General biology
tsmith | June 5, 2006Liam Scheff has now turned his attention from HIV to avian influenza, with predictable results. Analysis below...
Scheff's self-stated goal is to "...review some of the bright and shiny inconsistencies that have come into view on the bird flu." However, he's not exactly consistent himself, ranging from minor errors to total contradictions of his own words. He starts off discussing "stray cats and Chinamen:"
In March, 2006, The Associated Press reported: "In Austria, state authorities said Monday that three cats have tested positive for the deadly strain of bird flu in the country's…
tsmith | June 2, 2006John Hawks highlights a new article in today's Science, Metagenomic Analysis of the Human Distal Gut Microbiome. This goes nicely with the posts here recently on the topic of how our microbes affect our health and weight (part I; part II). A bit of discussion of the new article below...
First, I want to briefly mention what "metagenomics" means. There's a nice overview of it here on wikipedia. Basically, instead of sequencing and assembling a genome one at a time, you take a raw sample (such as dental plaque, sea water, soil, or fecal material, in this case), isolate the DNA, sequence it…
tsmith | May 31, 2006 It can't be said often enough that "nothing in biology makes sense except in the light of evolution." Moving from physical characteristics--color, bone shape, the form of bacterial cells--to genetic characteristics in order to classify organisms--and infer phylogenies--was a giant advance. That the molecular characteristics confirmed what was known using physical characteristics was a breakthrough, and allowed for more sophisticated analyses of organisms that don't have bones or other easily-observable physical features that allow for simple classification into groups: microbes. I've…
tsmith | May 26, 2006As pointed out yesterday, flu blogging has been light this month, even though there have been interesting developments. As such, to catch up a bit, I'm posting an overview of the current Indonesian cluster and some other thoughts below the jump...
As always, I point anyone who wants to keep up-to-date on the latest news over to Effect Measure for excellent analysis of what it all means, or to H5N1 for news from around the world on the topic. Obviously, the biggest news of the moment is the Indonesian family cluster, which appears to not only be an example of human-to-human transmission, but…
tsmith | May 26, 2006Species of the bacterium Clostridium have long been a scourge of humans. They are gram-positive, spore-forming bacteria that can be found in the soil around all of us. The spores then germinate when exposed to anaerobic conditions.
Clostridium botulinum is the cause of botulism, a serious and potentially fatal paralytic illness often caused by ingestion of contaminated foods. More recently, the bacterium has been used as the source of that anti-wrinkle miracle, BoTox: botulinum toxin type A, allowing all of Hollywood to smile without a wrinkly forehead (ah, the wonders of nature!).…
tsmith | May 25, 2006I feel a bit guilty. I still get occasional comments on this post about the outbreak of chikungunya on several islands in the Indian Ocean. Since I'm obviously not involved in the actual outbreak investigation, all I have to offer is news reported elsewhere--and it's not exactly been a landslide of information. However, Nature does have some news to offer, based largely on a new paper published in PLoS Medicine (summary here).
Previously, the complete genomes of three isolates of the virus had been determined. Two were from strains isolated in 1952 during the first known Chikungunya…
tsmith | May 23, 2006NBC's science and health correspondent, Robert Bazell, has an opinion piece today on MSNBC: Stop whining about intelligent design.
Scientists should stop whining about threats to the teaching of evolution and spend more time discussing values.
I should note here that most of the piece is strongly supportive of teaching evolution. Bazell presents a very brief overview of the history of anti-evolutionism in America, and notes that "serious efforts in biology and medicine can no more ignore evolution than airplane designers can ignore gravity." So, he's not messing around or giving any…
tsmith | May 21, 2006Or Saturday roundup, belated. Some interesting stories I didn't have time to cover:
The HPV vaccine, aimed at reducing the incidence of cervical cancer, has moved a step closer to approval.
The Institute of Medicine calls for more research into and oversight of vitamin supplements.
Continuing debate over "The Hobbit."
New research might eventually bring breathalyzers to your doctor's office. Not necessarily for alcohol.
An interesting study of experimental evolution: selecting for heat-tolerant bacteria over 1500 generations.
Yet another use for bacteriophage: diagnosis of…
tsmith | May 20, 2006Yesterday's Science had a letter to the editor regarding an editorial I mentioned previously (and that was touched on in the comments here as well):
Medicine might benefit most from embracing evolution theory's recognition of individual variation within populations of organisms, a property that Ernst Mayr has called "the cornerstone of Darwin's theory of natural selection". This "population thinking," as Mayr calls it, helped to undo typological thinking in biology, and it can help to dismantle typological notions of disease by highlighting individual differences in disease susceptibility…
tsmith | May 19, 2006 So, archaea are apparently the topic of the week. While I wrote here about the pathogenic potential of some species of these organisms, a new essay in Nature and a new review in Science focus more on their evolution (and the evolution of the other two domains of life) than any health application.
In the essay mentioned, Norman Pace discusses the eukaryote/prokaryote dichotomy. Currently the archaea are classified as prokaryotes since they, like bacteria, lack a true nucleus. However, molecular sequence analysis has shown that the archaea and eukaryotes are actually more closely related…
tsmith | May 18, 2006Welcome to the new edition of Animalcules!
First, a few housekeeping notes. If you note the schedule, I've not yet extended it beyond June 1st. I think that, at least for the summer months, Animalcules will be a once-monthly carnival, rather than every other week. If things pick up after that, I'll change it back to the current set-up, but that will be dependent not only on entries but also on additional hosts. So, if you'd like to host in July, August, or September, drop me a line (aetiology AT gmail DOT com) an I'll get you on the schedule.
Okay...on to the entries!
We have a few…
tsmith | May 17, 2006When I was in school, I was taught about the 5 kingdoms of life: Monera (all bacteria), and the eukaryotes: Protista, Fungi, Plantae, and Animalia. Since that time, there's been a bit of a change in the organization. This is largely due to investigation of the Archaea (sometimes still referred to as "archaebacteria"). It was recognized that these organisms were so unlike bacteria (and of course, unlike the eukaryotes) that they deserved their own grouping. Therefore, the most common strategy currently employs 3 domains of cellular life at a level above the kingdom: Bacteria,…
tsmith | May 16, 2006 On a recent episode of the drama House, the medical team finds that a patient improves from his illness when he's infected with a particular species of bacteria, Legionella pneumophila. Though mysterious at the time because the cause of the patient's illness was unknown, it was later determined that the patient was infected with naegleria, an amoeba. Legionella is an intracellular bacterium that just happens to naturally live in amoeba. Therefore, when the patient was co-infected with the amoeba and Legionella, the Legionella killed off the amoeba--using one microbe to attack another.…
tsmith | May 13, 2006More topics I'd have liked to discuss, given the time...
The Vigil after Dover. A free public forum, May 17, 2006 8 PM EST at The Florida State University College of Medicine Auditorium. Featuring Eugenie Scott, Michael Ruse, John Haught, Robert Pennock, and others, it will apparently be broadcast live as well.
An article on "Europe's unknown viral nasties", discussing the importance of surveillance (especially at the animal-human interface) to help detect emerging infectious agents.
Discussion of a new study that chipmunks and acorns hold the key to forecasting Lyme disease:
The…
tsmith | May 11, 2006I very briefly mentioned new research suggesting mercury fillings aren't harmful back here last month. In Saturday's Guardian, Ben Goldacre (who runs the Bad Science blog) had a short article on the topic. In it, he addresses the lack of coverage of the research in the UK media, despite stories in the last decade suggesting how dangerous mercury was. He notes:
Panorama did an excellently chilling documentary in 1994 called The Poison in Your Mouth. As far as I am aware there is no Panorama documentary in the pipeline covering the startling new research data suggesting that mercury fillings…
tsmith | May 6, 2006Just a few things that have either been sitting in my drafts box and I know I won't have a chance to get to, or stuff I saw elsewhere that deserves a mention.
Check out this excellent (and hilarious) post by Skip Evans on creationists and boobies.
I've posted previously here about our eagles here in Iowa. Phil at the Bad Astronomy Blog gives links to 2 webcams, where you can watch the nests of eagles or peregrine falcons (another favorite bird of mine). They've shut down the eagle one because the eggs didn't hatch and the parents left the nest, but there's a fluffy white falcon chick (…
tsmith | May 5, 2006I didn't have enough energy or stamina to do it yesterday, but John and PZ both have ripped it to shreds. Thank you, gentlemen, for your sacrifice.
tsmith | May 5, 2006I mentioned here my kids' penchant for catching, um, pets. Well, 'tis the season. I'll put the pics below the fold for those of you on dial-up or who lean toward arachnophobicity.
From the top of the jar:
Side view:
Eating a fly:
The last one was pretty cool because the kids watched her catch the fly; it was so quick, they almost missed it. One minute it's just buzzing around the jar, the next it's dinner. We always fed last year's spiders crickets, but they're not in abundance yet, so flies will have to do for awhile. This spider ("Wolfie McSpidery" is her current moniker) is also…
tsmith | May 4, 2006Cheyenne shelter dogs to be euthanized
All 70 to 80 dogs at the Cheyenne Animal Shelter will be euthanized because of an outbreak of canine influenza that has closed the shelter for more than two weeks, shelter officials announced.
Shelter officials said there was no way to test for the virus quickly and thus no way to tell which dogs were infected. Shelter director Alan Cohen said that unless all the dogs were killed, he couldn't guarantee that they wouldn't re-infect themselves and other animals.
"If I do not euthanize these animals, how can I let them loose knowing they might spread it to…
tsmith | May 3, 2006Andrea over at Pandas Thumb highlights a new JCI article with a call to action for scientists.
The Journal of Clinical Investigation is a top-notch journal, and their editors seem to "get it." They wrote an editorial last year which I discussed here (moved over from the old blog) discussing intelligent design, and why more scientists should pay attention to it. Good that they're continuing the effort by publishing this new paper.