Archive for the ‘Tweets’ Category


My August tweets

August 31, 2012

30 Aug
@WilliamsCollege chemistry professor Chip Lovett is organizing the first-ever marathon in the country of Belize!

27 Aug
Me, reviewing my luggage: “…OK, the toiletries are packed…” My 5-year-old: “What are toilet trees?”

27 Aug
My girlfriend gets home from a long trip and immediately starts baking. I think it’s hard for her to be away from her oven for that long.

25 Aug
Saturday night in Seattle…. I’m reviewing Romanian grant proposals while sipping diet cola. (And you thought scientists never cut loose?!)

24 Aug
Lance Armstrong gives up fight against USADA, raising questions about his innocence – Yahoo! Sports–raising-questions-about-his-innocence-.html

19 Aug
Seattle bus stop #1530, 9:10pm. My 5-year-old is grilling some smokers about how their cigarette lighters work.

15 Aug
Phil keeps confusing HAWAI’I (home of his Aunt Chris) and IDAHO (our road-trip destination). I think it’s all the vowel sounds.

9 Aug
My 5-year-old son: “The tooth fairy gives you toys even if you’re bad …”
“…because she really wants your tooth, and if she got your tooth and you got nothing, it wouldn’t be fair.”

8 Aug
The frustratometer paper ( offers frustration indices and frustratographs. Can frustromics be far off?

8 Aug
Article title of the day: “Protein frustratometer: a tool to localize energetic frustration in protein molecules” (

6 Aug
I went to a time management workshop this morning. Apparently I should spend less time tweeting.

5 Aug
Today some of my friends did a 3-hour run; I took a 3-hour nap. Who’s to say which is better, really?

2 Aug
My 5-year-old: “Kids don’t like to watch runners run. All they do is run run run run run, and we watch watch watch watch watch.”



My tweets from a talk on peer review by UW’s Fred Rivara, MD, MPH

August 13, 2012

Paper by @DynamicEcology: “Pubcreds: fixing the peer review process by ‘privatizing’ the reviewer commons.”
1:01 PM

Does doing reviews help you get promoted? Not really, Rivara says, but quality reviews help you get onto editorial boards, which DOES count.
12:58 PM

Rivara notes the problem of PIs who don’t do their share of reviews, but stops short of recommending PubCreds solution by @DynamicEcology.
12:55 PM

Rivara: “People who write the best book chapters aren’t my age. People my age just recycle what they’ve already written.”
12:52 PM

Rivara closes with a quote from Ziman (1968): “The referee is the lynchpin about which the whole business of science is pivoted.”
12:44 PM

@NIHforHealth Early Career Reviewer program trains young scientists in peer review.
12:43 PM

NIH grant review criteria: overall impact, significance, investigator(s), innovation, approach, environment.
12:40 PM

Discrepancies among reviewers were studied/reported in a 1993 Nature paper by E. Ernst, T. Saradeth, & K.L. Resch:
12:39 PM

Reviewing results sections: are figures and tables used effectively to tell the story? Discussion: are conclusions justified by the data?
12:35 PM

Brevity of articles is important, says Fred Rivara. The 1953 Watson & Crick Nature paper on DNA structure was 1 page!
12:32 PM

Why be a reviewer? Makes you a better scientist; helps develop your rep; leads to other national positions; a duty of scientific community.
12:30 PM

How do journals select reviewers? Author recommendations, journal database, editors’ contacts, reference lists, paid statistical reviewers.
12:27 PM

Ethics of reviewing: treat work confidentially; respect the intellectual property; tell editor if you had help with a review; disclose COIs.
12:24 PM

Journals have their own copy editors, so there’s no need for reviewers to correct spelling, etc.
12:21 PM

What’s NOT a reviewer’s role? Decide on acceptance/rejection; copyedit; be mean; nitpick; tell authors how they should have done the study.
12:20 PM

More on peer review as seen by Richard Smith (former editor of BMJ):
12:17 PM

Richard Smith’s problems of peer review: a lottery; a black box; “ineffective”; slow; expensive?; biased; easily abused; can’t detect fraud.
12:14 PM

Peer review started around the 1940s. Before that a small group of editors at each journal did all the reviews themselves.
12:12 PM

Most journals rate the quality of the reviews they get back from reviewers: excellent, very good, good, fair, poor, don’t use.
12:10 PM

1st slide: “How journals work” — from submission to acceptance or rejection. His journal rejects ~50% of submissions without review!
12:08 PM

Sorry — Fred RIVARA, not Rivera. He’s editor in chief of the Archives of Pediatrics and Adolescent Medicine (JAMA Pediatrics).
12:05 PM

Today’s UW Biomedical Research Integrity talk: “The what, why and how of peer reviewing” by Fred Rivera, Depts. of Pediatrics & Epidemiology
12:02 PM



Who gives a tweet about mentoring undergraduates?

August 1, 2012

Janice DeCosmo: Tell students in advance how to interact with you. Is it OK to interrupt frequently w/ questions? Or make lists for later?
10:14 AM

Jennifer Harris: Asking “What draws you to THIS project, in particular?” will help you gauge students’ level of interest and motivation.
10:09 AM

How to gauge interviewees’ technical skills? Ask for a reference from a professor or TA from a lab class. Also consider a trial period.
10:07 AM

Janice DeCosmo: Look for evidence of students’ initiative on resumes and at interviews.
10:01 AM

Janice DeCosmo: Disclose your limitations as a mentor (tendency to micromanage, or to have high expectations, or whatever) up front!
9:41 AM

Janice DeCosmo: Remember that mentoring is a relationship. Both mentor and mentee have expectations and needs.
9:37 AM

The 4 men at the seminar are all along one side of the square around which we are arranged. The 11 women are on the other 3 sides.
9:24 AM

My question: how can we best predict which undergrads will succeed in research?
9:20 AM

Question from seminar attendee: how do you get money for students without using your own grant?
9:16 AM

After 7 years of mentoring undergrads, it’s time to find out what I’ve been doing wrong. 🙂
9:05 AM

Today’s seminar: “Mentoring the Undergraduate Research Experience” with Janice DeCosmo and Jennifer Harris of @UW.
9:04 AM


July tweets

July 31, 2012

29 Jul
Me, to my 5-year-old: “Let’s go to the grocery store.” Him: “No, let’s go home.” Me: “Phil, we ARE home.” Him: “Then let’s just stay here.”

28 Jul
I have seen the future of American ultrarunning. Its name is Sage Canaday. 6:16:10 course record at #WR50 today — Holy Krup!

26 Jul
Overheard today: “Is that Z as in ‘zot’?” LOL. How should *they* know how to spell a word that you just made up?

26 Jul
John Boswell (@musicalscience) has already raised $12K for his next album of science songs! Go John go!

25 Jul
Phil wants to be a Smurf but doesn’t want to wear blue. “Smurfs wear clothes that aren’t blue, Dad. I don’t want to be a *naked* Smurf…”

22 Jul
Felt entitled to ice cream with friends on a cool, windy Seattle afternoon. Fed up with waiting for ice cream-appropriate weather!

21 Jul
Went to a contra dance last night & stayed for over an hour. Those who know me well know how remarkable this is.

19 Jul
Leila Z. ’00 cooked dinner for my 5-year-old, then explained Poe’s “The Telltale Heart” to him. A very @WilliamsCollege evening!

17 Jul
Today I caved in to my cravings and had corn on the cob and key lime pie for breakfast. Is this what it’s like to be pregnant?

14 Jul
My son insists that we watch the Air Bud films in order. Maybe he should worry less about continuity; 4 different actors play the dad.

11 Jul
Tonight my son cheered up a crying girl by repeatedly bashing himself in the head. I’m really proud of him . . . I think.

11 Jul
I’m heading to the annual barbecue of the UW Division of Allergy & Infectious Disease. I suspect the meat will be well-cooked.

9 Jul
Tonight I wandered outside and talked to 6 neighbors. That’s 6 more than last week. Summer has arrived in Seattle at last!

9 Jul
The woman in the apartment upstairs has a kitten whom she named Shalom. I guess that makes it a “Hello Kitty.”

5 Jul
My son Phil (5 years old): “Do you have socks?” Leila: “No, I’m not wearing any socks.” Phil: “But do you live with socks?”

2 Jul
My 5-year-old son, to the bus driver: “Have a good day!” Then, to me: “That’s the nicest thing I could think of.”

1 Jul
Just saw “We Bought a Zoo.” My 5-year-old son: “I wish *we* could buy a zoo … so I could wear one of those little [zookeeper] shirts.”


Ethical tweeting

July 27, 2012

@smfullerton on the video’s strength: a realistic depiction of the many chances we have to speak up or stay silent, and the consequences.

OK, this “Reverend Lee said that my daughter is a hero” part IS a bit hoaky.

The villain of “The Lab,” who falsified data, is a postdoc named Greg Anderson. Same name as Barry Bonds’ sketchy trainer!

“… The little punks have always counted because, in the long run, the character of a country is the sum total of its little punks.”

Kim’s cousin, quoting Gary Cooper: “I know a lot of you are saying, ‘What can I do, I’m just a little punk. I don’t count.’ …”

Quote from grad student’s mom: “Why didn’t you go into law like your brother? He never has [ethical] problems like this!”

Video interlude: postdoc creates Johnny Cash / Wu Tang Clan mashup. Hilarious!

(I am texting my poll responses via , not via my phone.)

1st vote: Should Kim just sign the proofs, or tell Greg she needs to read them? “No, slapping him is not an option.”

American Idol-style polling on the seminar will begin soon!

When the Office of Research Integrity first came out w/ the video “The Lab,” @smfullerton thought, “Oh, how hoaky.” She likes it better now!

Research misconduct: “The big ‘duh’ of the BRI series,” says @smfullerton … Don’t lie, cheat, or steal! Yet not always black & white.

Seminar presenter/moderator: @smfullerton. Website for “The Lab” (cool interactive video):

Today’s UW Biomedical Research Integrity seminar: “Avoiding research misconduct: a virtual experience interactive learning simulation.”


Another seminar, tweetified

July 26, 2012

I’m continuing my test of whether live-tweeting from seminars improves my attentiveness. Below are today’s tweets (in reverse chronological order, as usual).

* * * * * * *

Slide title: “Integrating phylogeny with GIS [geographic information systems].” Again, I’m lost, but this sounds sexy as hell.

Hepatitus C genome: only ~9600 bases long (not base pairs — it’s RNA!). About the same length as HIV.

“Occult” HCV infection: patient seems cured, then (years later) presents an infection related to the original one (not a new infection).

“Bayesian Skyline” plot. Don’t understand it, but love the sound of it.

Rebecca Gray’s talk is reminding me how bad I am at understanding phylogenetic trees. @phylogenomics would be ashamed.

Where data are lacking, HCV is often assumed to be like HIV, a fellow RNA virus.

Problems with studying HCV: lack of animal model, difficulty with in vitro culture, long asymptomatic period.

Global burden of hepatitis C virus (HCV): 180 million people are infected! That’s ~3% of the world!

URL for Rebecca Gray:

Today’s UW seminar: “Infectious disease evolutionary dynamics: the strange case of hepatitis C” by Rebecca Gray, Ph.D.


Tweetomics: an omics seminar summarized via Twitter

July 19, 2012

[my tweets from a seminar I went to today, presented in reverse chronological order]

The middle-author problem: if you get little credit for your role in a study, where’s the incentive to check & vouch for the whole project?

Larry Kessler: As part of their training, grad students can re-run publicly available code and see whether they get the same results.

One Duke prof falsified a line of his CV, saying he got a Rhodes Scholarship … to Australia. Not really Rhodes Scholar material.

Kessler: Also, letters of concern to journals should not just be forwarded back to the authors of the article under suspicion.

Witten: How can 2 reviewers fairly evaluate a multidisciplinary 30-person paper? No way to do that, plus it isn’t their job.

Question from audience: role of journal editors and peer review in Duke case?

Kessler: Duke scientists wanted fame, promotions, grants … but weren’t aiming for royalties on diagnostic test. Wasn’t about $$ per se.

@smfullerton asks about conflict of interest, the elephant in the room. Duke scientists had vested interests in clinical trials?

Funders support discovery of exciting new approaches but are reluctant to support validation, so validation naturally gets neglected.

FDA needs to develop a guide on how to bring an omics test to the clinic. It’s been “putzing around” for a decade, Kessler says.

Institutions don’t always support multi-discipline work to ensure proper credit and accountability. What about middle authors?

There is a “bright line” between test discovery/validation on one side and evaluation for clinical utility/use on the other.

Kessler says we think we know how to do discovery and test validation, but lots of mistakes get made. Don’t validate on already-used data!

IOM report explains how to “correctly” translate omics diagnostics from bench to beside, and lists responsibilities of various parties.

Institute of Medicine report was released in March. Larry Kessler (who served on the IoM committee with Witten) will tell us about it now.

Aftermath of Duke debacle: dozens of papers retracted, careers of 162 coauthors jeopardized; public faith undermined.

The Duke problem was not just an academic one. The Duke papers, with their mistakes, were being used to guide clinical trials!

Keith Baggerly & Kevin Coombes of MD Anderson reported mistakes in publicly available Duke data (Annals of Applied Statistics 2009).

Concerns about Duke work were initially brushed off as “squabbles among statisticians.”

2006: Duke people started publishing high-profile papers on using omics to predict cancer outcomes. Others had trouble replicating results.

Challenges of omics data: (6) multidisciplinary analyses require cooperation and trust.

Challenges of omics data: (5) it’s hard to apply intuition to models with thousands of genes. Hard to tell what the data *should* look like.

Challenges of omics data: (4) expense of experiments and limited samples mean that results aren’t always validated.

Challenges of omics data: (3) complicated experiments and analysis increase the likelihood of errors.

Challenges of omics data: (2) Batch effects may cause results in one lab not to generalize to other labs.

Challenges of omics data: (1) many variables (e.g., genes) vs. number of observations (e.g., patients) leads to high risk of overfitting.

Recent @nytimes series “Genetic Gamble” highlights promise and difficulty of using genomics to guide cancer treatment.

Daniela Witten’s definition of omics: characterization of global sets of biological molecules (DNA, RNA, protein, metabolites, etc.).

Today’s topic: recommendations of Institute of Medicine panel on responsible use of omics data in clinical research.

Website for UW Biomedical Research Integrity program:

BRI seminar will feature Larry Kessler and Daniela Witten, with moderation by @smfullerton.

Now attending the UW Biomedical Research Integrity seminar “Responsible Research in the Era of Omics: Past, Present, & Future.”


Short and tweet: June Twitter highlights

July 1, 2012

28 Jun
My 5-year-old, after school: “Remember those cookies we made for my teachers [last month]?” Me: “Um … yeah?” Him: “They want some more.”

28 Jun
My son, 5: “Dad, why do tears come from baseball players who win a game?” If only I had the time & knowledge to answer that question fully!

18 Jun
My 5-year-old boy on John Williams’ Star Wars soundtrack: “I like the flute.” What a sensitive kid he is, occasionally….

18 Jun
Monday morning heaven: “Centerfold” cover by @Prydein with bagpipes on the “na-na” part. Stream it at!

17 Jun
Greg’s concise guide to language and politics: palindromes are cool; Palin-drones are not.

16 Jun
Surprise #2 of the day: a child vomiting all over the floor at a 4-year-old’s b-day party. These kids party HARD!

16 Jun
Surprise #1 of the day: @dominos pizza at the Cougar Mountain 8-mile trail race! Thanks, @SeattleRunning and @NWTrailRuns!

13 Jun
This may be the closest I ever come to giving a TED Talk: Songs are at 15:00, 21:05, 30:17, 36:10, 39:00, and 43:02.

5 Jun
Wed., June 6: I will be the guest (9:30-10pm) on the MetaQuizzical Cafe radio show (9-11pm) hosted by @4concerts!

2 Jun
I’ll sing 3 science songs today at the @Seattle_SciFest Science expo (3:15 at Seattle Center’s Fisher Stage). Thanks to @PacSci for helping!


Selected May tweets

May 31, 2012

30 May: Q. What do you call a neutral tweet with positive and negative aspects? A. A twitterion!

30 May: <36 hours left in which to donate to my "Sing About Science" #SciFund project! Great rewards, eternal gratitude, etc.

27 May: My 5-year-old, betraying his Seattle roots: “Santa can do anything with magic…. He can *even* use magic to MAKE COFFEE!”

24 May: … to a mellow electric guitar piece representing the stages of sleep ( #BioExpo12

24 May: … #BioExpo12 student compositions ranged from a wailing saxophone piece representing schizoaffective disorder ( …

24 May: It was great fun to judge student science music (and catch up with @brianglanz) again this year at #BioExpo12….

23 May: My math and science song database has just surpassed the 6000-song mark. ~2200 of these can be heard online for free!

23 May: From Facebook friend Scott Smith (San Antonio, TX): “Is life fair? Short answer: No. Long answer: Noooooooooooooooooooo.”

21 May: The brownies I was making for this AM’s lab meeting came out badly, and I had to eat a mound of half-cooked brownie goo. Where’s my medal?

19 May: One key to happiness is modest expectations. Especially when sitting down to watch “Alvin And The Chipmunks” with one’s 5-year-old.

19 May: The 2012 Seattle Parasitology Conference at @SeattleBioMed included a Plasmodium life cycle sing-along!

15 May: Egads! I think I have a data hangover from consuming too much data at #soSEA last night. It was fun at the time….

14 May: @DustinSmith of @tableau: Data are more like food than like money. Over time, staleness ensues! Get the data out there while fresh! #soSEA

14 May: Eugene Kolker is Chief Data Officer at Seattle Children’s. Hadn’t heard that title before, but I like it! #soSEA

13 May: This morning’s Lego-building innovation: a police convertible. Possibly less safe than normal police cars, but VERY chic.

12 May: Phil’s much-anticipated playdate with his pal Addison is this PM. We’ve been chanting, “Saturday is Addi day! Saturday is Addi day!”

11 May: 5K time trial in 16:33 at Green Lake this morning with Tim Billo. Just like the old days at @WilliamsCollege, only much slower!

11 May: Last night Phil objected to having to write his five teachers’ names all in one sitting. You’re right, poor thing…. What was I thinking?

8 May: To quote Curley from Oklahoma!: Oh what a beautiful mornin’, oh what a beautiful day….

7 May: Dear Internet: Can I have some money? It’s for SCIENCE!

5 May: In an adventuresome mood today; bought provolone cheese slices instead of Swiss. Next stop, lowering sunscreen SPF from 50 to 30.

2 May: Today’s parenting milestone: Phil’s first eBay bid. He knows a good deal on Lego clone troopers when he seees one!

1 May: Was hoping a 4am run would help me fall asleep again. Got a great song idea along the way; now I’m more restless than ever.


@trappedinlab’s April tweets

May 1, 2012

29 Apr: I had almost given up on cleaning behind the fridge, but finally managed to do it this morning. Don’t stop believin’!

21 Apr: I am psyched that Phil wanted to try kayaking, but wish that he had lasted more than five minutes.

19 Apr: Phil saw tasers at the UWPD open house; now his lego clone troopers are tasering each other. Great to see him apply what he’s learned.

16 Apr: tweets from #soSEA

13 Apr: Just mixed hot cocoa mix with cold milk instead of hot water — big mixtake. What a clumpy mess.

9 Apr: I’ve decided to write a Nora Ephronesque rom-com novella. Here goes nothing.

8 Apr: I wanted to clean the patio, but Phil wanted to play jail. The compromise: a prison-camp game where the prisoners must sweep the patio.

7 Apr: New bedtime story routine: Phil offers his bed with the phrase, “Sit anywhere you’d like.” It’s a small bed, but I like the hospitable tone.

5 Apr: Global Health Trivia Night at Seattle BioMed was a hoot, but I missed the bonus question about Bon Jovi’s “It’s My Life.” Zut alors!

3 Apr: Just got a smartphone. After 10 days & 2 trips back to the Sprint store, I can finally make hands-free calls & retrieve voice-mail.

2 Apr: Tonight I’m blowing off steam by playing loud, angry piano ballads.