in cellulo?

July 30, 2007 at 10:27 am | | help me, literature, open thread

What do you call experiments done in a live cell? Some call it in vivo, but that seems to make more sense for in an entire organism (and some of the cellular work is done in single cells of more complex organisms, such as CHO cells). But it definitely should be differentiated from in vitro experiments, because you’re dealing with life!

How about in cellulo? Sounds sorta weird to me.

Is there an accepted term, even an archaic one? Does anyone have a preferred term?

UPDATE: Andrea in the comments suggest that the correct Latin for would be in cellulis.

From “publish to perish” to “patent and prosper”

July 25, 2007 at 12:35 pm | | everyday science, grad life, literature, news, science community

Hey folks,

I recently came across a very interesting retrospective in the Journal of Biological Chemistry written by Howard Schachman, who’s been engaged in biochemistry research in Berkeley for over 50 years.

Schachman lays out the changing nature of research and academic life as he’s observed them over the past 50+ years. I, for one, am always interested to read about how things have changed and where they’re heading. Here’s a particularly interesting quote:

In 1953, while McCarthyism was rampant, the Federal Bureau of Investigation (FBI) began screening grantees. Based on FBI reports, Oveta Culp Hobby, as Secretary of Health, Education and Welfare (HEW) in the Eisenhower administration, interceded and ordered the cancellation of grants to Linus Pauling and other prominent scientists.

Read on to find out what happened! I guess that president Rove’s clumsy meddling isn’t as bad as it can get.

monkey hard—with a vengeance

July 25, 2007 at 8:23 am | | literature

Well here’s a great paper title. I don’t really know the difference between spite and venge; I’m a human, so I’m full of both. Stupid monkeys don’t even know how to spite others! They probably don’t hate the gays, either.


(click to zoom!)

Andrew sent this article to me and explained it thusly: “this is essentially a scientific study trying to explain why chimpanzees often help people win the $10,000 prize on America’s Funniest Home Videos.”

I thought it was more about researchers getting bitten by monkeys.

sam the nerd

July 24, 2007 at 11:57 am | | nerd, wild web

Oh, no. People are searching for me on Google. Two people came to EDS via an embarrassing search term:


How did they know my nick-name?

pi day

July 23, 2007 at 4:12 pm | | nerd, news

More bad news, everybody: We let another Pi Approximation Day (July 22, or 22/7) pass without any kind of celebration.


We’ll have to be more careful to remember next March 14. Or just celebrate a little every day at 3:14 AM.

(Thanks for the tip, Todd.)

Gone for Good: Tales of University Life After the Golden Age

July 20, 2007 at 7:46 am | | grad life, literature

Somebody recently raised the question: would our professors survive as young scientists in today’s competitive academic environment? After all, their Ph.D. was 4 years, and doing a postdoc was unheard of. I’ve asked this question of several established faculty (John Brauman, Mike Fayer, Vijay Pande, Steve Boxer) and I am watching my cousin go through the tenure meat grinder as I prepare for it myself.

To anyone considering a life in academia, I strongly recommend reading this book by Stuart Rojstaczer (available in the Stanford chem library):


From the blurb:

During the “golden age,” research money flowed freely. But the end of the cold war reduced competition within the international research community and government dollars diminished correspondingly, forcing schools to seek funding elsewhere. These days, Rojstaczer writes, overburdened professors must deal with making their courses easier for students (who seem more interested in heading out into the job market than in getting a quality education), which in turn increases the teachers’ popularity and assures future full classes. The educators must also contend with writing grant proposals, student athletes, and campus politics. Rojstaczer’s is not a pretty picture, but Gone for Good is an important book that suggests that the halls of ivy are not as green and fresh as one might hope. Ron Kaplan

If you’re seriously considering going into academia, reading this book is a must.

Graduate School Money VI: A Comparison

July 19, 2007 at 4:31 pm | | grad life, stipends

Speaks for itself


Graduate School Money V – Return of the PostDoc

July 19, 2007 at 12:54 pm | | grad life, stipends

To follow up on Charles’ theme, I decided to post what you can expect to make as a postdoc in the sciences. The information below comes from the excellent Sigma Xi postdoc survey. Read it and weep.

The salary increase from graduate student to postdoc is not too bad ( ~35%) but one must not forget that the average postdoc is in his/her early 30s, already has a partner/spouse that may or may not be working, and may be looking forward to starting a family:
Most schools base their postdoc salary from the current NIH postdoc stipend rate. These rates are only marginally adjusted for years of experience and do not reflect the differences in cost of living between, say, Ohio and NYC. Furthermore, most schools do not treat their postdocs as students so on-campus housing, medical, gym, and other “perks” are significantly more expensive.

Graduate School Money IV – Revenge of the PhD

July 19, 2007 at 12:08 pm | | grad life, stipends

After reading Charles’ excellent summary, I ran around our lab @ Columbia and surveyed the grad students:

Subject A – Biochemistry Graduate Student

Base salary: ~$28,000
After taxes: ~$24,000

  • Medical insurance covered by Columbia.
  • Monthly Transportation Cost: $100 for MetroCard and occasional taxi
  • Columbia subsidized studio: $900/mo
  • Basic cell phone plan: $55/mo
  • Monthly food expense: $300

Disposable income: $7,740/yr or $645/mo

Subject B – Biology Graduate Student

Base salary: $27,600
After taxes: ~$23,500

  • Medical insurance covered by Columbia.
  • Monthly Transportation Cost: $90 for MetroCard
  • Columbia subsidized apartment share: $770/mo
  • Basic cell phone plan: $55/mo
  • Monthly food expense: $400

Disposable income: $7,720/yr or $643/mo

There you have it – two very consistent data points. Even though the cost of living in NYC is greater than Palo Alto, generous student housing subsidies and inclusion of medical insurance make their disposable income greater than what you have.

stipends changing

July 19, 2007 at 9:07 am | | grad life, stipends, teaching

Charles has been posting his calculations about graduate student pay partially because he is moving and partially because our department has recently had a clandestine change in the pay policy for teaching assistants (TAs).

From the plots below, you can see that, over the last few years, while a TA position pays more or the same one year to the next, the pay increase above the base research assistant (RA) stipend has been decreasing. (HTA and ATA are two different types of non-first-year grad student TAs.)

stipends_real.JPG stipends_ratio.JPG

The real reason for this is that, in 2007-2008, graduate student TAs will now be paid less by their PIs during the quarter they are teaching. And, because our Department Chair went to bat for the students to the University, TAs will be paid above the minimum rate.

It actually makes sense that a PI shouldn’t have to pay his teaching students as much, and that the department should pick up the tab. But that’s not the way Stanford Department of Chemistry has done it in the past. I suspect we’re now in line with how most other schools pay TAs.

Motivated by unhappy granting agencies and an auditing University administration, the faculty decided to fix the students-being-paid-more-than-100% issue by, effectively, paying TAs less.

Frustrated grad students have been reacting to rumors of this happening for the last few months, and then it sorta happened while our back was turned.

Personally, I think it makes sense that a PI not pay a student full-time while he or she is TAing (on top of paying the student’s full tuition and overhead on the stipend)—I don’t want my PI spending more time working on grants. And students should TA for the sake of TAing, not for the extra pay itself. But it’s alway too bad when the University, the Department, and the Faculty make decisions that negatively affect student without even warning them of the impending change, or without explaining the reasons for what feels like a pay cut.

Graduate School Money, Part 3

July 19, 2007 at 7:28 am | | grad life, stipends




Graduate School Money, Part II

July 18, 2007 at 6:41 pm | | grad life, stipends


Graduate School Base Stipend: $26,600


Federal/State Income Taxes at ca. 12.5% : $3,325

Rent at Palo Alto Average* of $904/month (US Census Bureau): $10848

National Average Food Expenditure for Single Male with Moderate Budget of $238/month: $2856

Subsidized Stanford Cardinal Health Care at $342/quarter: $1368

Averge Car Insurance for California at $847/6 mo.: $1694

1/2 Annual Automotive Travel (6250 miles) at average 21 mi/gal at Palo Alto gas price of $3.21/gal: $955

Cell Phone Cost (Cheapest Cingular Plan) at $40/mo: $480

*Note: Stanford Graduate Single Occupancy (i.e. 1 person/room) Housing rent ranges from $640 for Crothers to $994 for the EV studios. The Rate for Rains, Lyman, and EV 2Br is $790. There is an additonal a $27/month mandatory fee for telecommunication and laundry.

Total Income: $26,600

Total Expenditures: $21,526

Estimated Disposable Income: $5074/year or $423/month ($211/paycheck).

Graduate School Money, Part I

July 18, 2007 at 6:37 pm | | grad life, stipends

Stanford Graduate Minimum Stipend (what we’re paid in Chemistry): $26,600

Average Work Hours for a U.S. science postdoc (probably similar to / less than graduate student): 49.8 U.S. citizen (Brumfiel, Geoff; “Taking a Stand,” Nature, 2005, 438, 278-279.)

Average pay/hour (50 weeks): $10.68

Average pay/hour (52 weeks): $10.27


Federal Minimum Hourly Wage: 2008 – $6.55, 2009 – $7.25


Living Wages: Encouraged in Cities/Counties by Ordinance (tax/property incentives)

San Jose Living Wage: $11.35

Santa Clara County (our county) Living Wage: $10.00

Berkely Living Wage: $12.55

Oakland Living Wage: $10.50



2004 Estimates of Retailers Bay Area (Annual Estimates for 40 hr work week, 50 weeks a year)

2004 Average Hourly Wage for Walmart Associate in Bay Area: $10.93

Walmart Annual: $21,860 (Stanford Salaray -$4740)

2004 Average Hourly Wage for All Large Retailers in Bay Area: $17.01,

Large Retailers Annual: $34,020 (Stanford Salary +$7420)

2004 Average Hourly Wage for Unionized Grocers in Bay Area: $15.31,

Unionized Grocers Annual: $30,620 (Stanford Salary +$4020)


Laugh it up, Fuzzball

July 18, 2007 at 9:16 am | | crazy figure contest

The figure is from an economics editorial from the Wall Street Journal. Since nothing I could say can do a better job than Dr. Chu-Carroll, I’ll let him do the discussing. I guess us crazy chemists aren’t the only ones that can fit a 10th order polynomial to 2 points.

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