Tuesday, February 27, 2007

Prayer Study Hasn't Got One

What? Another bogus study?

This entry is a shift from my standby controversial topic (stem cells) to another one (religion), but the story is actually the same. Only the names have changed to protect... Actually, I am not changing any of the names.

From the Chronicle of Higher Education:
Doctors were flummoxed in 2001, when Columbia University researchers published a study in The Journal of Reproductive Medicine that found that strangers' prayers could double the chances that a woman would get pregnant using in-vitro fertilization. In the years that followed, however, the lead author removed his name from the paper, saying that he had not contributed to the study, and a second author went to jail on unrelated fraud charges.

Whoa! Jail! Pardon my flippancy, but who's praying now?

Evidently, the study's third (and only remaining) author, Kwang Y. Cha published a separate paper copied from a Korean doctoral student without his permission in an American journal. That's called plagiarism.

On a related note, when will people stop trying to use science to 'prove' faith?

Sunday, February 25, 2007

Flawed Studies

It seems like there are new revelations of scientific fraud every week. Before I make any conclusions, I need the answer to a few questions:
  1. Have there always been this many cases of scientific fraud?
  2. Is the scientific establishment more adept at identifying misconduct?
  3. Why am I hearing mostly about fraud involving charged topics? (prayer, stem cells, etc.)

Maybe there is more fraud because there is simply more science being done.

Perhaps science these days is a higher pressure environment that induces folks to make unethical choices.

Am I (or the media) just paying more attention to these things these days?

What are we as scientists to do about this? Already, I have heard the line about a few bad apples too many times. I hope it takes more than a few to sour the public on science!

Saturday, February 24, 2007

Stem Cell Research Misconduct... Again

Could the stem cell field PLEASE get its act together?

In a not-so-covered story last week, the New Scientist reported that ground-breaking research from the adult stem cell field may have been falsified. They did not go so far to claim research misconduct, and no action has been taken by the journals. The basic scenario is this:
  • In 2002 Catherine Verfaillie (pronounced Ver-fi-yee) described in Nature magazine a population of adult stem cells that can differentiate into most cells in the body, including brain and heart cells. She publishes separately that these cells can be isolated from the blood, heart and brain.
  • Immediately, politicians opposing embryonic stem cell research touted this finding as proof that ESC research is unnecessary.
  • For 5 years, many of the world's leading stem cell biologists tried to reproduce this monumental finding. Several even traveled to Minnesota to learn the technique. Along the way, reports surfaced that the Verfaillie group even had trouble reproducing their own work.
  • The New Scientist (for some reason at this late date) looked into this issue in depth and found that 6 of the graphs presented in the Nature paper were also published in the other article.
  • After this was discovered, an expert panel (I wonder who this was) re-examined the data and found it 'flawed.' Strangely, the flawed data has nothing to do with the duplicated data. Verfaillie claims that the doubly printed figures were the result of a clerical mix-up.

What went wrong here? Let's start with the basics: the same figure cannot be printed twice in different articles without proper citation. This is called plagiarism. It doesn't matter if it was a clerical error, it needs to be called what it is.

At the next level we have the question of reproducibility. Like my colleague JG likes to point out, scientific articles are a little like muffin recipes. If the recipe doesn't include the very specific ingredients, how and when to mix them and instructions for baking and cooling, the likely outcome are dry and lumpy excuses for Otis Spunkmeyers. The New Scientist article leads us to believe that this adult stem cell recipe is so lacking, that the original chefs could not even get it right the second time. (The nagging question is whether they only were able to do this once, so used the same data twice.)

Finally, we have some questions about the unchecked progress of science. I am not referring to doomsday scenarios, just that the stem cell field is sooo hot that careful science is sacrificed for flashy findings. This is the result of zealousness positioned where skepticism should reign. (For all of you editors of major scientific journals out there reading this post, I'm talking to you.)

Something about this situation sounds really familiar... it sounds just like another report involving amniotic stem cells' abilities to regenerate every tissue in the body.

Tuesday, February 20, 2007

Burden of Proof

Just in case you thought I was making this up, here is a scanned image of the two stories side by side! Visit my Flickr site for a few more points. Don't worry: after this post, I'll move on to more pressing issues.

Monday, February 19, 2007

Sasquatch Rears His Head

On Sunday morning I like to read the newspaper. My wife goes for the glossy pages from the ads, while my goal is a grey thumb. Sure, I probably have heard much of the news from the past week, but the leisurely atmosphere of the weekend affords me a little more time to read some specifics and think more about the context of the reports.

So wasn't I surprised to read the front page news: "Science knowledge increases, but ..."

A science story was on the front page! It helped that the annual AAAS meeting was this weekend, and with it comes a blip of science media coverage, but I'll take it.

So what's the 'but...'?

Americans know more about basic science today than they did two decades ago, good news that researchers say is tempered by an unsettling growth in the belief in pseudoscience such as astrology and visits by extraterrestrial aliens.
In 1988, only about 10 percent knew enough about science to understand reports in major newspapers, a figure that grew to 28 percent by 2005.

So, how does the Seattle Times react to this news? By printing the latest evidence proving the existence of Sasquatch, of course. A syndicated article from the Washington Post (the other Washington) proclaimed that, "Officials, not Sasquatch fans, puzzled by nonhuman foot." The best part was that the two stories were immediately adjacent to one another!!!

Basically, someone found an 8 inch long, skinned foot in a landfill in Spotsylvania, Virginia. A gross picture and an assortment of other Bigfoot related information is available at searchingforbigfoot.com. Gee, it looks like a bear paw to me. Poor bear.

This situation offends me for three reasons:
  1. From a public interest perspective, the Bigfoot article is more fun to read. It involves a forensic analysis, a search through a landfill, several good jokes and comments by the chamber of commerce. Conversely, the scientific literacy article has going for it citations of a Brit as well as a bunch of professors and then a laundry list of statistics. References to astrology and evolution could have been fleshed out better.
  2. I wonder who is to blame for science illiteracy... Could it be that newspapers and the 500 word article just can't do the job of helping the public sort out science from psuedoscience? This is surely related to a conflict between providing news and selling papers...
  3. Back off, Spotsylvania! Sasquatch is ours! I'm with the Fredericksburg, VA barista who is "from Washington state, home of the Bigfoot, so no way [is this foot from a Sasquatch]," she said. "It's too warm [in Virginia]."

Well there we have it. Science is only as good as its use in public interest stories.

AAAS in San Fran

The American Association for the Advancement of Science is wrapping up its annual national meeting this weekend in San Francisco. If you are interested in the interface between science and society, this is a place to meet folks that are passionate about science. The meeting attracts scientists, educators, policy makers and media from every branch of science, and several peripheral to it (religion, history, economics). There are a number of events that bring folks whose paths may never cross into the same room. I have attended two meetings and found them useful for identifying interdisciplinary projects, meeting people that could help my future career, and canvassing potential speakers for the Forum on Science Ethics and Policy at the UW. In fact four of my FOSEP colleagues are in San Fran now.

Like a lot of the giant science meetings these days, the conference is a time when the media have easier access to potential science stories. In addition to a spike in science stories in your local paper over Presidents' Day weekend, AAAS hosts a news blog, and some other meeting updates. The AAAS website also hosts Eurekalert as a daily science news story resource.

Next year's meeting is in Boston. Hmmmm. Boston in February....

Friday, February 16, 2007

Would You Like Peanut Butter With your Spinach?

I recall my mom preparing lightly steamed spinach salad cooked with a small dollop of chunky peanut butter. I find it ironic that the two most recent reports of food-borne illness refer to ingredients from the same fond culinary memory.

But seriously, what's the deal with these outbreaks?

How is it that a peanut plant in Georgia causes illness in Washington state, spinach from California gets recalled in Massachusetts and the lucrative carrot juice market takes a hit everywhere?

A Centers for Disease Control spokesman (Robert Tauxe, chief of the CDC's Foodborne and Diarrheal Diseases Branch) recently said, "Nature's been throwing us curve balls. We've had seven major product outbreaks in the last five months, and three have been in brand-new foods — botulism in carrot juice, E. coli in spinach, and now this."

Excuse me: NATURE's been throwing us curve balls?

Each of these contaminations were in food processed at large manufacturing centers or distribution points. Perhaps if we relied less on the global industrial complex for our food and more on in-season produce and local meat, we really would be more healthy! You won't catch me in the aisles of Whole Foods quite yet, though. I have to make more than a graduate student's salary to be found there doing anything more than collecting some delicious free samples on the way to work.

In case any of you have Peter Pan or Wal-Mart 'Great Value' brand peanut butter with the numbers 2111 on the lid, you can avoid an interaction with the CDC's Diarrheal Diseases Branch by throwing that container away. If you need other reasons to avoid Wal-Mart, I could connect you with more resources on that front.

Tuesday, February 13, 2007

This Just in From Kansas...

Did you think that the new school board elected last year in Kansas would solve the political dilemmas in that state about evolution and creation? If so, you should reconsider your ideas about the appropriateness of elected officers defining education standards. The political pendulum will always swing, but the recent pass has opened a new can of worms. This time, defenders of evolution must deal with topics that has plagued this debate for a century: the problems of eugenics and social Darwinism.

First, a brief timeline from Kansas:

August '99: Kansas state school board de-emphasizes evolution in science standards.
August '00: Two conservative board members booted.
February '01: Evolution teaching restored.
August '02: Board split 5-5 on evolution.
August '04: Conservative resurgence led by Kathy Martin: Creationism 6, Evolution 4
February '05: Announcement that evolution will be reconsidered.
November '05: Science standards criticizing evolution approved.
August '06: Pro-evolution members regain majority.
February '07: Standards including evolution adopted.

So what's the fuss about?

Well, it turns out that not only is the new school board removing the creationist and intelligent design (ID) material from the science standards, they are removing references to the two most egregious examples of scientific misconduct from the twentieth century. It happens that in November 2005, the standards that inserted ID in the science curriculum, also for the first time included accounts of the Tuskegee syphilis study and Nazi human experimentation. My guess is that these were thrown in as tools to discount everyday science as immoral. In fact, it is the pseudoscience of eugenics that should be criticized! Now ID proponents, including Seattle's Discovery Institute, are using this example of 'censorship' to point out that science education is being improperly sanitized.

So I guess we need to talk about what students actually learn about science in school... Every science student is introduced to the scientific method, but most scientists (and every philosopher of science) who read a high school textbook will agree that the accounts of the history of science are sanitized. It's not really until upper level college courses that budding young experimentalists learn that science is not exactly tidy. Experiments rarely work the way you think they will, and the discoveries that are so succinctly accounted in the textbooks were preceded by years of failure. That does not even touch on the fact that ethics and the responsible conduct of science are hardly ever taught on through the graduate levels. So is it a step in the right direction to include these crimes of human experimentation at the high school level?

I have to agree with these ID proponents that introducing students to horrors conducted in the name of science is acceptable. The examples of Nazi science and Tuskegee belong in science education within the context of learning about the practice of science. A condition of including these accounts should be a proper discussion of the Nuremberg Code and the Belmont Report as efforts to reach consensus on the limits of scientific experimentation.

As a final side note, I have yet to see an account accessible to the public that distinguishes evolutionary biology from social Darwinism and eugenics. Does anyone know of one?

Monday, February 12, 2007

Pit Bulls, Barbie Blending and Science!

Boy was I surprised to read in the Sunday newspaper about a relatively obscure movement in scientific publishing: public access to scientific journals. Even I may have passed by this page 6 story had not the title been, "Research-Result Battle Now Pits PR 'Pit Bull' Against Barbie Blenders."

The basic argument presented in this article is that some people (mostly patient advocacy groups) want all government-funded research (uhhh- that's just about all of it...) to be available to the public 6-12 months after it is published, but the publishers want that information to remain only available to their subscribers. This is a hard argument to settle, but there are two items that seem to always be overlooked.

  1. This research is already available to the public, albeit in a limited manner. Any major city with a university or academic medical center has a library with all of these journals. If you really want access to this information, you can look it up the same way that we scientists do: photocopies and .pdfs.
  2. Scholarly work presented in scientific journals is hard to understand outside of the field in which it is published. The amount that is freely available - the abstracts - is all that patient advocacy groups and the press use anyway.

My main point here is that even if this information is freely accessible, it will still be intellectually inaccessible. This is not some sort of Ivory Tower pronouncement. The truth of the matter is that the scientific article is not the same as an encyclopedia entry or lay press article.

Thursday, February 08, 2007

Is Big Science is Here to Stay?

Reported in the New York Times today is a story about a planned $6.7 billion 20 mile long supercollider. It's no Superconducting SuperCollider (Cancelled by the US Congress in '93), but is seems pretty cool to me.

The most interesting paragraph in the article is:
Particle accelerators derive their punch from Einstein’s equation of mass and energy. The more energy they can pack into their little fireballs, the farther back in time they can go, closer and closer to the Big Bang and perhaps ultimate truth about nature, recreating particles and laws that once ruled the cosmos, but have since vanished more completely than the dinosaurs. But as physicists have pushed inward and backward, their machines have gotten bigger and more expensive.

Can you guess which phrase made me laugh? You win a prize if you identified "ultimate truth about nature." Wow. We've got the credibility of the most famous scientist ever, conjuring of Hollywood's fireball special effects, the elusive dream of time travel, questions of origins of existence, and to top it off, the answer to life, the universe and everything!

Gee, $6.7 billion seems like a deal to get all of that!

Monday, February 05, 2007

Jonesin' for Sugar

Are you concerned about your corn syrup intake? Jones Soda, the independent soda maker headquartered 3 blocks from where I work, has announced a switch on all of their production lines to cane sugar effective in a few months.

When I first heard this, I thought, "finally someone is making a healthier soda." What did I base this judgement on? Outdated science of course. Tales of the evil of corn syrup abound 'out there,' but it turns out the researcher who first said there might be a link between high fructose corn syrup and obesity says there is no evidence to support his earlier speculation. But what about that guy on Oprah from some the cardiovascular institute at some fancy hospital in New York City? He says on Winfrey's Web site that "corn syrup alters the body's ability to regulate appetite." It's nice to hear when another scientist (again the one who did the original studies) says, "I can find a doctor who will say anything. That's not research."

Jones has a 'free soda Friday' after 3:00 PM every week. Chances are I'll spring for the Splenda sweetened variety though. Cane sugar still has a bunch of calories...

Saturday, February 03, 2007

Obama on Science Funding

In my first overtly political post, I have chosen to include text from The Audacity of Hope. I was struck by how in two pages he:
  1. Outlined a brief history of government sponsored research.
  2. Relayed a personal vignette of a conversation with one of the world's top scientists.
  3. Offered hope for a plan to reinvgorate academic research.
Well, okay - the last element consists of letting the highways get a few more potholes in the name of scientific research. Maybe he will need a better plan than that...

This is from pages 165-167.

There's one other aspect of our educational system that merits attention - one that speaks to the heart of America's competitiveness. Since Lincoln signed the Morrill Act and created the system of land grant colleges, institutions of higher learning have served as the nation's primary research and development laboratories. It's through these institutions that we've trained the innovators of the future, with the federal government providing critical support for the infrastructure – everything from chemistry labs to particle accelerators – and the dollars for research that may have an immediate commercial application but that can ultimately lead to major scientific breakthroughs.

Here, too, our policies have been moving in the wrong direction. At the 2006 Northwestern University commencement, I fell into a conversation with Dr. Robert Langer, an Institute Professor of chemical engineering at MIT and one of the nation's foremost scientists. Langer isn't just an ivory tower academic – he holds more than five hundred patents, and his research has led to everything from the development of the nicotine patch to brain cancer treatments. As we waited for the procession to begin, I asked him about his current work, and he mentioned his research in tissue engineering, research that promised new, more effective methods of delivering drugs to the body. Remembering the recent controversies surrounding stem cell research, I asked him whether the Bush Administration's limitation on the number of stem cell lines was the biggest impediment to advances in his field. He shook his head.

“Having more stem cell lines would definitely be useful,” Langer told me, "but the real problem we're seeing is significant cutbacks in federal grants." He explained that fifteen years ago, 20 to 30 percent of all research proposals received significant federal support. That level is now closer to 10 percent. For scientists and researchers, this means more time spent raising money and less time spent on research. It also means that each year, more and more promising avenues of research are cut off – especially the high-risk research that may ultimately yield the biggest rewards.

Dr. Langer's observation isn't unique. Each month, it seems, scientists and engineers visit my office to discuss the federal government's diminished commitment to funding basic scientific research. Over the last three decades federal funding for the physical, mathematical, and engineering sciences has declined as a percentage of GDP - just at the time when other countries are substantially increasing their own R & D budgets. And as Dr. Langer points out, our declining support for basic research has a direct impact on the number of young people going into math, science, and engineering which helps explain why China in graduating eight times as many engineers as the United States every year.

If we want an innovation economy, one that generates more Googles each year, then we have to invest in our future innovators by doubling federal funding of basic research over the next five years, training one hundred thousand more engineers and scientists over the next four years, and providing new research grants to the most outstanding early-career researchers in the country. The total price tag for maintaining our scientific and technological edge comes out to approximately $42 billion over five years - real money, to be sure, but just 15 percent of the most recent federal highway bill.

In other words, we can afford to do what needs to be done. What's missing is not money, but a national sense of urgency.

Okay... I could be convinced that breakthroughs in science and engineering could figure out great new ways to fill in those potholes.