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Denmark provocation of a different sort

Update: Trivial prediction: more Muslims will die because of "protests" and riots because of the Danish cartoons than non-Muslims. Matt McIntosh has posted a piece titled We Have Met the Enemy, and He Is Us at my other blog. It has spawned a lot of comments. Many people were offended by the way Matt couched his thought experiment and the character of his exposition. I jumped in to defend him, and below is a somewhat florid summation at the end of the thread (excuse the lack of capitalization, it is not an affectation, just a way to save keystrokes when I'm entering comments): ok, here is…

Some Civil War Blogging

Sadly, too many Americans are probably unaware that the anniversary surrender of the Confederate rebels at Appomattox happened a few days ago. I've found three posts I highly recommend. First, Tony Wikrent: One thing I really would like you to take away from this diary is a basic sense of how the United States, as a self-governing democratic republic, cannot long tolerate oligarchic and aristocratic ideas in its body politic. This is becoming an increasingly urgent issue for us today, because the American conservative movement today is basically a replica of the slavery-defending, anti-free…

Theological beliefs by denomination

One of the problems with intellectual conversations is that they are generally restricted to intellectuals. By their nature intellectuals tend to value reflection and some semblance of comprehension and consistency. This is a "curved" scale; I'm not contending here that intellectuals really attain a very high absolute level of analytic clarity or coherency, but, the process itself tends result in a minimal baseline of plausibility to a propositional sequence. I've pretty much come to the conclusion that the problem with attempting to understand human cognition as a sequence of inferences…

Humanzee, please (?)

Ah...busy with other things, and Evolgen pounced on this story of hybrdization in the midst of the split between the pre-human and pre-chimpanzee lineages 5-7 million years ago. Carl Zimmer offers some social perspective, while John Hawks tears into the science (tears, cuts and bludgeons, actually). I don't know about the details of the science here, there is a lot of exciting hype. Talk of human-chimpanzee hybridization is trangressive and appeals to our folk mythologies of man-apes. I also know that only one chimpanzee fossil has been recovered, and the pre-Australopithecene history of…

Good godists

Rob Knop, physicist and Christian, offers us his ruminations on religion. But Rob is not an "orthodox" Christian from what I can tell, he says in a follow up post: ...do I really believe that Jesus was really bodily resurrected, in contrast to everything we have observed, and everything we know and understand about human physiology and the decay that happens even shortly after death? Let me give you a wholly unsatisfactory answer: probably not. There you have it, he believes that the balance of the evidence leans against the resurrection of Jesus Christ. That being said, I'm a big…

It's good to be an atheist

I've received several emails about this study, Atheists identified as America's most distrusted minority. This shouldn't surprise too many people, but I think some perspective is in order. I think the results are probably accurate, but, I also think that the belief is wide but shallow. I went to high school in an area that was about 75% Republican and half Mormon. One time during our American Government class the teacher, Mr. Nelson, was giving a talk about the First Amendment, and he stated that in the United States you could believe in any God you wanted to, or no God at all. This last…

Naked Mole rats are inbred

Viral Epizootic reveals inbreeding depression in a habitually inbreeding mammal: Inbreeding is typically detrimental to fitness. However, some animal populations are reported to inbreed without incurring inbreeding depression, ostensibly due to past "purging" of deleterious alleles. Challenging this is the position that purging can, at best, only adapt a population to a particular environment; novel selective regimes will always uncover additional inbreeding load. We consider this in a prominent test case: the eusocial naked mole-rat (Heterocephalus glaber), one of the most inbred of all free…

Injustices and ironies

Allow me to purge a few interesting stories from my mailbag: Keshia Canter was working the drive-up window at a burger joint when a sanctimonious customer handed her a pamphlet. Scripture tells us that when a man looks on a woman to lust for her he has already committed adultery in his heart. If you are dressed in a way that tempts a men to do this secret (or not so secret) sin, you are a participant in the sin. By the way, some rape victims would not have been raped if they had dressed properly. So can we really say they were innocent victims? To answer the question, yes. Yes we can. If a…

Milk digestion, it does a body good

A few weeks ago I presented a tentative model for how lactose tolerance (the ability of adults to digest milk easily and efficiently) spread throughout the world. Here is what I offered: 1) A haplotype block, A, associated with the LCT gene, and a particular SNP on that block, -13910*T, is responsible for Eurasian lactose tolerance (here are some numbers across populations) 2) In African populations which are lactose tolerant this haplotype, A, and the SNP, -13910*T, are not always found. 3) This implies that separate mutational events resulted in alternative genetic strategies which…

Maybe NIH Thinks Small Laboratories Aren't Translating Enough Research?

DrugMonkey asks "Is the NIH trying to get rid of smaller laboratories?" Before I get to my take on the answer, what I'll be talking about is based on private conversations, so I won't be attributing some things to specific people (sorry Ed!). Take this for what it's worth... I don't think NIH is specifically trying to tank smaller labs. Instead, NIH seems to be reacting to frustration, both within and outside NIH, about the pace (or lack thereof) of translational research. Without viewing the funding situation for independent PI-driven labs in the context of larger NIH-wide moves towards…

The Press Has Always Been Sycophantic...

...at least some of the time. While there has been much gnashing of teeth and wailing about the political press' recent socializing with John McCain (and appropriately so), let's not forget that this is hardly the first time the press has knelt before power instead of confronting it. Rewind to Guatemala, 1954. In 1954, at the behest of the United Fruit Company, the CIA organized and backed the overthrow of democratically elected President Arbenz. From Peter Chapman's Bananas: How the United Fruit Company Shaped the World, here's how the political press behaved (boldface mine): [United…

You Mean to Say That Rigorous Infection Control Actually Works?

Who coulda thunk it? There are two frustrating attitudes held by a fair number of antibiotic resistance/infectious disease specialists about MRSA (methicillin resistant Staphylococcus aureus). First, some argue that we really shouldn't be focusing on MRSA, since it's already evolved--the cat is out of the bag. Never mind that this particular cat kills more people annually in the U.S. than AIDS. While we obviously can't prevent the evolution of MRSA (that's already happened), we can contain the problem: we would rather have one percent of all staph infections be MRSA, rather than the…

Obama's Educational 'Reforms': More of the Same Old, Same Old

And they don't appear to actually fix anything either. From The Washington Post: But Duncan reiterated his commitment to testing and accountability: "I will always give NCLB credit for exposing achievement gaps and for requiring that we measure our efforts to improve education by looking at outcomes rather than inputs. . . . Today, we expect districts, principals and teachers to take responsibility for the academic performance of their schools and students." The standardized testing culture has sunk deep roots in public education under the federal mandate to assess students in reading and…

Some Concerns About the LA Times' Attempt at Teacher Evaluation

The LA Times has taken upon itself to rate school teachers in Los Angeles. To do this, the LA Times has adopted the 'value-added' approach (italics mine): Value-added analysis offers a rigorous approach. In essence, a student's past performance on tests is used to project his or her future results. The difference between the prediction and the student's actual performance after a year is the "value" that the teacher added or subtracted. For example, if a third-grade student ranked in the 60th percentile among all district third-graders, he would be expected to rank similarly in fourth grade…

Seattle Artist's Christmas Ornament Banned from White House Tree

Offensive Christmas Ornament created by Seattle artist, Deborah Lawrence. Image: Deborah Lawrence. Seattle artist, Deborah Lawrence, was one of 370 artists who were given the honor of creating a Christmas ornament for the White House's official Christmas trees. This was after Laura Bush invited all 435 Congresscritters to choose artists from their congressional district to design ornaments for the White House Christmas trees. Unfortunately, Lawrence's 9-inch ball was the only one that was banned from the White House trees, even though it fulfilled all the requirements set out by the…

Birdbooker Report 105

tags: Birdbooker Report, bird books, animal books, natural history books, ecology books "How does one distinguish a truly civilized nation from an aggregation of barbarians? That is easy. A civilized country produces much good bird literature." --Edgar Kincaid The Birdbooker Report is a special weekly report of a wide variety of science, nature and behavior books that currently are, or soon will be available for purchase. This report is written by one of my Seattle birding pals and book collector, Ian "Birdbooker" Paulsen, and is edited by me and published here for your information and…

Birdbooker Report 97

Birdbooker Report 89

Capture Some of the Magic in the World with Ant Farms and Microscopes

tags: DonorsChoose, science education, teaching, fund-raising, poverty I have a confession to make: I love ant farms. I love them so much that one of my readers bought me an ant farm to cheer me up shortly after I lost my funding and was experiencing a long run of bad luck in my job search -- the financial stress and loss of self esteem were almost unbearable. But even though I am an adult (well, I'm told I look like an adult), I found hours of joy watching "my ants." But imagine how eye-opening an ant farm would be for a bunch of impoverished second-graders who have never seen or…

Rabbi Avi Shafran wants to argue

I've received a personal email from Rabbi Avi Shafran—the fellow whose graceless and ignorant opinion piece I criticized a while back. It's a peculiar thing: he wrote a public editorial, I criticized it publicly, and now he asks that we have a private discussion on the matter. I won't post his whole email, but I will put up the main point, what he plainly says is the main point and a restatement of the thesis of his original editorial, and address that here. If Rabbi Avi Shafran wants to continue the discussion, he should do it publicly. I'm not going to convert him, and he's not going to…

Birdbooker Report 64

WHO Director General: on being careful what you wish for

In an example of the adage, "Be careful what you wish for," China's choice for WHO Director General, Dr. Margaret Chan, is already finding her reputation will be held hostage to the behavior of China itself, not an enviable position. The new chief of the World Health Organisation, Margaret Chan of China, pledged to put her nationality aside and to use her leverage on Beijing to combat major threats such as bird flu. "Now I'm elected as the WHO's Director General I no longer carry my nationality on my sleeve. I leave it behind," she told reporters after her nomination was endorsed by more than…

What the world needs now . . .

Two members of the UN Security Council, China and France, broke with tradition last week and nominated candidates for the position of WHO Director General. In the past Security Council members have not had citizens in that post. China's candidate is Dr. Margaret Chan. She has a controversial history as health director in Hong Kong during the SARS and 1997 H5N1 outbreaks. Whether she is fairly or unfairly blamed is a matter of debate, but Karl Greenfeld's book on SARS, The China Syndrome, does not indict her particularly, although it has harsh words for the Chinese leadership. Our concern…

Godless mutations and the sins of Dr. Smith

So what does my Scienceblogs colleague, Dr. Tara Smith of Aetiology know anyways? So she's got an advanced degree and is a practicing epidemiologist. How could she be so smart if she writes stuff like this? Those of you who have followed creationism/intelligent design literature over the years have probably felt as if you're living in an alternate universe sometimes. In that literature, many times it seems as if "up" means "down" and "highly supported by the evidence" means "a theory in crisis." [snip] Phylogenetic analyses based on genetic mutations are used to determine relationships for…

Thought experiment or reality: Walking away from the American Chemical Society?

Jenica Rogers is Director of Libraries at the State University of New York at Potsdam. Like so many institutions SUNY Potsdam subscribes to the suite of journals published by the American Chemical Society. Now, that's always a challenge since the ACS prices their products very aggressively as well as pushing the envelope with annual price increases. Well, push finally came to show and SUNY Potsdam is Walking away from the American Chemical Society. The problem: In May 2012, after much internal discussion and debate, three SUNY library directors from the comprehensive colleges (myself…

A Field Guide to ScienceBlogs' Friday Features

"Friday cat blogging," or the practice of posting something light-hearted and whimsical, is an end-of-week tradition in the blog world. While no one at Sb regularly puts up pictures of their furry pets, many of the ScienceBloggers do post weekly features on Friday. What follows is my attempt to orchestrate a complete guided tour of Fridays at ScienceBlogs. Phylogeny Friday at Evolgen "Phylogeny Friday is back, bitches! In the glorious return of PhyFridays, I give you the root of the tree of life. In the upcoming editions we'll zoom in on a few parts of the tree to illustrate the diversity…

Reading Diary: Wizards, Aliens, and Starships: Physics and Math in Fantasy and Science Fiction by Charles L. Adler

Only rarely in my life as a reviewer do I get books that seem to be absolutely perfectly suited for me. This is certainly the case with Charles L. Adler's Wizards, Aliens, and Starships: Physics and Math in Fantasy and Science Fiction, a book that combines my love for science and my love for science fiction. The premise is an ingenious one, one that's probably not anywhere near exploited enough in the popular science literature: use science fiction and fantasy stories as a way of elucidating science. Sure, it's been done to death in all those "The Science of X" books where X is some movie or…

Going into the Unknown, Together

The actors on the stage work their magic, turning a few disparate phrases - "challenge, giving birth, infinity, chaos, visiting a new country" - into a brief but charming improvised sketch, to the delight of the audience. But the viewers, filling a large auditorium at the Weizmann Institute of Science, expect more than to be entertained. Since the improvised play is part of a lecture by Prof. Uri Alon, a Molecular Cell Biologist, they know scientific insights are bound to follow. Indeed. Combining his two passions, science and theater, Alon has recently created a "theater lab" on the…

BEST paper in the urban heat island effect category

There's this notion among the climate denial community that somehow the entire professional climatology community has overlooked an obvious flaw in the science behind anthropogenic global warming. Their hypothesis is that too many of the thermometers used to record temperatures over the last 200 years have been located in or near cities, and so have produced a warming bias produced by the waste heat generated in urban areas. It sounds plausible. The problem with the notion, of course, is that it's so obvious a potential bias that climatologists long ago learned to take the "urban heat island…

Lomborg v Lomborg

Much is being and will be written about Bjorn Lomborg's volte face on climate change. After a decade of denial -- not of the reality of anthropogenic warming, but of the threat it poses to civiliation -- the Skeptical Environmentalist now says: "If we care about the environment and about leaving this planet and its inhabitants with the best possible future, we actually have only one option: we all need to start seriously focusing, right now, on the most effective ways to fix global warming." Is this worthy of a blog post? In a perfect world, no. But then, in a perfect world, I would be…

If you think the BP spill is bad....

The estimates of the just how much oil is spewing into the Gulf of Mexico from BP's Deepwater Horizon rig keep rising. The latest guess -- and it is just a guess -- is something like 210,000 gallons a day. It is almost certainly going to eclipse the Exxon Valdez catastrophe by the time things are brought under control. Who knows how much damage has been done to the Gulf Coast ecology and economy? But could it be that we're lucky this happened where and when it did, instead of a few years down the road in an even more difficult spot, say the Arctic Ocean? Canada has long been interested in…

Next Generation Learning with the Kavli "Science in Fiction" Video Contest.

By Stacy Jannis Connecting bright young minds with the tools and techniques they need today is the first step towards developing our work force tomorrow. Businesses and government have issued a challenge to educators to help this next generation acquire the creative high-performance STEM skills they need to better transform the world. The evolution of learning technologies, combined with new frameworks for learning standards, will help equip and propel our students forward towards this goal. So how could our "Science in Fiction" video contest help students practice and refine these much…

Role Models in Science & Engineering Achievement: Lewis Howard Latimer -- Inventor

His invention improved Edison’s electric light bulb, and he executed the patent drawing for Bell’s telephone. Get to know this creative genius! With his mind frequently in motion as a child, Lewis Howard Latimer -- born in 1848 in Chelsea, Massachusetts -- loved drawing at an early age and found himself doodling no matter where he would be. Little did he know these pastimes would evolve into a career as a noted draftsman and inventor, and result in him collaborating with two of the most famous innovators of his era. Lewis, the fourth child of George and Rebecca Latimer, was reared in Boston.…

An Interview With Greg Laden

For this week's ScienceBlogger interview, we present the star of Greg Laden's Blog: none other than the great Greg Laden. (The girl on his shoulders is his daughter, Julia.) What's your name? Greg Laden What do you do when you're not blogging? Not blogging? Oh, that. I am a part time biological anthropologist (I work in South Africa) and a part time advisor in the University of Minnesota's Program for Individualized Learning (A BA/BS program). More below the fold... What is your blog called? It is called Greg Laden's Blog. What's up with that name? I used to have a blog called "Evolution…

Subject: I need your assistance...a Message from Festival Director Larry Bock

I need your HELP and it will take just three simple steps: copy the link, Add your friends to an email and Send. For the past year I have been organizing the USA Science & Engineering Festival in what I hope will be the country's largest celebration of science and engineering -- a FUN, entertaining, educational and FREE event geared toward reinvigorating the interest of Americans in the Sciences. I have put as much energy and imagination and effort into this as any of the companies I started. And now I need your help getting the word out. Why is this important? In a nutshell: --…

Making Science Cool Again--One Kid at a Time

By Aimee Stern, Festival Communications Director "Fighting a forest fire with 1000 eye droppers." That's how David Washington, acting CEO of Change the Equation, a non-profit, described the current effort to improve STEM (science, technology, education and mathematics) education in the United States. There are hundreds of programs around the country addressing the nation's need for improving STEM education, but there is no centralized repository of information about them. The problem? Others can't learn from their success or failures. This discussion was part of a larger meeting at the…

BioDatabases 2017 - What's out there?

It's time for the annual blog about the annual Nucleic Acids Research (NAR) database issue. This is the 24th database issue for NAR and the seventh blog for @finchtalk. Like most years I have no idea what I'm going to write about until I start reading the new issue. Something always inspires me. This year's inspiration came from missing data. In 2017, NAR lists 1662 databases or 23 fewer than last year. As summarized in the database issue's introduction, Galperin, Fernández-Suarez, and Rigden tell us this year's issue has 152 papers. 54 of those describe new databases, 98 provide updates,…

Exactly 8.2% or 80% of the Human Genome is Functional

Science and its interpretation is wonderful. Today I saw a post on Twitter from @LAbizar, referencing an @GEN, post that stated 8.2% of Human DNA is Functional with a link to a GEN article: "Surprise: Only 8.2% of Human DNA Is Functional." The GEN writeup cited a PLoS Genetics article, "8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage," released today. How much of the human genome is functional? In 2012, the ENCODE (Encyclopedia of DNA Elements) project published a landmark summary, "An integrated encyclopedia of…

A biologist by yet another name

What do you call a biologist who uses bioinformatics tools to do research, but doesn't program? You don't know? Neither does anyone else. The names we use People who practice biology are known by many names, so many, that the number of names almost reflects the diversity of biology itself. Sometimes we describe biologists by the subject they study. Thus, we have biologists from anatomists to zoologists, and everything in between: addiction researchers, chronobiologists, epidemiologists, immunologists, microbiologists, neuroscientists, pharmacologists, physiologists, plant biologists,…

Spoiler Alert: Riddick

After thirteen years and three films, it's still hard to know what to think about Richard B. Riddick. No one calls him Dick. His luminescent mother-of-pearl cat's eyes allow him to see in the dark, when they're not protected by an iconic pair of black welding goggles. He is very talented at killing people and animals, especially with melee weapons or hand-to-hand. He's not based on any literary or comic-book character. Judging by his conversational abilities, he may be brain damaged or developmentally disabled. He is extremely strong. He is played by Vin Diesel. In Pitch Black (2000),…

My picks from ScienceDaily

Two Nerve Cells In Direct Contact: For the first time, scientists at the Max Planck Institute for Neurobiology in Martinsried near Munich have been able to show how two nerve cells communicate with each other from different hemispheres in the visual center. This astoundingly simple circuit diagram could at a later date provide a model for algorithms to be deployed in technical systems. A Silent Pandemic: Industrial Chemicals Are Impairing Brain Development Of Children Worldwide: Researchers found that 202 industrial chemicals have the capacity to damage the human brain, and they conclude that…

The TB guy. Others weigh in.

My defense of the TB guy has drawn a lot of traffic and some of the comments imply my view is colored by a case of misplaced compassion. Since I'm a physician I won't shy away from being called compassionate. Whether true or not in my case, it is a desirable trait for a doctor and nothing to be ashamed of. However I don't think my opinions about this case are due to sentiment. I would defend them on the grounds they are sound judgments of a public health professional. Since I am unlikely to convince the doubters by repeating my arguments (you can find them at these links), I will do something…

Not All in our Genes, The Sequel

Last November a WHO study "stated" there was evidence a genetic factor was at work in the susceptibility to H5N1 because it appeared an abnormally high number of reported clusters involved only blood relatives. At the time I expressed some polite skepticism (Not All in Our Genes). Whether the observed data actually had more blood relative cases than would be expected bdepends on what one would expect. What you "expect" is the so-called null-distribution, which in turn depends on a plausible underlying probability model. Now a doctoral student working with Marc Lipsitch and his collaborators…

Freethinker Sunday Sermonette: Hitchens, Collins and The Economist

The Economist, a right of center journal of news and opinion I find quite interesting (as do many other lefties), has noticed that atheism is big in the book market. Comparing Hitchen's book, God Is Not Great: How Religion Poisons Everything with Francis Collins's The Language of God: A Scientist Presents Evidence for Belief they come up with a rather bizarre conclusion: whether you are a rationalist like Hitchens who comes up on the side of atheism or a scientist/rationalist like Collins who cleaves to the devout depends on whether you "have an intrinsic feeling for religion or not." Errr…

The overlooked flu planners

An excellent article on the CIDRAP site by Maryn McKenna (late of the Atlanta Journal Constitution where she had the CDC beat) won't be news to readers here, but it is news that it is news. The subject is efforts by non public health types in preparing for pandemic influenza. McKenna notes that recent reports by two different but highly regarded groups has noted that governmental planners are not making full use of grass roots groups outside of professional boundaries. In fact they aren't making use of them at all. Communication with the public is one way. The first report, "Community…

Freethinker Sunday Sermonette: breaking a taboo

The big news in the world of atheism this week is the admission by northern California congressman Pete Stark that he was a nontheist. In officially making his declaration of non faith, Stark has breached what many think of as the last religious taboo in American politics. Mr Stark, who has served in Congress since 1973, admitted his "non-theism" after the Secular Coalition for America, an advocacy group in Washington, offered a $1,000 bounty to the person who could identify the "highest-level atheist, agnostic, humanist or any other kind of non-theist currently holding elected public office…

Pa-Doofus

You probably don't know what PDUFA is (pronounced pah-doofah) but it's about to expire. Which is good. If they let expire. "They" are our friends in congress. PDUFA stands for the Prescription Drug User-Fee Act and it is an integral part of the FDA drug safety program. You know. The one that brought us Vioxx. I wish I had the great cartoon I saw at the time of the Vioxx trial that showed a bottle of medicine with a label on it that said, "FDA Approved Drug." On the label was a small box that said: "Warning: contains FDA approved drug." So what's PDUFA? The idea behind PDUFA sounds very…

Clock Tutorial #12: Constructing the Phase Response Curve

The fourth post in the series on entrainment, originally written on April 10, 2005, explains the step-by-step method of constructing a PRC. After months of applying light pulses to your animals you are ready to analyze and plot your data. You will print out the actographs (see how in the post "On Methodology" in the "Clock Tutorials" category) and you will see many instances of phase-shifts, somewhat like the very last figure in this post. For each light pulse you applied to each animal, you measure the direction of the phase-shift (i.e., if it was a delay or an advance) and the size of the…

My Oldest Book(s) Meme

Apparently there is a meme going around the blogosphere in which people dig into their personal libraries on a search for the oldest book they have - originals, that is, not reprints or printouts. Considering that I am a book lover and a book hoarder, I was surprised to see how few of my books are really old. It is not surprising that history bloggers have much older books than us mere mortals. Check out the ancient texts collected by Duane Smith, Chris Weimar, Chris Tilling and their commenters! Some go back to 16th century! There is no way I can best that. There is also no way I can best…

Nationalism and Patriotism

OK, today I'd like you to superimpose a couple of very different articles that all look at the difference between patriotism and nationalism, but each from a different angle and see if, and how, they inform each other. First, I'd like you to read one of my old posts (which I may decide to re-post here one day, but for now, check it out on my old blog) - Nationalism is not Patriotism. That would be a bare-bone introduction to political psychology of patriotism and nationalism: Why is there a widespread belief that the difference between patriotism and nationalism is one of degree: loving one…

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