Tuesday, July 31, 2007

Dead Crows

Lately, my walks to and from bus stops or around campus have included a little foraging for berries, flowers, coyote scat and other cool stuff. A consequence of this is that I notice (more than usual) animal carcasses. Since I am on the lookout for an intact crow's head for a Wunderkammern project I am working on, there are a few health issues I need to pay close attention to. Namely, West Nile Virus. If you see a dead crow and live in a region where WNV has been detected, there's a good chance your county has a reporting system in place. In King County, you can call 206-205-4394 M-F 8a-5p, or go to the easy web-based form I just used to report two crow roadkills I saw on Saturday.

Grand Rounds 3:45

The Health Business Blog is hosting this week's medical blog entries. I contributed a mini-rant about the current political situation surrounding the United States Surgeon General. If you need a coffee break, there are several other good articles linked there.

Monday, July 30, 2007

Too Busy To Read This?

If you are too busy to read this article, then you should definitely read it. Dr. Free-Ride has posted some thoughtful takes on what it means to balance, er... juggle numerous tasks in the context of academia. She makes use of a good metaphor and makes it work really well. I'd say I am in a 'don't throw any more balls up into the air' phase of my life.

Research Subject Update

My long-time readers will recall a post I made back in June featuring some cousins of my research subjects.

Today, I am proud to present a sequel.

It's too bad that the rodent master calls them mice. These are clearly rats!

Sunday, July 29, 2007

Meddling With Public Health

Today's Washington Post revealed the specific machinations behind the Bush administration's gagging of former Surgeon General Richard Carmona. Carmona testified to congress earlier this month about the obfuscation and silencing of reports from the SG's office. There are no surprises here, except for perhaps the extent of nepotism and good-'ole-boyness in government right now.

The individual responsible for carrying out the long arm of the Bush/Cheney law is William Steiger. Heres some background:
Steiger, 37, is a godson of former president George H.W. Bush and the son of a moderate Republican who represented Wisconsin in the House and hired a young Dick Cheney as an intern. The elder Bush appointed Steiger's mother to the Federal Trade Commission in 1989. Steiger's parents, now deceased, were "lifelong friends" of the Rumsfelds and the Bushes.
In reference to a report on global health, Carmona said that a senior Bush aide (now known to be Steiger) told him "this will be a political document, or it will not be released." The Post reports that
Steiger said that "political considerations" did not delay the report; "sloppy work, poor analysis, and lack of scientific rigor did." Asked about the report's handling, an HHS spokeswoman said Friday that it is still "under development."
This all comes from a man without any public health or scientific experience or credentials. So what are his credentials, apart from being born into the right family? A Department of Health and Human Services spokesman invites us
"to look at his skills as an executive leader in spite of the fact that he doesn't have a medical degree or a public health degree."
I am not buying that. How about this insight from a different career HHS employee:
"Steiger always had his political hat on," he said. "I don't think public health was what his vision was. What he was looking for, and in general what he was always looking for, was, 'How do we promote the policies and the programs of the administration?'"
There it is! The chief qualification for being a Bush appointee: Never cautious about giving your boss an "Atta Boy!" Steiger had it. Carmona didn't. Carmona's out. Steiger's in. Let's tell him what he's won: Steiger is now awaiting a Senate vote on his nomination as Bush's ambassador to Mozambique. Send your senator an email. Ask him or her to vote no for Steiger. Tell the Senate you've had enough of Bush's patsies. For his political meddling with public health reports, Steiger gets a thumbs down from me on scientific integrity. From Bush et al., he gets an ambassadorship? Just say no!

Saturday, July 28, 2007


Two weekends ago, I traveled back in time to an age when science and art, nature and religion, and truth and beauty weren't so disconnected as they are now. In the Renaissance, rich men collected natural specimens for display in rooms and cabinets called Wunderkammern. They would host parties where guests would philosophize on the structure and order of the natural world. Two notable descendants of the wonder cabinet phenomenon live on today: circus freak shows and natural history museums. A very interesting article in Cabinets magazine presents more history of this phenomenon. For more info or nice photos, check out the Kircher Society, ArtLex, and this blog. World's Fair is even a blog inspired by cabinets of curiosity and wonder rooms.

My introduction to Wunderkammern was via the Pratt Fine Arts Center. I took an assemblage course called "Assembling The Modern Wonder Cabinet." It was cathartic for me to escape (for a few hours a day, at least) from the lab to engage in an activity more creative and less analytical than my current scientific endeavors. It was also really fun to work in a class environment where everyone was enthusiastic to help each other. Art, like science, can be more meaningful when conducted in a collaborative environment.

I have included here a few images of my colleagues' cabinets. Click on the photos or visit my Flickr page for larger images. We will all be part of a show at Seattle's Center on Contemporary Art from August 25-September 25, 2007. Stay tuned for more information about that.

My piece (at left) is a 12" x 16" man's jewelry box that opens to reveal an arrangement of rodent parts. The bones were collected and sorted from owl pellets, while the soft tissue is fixed and paraffin embedded, as would be done for tissue specimens in research labs and hospitals. It is titled, Gratiaedonatus oriens. The italicized Latin name evokes the genus and species binomial nomenclature biologists use to classify organisms.

For a directory of the parts displayed and more cabinets, please visit my Flickr page.

This course opened for me many doors to new ideas. It will be fun to explore the intersection of science and art as I assemble future Wunderkammern.

Thanks to Ipei for the pictures.

Friday, July 27, 2007

Carbon Footprint: Cell Phone Chargers

Sorry for the skipped entry in the Carbon Footprint series. My footprint totally died and I had to recharge it for, like, two weeks.

Which brings us to this week's recommendation: battery chargers. Did you know that chargers use power even when the electronic device is not plugged in? In fact, 95% of the energy used by mobile phone chargers is wasted. Why is this? Most electronics these days use batteries, and batteries need direct current for charging. That little black box that blocks the other outlet whenever it's plugged in does not 'know' if the phone is plugged in at the other end; it just goes about its business converting alternating current from the socket into low voltage direct current for your battery. This activity is called a phantom load. This kind of appliance is known in green circles as a vampire.

My AC adapter is rated at 4.8 volts and a 350 mAmp current. That means that fully loaded the phone's battery resistance is almost 14 Ohms. Ohm, my! When the phone is not plugged in, the resistance has to be much lower, especially since the voltage from the wall is 120V, and according to some engineers at Cambridge, a lonely charger sucks a miniscule 0.472 Watts. Even so, according to a CNN article, chargers of all kinds make up fully 5% of your electricity bill every month. Unplugging them is an easy way to cut your bill and your carbon use. Plus, it will be easier to use other devices in the outlet without that bulky plug in the way.

Update 8/19/07: I have altered this column slightly to address concerns of accuracy brought up in the comments below.

Thursday, July 26, 2007


You think you get altruism from religion? Democracy? Aunt Edna?

The King of the Nerds notes over at The Stranger how waving someone through the intersection (Seattle drivers: GET A CLUE!) is a trait that even lab rats have. Sadly, this causes me to lose a little respect for those cute little rodents. A 500 word article in a free weekly that features a spot titled "Drunk of the Week" right next to the King's is not enough to convince me there is no learned component of altruism. But a weekly science column in a pop culture rag? Now, that's looking out for his fellow man.

Wednesday, July 25, 2007

Civic Scientist Role Model?

I want to be like this when I grow up. So excited about science! So talkative about science! As a bonus, Neil deGrasse Tyson blows Jon Stewart's mind.

I particularly like, "You carve through what is known and you come to this precipice between what is known and unknown, and that is where the research scientist lives."

Special K: Cures What Ails Ye

Ketamine is an injectable drug used in anesthesia that works by blocking the NMDA receptor in the brain. It is known on the streets as "Special K" because of its dissociative and hallucinogenic effects. (You're removed from pain and worries and see crazy stuff.) I use ketamine in the lab for rodent sedation and pain reduction.

A recent press release from the NIH, reported by Science Daily, announced a newfound effect of this drug: anti-depressant. Evidently one sub-anesthetic dose reduced the symptoms of depression in patients resistant to all other anti-depressant therapies. The effect was not trivial. From the NIH press release:
Depression improved within one day in 71 percent of all those who received ketamine, and 29 percent of these patients became nearly symptom-free within one day. Thirty-five percent of patients who received ketamine still showed benefits seven days later. Participants receiving a placebo infusion showed no improvement.
That is something else! Due to its status as a controlled substance and the hallucinogenic side effects, it may be a while before this treatment gets approved. It is exciting none-the-less that there could be an entirely different approach to treating depression.

Tuesday, July 24, 2007

Call for Entries

Having spilled 1.5 N hydrochloric acid on my pants and shoes this afternoon and witnessed with chagrin the chromatic effect of acid on leather and fabric, I thought that it might be fun to connect with others over 'ruined' lab garments.

In my case, the leather on the shoes turned from grey-beige to purple, but was rescued after application of a Borax buffer.

The pants turned from brown to pink and were not salvaged.

Anyone else out there have a sad story of lab-affected clothing?

Monday, July 23, 2007

Seattle Coyotes

I made a post recently about the coyotes that have taken up residence this year in the woods near my apartment complex, so was pleased to read on the front page of the web version of the Seattle P-I about the rise of the urban coyote in Seattle. Because my wife and I work long and odd hours in the lab, we regularly encounter these cute little beasties on our walks from the bus stop. We have seen a parent and 4 pups together in our parking lot, as well as numerous singles. Once one sat near the common pool area just checking out my wife as she walked by. We most frequently see the coyotes at the top of a parking lot, so I explored that area last weekend, and found lots of evidence of their presence. My treasures included freshly dispersed grouse feathers, worn paths, occasional tracks and lots of scat. I dissected some of the scat to find crushed large bones, a few rodent femurs and several bird talons. Some of the scat consisted entirely of fur and hair. Thankfully, my wife thought this little dissection project was interesting enough to allow me to do it inside our apartment!

Many of the comments about this article (& the content of the story) over at the P-I focus on the predators' impact on pet populations. Because of my allergy, I have never been very fond of cats, but my wife is. Whenever we encounter a friendly cat on our walks around the neighborhood, my wife pets it and give it a friendly reminder to stay close to home so as not to become coyote chow. I haven't heard her telling the same thing to the rats and moles...

For lots of great info about coyotes, visit the Washington Department of Fish and Wildlife site. If you see a coyote, you can report it at Northwest Coyote Tracker, as featured on King5 (click for video.) Monday 7/23. The Google map appears to be focused in south and central Seattle. I'll be emailing the mapkeeper my reports to get more representation from No'Seattle!

Saturday, July 21, 2007

Messin' With Me!

A couple of months ago, Qiagen took some liberties in representing the peer-review process in order to sell PCR kits, but a recent ad from Promega makes an offer that's tough to pass on!
It really is too bad that I've already purified all of the DNA I need for my dissertation... I may just have been convinced to buy this thing-a-ma-bob.

Friday, July 20, 2007

Framing Science in Seattle

It's almost final! Chris Mooney and Matthew Nisbet will be coming to Seattle October 5 to give their Speaking Science 2.0 presentation. The Forum on Science Ethics and Policy is excited about this opportunity to introduce both scientists and the public to the importance of understanding and controlling the context in which science is discussed.

Mooney is the author of The Republican War on Science and recently Storm World, a Seed Magazine writer and Science Blogger. Nisbet is a communications professor at American University, studies framing theory, and writes the Framing Science blog.

To prepare for the event, check out this Daily Show clip of Mooney talking about his first book.

Stay tuned for more information!

Thursday, July 19, 2007


Want to plug in to your local blogging community? Register at We101. And then get your friends to register. It's a new site, but it seems like a better way to meet local bloggers than any other blog cross-reference I have yet encountered.

Wednesday, July 18, 2007

Damage Control...

Today's Science Daily reported a study by a Boston research group (Mark Keating's) that has identified a drug delivery technique using a drug called periostin that could rebuild heart tissue without stem cells. This drug causes heart cells to re-enter the cell division cycle 100 times more than normal 12 weeks after a mouse was given a heart attack. In any other tissue, this abundant increase in division would cause a tumor. But since heart cells hardly ever divide, what they saw was an increase from 0.01% to 1.0% when the marker for cell division (BrdU for my biologist readers) was given for 6 days. Just as a way of reference, that much BrdU given to an animal would cause almost 50% of the intestine to be positive.

These drastic increases in cell division are what is needed in order to harness any latent ability in the heart for cell division. While this group did find that heart function improved after treatment with their drug patch, it is unclear to me whether this is due to the effects of cell division or other effects of the drug, namely different scar properties.

The original document (needing institutional subscription) is here.

Canada Declares War on Pittsburgh

Following the revelation that federal and county officials rounded up and exterminated 272 Canada geese in Allegheny County's North Park, Canadian Parliament moved to honor a long-standing treaty with GeesePeace by declaring war on Pittsburgh, Pennsylvania. The Canucks are in for a tough battle, however. County parks director Andy Baechle reports that
they had two people out on the lake in canoes and a guy on land with a laser
rounding up the geese. The geese were collected in cages and shipped to a meat processing plant in Latrobe, PA. No word yet on whether the plant is in any way connected with Rolling Rock beer. The Pittsburgh populace has little to fear. Unlike some countries, in Canada, 'declaring war' is synonymous with 'pursuing diplomacy.'

Monday, July 16, 2007

Grand Rounds

This week's Grand Rounds carnival is excellently curated at Vitum Medicinus. Head on over there for some coffee break reading about all things medicine.

Friday, July 13, 2007

Wave Metaphor

I think I just let go of the tow rope.

I can't wait to drop in. Hopefully there will be more to my dissertation by the end than a bunch of sea foam...

Thanks to blogfish for the link.

Thursday, July 12, 2007

Movie Review: Arctic Tale

Yesterday could well have been the hottest day Seattle will see this summer: 97°F.

Consider now how I spent that hot evening: sitting in an air conditioned theater watching a movie about polar bears and shrinking ice fields. The irony is thick enough to walk across.

I snagged a pair of the UW's Program on the Environment's free passes to an early screening of Arctic Tale, so took a little break from labwork to treat my wife to a nature movie. The bottom line is that this film has amazing cinematography, colloquial narration and a message: the earth is warming, the ice is shrinking, arctic wildlife is in peril.

Two summers ago, America's hearts belonged to a pair of emperor penguins. Morgan Freeman introduced these birds' mysterious life cycle in an anthropomorphized account of the power of family. Never mind that the penguins spend much of their time in same-sex arrangements... This time, Queen Latifah has the task of telling the coming-of-age account of Nanu the polar bear and Seela the walrus.

Let's start with the pictures in this film - they are its best attribute. Who out there has seen footage of underwater walrus courtship? Cameos from pods of narwhals under the ice scrappy foxes and several species of bird keep the animal diversity quotient high. And everybody loves polar bears, right? Kids will like that the film's stars are just kids themselves, and adults will appreciate the beauty of the white landscapes. In a nod to the families with small children, when the bears catch prey, the most gruesome parts are kept off the big screen. The cinematic innovations, including polar shark cages and adaptations for the sub-zero temperatures made by director Adam Ravetch pay off big time. I was sad when Seela and Nanu had their own daughters, because that meant the nature eye-candy was running out.

More than in March of the Penguins, Arctic Tale integrates the urgent message of the negative human impact on the arctic climate. That Al Gore's daughter contributed to the script could have something to do with this. Everyone will catch the not-so-subtle message that these arctic mammals' ways of life are in serious trouble because humans use the wrong lightbulbs and don't carpool. You know the 'ice is melting' message will show up sometime, and part of the film's suspense lies in waiting for it. Anthropomorphizing the cubs' adventures may not be the only way to get climate change on the big screen (Don't forget about The Day After Tomorrow's Inconvenient Truth!), but it may be the best way to connect with kids and families. Some people might complain about Queen Latifah's cutesy descriptions of the animals' escapades. Corny is my style, so I'll let the others complain.

One element of the film that I appreciated is that the directors did not feel the need to balance time between the male and female 'characters.' With walruses and polar bears, the moms do the parenting. I learned that a walrus sow teams with an older female in the herd family unit to assure offspring survival. While Queen Latifah calls that partner "Auntie," it is unclear how close in relation the parents are. Here's an echo from Penguins: maybe same sex parents confer increased fitness in a population. Males make appearances as potential agents of infanticide and food hoarders and then have a short stint as boyfriends. Sounds about right. In the end, this is a story about preparing young for a challenging future. Seela and Nanu succeed, but what about our children?

Although some accounts of release date vary, I think Arctic Tale is set to debut in selected theaters July 25, with a wide release planned for August 17. A website, http://www.arctictalemovie.com/ has a trailer, but it takes a while to load, even with a fast connection. If you have time, stick around for the credits - I learned some new ways to decrease my carbon footprint. And if you are really patient, look for the message after the production company's mastheads. (Where the 'no animals were harmed' message usually is.)

Wednesday, July 11, 2007

Science Writing

Now that I have a good collection of experimental results, I need to shift from amateur science writing to writing science professional for the next few weeks. I'll be posting here only the most interesting ideas that cross my desktop. In the interim, consider checking in on some of the topics I post about the most. I've made some recent contributions from the center about one element of the abortion debate. Or, while I sort out some stem cell data, you could mull over some stem cell policy. Give the planet a break and consider some ways that you could lessen your impact on global warming. Maybe you are interested in some of my takes on the MD/PhD combined degree physician scientist training program and the interface between science and medicine. Finally, this week I will be collecting hearts from the last of my animal research subjects. While I do that, you should surf over to check out some of their cousins hamming it up for the camera.

If you have already read all I have to offer and need more, there is good stuff at two carnivals I recently participated in: Carnival of the Blue and Christian Carnival CLXXX. Dr. Free-Ride and DrugMonkey reliably provide thought-stimulating posts at their blogs, so give them some visits as well. Have a great week!

Tuesday, July 10, 2007

America's Next Top Doctor

The confirmation hearings for America's Next Top Doctor are in a couple of days, so hopefully you will start to hear something about that in the media. The first big story I came across came by way of a House Oversight and Government Reform Committee hearing where the former Surgeon General spoke. From what I can gather, Dr. Richard Carmona, a Bush appointee, was interested in applying scientific evidence to the practice of medicine and public health. He was most notably silenced on his perspectives concerning human embryonic stem cell research, and a commitment to comprehensive sex education.
Carmona reported that his Surgeon General predecessors - Republican and Democratic appointees - told him, "We have never seen it as partisan, as malicious, as vindictive, as mean-spirited as it is today, and you clearly have it worse than anyone's had."
It is sad how familiar this refrain has become. From his prepared comments (I recommend listening to these words from his own mouth in an online NPR segment):
"The reality is that the nation’s doctor has been marginalized and relegated to a position with no independent budget, and with supervisors who are political appointees with partisan agendas. Anything that doesn’t fit into the political appointees’ ideological, theological, or political agenda is ignored, marginalized, or simply buried."
For respecting the principle that public health should be based in sound science rather than a political agenda, Carmona's term was not renewed. Let's see if Dr. James Holsinger, the next appointee in line for this will be able to toe the Administration's line. If he does, he deserves to be sacked in 2008. If he doesn't, good for him. Holsinger might be facing an uphill battle; comments denigrating homosexuality have already earned him two 'no' votes on the Senate Committee on Health, Education, Labor and Pensions, who will be holding the confirmation hearings this week.

Update 7/13/07: Yesterday, Dr. Holsinger testified for the first time. Of note was this statement referring to an anti-gay position paper he wrote for the Methodist Church in the early '90s:
"First of all, the paper does not represent where I am today. It does not represent who I am today," Holsinger replied. He said he was not anti-gay, and that he wrote the paper in response to a request from religious scholars who wanted him to summarize the medical literature.
Which scientist among us has never changed his or her mind in the face of evidence that contradicts previous assumptions or hypotheses? Isn't the point of bringing science and/or rationality into the political process so that people will change their minds to adopt a truer course of action. Somehow this always gets mixed up in that political character flaw known as flip-flop.

Carmoma's prepared remarks to the committee are available here.
A nice NPR review of Holsinger's testimony is here.

Post-Abortion Syndrome

A continuing debate about "post abortion syndrome" is raging over at the Seattle Post-Intelligencer editorial page. For a quick summary, see my post from a week ago. In a guest column, Sarah Prager plays some denialism cards in an effort to snuff out the possibility that such a syndrome exists, or that there are negative emotional consequences of abortion. Check out the entire deck at the denialism blog. The first card she plays is the "No Problem" card, which happens to be a common chorus in denialism. By citing that 76% of women experience relief after an abortion, she relegates the 17% of women who do feel grief into a category of extraneous side effect.

In citing that 39 million women undergo abortions sometime in their life, Prager plays the "Consumers Want It" in reference to the service of abortion. That a quarter of the female populations receive abortions is a remarkable statistic, and is one that deserves attention. It should not be cited as proof for the status quo.

I am glad that the columnist did not make the most frequent argument made in the abortion debate, the "Our Rights" card. When this one is played, it becomes impossible to keep an open discussion about the topic. And in an environment where opinions about abortion are so divided, I think that closing the door to dialogue is a bad idea.

Don't misunderstand me, I think that abortion is well within a woman's right to choose her own health care options. I also subscribe to the Clinton dictum that abortion should be legal, safe and rare. I am frustrated when folks use statistics as a screen for issues that could lead toward a resolution of the argument. What am I saying? This argument will never be resolved!

Monday, July 09, 2007

Combined Degree Programs

I am part of an NIH-funded program that has been around for more than 30 years. The combined degree MD/PhD training program, called the Medical Scientist Training Program (MSTP, pronounced "messed up" by some of us) serves a need to better bridge basic science with clinical implementation. The idea is to train impressionable young scientists and clinicians in the ways of science AND medicine so that when they grow up, they can speak the same language and navigate the varied cultures of science, medicine and engineering. The result is a long, sometimes grueling path leading to a career in academic medicine. Every year, another 300 or so students sign up for this gig. One benefit of these programs is that we trainees don't have to pay for school, and get a livable stipend. The other side of the coin is that upon graduation we each enter a lifelong fundraising campaign to support our research. The big donors here could be private industry, but usually the benefactor is the Federal Government, via the National Institutes of Health.

Well, the NIH is seeking advice about how to reform the granting process so that the money (your taxes) they spend is most effective. For instructions on how to give advice, switch to this post. To hear one of my 'creative' ideas, keep reading.

I recently entered Seed Magazine's science writing contest. (The topic was science literacy.) Having only this blog as my science writing experience, I do not expect to win anything. For me, the contest helped me form an idea about what is missing in the public science communication complex. At the core of science literacy today is the need for effective translators; between religious folk and scientists; between doctors and newspapermen; between researchers and housewives; between professors and policymakers.

The MSTP has filled a critical need to connect the bench with the bedside. Sure, it takes too long for us to finish, and there is an attrition rate, but MD/PhDs tend to get grants because they understand what is needed on either the medical or the basic science side. Furthermore, several competitive programs exist to fund slightly higher risk efforts in translational medicine. Following these leads, the NIH would do well to support a small and competitive initiative to better train civic scientists. These would be professionals who garner some of their salary support solely to communicate with the public or with policymakers. A small number of students could earn dual degrees in hard science and communications or engineering and political science. These people will be the go-to resource for the public's questions and concerns about controversial topics like stem cell research, nanotechnology, designer genomes and drug safety. They also will be trained to develop innovative mechanisms to instill in Joe Public a scientific sense - that science does more than generate trivia.

This is my charge to the NIH (and other Federal funding agencies, for that matter):
Support Translational Science

Translators to the public and for the public. That will be money that can only feed back into the system.

The NIH wants YOU!

The NIH is seeking comments regarding NIH’s support of the biomedical and behavioral research, including peer review, with the goal of examining the current system to optimize its efficiency and effectiveness. The NIH is especially interested in creative suggestions, even if they involve radical changes to the current approach. Responses will be accepted until August 17, 2007 online or via e-mail (PeerReviewRFI@mail.nih.gov). I hope that all of you reading this - whether you are a grant recipient, a student or a taxpayer - will offer advice to Uncle Sam.

I made this post as part of a pyramid meme initiated by Writedit and sent to me by DrugMonkey, both individuals who know more about the nitty-gritty of NIH grants than myself. If you blog and want to tag yourself to write about this, here are 4 rules:

1. Include in your post the links to the NIH RFI and the comments page.

2. Include the list of six topics the NIH wants information about.
  1. Challenges of NIH System of Research Support
    Please describe any specific challenges presented by NIH’s support of biomedical and behavioral research such as the current array of grant mechanisms, number of grants awarded per investigator, and the duration of grants.
  2. Challenges of NIH Peer Review Process
    Please describe any specific challenges presented by the current peer review process at NIH.
  3. Solutions to Challenges
    Please concisely describe specific approaches or concepts that would address any of the above challenges, even if it involves a radical change to the current approach.
  4. Core Values of NIH Peer Review Process
    Please describe the core values of NIH peer review that must be maintained or enhanced.
  5. Peer Review Criteria and Scoring
    Are the appropriate criteria and scoring procedures being used by NIH to evaluate applications during peer review? If not, are there changes in either that you would recommend?
  6. Career Pathways
    Is the current peer review process for investigators at specific stages in their career appropriate? If not, what changes would you recommend?
3. Comment on one or more of these issues.

4. Decide who the next seven vectors will be for this meme.

I decided to forward this request to 7 other bloggers. The lucky winners here are:

The Daily Transcript
King of the Nerds
The Scientific Activist
Science to Life

Check their sites to learn more about other folks' ideas, but most importantly, comment to the NIH!

MD/PhD Interest?

I've noticed a surge of referrals from an online forum about folks interested in MD/PhD programs. I am a student in the University of Washington's MSTP, and am happy to answer specific questions about our program or about my take on training the physician scientist. You can find one of my email addresses with only a little digging, OR you can comment on this entry. I am scheduled to defend September 13, and am very happy to be getting back on the wards.

You will probably notice that only a portion of my posts deal explicitly with medical research and graduate school. That's because I believe some physicians and scientists should assume more of a citizen's role - able to communicate about science and medicine in the context of public policy, general understanding and pop culture. This blog is meant to improve my communication skills in those areas.

Thanks for visiting!

John Edwards on Science

While I was reading Barack Obama's Audacity of Hope, I posted a segment of the text with some of his views about publicly funded science. Well, Coturnix at A Blog Around the Clock snagged an exclusive interview with John Edwards, and focused on science questions. You should note that the interviewer is from North Carolina and is a big fan of Edwards before. It is clear who he will be voting for in the primary. His conclusion statement is:
Thank you, Senator for taking your time to answer my questions. I hope the American voters give you the chance to implement your ideas in the near future.
Even so, many of Edwards' remarks are right on the money. Such as:
The Office of Science and Technology Policy will play a central role when I'm president. We need to encourage science, and do it honestly and openly. It's unfortunate the Bush administration hasn't shared that view. The censorship and suppression of science on climate change, on air pollution, on stem cell research--all to advance a political agenda--is wrong. Policy should be science driven; science shouldn't be politics driven.
We need to invest in the next generation of math and science teachers for our schools. Ninety-five percent of urban high schools report problems getting qualified science teachers. We need higher pay for teachers, college loan forgiveness, and better teacher training programs.
Unfortunately, the questioner did not ask (or the subject declined to answer) about embryonic stem cell research.

I wonder if the other candidates would differ in opinion about these replies. If any of you readers come across other candidates' answers about science issues, give me a heads' up!

Sunday, July 08, 2007

Carbon Footprint: White Roofs

Now that the summer has had a couple of serious heat waves, it's a good time to talk about how we Americans need our cool refuges from the hot and humid air. One obvious strategy to reduce your carbon footprint is to turn down the A/C or keep it from running when you are not at home. This keeps carbon from the atmosphere and dollars in your pocket.

But here's another creative solution: The next time you re-shingle your home, consider light colored material; White tile, silver paint, or cedar shakes each have a high reflective index. Instead of absorbing all of that energy and transferring it into the buildings below, as much as 15% of total energy could be reflected back into space. White roofs do the same thing as clouds and snow, in that they reflect incident energy like a mirror. The quantity of total energy reflected is referred to as albedo. White surfaces have very high albedos for light in the visual range, but are less efficient at reflecting ultraviolet or infrared wavelengths (hence the ~15% value cited above).

Evidently, there is a movement afoot to design new roofing materials that reflect light not only in the visual range, but in the longer more energetic wavelengths. These could be used as tiles to keep homes and other buildings more energy efficient. California is also sponsoring research that could make pavement more reflective. Combined with lighter roofs, this could go far in reducing the heat islands that form in urban areas. It's hotter in cities because more energy is absorbed by man made structures! And in heat waves, we have to cool those structures.

So painting your roof white may not have an immediate impact on your carbon footprint, but it should keep your cooling bills down in the summer. Now whether any of you cold winter dwelling folk benefit from darker roofs in the winter is something I don't know. Having done my fair share of attic crawling as a boy, my experience with dark colored roofs is that attics always got really hot in the summer, yet retained frigidity in the winter.

I found some fuzzy math on this subject in an article in Business Week, and a lot of commentary on it at the Island of Doubt, so if you are interested in this issue or are considering a new roof, check those sources out first.

Pumpkin Seed Oil

What is pumpkin seed oil doing on a science blog? It turns out it has something in common with a histology stain I use all the time in lab. Eosin is a dye responsible for the pink stain you see on microscope slides. According to a recent study from Slovenia, both eosin and pumpkin seed oil are bichromatic. I've only experienced this with eosin, however. In its concentrated state, that dye is an iridescent green tinged with pink, but when it is diluted in alcohol for dipping slides into, it is a bright fuscia. And the end result is a robust pink. My experience with pumpkin seed oil is via my mother-in-law, a native Austrian and a chef by profession. Her recipes for this dark substance include tasting oil for bread and in salad dressings. I like it in small doses! According to this paper (featured in Science Daily) , liquids containing multiple perceived colors play upon the boundaries of perception of cone cells in the retina. Some cones see red, others, green and others blue, but perception occurs along a curve. Red cones 'see' a little bit of blue and green; they just specialize in red. I've never seen pumpkin seed oil as anything but black or green (that's a small cantor of it at right), but maybe that's because I only have one X chromosome. As usual, King of the Nerds has something to say about this, too. (Although his editors oversimplified a couple of his sentences!) I do agree with the Science Daily assessment of pumpkin seed oil as having
a strong characteristic nutty flavor.
Sort of like this blog.
Tip to Bora for alerting me of this important story.

Saturday, July 07, 2007

Ant Cup

- Ladies and Gentlemen, welcome back to the friendly match between the antional soccer teams Japant in the red and white jerseys and Spaint in yellow. The outcome of this contest today will not affect either of the team's rankings, and is just to keep the players legs limber and antennae at their peak condition.

- The home team seems to have an advantage today, not having to suffer the excruciating pressure changes during altitude change involved in the plane ride.

- I don't think the Spantiards are used to all of the sushi, either.

- Spaint also had to transfer its captaintcy to a rookie drone after an unfortunate accident on the sidewalk out front.

- With the second half now underway, Japant's striker has firm control of the ball at mid field. I wonder if we will see any of the precision ball handling the Japantese players are known for?

- Or will Spaint's coach bring out some of the sociobiological tricks that team is known for?

- You never know with E.O. Wilson.

- Let's switch to the overhead cam for a view of the entire field. Sometimes we can get a better sense of the action from these shots. Our overhead view is presented today by the folks at GoodYear tires. "We keep you in the car and off the sidewalks."

- I bet the Spaint players wished some more folks were kept off the sidewalks before this match.

- I can't seem to make out any semblance of order, however, and the ball still has not left center field.

- Our antgineers in the control room say that we're getting good signal from the ant-cam. The ant-cam is brought to you by Hoy-Hoy Trap-a-Roach. "It works for spiders, too!"

- Wow! Look at those ants push the ball. Note the players' strict observance of the rules barring forelimbs from touching the ball.

- I'm just glad it's left the center circle.

- You' know, these playants train in the off season with regimented schedules. Busy as their fellow hymenopteran cousins, they devote themselves to amassing large quantities of food all year, just so their little sisters have a chance at survival.

- Enough entymology - back to the game. It seems like E.O. Wilson's team is in serious trouble; the ball is deep in their backfield. Japant's players are poised for a Raid!

- Funny, it doesn't seem as though anyone is paying attention to the ball right now. The Japantnese team is really passing up a golden opportunity here. It's as though a fine particulate mist has fallen on the pitch.

- A good number of defenders are in the vicinity, should the need arise to expel the invading orb. I wouldn't really worry until the ball is in the keeper's box. Team Japant seems prepared to take this food back to the nest. The Spantiards might as well fold up their legs and roll over.

- What happens now? Team Japant has penetrated the keepers box and seems to be poised to score, yet something is missing... Hey, where are the goals?

- I'm guessing they got lost in the shuffle. Let's just count this one a victory for Japant.

- Tune in for next week's match between global powerhouses Antgentina and Frant. I think we can expect some serious social behavior in that game.

- From the leader in world wide sports, AntBC, that's all from this week's Ant Cup.

Friday, July 06, 2007

More on the Stem Cell Map

Attila over at Pimm has recruited a number of additional stem cell labs for his Stem Cell Labs on the Globe project, and is working through some of the issues related to curating such a resource. Check out this post for more details. You will note that my lab has not yet joined the list...

Sherley It's Time For An Update

The case of James Sherley's employment at MIT is still one of the most common searches leading to my web site, and there continue to be developments. To catch up, check out my first entry on this topic. (For you bloggers trying to get listed higher on Google, it actually *helps* to make a little spelling error deep in the entry...)

According to a news feature in Science Magazine last month, the biological engineering professor was asked to leave his position on June 30, 2007. Of note is that Frank Douglas resigned because MIT's handling of Sherley's case for tenure creates a hostile environment for African-Americans on campus. Douglas was the director of MIT's Center for Biomedical Innovation. He held faculty appointments in the science, engineering, and management schools.

It sounds to me like MIT has a problem with race. Philip Phillips, another Black scientist, formerly at MIT and now at the University of Illinois, predicts that Douglas will be treated as was Sherley—“as just another irrational person.” This got me thinking: I wonder how many irrational White, South Asian or Hispanic people there are who were denied tenure at MIT. Or is irrational a word only reserved for Black professors. I wonder also, how irrational individuals received appointments at the premier science institution in the world, if they were irrational.

I admit that some of Sherley's actions and his use of hyperbole (on this issue and others) can easily confuse what is the real issue at hand, but it is hard to lay the blame entirely on one man. Is MIT just offering lip service to issues of race? Do they have anything more than official statements to try and improve this situation? Is the environment there really hostile to African-Americans? What will James Sherley do next?

Thursday, July 05, 2007

Real Time Ocean Science

Just northwest of SeaTac Airport on the shores of Puget Sound are two inconspicuous moorings that house what could be important new tools in oceans research. The Seahurst Observatory, located at Seahurst Park in Burien, consists of installations designed to collect marine information including salinity, temperature, pressure, chlorophyll concentration, currents, sound and video. The innovation in this system is the remote deployment and automated data collection. The researchers intend for this placement to serve as a test-run for installation in 3,000 feet of water in Monterrey Bay and eventually as deep as 2 miles on the Juan de Fuca plate off Washington State's Pacific Coast.

The armchair oceanographers amongst us will be most interested in the project's videos. The Applied Physics Lab at the University of Washington hosts several clips of the most interesting animal life, each collected after motion sensor activation. I recommend checking out the jellyfish on this page, the seal(s) on this page, and the sunflower star on this page.

Wednesday, July 04, 2007

Hot Dog!

Enough principled posts; it's the 4th and that means Americans are in the process of consuming 150 million hot dogs. Mmmm... delicious. Well okay, maybe not. In related news, you may already know that Takeru Kobayashi, the Lance Armstrong of competitive hot dog eating, has been dethroned by California boy Joey Chestnut. In twelve minutes, San Jose State student Chestnut racked up 66 HDBs - that's hot dogs and buns eaten - beating out Kobayahi's 63.

So the issues that strike me as important in a post about the new Nathan's champion include:
  • The consequences derived from equating competitive eating with American freedom.
  • The attention (including my own) placed on this event.
  • This was televised live with color commentary on ESPN.
  • The distraction this is from real problems of hunger and resource disparity in the world, and
  • A medical condition called Boerhaave's syndrome
Since rare medical conditions are sometimes cool to learn about, that's what I will focus on for the rest of this entry. Also known as effort rupture of the esophagus, Boerhaave's syndrome can occur when folks vomit too much or have other underlying disease in the tube that connects your mouth to your stomach. Most commonly, esophageal rupture is caused by doctors poking too hard during endoscopy procedures. Given the intense effort displayed on the new champion's face and the immense quantity of processed meat and bread passing through his esophagus, I would bet he has a greater chance than most of rupturing that tube. From a medical resource site commonly used by doctors and med students:
The condition is associated with high morbidity and mortality and is fatal in the absence of therapy.
Treatment is surgical repair.

I am sure my sister will complain that I even turn a simple story about hot dogs into some nerdy scientific explanation. Sorry, kiddo.

Hey America!

You say it's your birthday
It's my birthday too, yeah
They say it's your birthday
We're gonna have a good time
I'm glad it's your birthday
Happy birthday to you!
by Lennon-McCartney
Given that everyone will be celebrating the nation's birthday this afternoon and evening by eating lots of animals and blowing stuff up, this post is probably a vain attempt to insert a little bit of scholarship into an otherwise consumptive day. Some of you might be interested in touching up on one pretty rusty part of what it means to be an American.
The Conventions of a number of the States having, at the time of adopting the Constitution, expressed a desire, in order to prevent misconstruction or abuse of its powers, that further declaratory and restrictive clauses should be added, and as extending the ground of public confidence in the Government will best insure the beneficent ends of its institution...

Amendment I

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof; or abridging the freedom of speech, or of the press; or the right of the people peaceably to assemble, and to petition the government for a redress of grievances.

Amendment II

A well regulated militia, being necessary to the security of a free state, the right of the people to keep and bear arms, shall not be infringed.

Amendment III

No soldier shall, in time of peace be quartered in any house, without the consent of the owner, nor in time of war, but in a manner to be prescribed by law.

Amendment IV

The right of the people to be secure in their persons, houses, papers, and effects, against unreasonable searches and seizures, shall not be violated, and no warrants shall issue, but upon probable cause, supported by oath or affirmation, and particularly describing the place to be searched, and the persons or things to be seized.

Amendment V

No person shall be held to answer for a capital, or otherwise infamous crime, unless on a presentment or indictment of a grand jury, except in cases arising in the land or naval forces, or in the militia, when in actual service in time of war or public danger; nor shall any person be subject for the same offense to be twice put in jeopardy of life or limb; nor shall be compelled in any criminal case to be a witness against himself, nor be deprived of life, liberty, or property, without due process of law; nor shall private property be taken for public use, without just compensation.

Amendment VI

In all criminal prosecutions, the accused shall enjoy the right to a speedy and public trial, by an impartial jury of the state and district wherein the crime shall have been committed, which district shall have been previously ascertained by law, and to be informed of the nature and cause of the accusation; to be confronted with the witnesses against him; to have compulsory process for obtaining witnesses in his favor, and to have the assistance of counsel for his defense.

Amendment VII

In suits at common law, where the value in controversy shall exceed twenty dollars, the right of trial by jury shall be preserved, and no fact tried by a jury, shall be otherwise reexamined in any court of the United States, than according to the rules of the common law.

Amendment VIII

Excessive bail shall not be required, nor excessive fines imposed, nor cruel and unusual punishments inflicted.

Amendment IX

The enumeration in the Constitution, of certain rights, shall not be construed to deny or disparage others retained by the people.

Amendment X

The powers not delegated to the United States by the Constitution, nor prohibited by it to the states, are reserved to the states respectively, or to the people.

Tip to the King of Nerds for planting this idea.
You will never guess which was the first Google result to provide me with the lyrics to "Birthday."

Tuesday, July 03, 2007

Fertile Biblical Debate

The hinge for many arguments about stem cell research is the same as for the abortion debate. When does personhood begin? Since, I recently made a post referring to abortion, I thought I would follow it up with a position statement on that topic.

I think the least-read entry on my blog so far is one from last month concerning the theological concept of concordism. I want to come back to that term now in conjunction with a presentation of one Christian perspective that is consistent with the moral use of human embryonic stem cells in research and to an extent does not rule out a pro-choice political perspective.

What follows is a lengthy post by someone without theological training, but who is committed to the struggle of reconciling his personal religious, political and scientific world-views. My intent is not to draw you to anger, but to understand a perspective on abortion that you might have yet to consider.

First, some reminders about concordism:
  • Concordism is the view that the biblical accounts, when properly understood, will be in agreement with scientific accounts of the natural world.
  • The extent that individuals attempt to reconcile conflicting biblical statements with each other and with what scientific study has demonstrated depends on whether that individual pursues a verse that supports his or her opinion or tries to assemble a comprehensive concordist explanation.
  • Concordism occurs in both the literalist approach to interpreting the Bible and in the position that the text concerns the relationship between God and his creation rather than a scientific account written in a pre-scientific era.
I have identified several verses from the Bible that are commonly cited as support for personhood occurring at fertilization. Quotations are from the New International Version, available free here.

These include:

Psalm 139: 13-16
For you created my inmost being; you knit me together in my mother's womb. 14 I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well. 15 My frame was not hidden from you when I was made in the secret place. When I was woven together in the depths of the earth, 16 your eyes saw my unformed body. All the days ordained for me were written in your book before one of them came to be.
Job 31:15
Did not he who made me in the womb make them? Did not the same one form us both within our mothers?
Jeremiah 1:5
5 "Before I formed you in the womb I knew you, before you were born I set you apart; I appointed you as a prophet to the nations."

Each of these point to God's knowledge and creative activity before birth. This could refer to omniscience or activity even before fertilization. No specific comment on fertilization occurs here. In fact, Jeremiah 1:5 emphasizes God's relationship with Jeremiah even prior to his conception. It is a relationship verse rather than an explanation verse, but some strict concordists might disagree.

Other frequently cited sections in the abortion dialogue are:

Job 3:3
3 "May the day of my birth perish, and the night it was said, 'A boy is born!'
Isaiah 49:1
1 Listen to me, you islands; hear this, you distant nations: Before I was born the LORD called me; from my birth he has made mention of my name.
Psalm 51:5
5 Surely I was sinful at birth, sinful from the time my mother conceived me.
Luke 1:41-44
41When Elizabeth heard Mary's greeting, the baby leaped in her womb, and Elizabeth was filled with the Holy Spirit. 42In a loud voice she exclaimed: "Blessed are you among women, and blessed is the child you will bear! 43But why am I so favored, that the mother of my Lord should come to me? 44As soon as the sound of your greeting reached my ears, the baby in my womb leaped for joy.
Luke 1:15
15He will be great in the sight of the Lord. He is never to take wine or other fermented drink, and he will be filled with the Holy Spirit even from birth.
Galatians 1:15
15God set me apart from birth (OR from my mother's womb, depending on translation) and called me by his grace.

None of these say anything precise about the origin of personhood. One of them even makes a nice prescription against pregnant mothers drinking alcohol.

The major references to personhood are:

Exodus 21:22-25
22 "If men who are fighting hit a pregnant woman and she gives birth prematurely but there is no serious injury, the offender must be fined whatever the woman's husband demands and the court allows. 23 But if there is serious injury, you are to take life for life, 24 eye for eye, tooth for tooth, hand for hand, foot for foot, 25 burn for burn, wound for wound, bruise for bruise.
Numbers 5:11-31
(A long passage about what is to be done if a woman is suspected of unfaithfulness to her husband that treats the husband and wife as the only persons involved in a cleansing ritual. The swelling of the abdomen is fully part of the woman. An irreverent interpretation may be found here.)

These last two actually suggest that personhood is not immediately present at fertilization. In order for one to draw a conclusion about fertilization, a concept from modern science must be retroactively applied to the ancient words. For example, some folks like to think of the unformed body in Psalm 139:16 as the morula or blastocyst (stages of development that occur days after fertilization), but it could just as easily be a 'twinkle in your father's eye' or cosmic dust.

Why are these verses so often cited as supporting a pro-life political perspective? My guess is that people try to apply science and what we know about life today to text from the Bible written long ago. I think that it is wrong to apply new meaning to old words, particularly if you consider them sacred, holy, or (separate from religious significance) just an important account of a moral code.

It is within their right for fellow Christians to offer perspectives that differ with mine regarding this issue. I begin to take offense when people uncritically accept others' uses of words from the Bible - what I consider a catalyst for God's relationship with humans - to support political perspectives that are at the periphery of what it means to be a Christian, and then tell me that my reading is wrong.

So if there are any atheists out there who use the refrain that moderate Christians are complicit with fundamentalists by not speaking out, here is one voice saying, "Wait a minute!"

Thanks to an article by Robert Boomsma for helping identify these verses.

Monday, July 02, 2007

Carnival of the Blue (II)

Swim on over to the second Carnival of the Blue, hosted by blogfish. I am proud to be able to contribute this month. Blogfish and the other carnival hosts focus on any issue related to ocean science and policy.

Objectivity in Studying Abortion

Do women who receive abortions experience lasting psychiatric trauma as a result of that choice?

A lot of (pro-life) groups claim yes, while (pro-choice) women's clinics say no. The mere existence of post-abortion syndrome (PAS) is controversial. Cherie Black of the Seattle Post-Intelligencer wrote a nice article in today's paper about this topic. She seemed not to favor a particular view, and objectively presented opposing sides on this debate (both a Christian program called Project Rachel and physicians decrying the hijacking of medical terminology); Black even addressed the misuse of science occurring in each groups' claims.

One question the author did not raise was whether it is even possible to set up an objective study of whether there is anything real about post-abortion syndrome. I can imagine that the academics or interest groups that have the skills and means to conduct a study might also have considerable underlying bias. If such a study were conducted, what methods could be applied to assure objectivity?

The anecdotes presented in Black's article suggest patients' backgrounds and beliefs before the treatment might inform their response to having an abortion afterwards, but that women report mental trauma should keep open the possibility that their psychiatric pain is real. One side claims support from science, while the other (populated more heavily with scientists) claims uncertainty.

Could there be other situations that could inform this one? What other sorts of personal experiences have the potential for lasting effects from a personal decision? Military post traumatic stress disorder doesn't count in my book - soldiers don't make explicit decisions to see specific horrific situations. Nor does criminal remorse provide the same situation - abortion is legal.

Unless we can find someone familiar with this issue who is undecided on abortion (good luck!), the only way to honestly purse the question of post-abortion syndrome is to form a team consisting of investigators with opposing viewpoints. Such a team will need more than luck!

Update July 3: The Seattle P-I printed a vitriolic editorial today criticizing Project Rachel's misrepresentation of science. I think the emotion was justified if targeting the misuse of science, but I have the feeling that collateral damage could include the individuals seeking counsel for their grief. I responded in their Soundoff comments section, and a commenter named veritas rex offers there more scientific data and medical history related to this issue.

Update July 5: Some folks asked me what my personal take on the abortion issue was. My answer: I find dubious the claims made by many fellow Christians that the Bible prohibits abortion, but am uncomfortable with the widespread acceptance of abortion as a birth control method. My reading leaves ambiguous the Bible verses often cited as determining fetal personhood. (These are the same as those championed by Pro-Life advocates as proof that abortion is murder.) Please see this post for more details.

Update July 10: An OB/GYN doc has a guest column in the Seattle P-I today and offers a retort against there being any evidence of post abortion syndrome. The problem I find with her rebuke is that she stakes her claims on statistics that could actually be used against her argument. Pointing out that "76 percent of women report feeling relief after abortion", she asserts that
no negative medical or psychological consequences
arise from abortion. Okay, I follow that - in politics, this would qualify as an overwhelming majority. In medicine however, 17% is a pretty high rate for side-effects.

17% is particularly important given the columnist's take-home message:
There are 1.3 million abortions performed every year in this country and one in four American women has at least one abortion while reproductively active.
Every year, 221,000 women feel guilt from abortions, and that its possible that 6.7 million women in America regret undergoing the procedure. Don't you think there is a small chance that a few of these women could experience more serious psychological consequences? Will you not take these women's claims seriously? Even if the grief does arise from existing social or religious constructs, isn't it the care provider's prerogative to address these concerns? Perhaps physicians' refusals to acknowledge these women's pain belies the success of programs like Project Rachel.

The more this argument escalates, the more devices from the denialist's deck of cards are employed. I've identified a couple for you in this post.