ScienceBloggers

Living in Glass Houses with Bricks: What about science should concern us?

2010-02-24T08:43:29Z

This weekend, I attended several seemingly-disparate panel discussions on agriculture, statistics, science playwrights, and doomsday theories, but in the end, a theme-type message started to form itself. The conference focuses on educating the world about science, and that goal requires facing one particular major challenge. Education isn't just about offering up new information, it is also about battling misinformation, which somehow manages to sneak into everything. False information even makes its way into the world of the scientist, despite all best efforts towards safeguarding against such an invasion.

1. In which we learn how to survive an earthquake, and how to really scare people that need scaring.

One day last year, I had just finished attending to some brains in lab, when I suddenly felt very dizzy. Once I finally figured out that it was the earth that was shaking and not me, I really freaked out. As a child I was terrified of natural disasters, but just then I realized that I had absolutely no idea what to do in the actual event of one. I ran out into the main corridor of the lab, and then, intent on saving my life, left the building.

]]> Turns out, I did exactly the opposite of what you are supposed to do in an earthquake. You are supposed to get under a table. I forgot to learn about this, and apparently didn't care enough to prepare myself. Many people in California feel the same way, even the natives, for anyone can get too distracted or busy with more immediate concerns. But today, after listening to a panel discussion on earthquakes in southern California, I'm ready to go out and get some jars of Peanut Butter and a flashlight and make a few earthquake kits. Let's just say that the earthquake talks were not as boringly reassuring as I had hoped.

"We are overdue for a massive 7.8 magnitude earthquake. The Big One. Historically, on average, every 150 years southern California gets hit by a major earthquake, and the last one was 300 years ago." The first speaker, Lucille Jones, a seriously super-prepared woman in perhaps her mid-fifties, probably had a fallout-shelter, twenty gallons of emergency water, and a storehouse full of power bars in her backyard.

"The Big One. What does it mean? There are two groups of responses. Some people say 'why bother?'" These people, she explained, are convinced that California is going to break in half and fall into the ocean, so nothing they could do could possibly help. So why bother?

"Others think, 'I have been through some big earthquakes. Nothing really happened. This one can't be any worse, so I don't need to bother.'"

The goal, she insisted, was to teach people that they should actually just bother. This is because the quality of our lives before, during, and after this scary apocalyptic-sounding disaster rests on our own preparedness. When she said this, everyone in the room suddenly became very concerned. For now, any minute, we would have a 150-year overdue earthquake. Thank God we were attending an earthquake seminar. I felt badly for everyone else in the conference who was learning about microorganisms at that particular moment. They would have no idea what to do when The Big One came.

The Coming of the Big One, it turns out, is a very scary story. The predicted stats did not sound so nice. Based on historical data and models created by a troupe of scientists, hundreds of thousands of homes and buildings would likely collapse, 1,600 major fires would break out in its aftermath, and a thousand people would die. How do you convince people that they should be afraid enough to prepare? How do you scare people enough to see the risk involved with a natural disaster that we cannot control or even predict - a disaster that is out of sight and therefore out of mind?

The panel members were on a mission to help the state get through The Big One as well as any smaller ones that could come along. Two years ago, "The Great California ShakeOut," an educational program to get people to bother preparing for earthquakes, introduced the largest earthquake drill in the US. Since then, outreach programs have gotten more than 5 million residents involved, and all based on several simple principles. One of these principles was "Avoid Sensationalism," which sounded practical, until the next principle was introduced, perhaps a more useful one: "Use Engaging Imagery."

The imagery probably worked the best of any of these techniques. The panelists showed a video produced as part of the ShakeOut -- an animation graphically depicting all the horrors that we would have to deal with and how much worse things would be if we didn't have fire extinguishers and 3 gallons of water per person per day. It was pretty terrifying. Seems like you would need some very scary movies to push Californians that little extra bit required to get us prepared.

2. In which we are reminded that science aims to discover and not destroy the universe.

"We are experiencing some technical difficulties. Nothing to be concerned about" said the pilot right before the plane exploded in the catastrophic nuclear blast.

I had walked into the symposium entitled: "Doomsday Verses Discovery" about a half an hour late, just as the room was finishing up watching some movie clips from the end of the world.Turns out, everything from our psychology to our religion, our distrust in science and new technology, and media sensationalism leads us to panic about dangerous-sounding scientific experiments. And since we can only spend so much time worrying about things, these irrational fears prevent us for attending to and assessing real concerns, such as the aforementioned earthquake issue, as well as dangers that come from crossing the street in the rain, riding a bike without a helmet, and baking while fatigued, to name a few.

3. In which we hear all about accidental lies in research, and learn that we shouldn't accept other peoples' analyses.

On Saturday afternoon, I attended the symposium entitled: "False Discoveries and Statistics: Implications for Health and the Environment." This, perhaps, was the scariest talk of them all. For any scientist, the end of the world as we know it might not quite measure up to the idea that much science is actually based on lies. Even if these lies are innocent and accidental, they are still misinformation that can not only affect the direction that science takes and the methods and resources that researchers use to get there, but can also have a culture-changing affect on citizens who trust research completely and blindly. How sad it seems that people loose when they mistrust science as well as when they trust too much.

"There are three types of lies: lies, damned lies, and statistics," goes the old unidentified quotation. The symposium just rubbed it in. The panelists discussed atrocities such as not controlling variables, claiming too much from uncontrolled experiments, and going along with findings that are "totally biologically impossible," simply because of a few manipulated numbers. As an undergraduate, I was always taught that you could say anything you wanted with statistics, if you did them wrong.

"Experimenters always want to find something positive. The more they find, the happier they are," Said Juliet Shaffer of the University of California in Berkeley. While this is definitely true, it seems a bit of a stretch to say that researchers will drop their ethical obligations to honest science just to find something positive. If this were true there would be many more successful grad students out there.

Stanly Young, a panelist from the National Institute of Statistical Sciences, claimed that it was the system of applying for funding that pushed researchers to emphasize the exciting-sounding new results over being sure of the old ones. "The problem is with the system," he repeated over and over, "The problem is not the worker, its the manager, because they set up the system."

"Science is supposed to be self-correcting," Young sighed, "I won't criticize your statistics, you won't criticize mine. We both live in glass houses, we both have bricks, we just won't throw them."

How do we fix this problem of not holding scientists to the highest statistical standards? From my experience this is very difficult, because statistical methods often have to be so carefully tailored to the experiment to be very difficult even for other scientists to completely understand, even after putting in a lot of time and effort. Here are a few ideas that I have heard/come up with:

1. Journal of Articles in Support of the Null Hypothesis. This is a good idea -- whenever you don't find something interesting, publish it so that people at least know the truth.

2. Journal of Failed Experiments. Just a blog now, but maybe in the future...

3. Holding more scientists responsible for research. In order for a paper to be published in a credited journal, it has to be "peer-reviewed" or read and given the thumbs-up by a few readers. If these reviewers had to put their names on the articles that they vouch for, then perhaps publishing would get a bit more stringent?

Making an Apple Pie, and the Creation of the Universe

2010-02-24T05:49:06Z

I. In which I make an apple pie almost from scratch.

"If you want to make a pie from scratch, you must first create the universe" --Carl Sagan

I had the butter, flour, sugar, and requisite spices, but no apples. And I didn't exactly know how to make a universe. How would I ever learn that?

The first problem was easiest to solve, so after spending the day at the San Diego Conference Center attending the American Academy for the Advancement of Science (AAAS) annual meeting, I drove to Vons. After circling the apple portion of the produce department, I determined that I probably should just create a universe, because then I could create one in which Vons carried pie-variety apples. I settled for some random type, although in my universe, the Macoun would have made it into my pie. I was making an apple pie specifically for a party I was attending that very evening at the home of some physics PhD students. My friends have a wonderfully obsessive love of nerdiness, wine, and cheese. Put these all together, and you have a group that spends their Sunday nights watching old episodes of "Cosmos: A Personal Voyage," an 80s tv show written by and starring Carl Sagan, a famous scientist, astrophysicist, and teacher. Tonight was our last party -- the viewing of the ultimate episode, entitled:

Episode 13: Who speaks for the Earth?

"Through the use of special effects [hahaha "special effects" from the 80's] we retrace the 15-billion-year journey from the big bang to the present. This is the famous episode on nuclear war in which Dr. Sagan argues that our responsibility for survival is owed not just to ourselves, but also to the cosmos, ancient and vast, from which we spring." - (From http://science.discovery.com/convergence/cosmos/episodes/episodes.html)

]]> Who indeed speaks for the earth? We do. In fact, so far as we know, we also speak for the universe, too. And if we want to speak with authority, there is only one way to do this: by conducting Big Expensive Physics Experiments to ask the really exciting questions. Like what is the universe, and how did it get here? Only then can we really make an apple pie from scratch.

We would like to know more about the universe than what is depicted in this pie chart here. For example, how was this pie made? How was the universe created?

But, as Robert Crease, a speaker at the AAAS conference pointed out, "great events attract great fears." And that seems to me to be one of the largest and scariest impediments to research.

II. In which I attend the AAAS scientific seminar "Doomsday vs. Discovery." In which we ask "how do we ease the fears about the LHC and other scientific adventures?"

The message that I got from John Ellis, Alan Boyle and Robert Crease was: It's really, really hard to ease people's fears, because of:

1. The natural irrationality of fear.

Figure 2 shows a famous chart about types and perceptions of fear, from Paul Slovic's 1987 paper in Science. Having different categories of fears makes sense, but it is so easy to wrongly attribute or categorize some of these dangers. For example, I have put a star where I think that the dangers of the LHC are located -- in the "very safe" part of the graph, but perhaps in the "not very well understood" area. The problem comes when people take this star and move it in the direction of the yellow arrow -- to the "very dangerous" side of the chart. How does this happen? Part of it is that we don't have any internal sense of how statistics work, and humans in general haven't internalized the fact that just because you can't prove something is impossible, doesn't mean it's possible. Seems like there will always be some amount of irrational fear in the world, and for science to free itself from this it must somehow distract people with worries about all the unlikely comet collisions, Y2K bugs, 2012 apocalypses, etc. Or even better, the real-life imminent energy, natural, and human-health related disasters that come along with global warming.

2. History and preloaded imagery makes things worse.

"Humans always f%#$ up, especially when they are really, really smart," Crease pointed out, quoting the long-standing distrust of science. What does this mean for LHC, and our exploration into making our apple pie from scratch? Even before the LHC, other experiments and other ion colliders have set a precedent for fear. In 1974, at the Bear Mountain Conference Center outside of New York City, panels met to discuss the possible dangers of Relativistic Heavy Ion Collider (RHIC) being built on Long Island. Some completely science-free "theories" were discussed and then dismissed, but no records were kept because everyone was afraid of a PR disaster. This seems like the mistake here: discussions should be carried out in public and not in private. The public nature of science is one of its greatest strong-suits, and keeping it hidden is only going to lead to an increase in distrust. Full disclosure is clearly necessary.

3. Theology also has its effect.

"Science shouldn't be doing this, only God should be doing this. Humans get in trouble when they play God. And what better way to play God than to try to re-create the universe." Crease brought up the fact that we haven't always blamed science -- before World War I, the majority of Doomsday predictions were based on natural disasters. And after the associated technological advancement in warfare, the tides turned. Now scientist-based concerns have over taken nature-based concerns.

4. Media and Conspiracy Theories.

Alan Boyle from MSNBC.com, and Crease talked about how the news coverage can lead to a downward spiral of terror. The media can cloud the atmosphere of knowledge, of course, highlighting big bad news over the real story. It is often unclear to the audience who is the expert, and there is often a melodramatic structure to the coverage. Crease described this quite well. "The approach to coverage," he explained, "is that there is an innocent space with innocent people, and then dramatic images of Apocalypse. It boils down to those worried about the ending of the world [the good guys], vs. the detached scientist who has lost his ethical compass."

So, what should we do? "The best thing to do," said Crease, "is to hold up a mirror and show history and philosophy and expose the atmosphere in which events get distorted and blown out of proportion." Yet this idea seems vague and hard for me to imagine implementing. Anyone have any ideas? Maybe the best thing is to tease people into realizing how silly some of their fears might be. This is where Jon Stewart comes in.

**************************************************************************************************

April 30, 2009: Large Hadron Collider Episode

"Scientists," Jon says, leaning into the camera and pointing an accusatory pen at the audience, "we assume that they are working for the benefit of humanity. But... does their quest for understanding have a dark side?"

"Nobody with any expertise in physics or astronomy or astrophysics thinks there's the slightest risk of any danger whatsoever," says Dr. John Ellis, project leader for CERN, in an interview about the LHC. In this Daily Show episode, Ellis's interview leads to some serious teasing of some non-scientists, in regard to their fear of the end of the earth. I would recommend this show to anyone interested in the subject.

Blinded by the Sound

2010-02-23T16:16:05Z

You're at a rockin' party. You see this guy or gal alone across the room who's reeeeally easy on the eyes, and you would love to say hello. You start walking over when suddenly, the strobe lights go crazy.

It's like a million camera flash bulbs going off one after another. Blinding, flashing lights overload your senses. It stops after a minute, but by the time your eyes adjust, your potential date has moved off, whereabouts unknown.

That's what it's like for baleen whales in the modern world of human sonic technologies and shipping lanes.

Christopher Clark discussed the impacts of sound pollution on whales during the AAAS 2010 sessions on Sunday. An acoustic ecologist at Cornell, Clark says whale song is the equivalent of visual communication for human beings. When miles and miles of water separates you from your nearest neighbor or potential mate, singing in very low frequencies is the only way to "see" and talk to one another across a room.

]]> But like an errant strobe light, sonic energy generated by large ships and petroleum exploration vessels can cancel out a whale's ability to communicate. This "communication masking" shuts down natural whale behavior across great distances; constant agitation over time may drive out the whales from a region entirely.

Clark's team measures underwater sound waves from ships and whales to paint better pictures of this sonic impact.

These are long-living species, Clark reminded the audience. Activities like sonar and acoustic exploration are relatively new to the world. Imagine growing up in a quieter world as a teenager, Clark says, then experiencing an increasingly noisy world as an adult.

Sonic effects on cetaceans is a controversial topic amongst the scientific, industrial, and military communities. Data like those recorded by Clark's team -- translated into visualizations that humans can relate to -- should add more food for thought to this conversation.

Blinded by the Noise

2010-02-23T07:57:15Z

Credit: Wilma Passchier/Creative Commons

A new visualization reveals the dramatic impact of shipping traffic on Right Whales in New England

Before the invention of the Diesel engine, life was good for the Right Whales living off the coast of Boston. For thousands of years, the calls and songs they produced to keep track of each other over great distances were the only sounds probing the murky depths.

"The place in which these animals live is defined not only in terms of space, but in terms of sound - they live in an acoustic habitat," says Christopher Clark from Cornell University, who has been listening in on the whales to get a better understanding of how noise impacts their acoustic habitat. "Imagine living in a village where people can't see each other or where they're going. They have to rely on sounds and calls to keep track of each other and go about their lives."

Once a shire shrouded in peace and quiet, the Right Whales' village has since been drowning in the cacophony of cargo ships' and ocean liners' propellers that churn the waters.

]]> Using an array of underwater listening devices installed on the sea floor, Clark and his research team have been able to record and monitor the sounds that define the Right Whales' acoustic seascape over long periods of time.

What the researchers found is alarming: Just like terrestrial habitats shrink in space, the whales' acoustic habitat is being destroyed.

"Each time a ship passes through the area, the acoustic habitat around the whales basically collapses," Clark says.

He has developed visualizations that show the impact over time and space. As long as no ship is in the area, only the whales' calls and counter-calls make up the acoustic seascape, as can be seen in the image: Like the soft twinkle of stars in a dark night sky, each spot marks the acoustic signature of a whale. As soon as a ship approaches, the 'night sky scene' turns into an exploding supernova, obliterating the light emitted by the stars and rendering them invisible in the process.

"The ship's noise bleaches out the whales' vocalizations," explains Clark, "robbing them of their acoustic habitat and essentially rendering them 'blind,' over and over again."

"Every day, five to six large ships move into and out of Boston, and their acoustic footprint can last for hours. As a result, the Right Whales trying to make a living off Boston are losing about 80 percent of their opportunities to keep in contact every day, day after day, month after month, year after year."

Although nobody knows for sure yet what the constant onslaught of noise does to the whales, whale researchers have found alarming indications of stress.

"Right whales are long-lived animals. When they were kids and teenagers, their world was normal," Clark says. "Acoustic habitat loss is a stressor and there are multiple stressors on a species."

His team has found that the whales often no longer bother answering calls from their peers. In this world of constant noise, they wouldn't be heard anyway.

"Their social network is constantly ripped apart," says Clark. "In one area, noise levels are now 105 decibel where they should be 75."

Other researchers from the Right Whale Consortium found that the animals show dramatic loss in vital body fat: In some individuals, the blubber layer is thinner than normal, hinting at the possibility that they no longer find enough food due to the noise.

Referring to the village metaphor, Clark says, "If you're one of the blind villagers but can't hear the dinner bell because of the deafening noise around you, you're going to go another night without food."

Moreover, the females give birth only every five years on average instead of every three.

Assembling the data from sound recordings taken in the field, Clark has developed a computer animation showing what happens when a ship passes through an area with Right Whales (follow link below to watch video).

Acoustic-space-loss_1-ship_Right-whale.mov (Video kindly provided by Christopher Clark)

The blue area shaped like a 'Hershey's Kiss' represents the 'communication space' for a calling right whale, in other words, its acoustic habitat at a given point in time. As the ship approaches, this area starts to shrink and is virtually obliterated when the vessel is closest to the whale.

"When the area in the animation goes black, it means that other whales cannot hear the calling animal," Clark explains. "They are now living in an urbanized, even industrialized, habitat and there is no rest for the weary."

"Keep in mind that Boston is not even a heavy shipping port," he adds. "What the whales are going through there is in fact happening all over the world."

Student Poster Competition

2010-02-23T07:50:42Z

I was first time in 2010 AAAS meeting this year but it was great opportunity to learn and meet the scientist in different fields. I served as a judge in Student Poster Competition. Most of the posters are from students of undergraduate entry level but I was surprise to see the quality of knowledge and work presented by budding scientist. It was really tough to give first rank between two equally good students. We discussed with other judges in same group and finally went again to poster but it was hard to finalize which one will be first and then we decided to give two first and second places to two equally good students. Most of the quality posters are from UC Irvine, California Institute of Technology, Arizona State University SDSU and some other places, in Developmental Biology, Physiology and Immunology group. These types of competitions are encouraging the young scientist to attract towards science. I hope AAAS will start some more these type of competition for young scientist. I will also suggest to undergraduate students that they have to prepare poster for next 2011 AAAS meeting.

Back from AAAS 2010 Meeting, as expected, a disappointment

2010-02-23T04:41:29Z

I've been to three AAAS meetings in the past 20 years, the first in San Francisco, about 14 years ago, the second in Seattle, about 6 years ago and now this past week in San Diego. I am a Medical Oncologist / Hematologist and go to one or two major meetings a year, usually in Clinical Oncology or Basic Science Oncology.

I guess I am spoiled by the annual meetings of the American Society of Clinical Oncology and the American Association of Cancer Research because they actually teach one about Medical Oncology at those meetings. For the most part, AAAS meetings discuss the politics (in a very broad sense) of Science rather than Science itself.

Now, of course, that is not entirely true. There were a few seminars on basic science and the family series event was much about science and the lectures on Neutrinos was a fairly decent review of neutrino science. But the seminars on Neutrinos was very much the exception. One has only to read the titles of the lectures to see that the subject matter was bent towards politics, or economics of science rather than reviewing science itself.

]]> And it seems that every AAAS meetings is the same.

Now perhaps I misunderstand the intent of these annual meetings. Maybe I should go (or not go) to the annual meeting with the understanding that the purpose of the meeting is that of learning the political aspects of science in today's society. That is, I should welcome understanding what can be done, what should be done about marine estuaries, how science is taught in some other country or rumors of doomsday from the large hadron collider.

I would rather learn science. Look, I have several textbooks on oncology and hematology. Take any chapter in the textbook. Say, take the topic "Multiple Myeloma." Now, I go to the annual oncology conference. What are the chances that there will be an "up to date" seminar on "Multiple Myeloma?" One hundred percent. They would never miss it. What are the chances that there will be a review seminar on "Sickle Cell Anemia" at the annual Hematology Conference? 100 percent. They would never miss it. What are the chances that there will be a review seminar on "Latest information on particle physics" at the AAAS meeting? Not much of a chance. What is the likelihood of finding a lecture on superstring theory at the AAAS meeting? Hardly any. What chance is there to learn about linguistics? Plate tectonics? Improvements in energy sources? New trends in Agriculture? Cell biology? Deep space astronomy? Unfortunately not likely.

I am a scientist oncologist. I know oncology pretty well. I have an interest in other areas of science, but I don't have time to become an expert in plant biology, particle interactions, astrophysics, linguistics and many other subjects that I read about in Science magazine, Nature, Science News and 5 other science journals.

I would like an annual conference that could give me some "up to date" information in those fields. Unfortunately the AAAS meeting disappoints me every time.

Unexpected Optimism: Coral Reef Ecologists Stay the Course

2010-02-23T00:27:44Z

"I want to study coral reefs, but, I hear that they probably won't be around for much longer, so I am not so sure that is such a good career choice." Prospective student, Steve Palumbi's office, a few months back.

Dr. Steve Palumbi is not easily ruffled. A veteran field scientist, he has taken on Japan's powerful whaling industry (conducting clandestine tests of commercially sold whale meat by cloning the DNA in hotel bathrooms to accommodate CITES restrictions)-- and successfully exposing the rampant illegal hunting that exists. He has used molecular techniques to determine historic abundances of whales, challenging pro-whaling countries' argument that some species have receovered enough to lift the global moratorium. But, all this experience didn't prepared him for that prospective student's decidedly depressing proclamation about an inevitable demise of coral reefs.

]]> The surprise comes because we coral reef scientists know that while the news about climate change is dire, and the future of coral reefs is disturbingly precarious, it is not yet written. I say this not out of a desperate, deluded hope--I'm no Scarlett O'Hara fantasizing that Rhett may just come back. My certainty is grounded in the evidence of corals' natural capacity to adapt and the potential that still exists within the policy realm to halt further climate change (granted, the latter requires a slightly more desperate form of hope than the former).

But this perspective is clearly lacking in the next generation of would-be coral reef ecologists and likely lacking in the public at large. It's the unfortunate consequence of warnings gone awry: instead of motivating people to act to stop the worst, dire predictions result in a passive acquiescence that defeat is inevitable.

But coral reefs not destined to disappear, and certainly not by a force beyond our control.

Take the reefs of Ofu, in American Samoa. Dr. Palumbi described how periodic exposure throughout the year to pulses of warmer water seems to have conditioned resident corals to have greater resistance to bleaching than nearby corals occupying a different and cooler lagoon pool. So some corals may be able to adapt to warming waters caused by climate change, at least to changes predicted for the next few years to decades.

And the same may be true for ocean acidification. In the session, "Will Coral Reefs Disappear? Separating Fact from Conjecture," water chemistry data across the reefs of Bermuda showed there were significant seasonal effects. So while continued unabated acidification of seawater will undoubtedly lead to dissolving coral reefs, the frequent and regular exposure to more acidified waters in the summertime may allow for corals in Bermuda to adapt to global ocean acidification more readily than we might have first thought.

This is the silver lining along the edge of the darkening storm cloud: reefs on the margins may serve as refuges of hope, and not just canaries in the coal mine. In other words, living on the edge (in terms of geographic distribution, depth, water quality or other environmental parameter), may confer resilience or resistance to corals that will help them hold out against climate change for longer than we anticipated.

But not forever. It's an intelligent optimism we hold, bound by the realities that the situation is indeed, grave. We must act now to protect potential refuges from other stressors (such as coastal development) as we continue to work to stop climate change. Not to act is to resign coral reefs to the realm of paleontologists.

So to the future grad students or the despondent masses out there: those who know the most continue to push for action, to argue that coral reefs have not yet given up the ghost (though they may indeed be changed). I spent all day in those lectures halls and can assure you there were no fat ladies singing. Until the experts say the gig is up, I say we stay the course and keep working for solutions.

Photo credit: Tim Taylor

Genetics and ethics

2010-02-22T21:41:42Z

A rabbi, a theologian, and a geneticist walk into a conference room...it's not the start of a joke, but rather the start of yesterday's session on Genetics and Ethics, at which the session's speakers really tried to reach beyond their disciplines to talk to one another.

Walter Doerfler, one of the session's organizers, emphasized that science "should seek a wider perspective" and encouraged a dialogue between academic cultures to further understand the complexity of life. Since new technology in genetics and genomics is growing at a rapid rate, it's sometimes difficult for society to comprehend the ethical implications of these advancements. After thinking so much about translational research and personalized medicine over the past few days, I found it really refreshing to take a step back to think about some of the ethical challenges that these new discoveries could imply.

]]> The first speaker, Uta Francke, is a geneticist at Stanford and is also a consultant for the direct-to-consumer personal genomics company 23andMe. Dr. Francke is interested in the genome as personal property: what does it mean to post the contents of your genome in the public domain? And what does it mean for your family?

Dr. Francke mentioned our ability to examine the genome for clues about ancestry and described the concept of race as no longer particularly useful in this area of research. She showed a striking map that showed how genetic variation mirrors geography in Europe. In addition to ancestry, Dr. Francke noted that researchers are beginning to find genes associated with differential drug response and predisposition to disease.

Personally, I think it's a little too easy to over-estimate the predictive power of SNPs right now (and certainly in the best interest of personal genomics companies to anticipate this power with much excitement), but I really enjoyed the next point that Dr. Francke raised: is your genome really yours? What about your family?

For complex diseases, we are so far away from being able to make accurate predictions about whether or not an individual will develop a condition that some of the ethical questions are premature at best, but it's still fascinating to think about these questions for Mendelian diseases. Huntington's disease, in which one gene really does definitively show whether or not a person will develop the disease, may be the most striking example: if one sibling wants to have her genome sequenced and share it with the world, should she get her family's consent? Do parents have the right to know if a child has the gene for Huntington's? What about the rights of the unborn?

It's a great thought experiment...for Huntington's disease. But it does seem like examples of genes with a clear link to disease are few and far between. This also made me wonder if companies like 23andMe even test for Huntington's disease. It's always disturbed me that the companies can't test for BRCA1 and BRCA2 (oncogenes implicated in breast cancer) - I wonder what else is off limits.

In 2008, the Genetic Information Non-Discrimination Act was passed, but Dr. Francke pointed out that this law only protects people from discrimination for health insurance and employment, not life insurance, disability, and long-term care.

During the q&a, there was an interesting discussion about the drug Warfarin (which came up in an earlier post I made here). The audience member pointed out that getting the dosing right is most important for the first dose of the drug a patient receives. The only way for the patient's genetic information to be helpful is to have it ahead of time rather than waiting a few days for the results of genetic testing. Dr. Francke agreed completely with this audience member's comment.

The second speaker, Amy Hall of Duke Divinity School followed up with a talk on Race, Protestantism, and Reproduction in the US. She embraces the ability of genomics to celebrate human progress and identity (how similar our genomes are, "what makes us us", etc.) but brought up several disturbing examples of the way that genetics and genomics can still be twisted today to support social Darwinian or ethnocentric thinking. One of the slides she showed was of images from Spencer Wells's "Journey of Man," in which the Bushmen of South Africa are labeled the "direct descendants" of our ancestors (as an audience member noted, "Aren't we all 'direct descendants' of our ancestors?"). The images showed the Bushmen as stand ins for ancestors, which might have made for great footage, but from an ethical perspective, it's an unsettling, deceptive tactic. Dr. Hall also read from a David Brooks New York Times story from January 15, 2010 in the wake of the Haiti earthquake. Brooks called for shoring up paternalism in a piece that clearly disturbed Dr. Hall.

Dr. Hall was less interested in trying to enforce some sort of political correctness, and far more interested in trying to get scientists (and members of the media) to think a bit more deeply about the way that we consciously or unconsciously present findings on race. The right answer is not to simply ignore race, even if, as others have noted, the concept of "race" has no biological basis and is becoming irrelevant in genomics. "Neo-liberalism and color-blind racism catapults us out of the conversation," Dr. Hall said.

An audience member asked why it was so easy for those outside of science to misrepresent scientific thought to prop up their agendas, but it's so difficult to reverse this. I think this probably has to do with how easy it is to form a misconception and how impossible it is to unlearn it. In the exhibit halls, I was talking to a AAAS staff member involved in Project 2061 about educating children - she mentioned a study I've seen before (but can't find right now!) about trying to correct children's misconceptions about science. It's not enough to tell them how photosynthesis works or how the Earth revolves around the sun - if they've learned it incorrectly somewhere along the road, it's incredibly challenging to get them to adopt a new mode of thinking.

Unfortunately, I think the same holds true for Dr. Hall's points on race. The concept of race, as unscientific as it may be, is so firmly entrenched in our view of the world that if we simply state that race is irrelevant to genomics and has no biological basis, we stop the conversation. Dr. Hall's suggestion to emphasize the commonality of the human genome and to be aware of the pitfalls that Wells and Brooks represent seems like a great way to stay engaged in the ethical conversation.

DNA repair mechanisms to the rescue

2010-02-22T20:17:16Z

Each cell in your body suffers 10,000 to 100,000 DNA lesions per day. But repair systems in your cells are hard at work eliminating this damage. One of the most troublesome kinds of DNA damage a cell can suffer is a double strand break - losing genetic material on one strand isn't too much of a challenge for a cell since DNA machinery can use the complementary strand to repair it, but if both strands are broken, it can be a major problem. Cells have repair mechanisms and back-up systems that kick in when double-strand breaks take place, but cancer cells, which are pros at accumulating mutations and dividing rapidly, may not have as many layers of back-up repair, making them more dependent on one repair mechanism and potentially vulnerable if that mechanism fails. At a session on Saturday morning and press conference Saturday afternoon, Graham Walker from MIT, Richard Kolodner from UCSD, and Tanya Paull of University of Texas, Austin discussed DNA repair and how understanding it could lead to cancer treatment. This was another cool topic that linked basic research using humble model organisms to profound implications for cancer in humans.

]]> BRCA1 and BRCA2 are well-known breast cancer oncogenes involved in DNA repair. Cancer cells mutate rapidly and divide rapidly and like regular cells, must have a way of fixing double strand breaks. However, if BRCA1 or BRCA2 are mutated, a DNA repair mechanism known as homologous recombination can't take place. Cancer cells must therefore rely on a different repair mechanism known as base-excision repair. Drugs called PARP inhibitors can interrupt this latter mechanism. Dr. Paull noted that cells can survive if they lose one pathway, but not if they lose both (known as synthetic lethality). Targeting the "redundant" pathway allows researchers to specifically target cancer cells with BRCA1/BRCA2 mutations; normal cells will just switch to their "back-up" repair mechanism, but cancer cells won't have that luxury.

Dr. Kolodner reminded us that every time a cell divides and makes a copy of DNA, there's plenty of room for error. He invited journalists in the audience to imagine retyping an article - you're bound to introduce spelling mistakes. Cells need a "spell check" or mismatch repair mechanism. He also noted that many of the discoveries about DNA repair mechanisms have been made in yeast - the results have translated well into humans.

In the 1970s, researchers discovered the "SOS response" in E. coli - this allows DNA machinery to breach a DNA lesion - but the prevailing sentiment at the time was that this only took place in bacteria. Until the 1980s, DNA repair research focused on biochemical descriptions of pathways, but now the focus is on identifying genes and linking them to proteins and phenomena. The field has blossomed from biochemical descriptions to mechanistic explanations.

Restoring The Scientific Method to All Its Glory

2010-02-22T09:31:11Z

Take that you doubters of scientific vigor! Yesterday, the session, "Denial, Détente, and Decisions: Fisheries Science at the Crossroads," provided a shining example of the power of the peer review process to root out inaccuracies and refine results, and bring us one step closer to unraveling the mysteries of the universe. Amidst the growing din of skepticism and doubt surrounding the validity of the scientific process, fueled most recently by the slip-ups by the IPCC (which really should have been caught earlier), this story emerges a reminder that the scientific endeavor remains alive and well and worthy of our confidence; it just requires our patience.

Dr. John Lynham, at the University of Hawai'i, presented a fantastic talk about the relationship between catch share management systems in fisheries, and declining fish stocks. This research, conducted with colleagues and published last year, provided the first evidence of a positive effect of catch shares to halt or sometimes reverse declines in fish populations. And while the authors were careful to emphasize that the relationship they found was correlative, and not necessarily cause and effect, their publication caused quite a stir, as catch shares have been fairly controversial in the U.S.A.

]]> Not surprisingly, they received a whole host of criticism. And, as Dr. Lynham carefully pointed out, some of it was extremely valuable, especially the one criticism that turned out to be right.

Dr. Lynham presented the new findings, based on the refined analysis motivated by the thoughts and insights of this critic. The result was that catch shares still do have a positive relationship with preventing fish stock declines, but not quite as strong an effect as the previous results had implied. They weren't wrong, but the new analysis has helped increase accuracy and account for another factor that contributes to the observed relationship.

This is how science is done. It is a constant conversation, an iterative process that allows for one idea to build and shape the next through refinement of the last.

For many outside the walls of academia, the scientific process remains largely a figment of imagination: a fuzzy blurring of Hollywood CSI-style lab detectives mixed with the mad chemist filling bubbling test tubes or the eccentric natural historian filling bug jars of pickled insects. Many haven't heard of "peer-review," a pillar of modern science, and for those who have, my guess is that they don't understand the full scope of the process. Thus, the (flawed) argument that errors in published papers are evidence of a system gone awry; the assumption is that the review process is supposed to catch all errors before publication.

But peer-review is an on-going process whereby the entire scientific community is able to read, review, and then respond to published work. The majority of the time, the first filter of publication catches most of the errors or inaccuracies. But, sometimes, especially with complex systems, the second filter, comprised of the entire scientific community, will unearth a missing piece of the puzzle. More often than not, this piece does not completely negate the findings (though sometimes, it can); instead, it refines the outcomes.

Like the natural world it seeks to understand, science evolves. Making this process known would help alleviate concern about the mistakes within or revisions made to published works and would go a long way towards restoring confidence in the scientific endeavor.

Photo credit: wikimedia

Bridging the Bridge Metaphors

2010-02-22T07:46:27Z

Yes, this weekend at the 2010 AAAS annual meeting, we've bridged science with society, science with the public, science with Hollywood (with the White House and White Castle), scientists with hostile regimes, scientists with other scientists, scientists with journalists, and not the least, scientists with a lot of wine and beer.

But what about that big bridge thing just outside the conference? What does that bridge?

That would be the San Diego-Coronado Bridge. It bridges, uh, San Diego with Coronado.

Cheeky attitude aside, I was curious about the Coronado Bridge after looking at it all weekend. So, here are some Coronado Bridge facts from Caltrans:

]]>

It's about 2 miles long and at its tallest, about a 200-feet clearance over the water. Sorry, I mean it's about 3.2 kilometres long and 61 metres tall.

The concrete piles it rests on are driven 100 feet into the sediment at some places.

Construction began in February 1967 and completed August 1969. What did you do get done with your research in two years? (Kidding, kidding...)

The steel superstructure of the bridge span was built and partially erected in the San Francisco Bay Area -- over 500 miles away -- then barged down down the coast.

It's got a movable median barrier -- you can switch from two eastbound/three westbound lanes to three/two, depending on traffic needs. Imagine that for your lab commute.

It has concrete railings designed to be low enough to give people an unobstructed glimpse of the surrounding vista, but still safely corrals errant drivers. Engineers have hearts, it seems.

More at http://www.dot.ca.gov/dist11/facts/corbridge.pdf

Technological Help-Seeking Behaviors in the Science Newsroom Environment

2010-02-22T00:20:31Z

Here I am in the newsroom at the AAAS meeting, the most important scientific meeting in the country and perhaps the world, sitting shoulder to shoulder with giants of my profession. Well, not literally. There's a couple of yards between me and the editors of the two largest science journals in the United States. It's not a good time to pull up a YouTube video of yo-yo-chasing kittens. It is a time to be a true professional.

Professional science journalists, like scientists, look for good questions and the answers to them. As I sat down at my newsroom computer station, I was struck by a compelling question: Are professional science journalists any better with computers than the average Joe or Jane?

Literally struck, that is. I ran into the corner of the computer help desk, which, is thankfully, rounded and padded with a thick curtain. Michael Weisman sits behind the desk, and he was kind enough to act as an expert for my investigation.

]]> Weisman's own observations suggest that the subjects may be confining their computer usage to relatively simple software, thus explaining the relatively low frequency of requests for help. I would add that many science journalists are themselves scientists, and have a generally higher level of technical knowledge than society in general, which ought to translate into relatively high computer literacy as well.

Weisman noted, however, that the frequency of inquiries at the computer help desk increases with perceived reporter fatigue. That is to say, as the AAAS meeting plods on, and the reporters hustle to meet deadline after deadline, the frequency of questions such as "How do I print?" increases.

There are four large laser printers along the wall immediately to Weisman's left.

A pilot analysis suggested ample evidence to support using reporter posture as a marker of fatigue, as Weisman suggested. The obvious outlier visible in the third closest chair is an editor whose outrageous workload, politeness, and near-flawless memory for people have led many of my colleagues to suspect that he is not entirely human.

Even with a few posture problems, though, the newsroom contains a pretty good-looking bunch. One would suppose that there is normalizing selective pressure on journalists to maintain a fairly attractive, yet seriously intellectual appearance. They are in the business of getting scientists to talk to them, and I doubt many scientists would open up about their research to either a dazzling hunk or a hunchbacked ogre

Climate science: not just about science anymore

2010-02-21T23:29:17Z

Many scientists (and journalists, for that matter) argue that their job is to seek and deliver knowledge. They don't have much power over how people use it. Climate change historian James Rodger Fleming opened the Saturday morning symposium, "Can Geoengineering Save us from Global Warming?" He suggests that his next book on the subject ought to be called Losing It, because climate change scientists long ago lost control over the discourse on the subject.

Case in point: geoengineering. With international measures to reduce greenhouse gas emissions still suffering from political inertia, the U.S. and U.K., at least, are beginning to consider engineering fixes for climate change. These fixes include things like pumping sulfur dioxide into the atmosphere or seeding clouds to reflect more sunlight, and dumping iron into the oceans to encourage the growth of plankton that suck carbon dioxide out of the air and convert it to biomass.

]]> Quite tantalizing, the prospect of an elegant technological fix for a worldwide environmental disaster. But all of the geoengineering schemes currently under consideration have considerable drawbacks and limitations, the biggest being massive uncertainty. It'll take loads more good studies to get really solid evidence on how well they could work. Many geoengineering researchers are clamoring for political leadership and funding to support further investigation. But what kind of a message does a major geoengineering research effort send to the scientific community and the public at large?

It might cement the seriousness of the situation, said Daniel Sarewitz of Arizona State University. Sarewitz made a case for geoengineering in a Friday morning symposium entitled "Human Dimensions of Geoengineering." Searching for technological answers implies that the problem is real and that we're desperate for a quick fix. Yet the fix may stymie efforts to reduce carbon emissions and adapt to ongoing climate change, say the geoengineering skeptics. It may give us license to stick with bad habits, to continue with carbon crash diets and carbon bulimia instead of making long-term changes in the way we live.

But they all agreed that since climate is such an intricate global phenomenon -- picture a butterfly in the Northern California redwoods flapping its wings and shoving air currents round the world past a tipping point to generate a monsoon in Asia -- any effort to control climate must be an international one. The research itself might need government leadership or a major benefactor (Gates, anyone?) to spearhead it. And if we do the research and discover that our best possible simulation shows excellent results in most parts of the world, and long-lasting drought and famine in India and Brazil, do we and how do we convince India and Brazil to take one for the team?

Considering the decades that international climate change accords have spent mired in political mud, the prospects of geoengineering becoming a large-scale reality anytime soon are pretty grim.

We trust scientists because they can make things happen, said Harvard's Sheila Jasonoff in a Friday session about scientific integrity. Well, scientists, especially climate scientists, can't always make things happen anymore. At least, not without a lot of help.

Where's swine flu? Check the traffic

2010-02-21T21:16:58Z

The students poured into Carlos Castillo-Chavez's office soon after swine flu struck Mexico last spring. The graduate students, some from Mexico, a few from Puerto Rico, knew the Arizona State mathematician was an expert in modeling disease spread.

"They were very scared because they had relatives there," said Castillo-Chavez. "They asked, 'Is there something we can do?'"

The cadre of concerned students worked Saturdays and Sundays to model the ensuing outbreaks of H1N1, which peaked three separate times in Mexico. In the model world they created, people were either susceptible or exposed, vaccinated or not.

]]> They found that cases of H1N1 plunged when schools shut their doors, families went on vacation, and people intentionally isolated themselves, Castillo-Chavez reported here Sunday. But they also found an intriguing, smaller effect--the coming and going through Mexico City, the beating hub connecting 20 percent of the population, predicted the weekly variations in flu cases when school closed for the summer.

Delivering vaccines quickly--more than 40 days before the next outbreak--prevented severe outbreaks in the model. That's because even if the vaccine was in short supply, allocating it wisely made the difference between a severe outbreak and a mild one.

How the Mexican government actually responded, according to Castillo-Chavez, wasn't too far from his model's optimal solution.

"Mexico did a superb job given high levels of uncertainty," said Castillo-Chavez. "They took painful and extreme measures right away," he said, like closing down businesses and giving out surgical masks. Not every country might have responded that way--Chinese public health officials were slow to admit in 2003 that SARS had broken out, he said. The World Health Organization and French president Sarkozy praised Mexico's quick response, though some first-responding doctors have said Mexico did lag a bit.

But one shortcoming of his model, and of disease prevention worldwide, is knowing exactly how many people are infected at a given time, as the number of reported cases may be low estimates.

"We can't tell how bad things are. We don't have this extensive network of high quality systems. That would be the most important thing to put in place."

Early Plankton Blooms, Not Dams, Killing Washington Salmon

2010-02-21T15:33:38Z

SAN DIEGO -- Dams may not be causing the steep drop in Pacific salmon populations in Washington and Oregon. Instead, earlier plankton blooms in the ocean may mean salmon smolt reach the sea too late and starve to death.

A comparison of salmon populations in a Pacific coast river with dams and one without revealed that dams did not affect how many salmon made it out to sea.

Instead, earlier plankton blooms caused by climate change may be key. The findings were presented by Ron O'Dor in the "How New Tracking Technologies Can Help Manage Sustainable Fisheries" session of the AAAS meeting on Friday, February 19.

"It's not the dams that are causing the problems. It's actually happening in the open ocean as a result of plankton changes," said biologist Ron O'Dor of the Census of Marine Life in a presentation at the American Association for the Advancement of Sciences meeting in San Diego. "Less plankton means fish don't get to eat what they want to eat."

The salmon are born in river beds in Washington and Oregon, spend a few years growing into smolts and group together to migrate out to sea. They spend several years in the frigid waters near Alaska, then return to the rivers to spawn.

]]> For decades, salmon stocks in the Columbia river, which snakes northwest through Washington and into Oregon have been plummeting.

"Traditional wisdom was that it was caused by eight dams on the Columbia," O'Dor said. "And if we just tore down the dams, all the fish would be happy and healthy."

In this theory, dams thin the salmon population by blocking their habitat, killing young salmon as they pass through turbines, and increasing how long it takes them to migrate to sea, making them more vulnerable to predation and stress.

But the team wanted to see whether the dams actually affected salmon survival. They compared survival rates in the Columbia River, which has eight dams along its length, and British Columbia's Fraser River, which has none.

The team tagged hundreds of salmon smolts with an approximately half-inch sized acoustic tracking devices. The miniscule devices could be inserted into salmon as tiny as three-quarters of an ounce. To detect the fish, they also laid down hundreds of tiny acoustic receivers in both rivers, which sensed the position of each tagged smolt as it passed by.

There were no real differences in how many salmon made it to the mouth of each river, O'Dor said. However, very few made it back in their migration two years later, suggesting the smolts were dying once they reached the sea.

In another study, they showed salmon that shoot off from the main Columbia river into a smaller tributary with half as many dams have the same survival rates as smolts that migrate along the entire length of the river, O'Dor said. Both findings suggest the dams are not the key to the salmon population decline.

Because the team does not have receivers throughout the ocean, they turn off tracking devices in the fish once they reach the ocean. What happens out there is still a mystery.

However, they suspect that earlier plankton blooms may be a culprit in the salmon decline. Satellite images of chlorophyll show surges in plankton production have happened earlier in recent years, likely because of global climate change. That suggests only the salmon who reach the sea earliest can pack in enough food to sustain their arduous migration back.