A Free Man

Today is another in the long list of holidays that only I celebrate and then get sullen and resentful about not receiving gifts. A year ago today I posted my first little ramble about progressive rock, fraternity life and The Decemberists. Now, 365 days and 371 posts later here we are. In the spirit of retrospective introspection (or introspective retrospection) that these occasions call for, here are my top 10 favorite posts from year one of afreeman.org.

• All come to look for America
• How do you afford your rock’n'roll lifestyle?
• Words from Winnipeg
• Defiant in defeat.
• In A West End town, a dead end world
• Good Morning Son, I Am A Bird
• Great Interview Week: Iron Maiden Ruined Everything
• Braggin’ Rights
• He was the one made me what I am today
• Science Tuesday: In Response to an Animal Rights Apologist

To celebrate my first anniversary as a blogger I’d like to give my readers a gift, though I’m still waiting for my Father’s Day present. Regular readers should know that I tack a song onto most posts that I write. I’ve put together a mix CD of some of my favorites - the soundtrack to afreeman.org, if you will. I’m going to give away a few of these hand-made CD’s to you, my loyal readers.All you’ve got to do to win is tell me which post you’ve read here that turned your crank the most. The one that keeps you coming back in the vain hope that I may be able to write that good again. For example, Dr. O’C’s favorite is Apolitical Friday: Baby Bliss (she comes back because I badger her until she does). What is yours?

To enter, leave a comment with the title. Next Wednesday I’ll draw a few (depending on how many blank CDs I have around) entrants and send out your prize. Easy peasy. And hey, if you’re still lurking around on the banks of the comment stream what better opportunity to hop in as a commenter? The water’s fine.

 

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In last week’s lively Science Tuesday comment stream, Matthew pointed out that one of the things that many scientists struggle with is communicating with the public. I think that he’s dead on target. Scientists, particularly academic scientists, don’t do themselves any favors by not learning how to talk to the average Joe or Jane. I suspect that a lot of academics fall into the trap of believing that it is their job to do the research and someone elses, like the media, to explain it to the masses. In an ideal world - where we have a thoughtful, critical and industrious mainstream media - that is a fair assumption. Maybe the problem is that scientists don’t come out of their ivory tower often enough to watch FoxNuz or read USA Today and to conclude that we do not live in an ideal world.

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.

 

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The subtitle of this post my very well turn out to be “How I Alienated My Religious Readers” but I got a little something stuck in my craw while reading up for this week’s Science Tuesday. My last job, at Oxford, was working in a lab that focused on evolutionary developmental biology. This field of study, and in fact all life sciences, take as a given a modification of Darwin’s theory of evolution. Most educated people around the world operate under the assumption that life as we know it today is the result of changes in the inherited traits of a population of organisms from one generation to the next over millions and millions of years. Evolutionary biology, my field, documents the fact that evolution occurs, and also develops and tests theories that explain why it occurs. I’m here to report to you that evolution is as solid a biological tenet as you’ll find.

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.

 

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Before we go, here are some photos from our Florida trip:

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There’s something in the air or the water or the sun here that sucks the creative juices out of me as soon as I pass U.S. customs in Orlando. I’m having trouble coming up with the goods for two blogs this week never mind the other bits and pieces. So, I’m going to go all wordless on you guys and on a Wednesday no less, to demonstrate the fruits of Dr’ O’C’s haggling. One is Mum’s choice, one Papa’s - can you guess which is which?

Oh, and by the way Jamie, that grass ain’t nothin’ but Florida Sunshine and the crushed skulls of the Miccusukee.

 

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I’m as fond of animals as the next guy. Maybe even, as I contemplate the exorbitant cost of transporting my seven year old dog to Australia, a little fonder than most. Like most folks, I love little furry creatures and would be personally loathe to do them any harm. Like most people, I ignore the irony of pampering my pooch whilst eating and wearing another furry creature. Unlike most people, until very recently I made my living as a research scientist. Early in my career, I made a decision to avoid working with animal model systems and to concentrate on plant genetics. This was due only to personal squeamishness not a grand moral stand. Many, if not most, of my scientist friends do work on animal model systems and their work sometimes requires those animals to be killed. They are not doing this because they are sadists or monsters, they are doing it in almost every case with the goal of improving the lives of you, I and themselves.

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.

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Science Tuesday is running a day behind this week, but better late than never. Those of you who know me will realize how difficult it is for me to report this research. I am a carnivore. I find any meal that lacks a large flesh component as unsatisfying. I am extremely suspicious of people who chose a vegan lifestyle. But science is science and requires that I leave my prejudices at the gate. So, this week when BioMed Central featured a study on the effects of a vegan diet on rheumatoid arthrititis I felt duty bound to pass it on.

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.

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More About Wordless Wednesday

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“Breathe in all the diesel fumes
Admire the concrete landscaping
And doesn’t it feel free?”

-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 .

 

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Today at A Free Man: The Real Deal

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. Continue Reading »

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