lab, and the back-and-forth (or push– pull?) design process between the labs should serve as an example to what all collaborations should strive for. Bob’s students have made great compounds over the years, and I thank all of them for being super collaborators: Meng, Hui, Zhikuan, Na, Reichel, Ryan, Alex, and Jarrod.

Friends have made grad school a blast. I met the Moilanens immediately, and enjoyed marathon training and adventures with David and Hailey. Ben Spry was a great help studying for placement exams, and I enjoyed driving to San Jose with Ben so he could buy a Camaro. William Childs and Charles McCrory—after I finally decided to like them—were indispensible: grad school will be filled with fond memories of coffee, lunch, and arguments because of Wm and Charles. So many other friends made my time at Stanford wonderful: Nichole, Kate, Alicia, Jen, Drew, Ashley, John, Zalatan, Chad, Matt, Griffin, Kendall, Daniel, Adrienne, Adam, Avisek, Eric, Ethan, Kevin, Emily, Ken, Dan, Scott, and everyone else! It has been fun having Jordan and Maria in California, and so many other non-Stanford friends that I cannot possibly name them all. I have had positive interactions with several faculty members, and I thank Bob Waymouth, Chris Chidsey, Dick Zare, Bianxiao Cui, Steve Boxer, Justin DuBois, Vijay Pande, Bob Pecora, and Ed Solomon. I also must recognize the members of the Stanford staff who contributed to my work and enjoyment, namely: Roger Kuhn, Todd Eberspacher, Brian Palermo, Patricia Dwyer, Grace Baysinger, Steve Lynch, and all the Conways—Marc, Daragh, and Mariette.

I feel that I must also acknowledge those in my past who influenced me and led me down the path of science. My earliest memories of enjoying the natural world were at Audubon’s Mast Landing Camp, playing and learning about nature with Aaron and Ira and Matt. In the third grade, Mrs. Solari recognized and encouraged my inclination toward science, as have many teachers since. I thank Dr. Root, who mentored me for my 7th-grade science fair project; Mr. Plummer for dealing with 8th graders; Mr. Glick for the astronomy and recycling clubs and supporting me throughout high school; Mr. Herrick, for being the best physics teacher I never had; Mr. Gauger for insisting that Heisenberg’s uncertainty principle can explain why things still jiggle at zero Kelvin; John Anderson for arguing with me; Don Cass for teaching my first college chemistry class and making it so exciting; Tony Planchart for teaching biochemistry in a way that convinced me to be a chemistry major; Helen Hess for fun classes biology and biomechanics; Michael Rubinstein for his entertaining exploration of polymer physics; Royce Murray for teaching analytical chemistry; Max Berkowitz for stat mech classes; and Charles Schroeder, Eric Shaqfeh, and Steve Chu for a great summer research experience. I should offer a special bit of gratitude to Sergei Sheiko, whose lab I worked in as an undergrad, and who helped make my time at UNC spectacular.

This Dissertation is dedicated to my family: the Lords, the Cyrs, and the Hearns. My parents have always encouraged my interests, without pushing me too hard. I wouldn’t be half the person I am without their support. My brother Jackson has been a life-long companion, so I was very pleased when he moved to California and we could play together like when we were growing up. My grandparents Lord funded my education, which I greatly appreciate. I probably get some of my curiosity from my pépère Cyr. My first year at Stanford, I met Brenna Hearn and married her a few years later. She has made my life wonderful, and I thank her for her support throughout grad school. I cannot thank Brenna enough for her companionship, so I’ll stop there.

Looking back at this, I wish that I had made it 50 times longer and cut out the rest of the dissertation.

postdoc and grad student taxes

January 25, 2011 at 8:32 pm | | grad life, postdoc life

Before I say anything, I have to clarify that I am not a tax expert. Don’t listen to anything I say. If you prefer TurboTax advice, read this link instead.

OK, taxes for grad students and postdocs can be complicated, especially dealing with fellowship stipends and tuition reimbursements.

Tuition and the 1098-T

The way Stanford sends 1098-T forms is via some really sketchy website 1098t.com, run by Affiliated Computer Services. They send the most spammy looking emails I’ve ever seen:

But it’s not spam. The 1098-T is basically worthless for grad students whose tuition is paid for by their PI or their department. In those cases, the students can’t claim the tuition on their taxes, because they didn’t actually pay it. In general, the “Amounts billed for qualified tuition and related expenses” box should have a very similar number as “Scholarships or grants”, but they may be significantly different if the department ends up paying your tuition in a different year than it’s billed. If you just input those incorrect boxes into your favorite tax software, it will calculate that you have a tax burden or deduction. That’s not correct. (Of course, those should cancel out over your entire grad career, because the department’s payments made on the prior year’s bill will eventually catch up. But it’s simpler to just report what actually happens, not what the 1098-T thinks is happening.)

I think the best thing to do is ignore the 1098-T. Instead, add up all the bills you get from the university that year, and add up all the payments to the university from your department, and report the difference that you actually paid. The difference should be what you actually paid: the fees billed directly to you and not reimbursed by the department. [Edit: Only required fees are eligible for a deduction.] This will be a small number, and probably won’t affect your taxes. Keep those documents in case the IRS comes calling!

[Edit: Of course, you must also report your stipend as income on your 1040 as a taxable scholarship.]

The most risky thing to do is claim that you paid tuition that you actually didn’t. I suspect that annoys the IRS. (Of course, this will be different for grad students who actually pay tuition. The Hope or Lifetime Learning credits are designed for those folks.)

Is a Fellowship Self-Employment?

Generally, the answer is no. And that’s a good thing, because you have to pay a 13.3% self-employment tax if you are self employed. Postdocs and grad students on fellowships may not be “employed” by their university, but they are not exactly self-employed, either. The way it’s been worked out, students and postdocs on fellowship generally pay their own income taxes (the university doesn’t take out taxes from their paycheck) in estimated taxes, but don’t pay the extra self-employment tax.

Do Postdocs Pay Social Security Taxes?

This question is more complicated. Students don’t have Social Security taxes (officially called FICA) withheld from their paychecks. But are postdocs “students” in the eyes of the IRS? Currently, they are. Universities usually don’t withhold FICA from postdocs’ paychecks. (Sometime, grad students have FICA withheld during summers, usually if they aren’t charged tuition and are paid as employees for the summer.)

There is some disagreement around this, and the IRS may start asking for Social Security payments from universities and postdocs. For instance, medical residents just lost a case against the IRS; now they have to pay Social Security taxes. It makes me wonder if postdocs will be next.

More Details



Photojournalism Tour

August 12, 2010 at 1:25 am | | everyday science, grad life, lab safety

These photos are from anonymous labs:

Like working at the MMS.

A monument to Thorlabs.

Money well spent.

Laser safety.


July 28, 2010 at 3:46 pm | | grad life, nerd, postdoc life, science and the public

One of my labmates attended Comic-Con last week in San Diego and decided to dress up as a TARDIS (a sort of time-machine from Dr. Who) in what can only be described as an epically awesome costume.

While there is a side-on photo of her with writer/director Joss Whedon (Firefly, Serenity, Buffy the Vampire Slayer, the Avengers, etc.) that’s been circulating on Twitter, below is an EXCLUSIVE photo from her own camera.

In addition to attracting the attention of the famous and powerful, she also managed to attract the very sketchy. Link

naturally depressed

May 14, 2010 at 10:36 am | | everyday science, grad life, science community

The documentary video “Naturally Obsessed” follows some graduate students at Columbia through their trials and tribulations in science. Personally, I found parts quite depressing. However, it is an interesting video and I wish they would film other labs to round out the picture.

Or watch here: http://www.thirteen.org/naturally-obsessed/

Here are some of my thoughts (spoiler alert!):

The nature of their research, protein crystallization, is especially depressing: because the results are all-or-nothing, the students work very hard and may see zero reward. In other bench sciences, this can also be true. However, it is often the case that there are many small discoveries and accomplishments along the way. Protein crystallization work, on the other hand, means that if you find the structure, you publish; if the protein doesn’t crystallize well enough to get a structure, you don’t publish. Ouch.

The person I felt the worst for was the blond kid, Kil. He was so positive at the beginning of the film—almost to a fault. Near the middle, he begins complaining about the strains being a graduate student has on his life and relationship with his fianceé. At the end, we learn that Kil and his fianceé broke up (at least partially because of grad school), and he has no interest in academic science. The viewer is at least relieved to discover that Kil gets a good job after graduation!

The ending of the film reminded me of the end of The Graduate: it was bitter, but maybe only intended it to be sweet? Rob, earns his PhD, has a baby, is happy, and becomes a postdoc. But I feel bad for him trying to raise a child on a postdoc’s salary (his wife is also a graduate student). Not to mention the fact that he is already over 30 years old and has several years of a postdoc ahead of him. I’m just not sure it’s the happy ending the film-makers intended. On the other hand, Rob seems really motivated and wants to become a professor, so maybe he’s on his way!

My overall opinion is that the film is interesting, and fairly accurate. However, I think a couple more episodes could really strengthen the documentary. This episodes follows a graduate student as he “succeeds” by toiling away for years, getting a chance success, and then publishing in Science. Instead, I would like to see the day-to-day, week-to-week, year-to-year successes of graduate work: positive interactions and collaborations with fellow students and postdocs, brainstorming in meetings, little “ah-ha!” moments while sitting over a sample, and publishing in J. Phys. Chem. B. In the end, I think this little documentary does a good job of portraying the ups and downs of grad school. However, I think another few episodes in different types of labs would reveal a more realistic overview. Moreover, I think it would be healthy to show students accomplishing smaller steps along the way to their PhD or best paper, instead of the view that students must toil away for 6 years with no rewards until the end.

(via BiteSizeBio)

lost my library proxy

April 13, 2010 at 10:36 pm | | grad life, literature

Stanford already took away my off-campus access to journal articles. I thought I’d have a couple months of access after I graduated, but I guess not. So keeping up with the literature means going to campus and sitting in the library like an undergrad.

I suppose I could rent articles, but I’m too spoiled by free access! Ah well, I’ll catch up reading my PDFs, then keep up better once I start my postdoc in a couple months.

obscure paper

April 6, 2010 at 4:35 pm | | grad life, literature

I was recently looking for a prep for p-bromophenylphosphine, and I found exactly 1 reference for it’s synthetic prep that’s cited by every paper that uses it.

It happens to be in (possibly) the most obscure journal in the world – “Phosphorus and the Related Group V Elements.”  It had all of 6 volumes in the 70’s before it merged with the “International Journal of Sulfur Chemistry” to form “Phosphorous and Sulfur and the Related Elements.”

I finally found TWO places in the world that had hard copies – the North Carolina State University library, and, of course, the National Library of Australia.

I’m beginning to think what I want must be some obvious synthesis, and that I’m just an idiot.  However, I did fail organic chemistry and am now working in a synthesis lab, so the “idiot” part is probably appropriate…

stanford grad students are NOT eligible for worker’s comp

January 20, 2010 at 4:36 pm | | grad life

According to this official document, Stanford graduate researchers are not covered by worker’s compensation. If we get injured on the job, we have to pay using our private insurance. Well that sucks. I can’t see any reason that a postdoc working in lab should be covered but a grad student doing the exact same thing is not.

Students at Notre Dame, Rice, UIUC, and Caltech are covered. Why aren’t we?

This means that we graduate students should be more vigilant at demanding safe working environments, refusing to even enter an area that is at all questionable, refusing to work with or around unsafe individuals, and asking postdocs or professors to perform all strenuous or risky tasks (such as heavy lifting or working in the machine shop).

UPDATE: I’ve heard of two cases of graduate students getting injured while in lab, and Stanford refuses to pay the workers comp. In one case, the student’s private insurance paid. In the other, the Stanford-branded health insurance (Cardinal Care) also refused to pay, because the injury occurred at work; that student got a hospital bill for nearly $2000. Something is wrong here!

UPDATE: I’ve read the California statutes on the subject, and I’m convinced that Stanford is breaking the law. The only exception that grad students could possibly fit under is the following:

“3352.  “Employee” excludes the following:

(i) Any person performing voluntary service for a public agency or a private, nonprofit organization who receives no remuneration for the services other than meals, transportation, lodging, or reimbursement for incidental expenses.”

But grad students are not volunteers. And we do receive payroll checks, not specific reimbursement for expenses.

Caltech agrees with me:

“Caltech is obligated by law to provide workers’ compensation coverage to its employees. Workers’ compensation laws are designed to protect employees and their families from the financial consequences of injury, illness, or death arising out of and in the course of their employment.

Caltech provides workers’ compensation coverage to all Institute employees (including students on the payroll), pre-approved volunteers, and professors emeriti.”

(From their HR website.)

Murphy’s Law of Water Titrametrics

January 17, 2010 at 5:47 pm | | grad life

It will ALWAYS be raining whenever you need to do Karl-Fischer titration in another building.


El Nino sucks.

tebow celebrates my PhD defense

January 1, 2010 at 7:35 pm | | grad life

In the Sugar Bowl tonight, Florida’s Tim Tebow kindly reminded the world that I’ll be defending my PhD Dissertation on February 8, 2010.

That’s nice of him.

even the computer gods don’t want me to work on my thesis

November 11, 2009 at 2:14 pm | | everyday science, grad life, great finds

The driver to my video card exploded yesterday, right in the middle of working on my thesis. Easy to fix (thanks to Brian), but it took a major chunk of my thesis-writing time.

Then, on top of that, SNL was hosted by the greatest musical artist since that hairy guy who banged two rocks together. I had to watch that.

OK, back to the thesis…

man bites dog

August 14, 2009 at 9:47 am | | grad life, news, science community, scientific integrity

Former Stanford graduate student Christopher Sclimenti is suing his former PI, Prof Michele Calos, for patent infringement and plagiarism. See stories here, here, and here. The complaint can be read here.

The summary is as follows:

  • Student was originally on a patent application.
  • At some point, Stanford and/or prof removed student’s name from application, which becomes this patent. Prof Calos is the only inventor listed on the patent.
  • Prof filed a second patent, which is a continuation of the first. Prof Calos is still the only inventor listed.
  • Prof filed two other applications (here and here), still the sole inventor listed, with significant portions copied from the student’s dissertation. (Stanford Daily found about 20 paragraphs in one application that were essentially identical to paragraphs in his dissertation!)

All parties agreed to an Alternative Dispute Resolution (ADR) with a neutral party. The ADR panel concluded that the student was a co-inventor and should have been included in the patent. As a result, Stanford agreed to add him to the issued patent (but I see no evidence that that has occurred yet).

CalosAccording to Stanford’s OTL page, inventorship is different than what most scientists would consider authorship. For instance, “A person who contributed only labor and/or the supervision of routine techniques, but who did not contribute to the idea—the concept of one of the embodiments of the claimed invention—is not considered an inventor.” For the prof and the University to claim that the student was not an inventor, they implied that he was only a technician and did not contribute to conceiving any of the claims in the patent. That’s possible, but the ADR panel disagreed. It seems pretty straightforward that the student should have been on at least the first patent!

Why would Prof Calos and Stanford University fight so hard against their former student, who clearly contributed enough to the invention to appear on the original patent application? Is splitting the royalties from one patent with one extra person, a student who contributed to the work, so terribly painful? Stanford’s policy is to divide the royalties (after paying for the patenting and lawyer fees) 1/3 to the inventors, 1/3 to the department, and 1/3 to the school. So the prof loses half of her royalties by re-including her former student as an inventor, but the University loses nothing.

Is the recent patent application plagiarized from the student’s dissertation? Only if the dissertation was not first self-plagiarized from an earlier paper. Who knows. Regarding the plagiarism complaint, Stanford had this to say:

“I think we’ve really done our part at this point,” Dunkley said. “The inventorship has been corrected. He has been made whole for any amount that he would have received if he had been an inventor from the beginning. So from the University’s perspective, all necessary action has been taken to rectify any differences on the inventorship issue.” (source: Stanford Daily)


That’s not really very satisfying. What if the roles were reversed and a student copied significant portions of his PI’s earlier grant proposal into his dissertation without the PI’s permission? Or submitted a paper without the PI’s knowledge? That student would probably be kicked out of Stanford at a minimum. The least the University could do is investigate this case and if Prof Calos has a history of taking credit for other peoples’ work. Maybe Prof Calos is innocent and the student is trying to steal credit, but it would be nice if the University would check into it.

All in all, the entire situation is not clear-cut. I suspect that the whole incident is the result of large egos, hurt feelings, and greed—from all parties! This is why it is very important to not burn bridges and to try to empathize with your PI or your student. I suspect this conflict could have been resolved early on if all parties had been more understanding and willing to listen and compromise.

Bottom line though, I find it unfortunate that the University would fight one of its own students.

P.S. Guess what Sclimenti is doing now?

Some lab motivation

August 12, 2009 at 10:46 am | | cartoons, grad life

A labmate made this motivational poster. Enjoy!


academic grandfather

June 18, 2009 at 2:45 pm | | grad life, science community

I met my academic grandfather recently: A.J. Sievers was my PhD advisor’s—W.E. Moerner’s—PhD advisor at Cornell. He is a really friendly guy. Also, he told me interesting stories of when he worked for the Varian brothers and beat Hewlett (or was it Packard?) in a ping-pong match!

Perspectives on Grad School

May 11, 2009 at 10:19 pm | | grad life

In the form of my iGoogle homepage

Words of the day:

  • Whinge
  • Fidelity
  • Otiose

Quote of the day:

If you put tomfoolery into a computer, nothing comes out of it but tomfoolery. But this tomfoolery, having passed through a very expensive machine, is somehow ennobled and no-one dares criticize it.
Pierre Gallois

Next Page >

Powered by WordPress, Theme Based on "Pool" by Borja Fernandez
Entries and comments feeds. Valid XHTML and CSS.