Clouds Are Breaking

It's a Saturday night - June's final day. The last streaks of sunset are receding across the Northwest sky, rainclouds have been banished until October, and Seattle is in its prime.

Some of you will recall the 40 day flood of experiments I inundated myself with back on May 22. If your calender is handy, that means the time is almost up. Tomorrow, we can expect a reprieve. As I write this, I am preparing the last batch of cells for my last surgical experiment of my graduate career. The clouds are breaking for me, too. The sky is lightening. I can almost feel the sun cooking my pale Northwest skin.

This feels good.

I sure hope it takes me less time to find land then it took Noah et al. I am ready for it to finish.

Stem Cell Labs as Targets

Let's make it easy for stem cell advocates/objectors to find their local scientist/target! It will be really easy with Stem Cell Labs on the Globe, a Google Maps application that will identify all of the stem cell labs around the country. Initiated at my new favorite blog Pimm, this resource could develop into something really useful. Just the other day I was trying to figure out how many human embryonic stem cell lines had been derived after August 9, 2001. This would help me track down contacts to gather that information. Students could track down locations for graduate schools or post-docs, and local journalists and politicians could easily track down expert resources via phone or the internet. To see the current version, follow this link or click on Pimm's image below.

A question for my colleagues: I have emailed Pimm to add our ISCRM to the map - should we list our location?

Misused Math

This morning, I received an anonymous comment on my post about farmers' markets and eating local. The post made from Alexandria, VA (Thank you SiteMeter!) at 3:30 AM Eastern Daylight Time links to a site that informs us of "which states are greener." The content doesn't have much to do with farmers' markets and would probably be better placed on my Live in the Northwest entry, but I checked it out anyway. It turns out that this site is a commercial supplier of solar panels called Hughes Solar Energy, that is based in... Alexandria, VA. It looks like this company is in the business of selling anything that could be remotely tied to solar power.

The section of the website referred to us offers a list all of the states and ranks them according to total carbon output. That metric is useful if you are an energy company marketing low carbon generators (like solar panels), but in terms of modifying individual behavior and identifying where meaningful mitigation can occur, it is useless. What you need to look at is per capita emissions. That number says something about where energy consumption can be improved. So I took 15 minutes to rearrange the data in a spreadsheet so you can see where we need to work the most at reducing emissions. It's also confusing that they order their information using the double negative of "Ranked Worst Pollution." This is the per capita data next to the information from Hughes Solar Energy, and here's a list where you can see which state is beating yours. What a surprise that the rankings nearly inverted! It seems as though high-density blue states use less carbon per capita than the rest of the country.

I remember in 8th grade I had to make a report about how statistics is misused by commercial entities. I think I focused on the Sylvan Learning Center's flawed comparison between American and Japanese school children's workloads and performance. If I were to wite this report over again, this solar energy company's clever (if not disingenuous) presentation of carbon emission data would be my topic!

This is not to say that buying a solar product from Hughes is a bad idea... I just don't like it when people mess around with data to serve their purposes. Okay - when other people mess around with data...

And don't forget how state emissions values can be altered due to geology. For a while, Mt. St. Helens spewed more carbon than all of the rest of the major polluters in Washington State combined!

100th Birthday!

Hope for Pandora turns 100 today! That's 100 posts. Thanks to all of you who are helping me develop my blogging voice. Extra bonus points go to folks who have made comments or clicked on ads! Use this entry to suggest topics or offer ideas about how to make my blog more interesting.

Science and Art

I stumbled across a pretty interesting feature in Slate magazine about science as art. It's a slide show, so you'll need to use a computer built after 2000 to enjoy it. I found it pretty interesting, but one of the guys featured (check out his mug - it's like he took a scientist's fashion sense and mixed it with an artist's absent-mindedness!) seems fixated on representing female nudes. And this green rabbit has always looked Photoshopped to me... If I haven't scared you off by now, you'll probably check it out anyway.

(American) Science Idol

Had enough with government interfering with science?

To have a little fun while drawing attention to this problem, the Union of Concerned Scientists is hosting Science Idol 2007: the Scientific Integrity Editorial Cartoon Contest.

Twelve cartoons have been selected, and now you need to vote. To do so, visit this site.

There are 12 pretty funny cartoons about how the science and policy relationship has broken down these days. Vote on one and find out how you can get more involved with issues involving the integrity of science.

Atheism in America

Have you noticed the recent increase in conversations about atheism lately? You've seen books, TV programs and more talking about atheism. If you read ScienceBlogs, you might think that a supermajority of scientists are atheists. Two recent posts there have shifted the conversation away from the screaming edges, and I would like to comment here on them. Matthew Nisbet at Framing Science posted a recent Barna survey showing that Christians tend to donate time and money to the needy more than atheists, and Josh Rosenau from Thoughts from Kansas posted a recent analysis of belief on America.

I'll say right now that I am a Christian, a liberal and a scientist. I wish to contribute to a dialogue about topics like this rather than pick a fight.

Nisbet's post and subsequent discussion centers on the image problem that atheists have in America, and the comments seem to me right on. If, however, he is interested in addressing the findings of the Barna survey, there seems to me an important consideration missing.

I believe that among atheist scientists, there are considerable negative stereotypes of religious - particularly Christian - people. A vast majority of comments (and posts) on ScienceBlogs refer to Christians is cynical hypocrites. I know that this text lashing is not representative of all atheists, but if ScienceBlogs is taken as a representative section of atheists, I might wonder if the negative impressions that society at large holds of of atheists are founded. I have had close interactions with a few groups of atheist secular humanists, and I would characterize only a very small minority of them as something resembling 'militant' or 'cynic.' So I think that Nisbet and colleagues are on to something when they suppose that community (as provided by a church, for example) is linked to good works. It is also possible that people interested in social justice are more social to start with, so seek out places like churches, community groups and political organizations.

My question related about what the Barna study says about atheism is: Are atheists willing to accept that Christians honestly pursue their religious teachings?

If you would like to understand how Christianity can be a religion of social justice, read the Sermon on the Mount. (The summary at Wikipedia is good as long as you don't read the muddled interpretation section.) Christ's teachings advocated giving alms (as the Barna study examined), reducing war, withholding judgment, healing sick, and were against materialism. Jesus interacted with and helped women, lepers, the underclass, tax collectors, priests and aristocrats. Paul preached to and formed friendships with Jews, Greeks, slaves, prisoners, soldiers and Roman leaders alike.

You will, of course, be able to cite contradictions to these points - mostly in the Old Testament. And surely you will find Christians that do not place the social justice commandments high on their priority list. I am just saying that there are stereotypes of atheists and stereotypes of Christians, and to shake off one, you may just have to let go of the other.

Finally, Rosenau identifies that there may be a trend toward a less religious America, and the Barna survey indicates that Americans are increasingly misinformed about the poor. Let's hope that we are not trending toward an era of callousness and fewer good deeds.

Reflection

There come times in life when we slip into contemplative reflection more than usual. Occasionally, this occurs conveniently - in which case we actually have quality time to reflect. Wise people devote a little time every day to the questions, "What am I learning?" and "What does that mean?" Others of us push these questions aside only to have them burst forth unexpected demanding address. Clearly I am experiencing a bit of 'bursting forth' if you are reading this!

I find myself pressed with some urgent questions these days, and have identified a regiment by which I can begin to answer them. If you are thinking, "Oh great. He's going to subject us to his personal struggles," you are only partially correct. My personal challenge is to wrestle with my questions on this blog in a way that will engage some of you. If anyone out there feels motivated to comment or argue with me, I'd be tickled.

My reflections of late have all been different faces of the question, "What is the meaning of graduate school?"

By the end of this series of posts, I expect to either:

1. tire of this topic
2. find a robust answer to the question or
   
3. defend my dissertation.

It is possible that all three of these will occur, as my scheduled defense is September 13, 2007.

I can identify a few reasons why I have not been able to silence my thoughts about this question. They include:

1. scheduling my defense and selecting a time line that resulted in a 40 day flood of experiments.
2. receiving a call from the labor relations office about my non-compliant status in the collective bargaining unit of graduate students at the University of Washington, and the subsequent discussions I had with folks about that.
3. my tendency to need numerous intellectual distractions whenever I am working hard on particular tasks.
4. the observation that if I don't comment on being a graduate student now, when will I?
5. a personal belief that questions that keep me awake for more than three nights are as close to any sign as I will ever experience.
   

I will still post entries similar to those you've been reading, but will spend a little bit of time on my latest burning question:

What is the meaning of graduate school?

No Vacation For You!

A week ago, the FBI made some recommendations to universities in the Northeast about zealous science graduate students. The bottom line was if grad students are really into the science they're doing, they might be terrorists. Zealous is defined here as working long hours, displaying an intense interest in the subject being studied, and communicating with other scientists about their work. If you think that's over the top, it doesn't stop!

Additional reports are that the FBI has suggested that these hard working graduate students not be permitted to travel outside of the country, for fear that they will be more able to transfer sensitive information to rogue scientists outside our borders. It's not like we need vacations with all of those late hours in the lab anyway!

This policy betrays serious misunderstandings about how science is done, and how knowledge is transmitted. I can understand how research involving weapons or bioterror agents could generate some sensitive situations, but these recommendations seem to target all graduate students.

Anyway, if you think your labmate's a spy, check this document for instructions about how to report him or her. I would also like to see these recommendations and not just read about them from reporters and bloggers...

The Heart of Hopeful Hype

This is a movie of beating heart cells that were derived from a presidentially approved (H7) human embryonic stem cell line. Show me an adult stem cell population that exhibits this behavior, and I will change my opinion that embryonic stem cells are the superior source of replacement heart cells.



Thanks to the King of Nerds for recording this and posting it on YouTube. If you are prepared for the alternative lifestyle ads on The Stranger's website, you can re-view this movie in a Slog entry he made referring to the recent stem cell bill veto.

Carbon Footprint: Buy Local Produce

Here's something to munch on: The average distance (in North America) that your fresh food has traveled by truck or plane to get to your table is 1,000-1,500 miles. You can imagine that more energy is being spent in such transport than in agrarian cultures elsewhere in the world or in our past. Activists have coined a new term surrounding the impact that food transport has on the environment: "food miles." Food miles depend on several factors:

• The distance transported.
• The transport mode.
• The concentration of the agricultural product.
• The relative agricultural productivity and the amount of fertilizer required in each location.

Each of these impacts the amount of carbon emitted to the atmosphere. What makes this issue a little complex is that concentrated or dehydrated foods decrease the amount of energy in shipping fuel, but the energy expended in dehydration, processing or freezing counters such efficiency gains. So what I am about to advocate is a complex issue that you should look into yourself. Here is a nice pro/con article, and here are two food carbon calculators. The second calculator is very detailed but only applies to the UK.

So what is my suggestion for you this week? Buy local produce. Not only will it probably reduce your carbon footprint, you will support diverse local agriculture, your food will be fresher, you will interact with more people, you'll have greater access to organic food, and if you consistently stick to local crop schedules, your diet will be more diverse. The other week, I took some photos of the University District farmers' market. For more, visit my flickr photo set.

Yesterday my wife and I stocked up on fruits, vegetables and kettle corn from the Lake Forest Park farmers' market. It is located in a shopping center adjacent to the Burke-Gilman bike trail, so we were able to pick up our produce without even firing up the horseless carriage. If you are in Seattle or Puget Sound, there are several markets to choose from. Find the closest one here. Some of the farmers will deliver produce weekly to you. One local company might even be advertised in the panel at right. Click on it to learn about them (and to give me a quarter!)

The things about farmers' markets that I used to worry about was cost and spoilage. It is true that you will have to eat fresh fruits from a market sooner than chain-store bought items, but my experience is that they taste a lot better, and you can prolong their shelf life by storing them in the fridge. The veggies - greens and roots - last just as long. I was pleasantly surprised that the farmers markets sometimes SAVE you money! Here is a price comparison of what we bought with our cheapest grocery store:

• $3 of raspberries at the market = $6 at Safeway
• $13 flat of strawberries = $8.50 at Safeway
• $2 of squash = $3.75 at Safeway
• $4 kettle corn at market = unavailable at Safeway
• $1 baby Walla Walla onions = $1 adult onions at Safeway
• $2 baby bok choy = $2 at Safeway
• $3 purple, red and gold potatoes = $4 for gold at Safeway
  

The these prices compare the local organic price to the Safeway conventional price. Only the delicious strawberries (picked that morning) were more expensive at the market. Boy are they tasty!

We might get a third of our produce from local farmers' markets in the summer. In a temperate climate of Seattle, the only excuse for not buying local year round is convenience. Sometimes the only time I have to shop for groceries is between 9 and 11 PM!

There you have it: Eating local is one more way to reduce your carbon footprint. This method seems to have a number of other benefits, too!

Chilly News

Certain political figures have been reminding us that there are only 10,000 frozen embryos available for research. By available for research, they mean that parents have given proper consent for unused blastocysts from in vitro fertilization (IVF) to be used for research purposes. This includes(but is not limited to) extracting the little mass of cells that can be turned into embryonic stem cell lines. Pundits have been noting (correctly) that embryonic stem cell (ESC) advocates are grossly overestimating the number of available donated blastocysts. Step into their shoes for a moment: If ESC advocates are exaggerating on this point, what's to keep them from overestimating the therapeutic potential of these cells?

Research to be published in Science magazine next week sheds important light on this issue. Here are some facts:

• There are 400,000 embryos are frozen in the United States. These are the 5 day old, pre-implantation balls of cells (called blastocysts).
• 87% are being held for patient treatment, of which more than two-thirds are eventually disposed of.
  
• 3% (11,000) are available for research because the donors have given consent for their use.
• Because it is not exactly easy to make a cell line from a blastocyst, these donated embryos could result in the formation of 275 cell lines.
• Currently there are 20 cell lines approved for use of federal funds

This new study indicates that half of all users of IVF clinics would donate cells to research, and almost two-thirds would donate if they knew the cells would be used to create ESC lines. The authors state

for most of the individuals who create embryos in hopes of having a baby, the preference is not that their remaining embryos have a chance at life, but rather that they be used in a way (research, and if not, simply destruction) that ensures that they do not.

Only one quarter of responders indicated they would be willing to donate the embryo to another infertile couple to create so-called "snowflake babies."

The study concludes with the assessment that

the way that infertility patients resolve the very personal moral challenge of supernumerary embryo disposition is consonant with the conclusions of the American public, the majority of whom support human embryonic stem cell research.

The disparity between patients willing to donate and embryos available for research is an order of magnitude off. It seems to me there is a lot of room for experts in informed consent to team with advocates for stem cell research to increase the chances families have to donate their embryos. Whether it's to other families or to the community of science, either will be better than bleach!

Making a Dent in Academia

One year ago, the former Dean of Engineering at the University of Washington committed suicide. For nine years, Denise Denton worked to increase gender and racial diversity in science and technology and devoted great energy to improving engineering education. She was the first woman to hold a deanship at an NRC-designated Research One university. Her final employer (University of California) now hosts a memorial web site, and today Dr. Free Ride posted a tribute to her.

Much can be done to build upon her legacy of making science and engineering a better place for women.

Who Is Sick?

Are you ever sick but not enough to bother with a visit to the doc? Do you wonder if you've just caught the bug that is going around? Thanks to an interesting new site, you can now dial up a snapshot of illness over the past two months in your zip code.

Who Is Sick? is a new website where users self-report their symptoms and can see if others have the same thing. I have some sniffles today, so took a first-hand tour of the system. Call up your zip code and you'll see a map with a bunch of little trivial pursuit game pieces. Averages of the reported symptoms and a bar graph of total illness reports in the past two months is also visible.

The default mode is for posting an illness. Users fill in their pies, but instead of Science, Arts or Sports & Leisure, they choose wedges like Fever, Stomach Ache or Cough. I clicked the Runny Nose box, filling in a red wedge. Select your age and gender before reporting more details. I entered, "General malcontent with sniffles. Could be allergies and/or stress & fatigue."

One 40 year old woman claims to have picked up her "Runny Nose, Stuffy Nose, Sneeze, Cough Sore Throat, Fever, Chills, Muscle Ache, Body Ache, Tired" illness "from a child at the KEXP's annual Father's Day dance party."

The site is inspired by other simple Web 2.0 functions like Craig's List and real estate mapping programs. It is easy to use and has a clever interface. I might use it again, but probably will not stake any personal medical decisions on it. As a future physician, I am not sure if I would rely on hearsay from other providers about what is "going around" more or less than a site like this. If it produced generalized reports for a city, I might give it the benefit of the doubt. Public health experts from Seattle give it mixed reviews.

This site would improve its utility if users were forced to report a date of symptom onset. Also, the bar graph indicating "# of sicknesses over the last 8 weeks" will be unreliable until some steady state usage is achieved. Right now, it doesn't seem to me that nearly enough people are reporting for there to be a reasonable chance of discovering someone with the same illness. This begs a question: How many different upper respiratory illnesses, stomach flues, influenzas, head colds and other contagious goodies are there out there at any time? Can we really identify a preponderance of particular causative agents based on symptom reports?

And who are the folks registering symptoms? I am going to guess there is a tendency for self-reporters to be slightly more hypochondriac than most. This or any similar skewing of the data is a data collection problem public health officials call reporting bias. I picked from one list at least ten other types of bias. If this data were to be used in any sort of study or health recommendations, it would have a number of problems. The website authors clearly indicate it is not their intent to use this for public health assessments. From their website,

Who Is Sick was started in 2006 with a mission to provide current and local sickness information to the public - without the hassle of dealing with hospitals or doctors.

There you have it. The motivation behind this site was the hassle of dealing with hospitals or doctors. Ouch!

Instead of tracking stomach aches and head colds, maybe someone should think about reducing the hassle of medicine!

Tell me what you see

Decide on your answer, then consider this.

Stem Cells or Die!

It's a political move sure to take the embryonic stem cell debate to the next level.

Senators Tom Harkin and Arlen Spector have inserted a clause into the Labor & Health and Human Services appropriations bill to permit funding for embryonic stem cell research on cell lines created before June 15, 2007. (The text is still not up on Thomas yet (6/24) - I will link to it when it is.) Initial reports are available here and here.

If this appropriations bill makes it to George Bush's desk, he would have to veto the entire spending bill just to protect his stance on the stem cell wedge issue.

So if Bush stands by his ideology, he will have to tank the entire budget of the National Institutes of Health, Medicaid, the Food and Drug Administration, No Child Left Behind, Social Security, Pell Grants and many more. All of this accounts to more than $150 billion in receipts. Anyone remember the actual amount of federal spending on embryonic stem cells has hovered around since 2003? $25 million.

Is this a dirty trick or an act of genius? I suppose it depends which side you are on!

As an insightful friend of mine pointed out, someone (Brownback) will probably introduce an amendment to strike that section when the bill comes to the Senate floor. But as the last bill made clear, there will probably not be enough support for such a change to pass.

This should be fun. Stay tuned!

(For a bonus prize, guess which elected official referred to in this post I have voted for.)

Hmmmm...

i give mice attacks
and inject human stem cells
the 71

Savage Science

He may not ever get the readership of his boss, Dan Savage, but Jonathan Golob, a.k.a. King of the Nerds, should. Check out his column about the stem cell issue in this week's Stranger.

Stem Cells Vetoed

No surprises today. George Bush put on his 'sanctity of life' mask as he vetoed the stem cell bill presented to him two weeks ago. Ellen Goodman from the Boston Globe wrote a pretty good editorial of the stem cell issue (syndicated here in my parents' home-town paper). Highlights from that piece include quotes that I hope hit home with the lay reader:

The reason researchers use embryos is not because they want to run a recycling program for in vitro fertilization clinics. Nor because they have a passion for wedge issues. It's because the embryo can do what scientists can't do yet.

and

In short, we'll need to use human embryos even to help us eventually stop using human embryos.

This is basically true. As I have advocated before, we need to support both embryonic and adult stem cell research, and not just with lip service. The counter-offer the administration is proposing is focuses on recent scientific advances that have the potential to sidestep ethical controversies involving embryonic stem cell work. The full text of the executive order is here.

Let me point out to you the important parts of this proclamation and also some of its nonsense:

Section 1 (a): The Secretary of Health and Human Services (Secretary) shall conduct and support research on the isolation, derivation, production, and testing of stem cells that are capable of producing all or almost all of the cell types of the developing body and may result in improved understanding of or treatments for diseases and other adverse health conditions, but are derived without creating a human embryo for research purposes or destroying, discarding, or subjecting to harm a human embryo or fetus.

• The leading techniques for doing this involve nuclear reprogramming or somatic cell nuclear transfer. You know what the lay press calls these techniques? Cloning! This is a good example of double-speak.
• "embryo or fetus" It sure is convenient that Bush's science consultants threw in an emotional term like fetus, even though it has no relevancy to the science.

Section 1 (b) iv: Within 90 days of this order, the Secretary renames the "Human Embryonic Stem Cell Registry" the"Human Pluripotent Stem Cell Registry."

• Hmmm... I am not sure if I like this or not. I've noted before that scientist failed to frame this properly by using the word embryonic, so I kindof like the idea of changing the terminology.
• It's the next point that pulls me in the other direction.

Section 1 (b) v: The Secretary must add to the registry new human pluripotent stem cell lines that clearly meet the standard set forth in subsection (a) of this section.

• Whoa!!! Let's just water down an already dilute stock of limited stem cell lines with some less potent, uncharacterized lines.
• The last time I checked, there aren't any human non embryonic pluripotent stem cell lines. Let me know in 5 years if there are any yet.

Section 1 (c) Not later than December 31 of each year, the Secretary shall report to the President on the activities carried out under this order during the past fiscal year, including a description of the research carried out or supported by the Department of Health and Human Services, including the National Institutes of Health, and other developments in the science of pluripotent stem cells not derived from human embryos.

• Over Christmas Cookies, Bush: "Hey Mikey, got any new-fangled stem cells that don't come from cute little babies?"
• Michael Leavitt: "No sir, but we're timing another mouse stem cell study to be released around the time those pesky congressmen give you another bill to veto."

Section 2 (b): It is critical to establish moral and ethical boundaries to allow the Nation to move forward vigorously with medical research, while also maintaining the highest ethical standards and respecting human life and human dignity.

• Exercise for the reader: try changing "medical research" to "international diplomacy."

Finally a note of practicality: the NYTimes points out that:

this effort appears largely symbolic — there is no money attached — and scientists were instantly skeptical.

Including the same scientists who published the recent skin stem cell work.

It is true that the August 9, 2001 Bush stem cell policy has caused an explosion of creative techniques to acquire non-embryonic pluripotent stem cells. But many commentators believe this work would have occurred anyway because of the desirability of personalized stem cells that are not rejected. What is too bad is that much of the US will be handicapped when these restrictions are lifted because, as Ellen Goodman writes, "the embryo can do what scientists can't do yet." The best way we will learn about what the embryo (and these potential new sources of pluripotent cells) can do is by, well, studying human embryonic stem cells.

Research Subjects

It's a good bet that the activity documented below was not sanctioned by an Institutional Animal Care and Use Committee. By the way, these animals are clearly rats, not mice as the film implies.



In the work I do, we are always pleased to report that the rodents are active and hanging off the top of the cages after their procedures. This implies strength, curiosity and foraging behavior. If we worked in a more surf-friendly climate, perhaps this would be a better indicator of resilience.

Click here for the sequel.

Graduate Terror

From Seed Magazine's I Can't Believe It's Science weekly feature:

Does a graduate student in your lab or local university keep strange hours? Does he show unusual interest in scientific information that lies outside his prescribed tasks? Does he secretly talk to foreign people? If so, beware! He is exhibiting several espionage indicators and might be a spy or terrorist. FBI agents are currently warning the nation's top universities that they should keep their eyes peeled for potential foreign spies or terrorists infiltrating research facilities. The FBI plans to travel around New England over the next few months, offering faculty training on how to spot a bad apple who hopes to steal research... So, professors, if you notice a quiet student in your lab who works late into the night and is really, really into your science, be afraid. Be very afraid.

Uhhh... Doesn't this apply to every graduate student?

Wild Spawned v. Hatchery Raised

Did anyone catch the latest news about salmon? By way of Kansas, I learned of an interesting ruling regarding salmon fisheries. The National Marine Fisheries Service, an executive branch administered department, had been counting hatchery-raised salmon the same as wild-spawned salmon in its environmental impact calculations. The hatchery-raised fish generally boost census counts, changing the status of species like steelhead trout from 'endangered' to the less restricted 'threatened.' Clearly, it was the developers that argued for including hatchery raised fish in the counts.

A Seattle P-I article details this story quite well, and Blogfish has another analysis.

Wouldn't it be nice if environmental agencies could listen to science BEFORE a judge has to take account of the situation? On the one hand, we probably only hear about the most egregious cases, but on the other hand, you have to wonder how else is science being ignored by the current administration...

Just as clarification, this ruling does not apply to "farm-raised salmon." Blogfish nicely points out that:

Scientists are careful not to call salmon wild if they're raised by people for part of their life cycle. For a scientist, there are three main types of salmon, wild, farmed, and hatchery. But fishermen and the seafood industry call salmon wild if they're caught in the ocean, no matter how long they actually lived free.

So if you eat fish, keep buying those wild salmon.

I spotted the salmon pictured above at this weekend's Solstice Parade.

Catholic ES Cells

The front page of the Wall Street Journal has an interesting article about the origins of an embryonic stem cell policy that the Bush Administration may offer to counter the recent stem cell bill presented to him by the Congress. The byline of the article is: "How Donald Landry reconciled science with religion and got the attention of Washington." This is an interesting work-around to a flawed policy, but identifies what can happen when smart people work honestly to reconcile their personal beliefs with a commitment to science. I have to admit that I didn't pay much attention to the original scientific articles, so want to read all of the background sources on this before commenting further.

Theological Concept: Concordism

When's the last time you thought about how the Bible relates to science? If you read science blogs like I do, this topic comes up quite a bit - often as the butt of jokes. Most of what I see in the science and (Christian) religion 'debate' are arguments from one side of how the Bible portrays a precise account of creation from the other side of how the stories in the Bible are mythological nonsense. There is an obscure school of thought from the 19th century that may offer some wiggle room for individuals interested in exploring the possibility that God played a role in creation, but who hold science as the best approach to investigate the natural order.

Concordism is the view that the biblical account of creation, when properly understood, will be in agreement with scientific accounts of natural history. Understanding where you (or the person you are talking to) stand on the spectrum of concordist perspectives will make it easier for you to understand what direction the discussion will go.

Does this mean that we are to take accounts of natural history in the Bible as correlating to modern day scientific observations?

Biblical literalists will argue that any allusion to natural history in the Bible must correspond to actual physical events. This is an approach with a very high degree of concordism. The problem with this approach is that literalist concordists are trying to find scientific data in a passage that is pre-scientific.

At the other end of the spectrum is the position that the Bible does not intend to teach us about natural history and is only using the language of nature to help our understanding of spiritual truths. This is the minimal degree of concordism.

Most theologians acknowledge that the primary message of the Bible concerns the relationship between God and his creation, not an account of the creation. Taking account of creation is where science comes in handy. The added bonus is that science in this role can be undertaken by anyone familiar with empiricism and the scientific method.

And perhaps in the end, we can note the similarities between the progression of Genesis creation account and the progression of species described by the paleontological record and say, "One wonders about that." Or we might be left curious about how it is that altruistic behavior arose and note that the central message of the New Testament is one of altruism.

Scientists: Meet Your Clergy

The Clergy Letter Project has accumulated statements of support for evolution from clergy and also promotes Evolution Sunday (the Sunday closest to Charles Darwin’s February 12 birthday). I am not so sure that we need to devote a sermon every year to evolution, the project's current effort at promoting scientist-clergy dialogue sounds worthwhile. As The Clergy Letter Project matures, they aim to provide more and better resources to clergy members who understand the importance of science and who do not find science to be a threat to their faith. (Wouldn't it also be nice if more scientists did not find faith a threat to their science?)

Here's where all you scientists come in to the picture. The project is beginning to create an on-line database of scientists who are willing to answer questions posed by clergy members. Consider if you are excited about the possibility of interacting with clergy members and their parishioners in an attempt to explain the beauty and power of science. If you are willing to provide technical advice to clergy members in need of such support, please sign up.

To enroll in this project, email Michael Zimmerman (mz at butler dot edu) with the following information:

Name:
Title:
Address:
Areas of Expertise:
Email Address:

This is a concrete way that you could help to build the relationship between science and religion.

Solstice Viewing

A few weeks ago I introduced you to Puget Sound's Mud Monster. He is a spokesman for MudUp, a local effort to clean up Puget Sound. I hear from a reliable source that he will make an appearance in Seattle at this weekend's Fremont Street Fair. Following the (in)famous Solstice Parade, there is a segment of the fair where you will be able to learn about all sorts of important steps you can take to improve your relationship with the planet.

What I want to know is whether the Mud Monster plans to ride a bicycle in the parade.

Dinner Conversation

Last week during the Republican candidates' debate, Mike Huckabee said,

Tonight, all over America, there are families sitting down to have dinner, and I doubt that any of them will say, ‘I wonder what the next president will think about evolution?’

My charge for you, dear reader, is that when you sit down tonight for dinner ask your family, "I wonder what the next president will think about evolution?"

Missed Stem Cell Paper

In all the hubbub last week about the skin cell reprogramming paper, I think everyone overlooked a report that actually may be more important in the long run - and to me it was more interesting.

A year or so ago a young faculty at Harvard named Kevin Eggan showed us how to reprogram mouse somatic cells by fusing them with egg cells. Now, he has another way of reprogramming mouse cells. This time, his group has been able to reprogram cells that are in the process of dividing. Check the Nature article here. By the way, Dr. Eggan is a really nice guy. We met at a stem cell meeting in San Diego a couple of years ago and he took a bunch of (poor) grad students out for drinks one night.

Why are these important? In both cases, the reprogramming occurred when the nuclear envelop was broken down. Scientists have hypothesized (there is a rather large bandwagon now) that reprogramming depends more on the epigenetic factors than the code itself. Actually, it is fair to say this theory is on its way to dogma. The thing is, we hardly understand HOW this happens. I'm placing my bets that the King of the Nerds will figure it out at some point.

In the mean time, it seems like breaking down the nuclear envelop is the way to go - either by cell fusion or by messing with the cells when they are in mitosis.

Don't forgetthat this is in the mouse! No human cell has yet been reprogrammed.

Carbon Footprint: Low Flow

This is the sixth entry in my series about reducing your personal carbon footprint. So far, I have suggested that you ride the bus, take the stairs, live in the water-powered Northwest, think differently about air travel and recycle aluminum. I enjoy writing these tips; I hope you enjoy reading them. That this is number six also means that I have been keeping up with my regular blogging for almost two months.

Today I want to share with you information that could reduce your carbon footprint, lower your electricity bill and conserve our watersheds. How much? Well... To start, the Department of Energy estimates that electric water heaters are the second biggest energy sink in homes without natural gas. (I am guessing this is after the fridge.) Where does the warmth in that guilty pleasure of a long hot shower come from? In most homes, gas and coal fired power plants. A utilities sponsored study found that a family of four could save 14,000 gallons of water a year just by switching to an energy efficient shower head. This amounts to 21 cents a day on water and 51 cents a day on electricity bills.

Energy efficient shower heads and faucet aerators work by inserting air into the water stream. The contents come out at the same pressure - there is just less water. Evidently, the water cools faster though. According to one site,

if you are tall, you may notice that the water has cooled a little before it reaches your feet.

Interesting. Hopefully this fact does not convince my wife that we should not switch the head in our household. But speaking of switching, you can get a FREE aerating shower head by calling 206-684-3800 or emailing rescons.scl@seattle.gov. In addition, many Puget Sound residents will soon be mailed forms with which they can receive two FREE faucet aerators and one shower head. You can go to this website and register before the crowds to make sure you get one. There are also numerous additional tips to reduce your water usage at that site.

Ombudsman

Tomorrow I meet with the University of Washington's ombudsman. Don't worry, it's nothing serious, and is of my own prerogative. If it is appropriate, I will certainly post more specifics in the future.

Just out of curiosity, does anyone out there have any experience interacting with ombudsmen?

Universities have come to rely on this person as a resource for personal conflict mediation and for processing claims of scientific misconduct (neither is the reason I am meeting with her). One prominent use of ombudsmen is the James Sherely tenure dispute at MIT. I also bet that legislation like the Whistleblower Protection Enhancement Act (HR 985) probably comes to bear on this office. The nature of ombudsmen's work is usually confidential, so it will be interesting to learn more about what the office does.

I figure that at the least, I will come away from our meeting with a better sense of how the ombudsman can factor into the academic structure. And maybe by the end of this I will be able to pronounce ombudsman without twisting my tongue.

Barking Up the Wrong Poll

Now that some of the hubbub surrounding the Creation Museum opening has died down (Well, okay - I guess it really hasn't), I thought I would comment on why of all the topics in science this is the one everyone cares about.

My colleagues and fellow bloggers love to quote polls about just how stupid Americans are when it comes to science. Since we are soooo stupid with science, the media makes it easy for us. As far as the newspapers are concerned, its either A or B. Take for example the recent USA Today/Gallup poll about evolution and creationism. If you bothered to go to the source, it would probably take you 5 minutes just to figure out what the questioners were asking. Then when you consider the results, you would discover that:

Two-thirds in the poll said creationism, the idea that God created humans in their present form within the past 10,000 years, is definitely or probably true. More than half, 53%, said evolution, the idea that humans evolved from less advanced life forms over millions of years, is definitely or probably true. All told, 25% say that both creationism and evolution are definitely or probably true.

Wait a minute... a majority believe in Young Earth Creationism and a majority believe in evolution over millions of years. The media has done it again. A complex issue for which people think they know more than they do is boiled down into cold, hard data. This time, however, everybody wins. Except that no one does. We are left with less information than we has to start with.

Michael Patrick Leahy has offered suggested questions that could actually set the record straight. So for all of you quoting how stupid Americans are, you will need to wait until this survey is taken before you can speak on evolutionary illiteracy.

On the topic of evolution and creation, which of the following schools of thought best represent your views:

1. Atheistic evolution, in which the earth is 4.5 billion years old, man evolved over millions of years and God played no part in it.

2.Theistic evolution, in which the earth is 4.5 billion years old, man evolved over millions of years and God had a hand in it.

3. Intelligent Design, in which the earth is 4.5 billion years old, and the development of species over time are the results of the design of an intelligent agent, which may or may not be God.

4. Old Earth Creationism, in which the earth is 4.5 billion years old, and man was created fully formed by God within the last 50,000 years.

5. Young Earth Creationism, in which God created the universe, the earth, and man in one week 6,000 years ago.

6. I’m not sure and I don’t care

7. I’m not sure, but I think God played a role.

8. I’m not sure, and I don’t think God played a role.

Make sure you know what you think on this issue before Gallup calls you!

40 Days

Let's see. It rained on Noah for 40 days and 40 nights. Moses was on the mountain for 40 days. Jesus fasted in the wilderness for 40 days.

I am also on a 40 day journey.

First, some context: As I type this, I am eating my ninth consecutive meal at the lab. You know work is busy when the porcelain is replaced with tupperware in the dishwasher at home. I now know the relative distances, operating hours and selection-economy axis of the three grocery stores closest to my lab. I am friends with Abdikadir, the late shift custodian in our building. I also know when to move from my lab bench to tissue culture to avoid being "mopped in." (10:30 pm)

The motivation for these recent developments can be traced to two dates: May 22 and September 13. On May 22, my advisory committee agreed that I could defend my dissertation on September 13. Of course, I do not have quite enough data to complete the scientific stories I am trying to tell. I presented an ambitious plan to finish all of my wet experiments (which for me includes those involving cells and animals) by July 1.

That puts me today at number 19 of a 40 day flood of experiments. Just like the one described in Genesis, this rain falls day and night. And while it may sometimes feel like I am in the wilderness, I am not fasting, nor do I expect at the end of it all to be tempted with world domination or anything like that. No, I will be tempted to embark on a second flood. One of words. That's right: I hope to have a draft of my dissertation, (and two accompanying articles for submission) by August 9.

Now that this information is out there for all 25 of you readers, I will have to commit to it. For you locals, here are the specs.

"Reducing Fibrosis and Cell Death in Transplanted Cardiomyocytes"
Thomas E. Robey
September 13, 2007
3:00 PM
Hitchcock Hall 132

By the way, you could select another "40" for me here or here.

Science Policy Tracker

Want to know what science-related bills are being debated in Congress? The American Association for the Advancement of Science tracks everything nicely at this website.

Remember that if you contact your legislators about these (or any other) issues, use email, the telephone or fax your letter. Since the anthrax incident, paper mail takes FOREVER to get through.

FREE TimesSelect

Were you as upset as I was last year when the New York Times limited its opinion columns and other features to subscribers only? If so, you will be as happy as I am right now that individuals with academic email addresses can receive complimentary subscriptions to the TimesSelect program. Just follow this link and you will have another way to while away those minutes between timepoints or incubations!

God's Merry-Go-Round

Around Christmas last year, Francis Collins (Director of the Human Genome Project) was interviewed on the Colbert Report. I wish I could stay up late enough to watch this every night, but these days, I can't even make it to Jon Stewart. Why is this on my blog? Well, Francis Collins is a really prominent scientist who is a Christian. He wrote a book about how he believes DNA to be the language of God. I spoke with him last year about his beliefs and was impressed by his humility, open-mindedness and accessibility. Note that he included in the subtitle of his text, "evidence for belief," not evidence for God.

Anyway, let the laughs begin.

Part 1:


Part 2:


Careful Francis - I know you are tall and all, but please don't kick that cute little lamb's head!

Cell Wars: A New Hype

Have you heard the news!!???

Skin cells can be reprogrammed into embryonic stem cells! We don't need to destroy blastocysts after all. All you need to do is scratch your nose, clean the debris out from under your fingernails, infect them with a virus and... voila! you've got pluripotent stem cells!

The New York Times - not to mention all the other papers that syndicated this news - had the story on their front pages. Nature printed a nice lay summary of this issue, too.

Wait a minute... Is this true?

Before I go on, I must remind you that I am a bioengineering graduate student who works with human embryonic stem (ES) cells. By my estimation, this both qualifies me to comment on this issue, and slightly colors my opinions. I applaud this work as instrumental in pushing forward regenerative medicine. These findings do not provide scientific competition for the projects I work with. My chief concern is with the way that pols, pundits and hypers will use this as evidence to invalidate the important work that scientists working with human embryonic stem cells are doing. I have chosen to use a few spare electrons to relay my early impressions about how this information is being transmitted to the public. Others (namely an excellent post by Mark at Denialism) have relayed scientific critiques of these papers.

Between last night and this morning, I read all three of these reports, and the science is looks pretty good. Just so you know, the techniques that these findings rely on were first reported a year ago (Cell 126, 663-676, August 25, 2006). This made a splash in the scientific community, but did not make so much impact in the lay press. Chances are that you remember the amniotic stem cell report more than the skin cell reprogramming. Why was that?

Well... It just so happened that the paper by Atala et al about amniotic stem cells came out at the same time as Federal legislators were debating stem cell bills (Recall that human embryonic stem cells were part of Pelosi's priorities for the first 100 hours of 110th Congress?) If you have interacted with the media at all, you know that the US House and Senate have passed their versions of a bill that would expand Federal support for human ES cell research, and that George Bush has threatened a veto of this bill. (Remember that his first veto came six years into the presidency on the first version of this bill.) It looks as though it is borderline whether there are enough votes for the override. According to the AP,

Democratic congressional leaders arranged to dispatch the measure today (June 7) to the White House with a flourish.

What a coincidence that this alternative to embryonic stem cell research is announced on the same day! Hmmmm... These are the seeds of a conspiracy theory, and I'm not the only one to notice. Evidently,

"whenever lawmakers are debating stem cells, you can guarantee some study about adult stem cells will be released," said a frustrated Senate Democratic aide about the reports.

If you need anything more to convince you of how politics and stem cells are mixed up, see this NYTimes article. I wanted to quote half of its text in this entry.

Along with Mark at Denialism and Alex at The Daily Transcript, I agree that these findings have great potential to move stem cell therapies into the clinic. As far as the science is concerned, my main concern is that the gene therapy methods used to modify these cells are inexact (and still potentially dangerous). These modifications are known (reported even in one of the papers) to cause uncontrollable tumors called teratomas. Specifically, Science magazine reports that:

the Yamanaka study showed a big downside to the strategy. The only author to study the offspring of the chimeras after birth, he observed that 20% of the 121 mice developed tumors. That finding, Yamanaka notes, shows the danger of using retroviral vectors, which can turn on cancer-causing genes.

What the press buries deep in its reports (I have yet to hear anyone talk about it on the radio) is the difference between mouse and human cells. Rudy Jaenisch, a fair bet for the title, 'stem cell expert,' and author on two of the recent papers indicated his perspective on when this will be used in humans.

"This is really dangerous. We would never transplant these into a patient." In his view, research into embryonic stem cells made by cloning remains "absolutely essential."

My concern is that the press will not pay attention to this appeal, and everyone else will never hear about it. This debate is being framed as adult vs. embryonic stem cell research, when really it should be adult AND embryonic stem cell research. The public wants to fund research. They want to fund embryonic stem cell research, and they want to fund adult stem cell research. (I hear that they do not want to fund a war.) That this is being presented as an either-or argument kindof makes me sick!

So why are we hyping this so much? The Daily Transcript projects a Nobel Prize for Yamanaka and Takahashi, the pioneering skin-to-stem cell scientists! I hope if that happens that they share the award with Jaime Thomson, the scientist who first derived lines of human ES cells.

This may turn out to be another great discovery, or it may go the way of previously hyped adult stem cell work. As with everything else, only time will tell. But you can be sure I will continue to point out where I think stem cell science has been misrepresented by the press, politicians or my lab coworkers.

SPUWing Science Ethics and Policy

For those of you Seattleites interested in science ethics and policy, here's a heads up for an ongoing happy hour that anyone can attend. Science Policy at the University of Washington (SPUW) happy hours are an informal place where students, faculty and community members can come together to talk about science and society. This is sponsored by the Forum on Science Ethics and Policy, and will occur the first Wednesday of every month. Currently, we meet in the back room of the College Inn Pub, at the corner of University Way and 39th St. We start around 5:30 and people stick around past 7:30. FOSEP pays for the snacks, leaving more funds for you to buy some pints. FOSEP's other events are much more structured - these gatherings are opportunities for camaraderie, networking, and the SPUWing of ideas. If you want more information, email me or post a comment.

Carbon Footprint: Stay Grounded

An editorial in today's Seattle Post-Intelligencer induced my choice of this week's Carbon Footprint series. Kathleen Braden, a professor of geography at Seattle Pacific University, relayed her reasoning for not supporting the Sierra Club's efforts to combat global warming because of duplicity between the group's positions and its member services. Don't worry, she doesn't spare other conservation groups that are as two-faced as Janus.

Braden is familiar with the consequences of international travel: she recently gave a seminar about ecotourism in Russia. (The 30 minute talk is available for podcast.) But the central premise of her P-I column was something else - carbon emissions from airplane travel. By offering members vacation travel packages to remote destinations around the world, she calculates that the Sierra Club will add 689 metric tons of carbon dioxide to the atmosphere this year, just so that members can enjoy nature in Nepal or Peru. The same duplicity comes from groups that send plush toys, t-shirts and other packages overnight by air freight to new members.

So what's the take home from this? Are we to take fewer plane trips? Reduce the number of overnight orders? Visit distant family less? The culture of academia is dependent on travel. Just like salesmen, professors travel the country to present their research and ideas to colleagues via conferences or invited seminars. NIH grant review occurs in study sections in Washington DC. Some societies plan 'destination conferences' in Waikiki or Sydney or Venice. On a more personal note, I expect to fly to eight to ten cities next year to interview for residencies. What are we to do about this culture of travel? Whatever it is, it will require system-wide changes in behavior. I am going to start by not worrying whether I will make 'MVP' this year on my Alaska Air frequent flier number. A 14 hour drive to visit my parents? That would be more difficult. And visiting my in-laws in Hawaii... Right now, we are limited by time and finances, so making that trip is still infrequent. Are there any frequent travelers out there - in business or academics - that have found ways to reduce their carbon impact without 'suffering' lost productivity or professional standing?

There's another little pearl from this column that I don't want to overlook, and it ties nicely with a recent post of mine. Here is a Christian - a professor at a Christian college - who is a member of the Sierra Club, the Ocean Conservancy, and probably others that sees no problem between the scientific claims made by these groups and her personal faith. I bet that Kathleen Braden sees her public scholarship on this issue as part of a Christian imperative to be good stewards of the Earth.

He's (Brown)ba-aack!

Mike the Mad Biologist brought my attention to the fact that Sam Brownback (R-Kansas) got a column published in the NYTimes about his (dis-)beliefs of evolution.

It is interesting to me that the gentleman from Kansas is making such a stand on this issue. I suppose he will guarantee some votes in the primary with this position, but to the rest of us, he seems more and more a moron. So please do not confuse my statements as supporting the man. I do however see something deep in his arguments that strikes a chord with me. Those that have read Gould (or a previous post of mine) will recognize this quote:

"the magisterium of science covers the empirical realm: what the Universe is made of (fact) and why does it work in this way (theory). The magisterium of religion extends over questions of ultimate meaning and moral value. These two magisteria do not overlap, nor do they encompass all inquiry (consider, for example, the magisterium of art and the meaning of beauty)."

Maybe this is where Brownback is coming from regarding his perspectives on faith and empiricism. Or maybe it is simply that:

"limiting this question to a stark choice between evolution and creationism does a disservice to the complexity of the interaction between science, faith and reason."

What? I agree with Sam Brownback??? (Speaking of agreeing with Brownback, did you know that Brownback and Barack Obama both appeared at Rick Warren's (The Purpose-Driven Life) church on World AIDS Day last December?) Our friend from Kansas may be mixed up about evolution, but he has some redeeming qualities when you consider some of the social positions he takes. That's for another post though...

A lot of people - many scientists included - see existence as consisting of more than empirically derived explanations. I think this is fine. It's been a part of human experience for millennia. The problem that Brownback is running into is that an issue at the periphery of his personal faith (an issue trumpeted as critical to that faith by certain religio-politico groups) conflicts directly with a central tenet of science.

For me, it's too bad that we can't talk about the different roles science and faith play in people's lives without inciting the vitriol of the creation-evolution 'debate.'

Christian Environmental Stewardship

Sometimes I think the chances of science and religion coming together in a meaningful way are next to nil.

If you take as proxy the evolution 'debate' for the science and religion discussion, you may be right. Maybe neuroscience will be the domain of the next schism. But maybe there is some hope. If you want to talk about environmentalism, scientists, community activists and religious people are more likely to be on the same page than not.

Specifically, consider the back page of the May/June newsletter from the church I attend. There's a story there about the church's Christian Ecology Group. They facilitate pickup of of organic produce grown by Southeast Asian and East African immigrant families living in Seattle's High Point neighborhood. This is part of a partnership between several churches, the local P-Patch Foundation and the city called Seattle Market Gardens.

By participating with this program, citizens are satisfying goals of living a more healthy lifestyle, providing meaningful supplemental income for immigrant populations, reducing the burden of carbon emissions involved with the global agriculture trade. Christians should identify that the Biblical imperative to have dominion over the Earth is one of stewardship, not exploitation. For a comprehensive article supporting this view, consider this paper. Another innovative thinker in this area is Holmes Rolston III.

I wonder what would happen if the fundamentalist Christians that are the face of religion in the United States these days added environmentalism to their political platform.

Scientific Integrity

I've been thinking about scientific integrity a lot recently, and want to put some of my ideas out there. It's almost summer, and this means that the Biomedical Research Integrity series at the University of Washington is about to start. The question I have for this post is:

When you teach ethics to scientists in training, how much do you talk about the history of science?

I think it's fair to say that most people enter science for altruistic motives, each of which could probably be categorized as 'improving society' or 'seeking the truth.' It's only along the way that we are introduced to financial gain, advancement requirements, prestige, funding pressures and the other incentives to lie, cheat and steal.

If we think about the development of empiricism and the scientific method, we can identify that the small number of men who were natural philosophers (there weren't even 'scientists' then) were in it for the altruistic reasons. Am I sugar-coating this to say that there was not motivation for scientific misconduct?

What I am getting at is that it might be useful to contrast the historical conditions surrounding the rise of the scientific tradition in relaying why integrity is such an issue today. We can all identify the pressures that lead to lapses of integrity, but fewer of us admit to temptations and I think fewer of us will (even anonymously) report actions of falsification or plagiarism. The last time I checked there is no Office of Research Integrity ethics topic on history of science.

Maybe it is altruistic to appeal to the traditions and foundations of science, but I think if more people held honesty as the scientist's prime directive, we would not see as many problems with scientific integrity.