A paper published in the latest issue of PLoS Medicine quantifies what most of us already know – that U.S. journalists are doing a poor job of accurately reporting on science, particularly in the field of medicine. The PLoS study was carried out by Gary Schwitzer, a journalism professor at the University of Minnesota. Schwitzer established HealthNewsReview.org, a website that publishes reviews of medical new stories, two years ago based on similar sites in Australia and Canada. The study that he’s published in PLoS reports the results of two years of analysis of the mainstream media’s treatment of health news. Schwitzer’s group monitors science news by the biggest newspapers in the U.S. and watch the morning and evening news programs of the three major networks on a daily basis. (If you think you’re job sucks, imagine if you had to watch all three morning shows every single day. Good god.) The researchers then assign a rating based on how well the story covers a number of criteria.

Even without Fox to skew the stats, the results are shocking yet unsurprising. Schwitzer claims that 62 – 77% of stories failed to adequately address costs, harms, benefits, the quality of the evidence and the existence of other options when covering health care products or procedures. The issue that was ignored most often by the media was cost of products and procedures. In a country in which 16% of the GDP is spent on health care, only one quarter of new stories addressed the minor issue of the cost of the technique they were discussing. Well done. Less than a third of news stories addressed issues such as the benefits or harms of products or the quality of the evidence reported by the primary source. For me, however, the most disturbing statistics were that nearly 40% of news reports failed to reveal that one of the “experts” that were cited had a financial tie to the product being discussed and 35% of stories did not go beyond parroting a news release from the manufacturer of the product.

Schwitzer’s conclusions are basically that he’s doing good work – and that is true. Take a look at his site – the “0 Star Stories” are particularly fun. Schwitzer places the bulk of the blame on the news outlets themselves rather than the journalists. He recognizes that in the era of media consolidation many newsrooms have eliminated trained science journalists. He urges the reader to check out his site for the best health care news analysis.

The problem is that not very many people know about Schwitzer’s site. I frequently rant about how shabby and corrupt the mainstream media has become and am a scientist and I hadn’t heard of it. The problem is that most people still get their science news from the mainstream media and they are being misled most of the time. With the continued consolidiation of media outlets, most of whom are owned by conglomerates who also have interests in pharmaceuitical companies, it’s not outlandish to believe that this is intentional. I know that I’m preaching to the choir – if you’re reading a blog then you’ve already discovered the new media. But if you’re still getting your science news from the Today Show then the best case scenario is that you’re not getting all the facts. The worst case scenario is that you’re being lied to. Here are links to a few good “new media” alternatives:

• Science Daily
• Science News
• New Scientist
• Nature News

Also check out some of the sites on my “Science” blogroll.

International readers may wonder where I’m going here.”Yeah, yeah”, they’ll say, “What’s the issue? Let’s see some more pictures of that kid.” The issue is, as one federal judge put it, “the utter waste of monetary and personal resources” that is the debate over teaching evolution in school. One of the lovely side-effects of six years of whack-job rule was that the far right got cocky and started pushing either the outright banning of the teaching of evolution in public schools or at the very least giving equal time to a bollocks “theory” known as Intelligent Design (ID). ID is nothing more than creationism in a lab coat. It espouses the theory that the world was created by an “intelligent designer”some time in the last 10,000 years and that life as we know it appeared at roughly the same time. It differs very little from the creation fable in Genesis.

Fortunately, the federal courts have ruled that ID, as with other religious alternatives to evolution, can not be presented in the public schools as doing so violates the Establishment Clause of the U.S. Constitution. This should protect at least the 90% of American students that attend public schools. According to a recent study in PLoS Biology, this is frighteningly not the case. A group of political scientists at Penn State University led by Michael B. Berkman performed a survey of public high school teachers regarding the amount of time they devote to teaching evolution.

Berkman’s group found that 98% of high school Biology teachers spent at least an hour on general evolutionary processes – OK so far, though I’m curious about that two percent. When it came to teaching human evolution – the shocking idea that we diverged from a common ancestor with apes a couple of million years ago – 17% of teachers chose to eschew the topic entirely. What’s even more disturbing us that 25% of public school teachers dedicated at least an hour to teaching creationism or ID – in direct violation of the law and common sense. For me, the most shocking finding reported in this paper is that 48% of the American public believes that “God created human beings pretty much in their present form at one time within the last 10,000 years.” Who are you, 48% of Americans? Could you please out yourself so we can have a serious discussion about science and the origin of life? I can understand the importance of religion and I respect that, I really do. But you don’t believe everything in the Bible is literally true, do you? Can’t we just read the creation story as allegory and move on?

I know that this post is probably going to anger some of my readers. I don’t apologize for that. It angers me that if I had a child in the secular, public school system in the U.S. – and I’m more and more grateful that this is not likely to be the case – that he may be exposed to a theory (no, “theory” gives ID too much credence) an insane belief that flies in the face of hundreds of years of scientific data. Even worse, he may be taught that what is basically the unifying principle of biology is no more valid than this myth of divine creation. I have lots of superstitions and crazy beliefs and I suspect that you wouldn’t want me to teach them to your children as an alternative to established truths nor I would presume to do so. I have the utmost respect for your faith – I have a fair bit of my own – but please, keep it out of the public schools.

All this is in preface to the topic at hand, a blog post that Maggie at Okay, Fine, Dammit wrote earlier this week. Maggie is an exceptionally good writer and her post reflects her skills. Like any good writer she seeks to convince the reader of a point of view or to take an action. What she wants her reader to do with this post is to think about scientific research involving animals. Certainly there are turns of phrase and particular questions posed that imply that the author frowns upon animal research, but it is certainly not a rant, not a polemic, not a diatribe. Maggie achieves her goal if the stream of comments that follows is any indication – she gets people thinking about animal welfare. The problem is that I fear Maggie is, perhaps unwittingly, supporting the position of and giving fodder to extreme anti-vivisectionists.

Maggie knows that it is unlikely that we’d be having this “conversation” without animal testing. Prior to the golden age of medicine that began with Alexander Fleming’s discovery of the anti-bacterial properties of penicillin (itself tested on mice) we would both be well past middle-age and perhaps to sick to be typing away into the interspace. The fact that both Maggie’s kids and my kid woke up this morning healthy and uninfected by crippling diseases like polio, which was eradicated by a vaccine that was originally tested on animals, is testament to the necessity of animal research. Most of the academic research done that involves animals is done on critters like nematodes, fruit flies, mice and rats – hardly the warm fuzzies that you see being abused in anti-research ads. Most of this research is done in the interest of gaining a better understanding of devastating human diseases – cancer, Alzheimers, ALS, diabetes, and so on. I’m not a fan of big pharma I can not and will not attest to what happens in corporate labs. This is where most of the horror stories come from – bunnies blinded by mascara and what not. But, as are most of the facts presented by anti-vivisectionists, these are the exceptions rather than the rule. As Maggie points out, all the drugs that are approved for human use must be tested on animals. Some of these drugs make you erect or put you at ease in social situations, but the vast majority save lives on a daily basis. They save your friends’ lives, your family’s lives and, at some point for most people, your own life.

Research scientists are not in the business of torturing animals. I have yet to meet a research scientist that is flippant about his or her use of research animals. I have yet to meet a scientist who approached the animal testing portion of their job with any more than grim determination of something that had to be done. Animal welfare is governed by strict ethical standards. The animals themselves are treated with as much respect and dignity as possible. Both the RSPCA and ASPCA recognize the need for animal testing and focus their attention on ethical treatment of research animals and the search for alternatives. The fact of the matter is that if there were viable alternatives then most researchers that I know would use them. The only alternative in most cases is to do primary testing on human subjects – most people would not consider that a viable alternative.

Many animal rights groups are completely blinded to these realities in their obsession to eliminate animal testing. Someone wiser than me said that opinions are like assholes, everyone has one and they all stink. I have no problem with animal rights activists as long as they don’t become like their opinions, as long as they don’t become assholes. An animal rights campaigner becomes an asshole when he stalks and threatens a contractor working on a building that is designed to improve housing conditions for research animals. An animal rights campaigner becomes an asshole when she torches a university building, without regard for whether or not it was occupied in protest of the school’s policy on animal testing. An animal rights campaigner becomes an asshole when he digs up the remains of a Guinea pig farmer’s mother-in-law in some kind of twisted protest against animal testing. I experienced some of this madness first hand. Before a series of court orders silenced protestors that stood outside my building on almost a daily basis, I would have these people hurling abuse at myself and my colleagues. They called us “torturers”, “killers” and “terrorists”. Just a reminder, I work on plants.

So, Maggie, my problem is not with your questions, your qualms or your desire to have people explore a topic that they may not think about enough. I agree entirely, people should be aware of what is happening in animal research labs. My problem is that they are getting junk information and junk science from animal rights extremists. Most animal rights campaigners are earnest, if in my opinion misguided, people with a real concern for animal welfare. Many of them are unknowingly being led by wild-eyed, violent, extremists that have no concern for the truth. They use shock tactics and horrifying images to mislead compassionate people. They have less regard for human life than they do for animal life. They are like climate change deniers, Maggie, they latch on to one or two poorly researched studies that say there is an alternative to animal testing and spout the same crap science over and over. By all means, then, think about animal research but make sure that you have accurate information in hand.

I would encourage people who want to know more about the truths behind animal testing to check out Pro-test and the Research Defense Society.

Rheumatoid arthritis (RA) is an autoimmune disorder in which the immune system turns on the body’s joints. It is a disabling and painful inflammatory condition, which can result in an increased risk in cardiovascular disease. RA is incurable and its causes are unclear, although there are a number of plausible theories.

Suffererers of RA tend to display abnormal lipoprotein (cholesterol and trigylceride) levels, which is often associated with disease symptoms. Bearing this in mind, a Swedish research group hypothesized that dietary changes, particularly those that would restrict intake of saturated fats, that regulate the levels of these lipoproteins may be part of an effective treatment for RA. Led by Johan Frostegard of the Karolinska Institute in Sweden, they randomly assigned (sentenced) volunteers to either a vegan, gluten free diet or a well-balanced normal diet for a year. Both diets were composed of roughly the same ratios of protein, carbohydrates and fat with the only major difference being the lack of animal and wheat products in the vegan diet. The researchers then analyzed blood lipid levels after both three months and a year.

First, it’s amusing that about one quarter of the patients that found themselves involuntary vegans quit the study before the three month time point. That would have been me. But for those that struggled through, the Swedish group found that a vegan diet induced decreases in total cholesterol, body mass index and in the ratio of LDL:HDL cholesterol. These changes in lipoprotein profile are more similar to those seen in healthy, non-RA individuals.

Frostegard’s group concludes that a gluten-free vegan diet are potentially anti-inflammatory and protective against RA. What they do not show is any alleviation of RA symptoms – probably the bigger issue for the patients. However, the biggest problem with this study is that it gives vegans, who already think that they’re saving the planet and all its fauna, something else to be smug about. Nonetheless, the results are compelling as the only difference between the two diets was in the amount of saturated fat. Dietary changes alone are probably not an effective treatment for rheumatoid arthritis, but the changes in lipoprotein levels that they can induce are certainly not going to hurt.

I wonder if the researchers are vegans? Ah well, never mind, all this talk about foot has made me hungry and it’s nearly lunch – today it’s that great British dish bangers and mash.

-Jay Farrar – “Feel Free”

There is nothing to induce a simmering fury in me on my morning bicycle commute like following a diesel exhaust spewing, and inconsiderately piloted, bus. The narrow streets of Oxford barely allow for two cars to pass side-by-side – nevermind buses, vans and trucks – and the dark stains on the beautiful sandstone buildings attest to the long term effects of pollution from vehicle exhaust.

A study that I found this week at BioMed Central explores the shorter term effects of one type of vehicle exhaust on peoples brains. It seems that there may be a biological reason for my frustration at tailing a bus into the Oxford city center. Writing in Particle and Fibre Toxicology, a group led by Paul Borm at Zuyd University in the Netherlands looked at brain activity of volunteers exposed to diesel exhaust and found some interesting changes.

Diesel fumes in general have previously been shown to cause pulmonary inflammation and other more systemic health effects. Borm’s group is focused on the particulate matter, particularly nanoparticles, that are plentiful in diesel exhaust. It has been previously shown that nanoparticles can moveto the brain through olfactory nerves. Many of these nanoparticles are strong inducers of oxidative stress, a chemical process that has been implicated in neurodegenerative disease like Parkinson’s and Alzheimer’s.

Based on these previous results, Borm and his colleagues exposed volunteers to either diesel exhaust or filtered air for one hour. During that time, and for an additional hour after exposure, the volunteers’ brain activity was monitored by quantitative electroencephalography (EEG). The researchers found that there was a significant increase in brain activity in response to diesel exhaust particularly in the left frontal cortex after a half hour of exposure. Interestingly, this increase in activity continues even after the diesel exhaust is removed.

So, the take home message is that exposure to diesel exhaust causing some kind of temporary but detectable change in brain activity. The left frontal cortex is a pretty general localization of this activity and there is no empirical data to determine the biological relevance of the increased activity. Borm interprets it as a cortical stress response – the brain trying to deal with potentially dangerous toxins – but they don’t carry out the experiments necessary to determine what is actually happening in the volunteers’ noggins. In addition, the Dutch researchers are really interested in the effect of nanoparticles in particular rather than diesel exhaust more generally so they kind of miss the forest for the nanoparticles. The changes in brain activity alone are interesting as this is the first study to demonstrate a quantitative neurological effect of exposure to diesel exhaust. The more interesting follow-up experiments would focus more specifically on what regions of the brain are being affected, how long the effects last and what level of exposure is required to induce changes.

Jay Farrar’s “Sebastopol” is available from Amazon and .

One of the several things that I will miss about working in academia is unfettered access to academic journals. The cliche of academics locked away in ivory towers is reinforced by the unfortunate fact that many, and certainly the most important, of our journals are protected by a heavy subscription fee. An annual personal subscription to Nature, for example, is $200 (US). It’s kind of a hefty cover charge to get into the club. Effectively this prevents the general public from participating much in the scientific discussion – particularly unhelpful for those lay people that are slightly suspicious of scientists and their work.

To counter this ivory tower attitude, groups of scientists got together in 2002 and 2003 to push for open access to scientific literature online. Currently about 10 percent of academic journals offer free access to all of their contents. The primary criticism of open access journals is financial. Because they don’t receive subscription fees, OA journals charge a higher publication fee to researchers. This is kind of a bogus argument as nearly all journals, OA or subscription, use a pay to play policy.

The other problem with OA journals is that they don’t get the hottest research. If you’re a scientist and you put together some groundbreaking work – you go to Nature or Science or the high impact journal in your field. Open Access journals may not get the “sexiest” science, but they often publish thought provoking, beautifully designed or controversial papers. One of my favorite Science Tuesday posts was from a PLoS journal discussing the origins of syphilis – great stuff.

All this is leading up to the announcement that Science Tuesday, from now on, will feature only Open Access research. Unfortunately this is due more to necessity than a grand moral stand, but it’s all about the ends. This inevitably means that I’ll miss out on a lot of the hot news science, but the traditional media outlets cover that anyway. So come here looking for the quirky, clever and subtle science that often gets missed by the big guys.

In that vein, I have an odd one for the first Open Access Science Tuesday. BioMed Central is an OA publisher with nearly 200 journals in their stables. Earlier this week they featured an strange little study coming out of the University of Maryland that caught my eye. A research group led by Amelia Arria report in Substance Abuse Treatment, Prevention & Policy results that may suggest that nosy parents, those that pay attention to what their kids are doing, are better at keeping their kids out of trouble with the bottle in college.

Yes, I can hear the “no, duh” chorus. But before we jettison this into the Journal of the Bloody Obvious, let’s take a look at what Arria’s group actually did. The Maryland researchers began this study with the hypothesis that parental monitoring in high school can have a long term protective effect on drinking once the kids leave home. To address this question Arria’s group surveyed over 1,200 students both the summer before they went to university and during the first year at university. They were asked not only about their drinking habits but also relationship with their parents.

There is a lot of statistical wrangling in this study, as the researchers are trying to eliminate variables other than parental monitoring in high school. For example, white students drink more than black students, men drink more than women and, surprise, members of fraternities and sororities drink more than non-members. Ground breaking research in College Park. After all the statistical manipulation Arria’s group find that the only real relationship between parental monitoring and college drinking is that those who drank less in high school due to parental discouragement continue to drink less in college. Once the variation in high school drinking was ignored there was no significant long-term parental effect. Take home message from the data as I see it – once kids leave the nest your influence as a parent wanes kind of quickly.

Arria, however, sees it differently. One of the things that really amused me about this paper was its built in disclaimers. Anyone who’s ever published a scientific paper knows that to avoid getting destroyed by reviewers you have to include little caveats – statements of uncertainty about your concusions, wiggle room if you will. Arria’s group has a couple of pages of these including (but not limited to) the recognition that college students are a pretty limited sample set, college drinking takes on many manifestations (binge versus daily), the measure of paternal monitoring is based on the children’s impression and that the study only looks at one time point in adolescence. A big one that they left out is that people lie, particularly those with substance abuse problems and poor relationships with their parents. Despite all these caveats and their own results, the researchers still conclude that parental monitoring is a key to curbing high-risk drinking in college. Probably true, but kind of not supported by your own data. Open Access Science Tuesday is going to be fun!

Image Credits:

Reaching

Atheneum

Helicopter Parents

The problem is that an increasing number of scientific studies are indicating that corn-based ethanol may not be the green giant that folks thought. Just before Christmas a letter to Science by a respected ecologist suggested that the jump in corn farming in the U.S. has led to increased Amazonian deforestation. Grain prices hit record highs in the summer of 2007 due at least in part to the massive increase in demand for ethanol. This week, two papers in Science propose that the real costs of the ethanol boom may not be an increase in food prices but, ironically, an increase in atmospheric carbon.

The first of these studies stems from a collaboration between scientists from The Nature Conservancy and the University of Minnesota. Led by ecologist David Tilman, they predict that the conversion of uncultivated land in Southeast Asia, Brazil and the U.S. that would be required to deal with the increased demand for biofuels will result in a “biofuel carbon debt”. Atmospheric carbon is the problem in global climate change. The hope for biofuels is that their use reduces atmospheric carbon because growing more plants sucks up more carbon dioxide from the atmosphere. The problem with that theory is that fallow lands sequester a lot of carbon. This is both due to existing plants which remove carbon from the air but also carbon that is sequestered in the soil and biomass. In other word, if you clear an acre of forest to plant corn you remove the photosynthetic trees and understory plants and then burn them, releasing their fixed carbon into the atmosphere. Tilman’s group claims that conversions like these would release 17 to 420 times more carbon dioxide than the annual greenhouse gas reductions that ethanol would provide.

The companion paper, written by a collaboration of scientists from Princeton University, Woods Hole Research Center and Iowa State University generally confirms the Tilman group’s results. These researchers, led by Princeton’s Timothy Searchinger, used a worldwide agricultural model to predict greenhouse emissions over the next several decade under a variety of conditions. They found that corn-based ethanol production will double greenhouse gas emissions over 30 years rather than producing a 20% reduction as previous models predicted. Other crops are slightly better – switchgrass, George Bush’s favorite, would increase emissions by 50% and sugar cane only induces a four year carbon debt. Of course, the latter only applies if tropical cattle ranchers conveniently disappear.

In summary, these studies suggest that if we are to sustain world food production at current levels, crop based ethanol production will produce more atmospheric carbon then what we are currently generating. It is worth noting that both of these studies rely on complicated ecological models rather than any empirical data and I’m not enough of a modeler to properly critique their methods. That being said, most climate science and most of our fears about climate change are based on predictive models. This is what allows the climate change deniers to maintain any level of credibility.

It is not, however, all bad news. There are other sources for biofuel production beyond corn, switchgrass and sugar cane. Municipal and crop waste is a ripe source of energy that otherwise will be released as carbon dioxide into the atmosphere. Use of these materials would also reduce landfill inputs. Perennial plants grown on abandoned agricultural lands are another source that would incur little carbon debt. The take home message from both of these papers is that we should pour resources into improving the efficiency of ethanol or other biofuel production from these waste products – effectively killing two birds with one stone.

Image Credits:

Carbon cycle

Biofuels