Mike Dunford was a graduate student in the Department of Zoology at the University of Hawaii, Manoa, where he studied evolution. Life as an army spouse has since moved him on to Pensacola, where he's currently trying to figure out what to do next. While he's doing that, he writes stuff here, although not usually in the third person. He's also a contributer to The Pandas Thumb. As is the case with everyone else here, his opinions are his own, and do not necessarily represent those of any organization he is affiliated with.
August 13, 2008
Category: Misc
Seed is trying to figure out who you are, why you read our material, and what you like. If you're willing to help us out, head over to the survey and fill it out. You'll help us, and you just might win a bunch of Apple stuff.
Posted by Mike Dunford at 10:24 PM • 0 Comments• View blog reactions
Category: Flaming Small-Minded Stupidity
I used to have a hard time explaining the anger, resentment, and hostility that many scientists feel toward the big academic publishing houses. It's been getting easier, though. Recent events have, unfortunately, provided people with an experience that makes it easier to relate to what the academic community has been going through.
Gas prices are going up. You've been combining trips, cutting your milage as much as you can, driving a more efficient vehicle, and your fuel costs are still going up. You drive home from work, stopping along the way to put $30+ dollars worth of gas into the 10 gallon tank in your Prius. You sit on the sofa, turn on the news, and hear that Exxon-Mobil just reported quarterly profits of about $1,500 per second. The price of something that you need to buy is going through the roof, it's making things inconvenient for you, and the people who sell it are making money faster than the mint can print it. How happy are you?
If you want to understand the anger that the major publishing houses are generating, that's a good place to start.
Posted by Mike Dunford at 2:44 PM • 21 Comments• View blog reactions
August 12, 2008
Category: Flaming Small-Minded Stupidity
Update: 13 Aug. I've added a new post that I think provides a clearer explanation for the reason that this sort of behavior is such an irritant when it comes from a company like Elsevier.
Like most bloggers, I have an ego. I'm not mentioning that by way of apology, but as an explanation for why I was browsing through my sitemeter statistics last Friday. Every now and then, I head over to sitemeter, call up the view that lets me see what websites referred people to my page. If I see a link that's coming from a source I don't recognize, I browse over and look to see what people are saying about me. Yeah, it's sad. Yeah, it's shallow and self-centered. And, yeah, I know a bunch of you have your own blogs and do it too.
Anyway, I'm almost at the end of the list from the last 100 hits when I come across this link. I don't recognize it, so I click on it and I'm taken to this page. (I saved it as a pdf because I've got a feeling that it won't be accessible at the link for much longer.) That page contains the majority of a post about open access that I wrote a few weeks ago.
The vast majority of the content on that page was written by me. All but the first 13 words in the "comment" at the top of the page were taken from my article. The remainder of the page contains the first 60% of my post. The links I included in the original have been omitted, but the text itself is unaltered. The source that is given for the material is simply "ScienceBlogs.com". My name is not given, and the only link to the original article is in the section of the page marked "related links." The copying that took place in the "comment" section is entirely unacknowledged. The only mention of copyright occurs at the bottom of the page, and reads, "Copyright © 2008 LexisNexis, a division of Reed Elsevier Inc. All rights reserved. "
I was not asked for, and did not give, permission for my work to appear on that page, much less in that format. Needless to say, I felt a little slighted.
Posted by Mike Dunford at 8:50 AM • 18 Comments• View blog reactions
August 11, 2008
Category: Science, Policy, and Management
This should come as no surprise, coming as it does on the heels of last week's revelation that the Bush Administration is planning to change the federal definition of abortion in an effort to make it easier for our homegrown religious extremists to deny women their right to good reproductive healthcare: we've just learned that the Bush administration is proposing rule changes that will eviscerate the Endangered Species Act.
This is no joke. The National Wildlife Federation has a pdf of the leaked proposal, and their own analysis of the proposed changes. I've looked at the proposal, and NWF description is, if anything, an understatement of the effects that this rule change could have.
I'm going to go over some of the more disastrous of the proposed changes, and what they'll mean for environmental protection efforts. I'll also finish up with some suggestions for things you can do, but, realistically speaking, things are grim.
Posted by Mike Dunford at 8:35 PM • 8 Comments• View blog reactions
Category: Education
The initial phase of the California Creationist Lawsuit is over, and quality education is the decisive winner. Kevin Vicklund has Judge Otero's decision, as well as a very nice analysis of the ruling up over at his blog. If you've been following the case closely, you can probably jump right over there for the details. If you haven't been tracking the events closely, or want a quick review of the case, keep reading. I'm going to go over the history first, then I'll talk a bit about what Friday's decision means, and what is likely to happen with the case in the future.
The lawsuit (ACSI v. Stearns) was filed in federal court in August of 2005 by the Association of Christian Schools International, Calvary Chapel Christian School, and parents acting on behalf of their children, who were students at Calvary Chapel. They were challenging the University of California's decision to refuse to accept several of their courses as fulfilling UC's admissions requirements. The rejected courses covered the academic spectrum, with English, history, and science classes all failing to meet UC's scrutiny. The common element in the rejected courses was that they did not actually teach the material that UC requires from incoming students. Instead, the rejected courses taught a radically wrong "Christian perspective".
For most of us, the rejection of the courses was nothing more than the natural consequence of the Christian schools' decision to reject reality and teach fantasy. From their perspective, it represented an unconstitutional attack on their freedom of religion. The court, obviously, did not agree. To see why, we really need look no farther than the introduction to the biology textbook used in one of the rejected courses:
Posted by Mike Dunford at 9:54 AM • 47 Comments• View blog reactions
August 10, 2008
The American Men's 4x100 freestyle relay team just gave the French a very painful lesson in why it's really not a good idea to talk smack:
"The Americans?" Bernard recently told the sports newspaper L'Equipe, "We're going to smash them. That's what we came for."
Bousquet looked at members of the United States team in the ready room Sunday and saw a few cracks. "They didn't look at us, although usually they do," he said. "We could sense that they were a little bit afraid."
The American Response? Beautiful.
Posted by Mike Dunford at 11:57 PM • 12 Comments• View blog reactions
August 8, 2008
Category: Politics
The camera at the opening ceremonies just captured our President, sprawled in his chair, binoculars dangling limply from one hand, looking blankly out in space, and generally appearing to be thoroughly bored. That appearance was not dispelled when he looked at his watch. Way to represent us to the world, Bushie.
Update: Daily Kos has the video up for those of you who missed it.
Posted by Mike Dunford at 10:02 PM • 4 Comments• View blog reactions
As I mentioned earlier, the current issue of Nature has a perspectives article by Donald Berry, a statistician at the MD Anderson Cancer Center that addresses problems with the current system for testing athletes. I more or less agree with the overall conclusion of the article - there needs to be more detailed scientific study of the tests that are used to see if athletes are using banned substances. Unfortunately, I don't think the entire article was as solid, or as well justified, as his conclusion. In particular, I think he seriously overstates the possibility of false positives.
Berry writes:
Landis seemed to have an unusual test result. Because he was among the leaders he provided 8 pairs of urine samples (of the total of approximately 126 sample-pairs in the 2006 Tour de France). So there were 8 opportunities for a true positive -- and 8 opportunities for a false positive. If he never doped and assuming a specificity of 95%, the probability of all 8 samples being labelled 'negative' is the eighth power of 0.95, or 0.66. Therefore, Landis's false-positive rate for the race as a whole would be about 34%. Even a very high specificity of 99% would mean a false-positive rate of about 8%. The single-test specificity would have to be increased to much greater than 99% to have an acceptable false-positive rate. But we don't know the single-test specificity because the appropriate studies have not been performed or published.
More important than the number of samples from one individual is the total number of samples tested. With 126 samples, assuming 99% specificity, the false-positive rate is 72%. So, an apparently unusual test result may not be unusual at all when viewed from the perspective of multiple tests. This is well understood by statisticians, who routinely adjust for multiple testing. I believe that test results much more unusual than the 99th percentile among non-dopers should be required before they can be labelled 'positive'.
This is misleading, because it ignores both laboratory procedures for identifying false positives and the use of multiple tests before a final positive result is confirmed.
Posted by Mike Dunford at 12:56 PM • 12 Comments• View blog reactions
Category: Science and Public Safety
The latest issue of the journal Nature has two articles (an editorial and a perspectives piece) on the topic of drug testing for athletes. Both the editors and Donald Berry (the author of the perspectives article) argue for the need for both more scientific testing to support standards for athletic drug screening and for more openness in the process.
From the editorial:
Nature believes that accepting 'legal limits' of specific metabolites without such rigorous verification goes against the foundational standards of modern science, and results in an arbitrary test for which the rate of false positives and false negatives can never be known. By leaving these rates unknown, and by not publishing and opening to broader scientific scrutiny the methods by which testing labs engage in study, it is Nature's view that the anti-doping authorities have fostered a sporting culture of suspicion, secrecy and fear.
From Berry's article:
Whether a substance can be measured directly or not, sports doping laboratories must prospectively define and publicize a standard testing procedure, including unambiguous criteria for concluding positivity, and they must validate that procedure in blinded experiments. Moreover, these experiments should address factors such as substance used (banned and not), dose of the substance, methods of delivery, timing of use relative to testing, and heterogeneity of metabolism among individuals.
Posted by Mike Dunford at 9:32 AM • 5 Comments• View blog reactions
August 7, 2008
Category: War and Peace
Sometimes the only thing that separates comedy from tragedy is the involvement of an actual living human being.
That certainly seems to be the case where today's military commission verdict in the trial of Salim Hamdan. Despite having the advantages of what we must, for the lack of a better word, call a legal system that was set up to give the prosecution the edge, despite the admission of hearsay evidence, despite the use of material taken from interviews that didn't come within a light year of the Miranda guidelines, and despite the use of secret prosecution testimony, the prosecution was unable to secure a conviction on the charges that Hamdan conspired to commit terrorist attacks.
He was, however, convicted on charges of providing material support (his services) to a terrorist organization. That part of the verdict is hardly a surprise, given that Hamdan admitted to being Bin Laden's driver.
Now you might think, as the White House apparently did, that anyone capable of driving Bin Laden's car must be a criminal mastermind, capable of planning devious attacks on unsuspecting civilian targets. Or, if you are less well grounded in the ideologically driven world, you might wonder if Bin Laden really needed much more in a driver than someone capable of understanding how and when to use the pedals, gear shift, and steering wheel. The question, of course, is how to tell which possibility actually fits Hamdan.
Posted by Mike Dunford at 12:21 AM • 4 Comments• View blog reactions
August 6, 2008
Category: Life in an Army Family
Don't get me wrong. Living on base has some huge advantages for military families. The kids are around other kids who also move a lot. My wife can bike to work (on days when she doesn't walk). There are good recreational facilities available close to the house, both for us and the kids. On the whole, it's a good deal - especially for the price.
But there are also some disadvantages. There are a lot of training programs here, and quite a few of the classes get to do their physical training together, as a unit, under the gentle direction of their instructors. Early this morning, a couple of those instructors decided that it would be a good idea to not only run one through our housing area, but also to stop their unit for some remedial instruction in the art of running together and following orders.
My morning wake-up today came in the form of, "HALT MEANS STOP!! STOP MOVING NOW!!!" WE CAN DO THIS ALL DAY!!! FALL IN!!!
Posted by Mike Dunford at 7:51 AM • 5 Comments• View blog reactions
August 4, 2008
Category: Politics
There have been a number of indications that the Associated Press isn't being as neutral in the election as we would expect from a major media outlet. At an event in April, two Associated Press employees gave McCain a box of donuts and a cup of coffee - both prepared to his tastes - while the Chairman of the AP asked Obama a question about Afghanistan, where "Obama bin Laden is still at large". Concerns have been raised regarding AP campaign coverage of Iraq and health care, among other issues. The hypothesis that there might be a solid pro-McCain bias at the AP has received additional support and attention following recent revelations that the man responsible for APs campaign coverage sent Karl Rove an email that signed off with "keep up the fight", and "seriously considered" taking a job working for the McCain campaign.
An AP article published this morning is going to to absolutely nothing to reduce those concerns. The article is allegedly about Obama's calls to tax oil company profits in order to fund a tax rebate for Americans who are hurting at the pump. It uses this as a hook to "discuss" the energy plans of both candidates. It also seems to use a reporting technique that originated at Fox News: if you're going to criticize a Republican, make sure you report their party as "Democrat":
Obama has said recently that he would reluctantly consider accepting some new offshore oil drilling. Obama previously opposed any offshore drilling.
Lately, however, he has cited "very constructive" talks between Senate Republicans and Democrats on this issue. He praised a plan unveiled by a group of Republican and Democratic senators to permit drilling while supporting an effort to convert most vehicles to alternative fuels in 20 years.
McCain's campaign accused the Democrat of flip-flopping. However, the Arizona Democrat recently reversed his own former opposition to drilling on the Outer Continental Shelf.
Posted by Mike Dunford at 9:31 AM • 4 Comments• View blog reactions
August 1, 2008
Category: Medicine
Apparently, the Bush administration has come up with another way to attack reproductive rights. The department of Health and Human Services has come up with a draft regulation that changes a number of definitions in an effort to make it easier for people to refuse to provide people with abortions, or birth control, or even with a referral to another provider who would be willing to provide these services.
The regulation is ostensibly intended to ensure that federally funded programs do not discriminate against people or institutions that have religious objections to abortion. This is a legal requirement, and it's nothing new. The Church Amendments date back to the 70s, and there are several other more recent laws that reinforce that requirement.
What the Bushites want to do is change the definitions of a few terms, so that the existing laws can be stretched to cover more people. The terms in question include "assist in the performance" and "abortion". Some of the rationales that they give would be hysterical, if this didn't have the potential to affect real people's lives.
Posted by Mike Dunford at 12:54 AM • 18 Comments• View blog reactions
July 31, 2008
Category: Animals
Every now and then I'm reminded of just how awesome the world we live in is. Today's reminder came during a walk on the beach, as I watched a young osprey hunting for lunch just offshore.
I had my camera, and was able to get a few pictures of the dive and catch. One's above the fold, and there are a few more below. As always, you can click on the pictures to see a larger version.
Posted by Mike Dunford at 3:34 PM • 1 Comments• View blog reactions
July 30, 2008
Category: Misc Science
My scientific background leaves me more inclined to trust laboratory results than people, and I'm no more inclined to give athletes the benefit of the doubt in doping cases than anyone else who's been paying attention over the last couple of decades. When I heard that Jessica Hardy had tested positive for a banned substance at the Olympic Trials, and most likely will not get to swim in the olympics, I wasn't really surprised. Swimming hasn't been plagued with the same sort of doping scandals that other sports have seen, but it would be shocking if there weren't at least a few cheaters out there waiting to get caught. That's why there are tests. Someone tested positive? Toss them off the team and move on.
But when I took a few minutes to read the full story, something didn't make sense. I looked at a couple of more stories, and the situation made even less sense. At this point, I'm hopelessly confused, but I'm going to keep writing this anyway. If you keep reading, one of two things will probably (hopefully) happen: either you'll be able to spot something I missed, and unconfuse me in the comments, or you'll join me in confusion and the hope that someone else will be able to clear this one up for us.
Posted by Mike Dunford at 10:44 AM • 20 Comments• View blog reactions
July 29, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:32 PM • 2 Comments• View blog reactions
July 28, 2008
Category: Politics
You are a Social Justice Crusader, also known as a rights activist. You believe in equality, fairness, and preventing neo-Confederate conservative troglodytes from rolling back fifty years of civil rights gains.
Take the quiz at www.FightConservatives.com
and what kind of Liberal are you?
Posted by Mike Dunford at 11:09 PM • 7 Comments• View blog reactions
Category: Daily Linkfests
Posted by Mike Dunford at 1:33 PM • 0 Comments• View blog reactions
July 23, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:34 PM • 0 Comments• View blog reactions
July 22, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:32 PM • 0 Comments• View blog reactions
July 21, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:32 PM • 1 Comments• View blog reactions
July 19, 2008
Category: Science, Policy, and Management
Yesterday afternoon, Judge Donald Molloy of the Federal District court for Montana issued a preliminary injunction reinstating Endangered Species Act protections for grey wolves in Montana, Idaho, and Wyoming. This is very good news for the wolves. Although a preliminary injunction will only protect the wolves until the lawsuit is resolved, a judge will only issue one if it appears likely that the party requesting the lawsuit is going to win at trial.
A friend of mine emailed me a copy of the decision. It's forty pages long, and very little of it is kind to the Fish and Wildlife service. It certainly leaves no doubt whatsoever as to which party the judge believes is likely to ultimately prevail when the trial is concluded. After examining the claims made by each party, Judge Malloy concluded that it appears that the FWS arbitrarily and capriciously reversed several of its own prior conclusions and decisions in order to justify their decision to delist the affected populations.
The timing for this decision really couldn't be better. Without the preliminary injunction, all three states would have been able to go ahead with plans for wolf hunts this fall. Montana and Wyoming hadn't yet published their hunting guidelines and quotas, but had they been anything like the ones proposed in Idaho, the consequences for the species could have been severe. (I can't honestly say that Idaho's guidelines would have decimated their wolf population, but that's only because "decimate" implies that the mortality would only be 10%. They were planning on shooting more than a third of the wolves in the state.) The decision also came on the same day that fish and wildlife officials in Washington state confirmed the presence of at least a small group of wolves in their state for the first time since the 1930s.
The plaintiffs (a group of environmental groups) made argued that the Fish and Wildlife Service should not have delisted the grey wolf populations for several different reasons. Let's take a quick look at at a couple of these reasons, why they're important, and how the court viewed them.
Posted by Mike Dunford at 1:32 PM • 18 Comments• View blog reactions
July 16, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:33 PM • 0 Comments• View blog reactions
Category: Religion
Apparently, Chad's dog has at least some of the issues surrounding the PZ Myers/Eucharist desecration issue figured out. I'm not sure, but I think she understands them much better than some of the folks who have been commenting here. And she expresses things with so much more grace and panache than I usually manage.
Posted by Mike Dunford at 8:57 AM • 2 Comments• View blog reactions
July 15, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:33 PM • 2 Comments• View blog reactions
July 14, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:31 PM • 1 Comments• View blog reactions
July 12, 2008
Category: Religion
I really had no plans on posting more about the whole PZ and the eucharist thing. I got my own views off my chest last night, and there haven't been any new developments in the case itself. The initial reactions to Paul's post are in, and the commenters have sorted themselves into three groups ("Rock on!", "Dude. Not cool.", and "Where's the firewood?"). It's unlikely that there's going to be a lot of movement from one group to another. Under the circumstances, writing another post on this issue has all the appeal of sticking my finger in a pencil sharpener.
But then there was the side issue. It was probably inevitable, but some of the discussion surrounding all of the lunacy has actually brought up a point that is worth discussing: what's the difference between what Paul said, and the publication of the infamous "Mohammed" cartoons a couple of years ago?
This point was raised by a couple of posts at Andrew Sullivan's blog. In the first, he condemned PZ's threat to desecrate the Eucharist. In the second, he responded to readers who wondered if he might be suffering from a double standard. Sullivan, after all, was a very vocal supporter of the Danish newspapers that received threats after publishing cartoons depicting the prophet Mohammed.
Jason Rosenhouse was among those who weren't very thrilled with Sullivan. To a certain extent, this is understandable. It's very easy to get the impression, Jason points out, that the different reactions might have been sparked more by the fact that in only one of the two cases was Sullivan's own religion insulted. There's another point Jason makes, however, where I think he misses something very important:
Posted by Mike Dunford at 8:34 PM • 52 Comments• View blog reactions
Category: Religion
Over the last couple of days, I've considered posting something on the controversy that's been sparked by PZ Myers' comments about the eucharist, and the reaction of Bill Donohue and the Catholic League to those comments. I've been putting it off because it's not an easy post for me to write. The entire incident has suffered from a lack of heroes. Instead, it's been a case where someone has behaved badly, but someone else has behaved worse.
I've interacted with Paul Myers on various internet forums for at least a decade now. In that time, he's done many things that I respect, and a few that I greatly admire. His recent post offering to publicly desecrate the Eucharist if someone would be so kind as to send him some does not fall into either of those categories.
To be fair to Paul, it's not like he pulled that idea out of the blue. A college student in Florida smuggled a consecrated host out of a Catholic Mass at the school. When this became widely known, a large number of Catholics became extremely outraged, and the student received a number of death threats. The college responded by supplying armed university police officers to stand guard - not over the student who received the death threats, but at Mass, to protect the eucharist from future kidnapping. The university police will apparently be receiving additional backup from a nun that the diocese is sending to help protect the Eucharist. (No, I'm not making any of that up.)
It's easy to understand why Paul - and, for that matter, any number of rational people - were outraged by that story. The kid removed something from the church that is, as far as anyone can tell from any measurements of any physical properties, a thin wafer made out of wheat. It's about the size of a quarter, costs a lot less, and has both the texture and flavor of glue. It is absolutely, completely, and utterly insane that there are people who are willing to threaten the life of another human being who failed to display proper reverence for an object that is, by all objective standards, nothing more than a Necco Wafer that's been subjected to a flavorectomy.
Regardless of what we believe about the Eucharist, we should all be able to get behind the idea that it's absolutely wrong to threaten to kill someone who treats it disrespectfuly.
Paul's offer to desecrate a host was made in that context. I'm not totally sure whether it was made in the spirit of standing in solidarity with the threatened student, to attempt to show the people making the threats that it won't work, to try to show everybody that there's no apparent difference between desecrating a host and mangling a cracker, some combination of the above, or for some reasons I've missed. To be honest, I don't think the reason really matters. Let's just say that it came in reaction to the absolutely outrageous behavior of others, and leave it at that.
Paul's response to the death threats was to turn around and threaten to do something that's guaranteed to offend (if not horrify) every Catholic who finds out about it, whether or not they were in the select group of pin-heads who wish they'd been born early enough to get an on-the-job anatomy lesson working for the Inquisition. He made it very clear that he has absolutely no respect for anyone who believes in something as irrational as transubstantiation, and absolutely no qualms about hurting their feelings.
Posted by Mike Dunford at 1:23 AM • 54 Comments• View blog reactions
July 11, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:32 PM • 0 Comments• View blog reactions
July 10, 2008
Category: From the Right
I don't know what it is, but there's clearly something about the G8 conference that interferes with George Bush's ability to restrain his inner frat brat. At the G8 two years ago, you might recall, the Commander-in-Chief grabbed international headlines when he gave German Chancellor Angela Merkel an impromptu (and uninvited and unwelcome) neck rub during a meeting. Apparently, disgracing his office and nation once at the G8 wasn't enough of a legacy for the man.
Various news sources in the United Kingdom are reporting that the President decided to unleash his inner frat brat on the global stage again this year. From the Telegraph:
The American leader, who has been condemned throughout his presidency for failing to tackle climate change, ended a private meeting with the words: "Goodbye from the world's biggest polluter."
He then punched the air while grinning widely, as the rest of those present including Gordon Brown and Nicolas Sarkozy looked on in shock.
Mr Bush, whose second and final term as President ends at the end of the year, then left the meeting at the Windsor Hotel in Hokkaido where the leaders of the world's richest nations had been discussing new targets to cut carbon emissions.
Isn't it nice to see that our President is still willing to show the rest of the world that he's got the maturity level you'd expect to find in a junior-varsity football locker room?
Posted by Mike Dunford at 4:55 PM • 5 Comments• View blog reactions
Category: Daily Linkfests
Posted by Mike Dunford at 1:35 PM • 0 Comments• View blog reactions
July 9, 2008
Category: Daily Linkfests
Posted by Mike Dunford at 1:33 PM • 0 Comments• View blog reactions
July 8, 2008
Category: Daily Linkfests