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Thursday, March 31, 2005 Damn, Flat Tire At least I was near a car repair shop and there were no blizzards. Which I suppose you could say is lucky because I don't own a cellphone and I don't know how to replace tires. The only other people waiting for their car to get fixed was a father and his two teenaged daughters who were engrossed in diddling with their shiny cellphones. The car repair shop was in the midst of remodeling. I had no idea that it was so easy to strip wallpaper off the ceiling. [posted by S. Y. Affolee on 3:53 PM : The Thursday Threesome: Hot Dogs and French Fries Onesome: Hot Dogs--Spring picnics and cookouts are coming! Is it hot dogs or hamburgers you want to have on your plate as you head back to the table? Anything but hot dogs and hamburgers. I'd rather have a sandwich. Unless that's the only stuff they're serving. Twosome: and-- ...and what else is on that plate that you just cannot be without as you work your way through the crowd? Potato salad? One of those huge pickles? Come on, there has to be something < g >! Not sure. When it comes to vegetables, I'm not that picky. Threesome: French Fries-- ...and the real toughie: do you have to have "fries with that'? ...or will chips do well enough for you. Just curious... I'm not especially picky about this stuff either. [posted by S. Y. Affolee on 3:24 AM : Wednesday, March 30, 2005 Linkage Food and Feasting in Ancient Rome. I might try the Nut Tart when I have time to bake again. Who Needs Harvard? The author argues that students can get just as good an education at schools other than the "top" schools. I agree--education is what you make of it and not where the school is ranked. Feynman Lectures. Eeee! Okay, so I didn't really scream like a crazy fangirl when I came across this link, but I was excited. All three volumes of the late great physicist's lectures are online in pdf and mp3. Lakota Winter Counts. "The Lakota marked the passage of time by drawing pictures of memorable events on calendars known as winter counts." Awesome anthropological exhibit from the Smithsonian. Like a subway map, for SNIPs. A Metafilter thread with links to maps of haplotype networks. Flesch-Kincaid: Threat or Menace? The works of bestselling authors have surprisingly low reading levels--which makes sense if you think about it. "Normal" people won't buy your books if you use too many big words. Admission. (via Reflections in d minor) Oh great. Do I really have to spill the beans? Well, I have only two words for you: Microbe Overlords. (What? And you thought all my science posts were just for fun?) Hugo Award Shortlist. I've only started reading one of the novels, I've read one of the novellas, seen two of the movies, read stuff that have been edited by three of the editors, remember two of the artists, seen three of the semiprozines, only heard of one of the fan writers, and visited three of the nominated websites. I am such a sci-fi slacker. [posted by S. Y. Affolee on 7:48 AM : Tuesday, March 29, 2005 Microbe Masquerade For the past couple of days, the blogosphere has been oohing and ahhing over the observations that octopuses can troll around the sea floor looking like coconuts and algae, but this is hardly unique in nature. Even seemingly "dumb" bacteria can don disguises and sneak right past watchful eyes. And they don't even have to go through the trouble of walking on two legs. A recent review in Science tells us that our gut contains up to 100 trillion microbes with genomic material that may exceed 100 times the number of our own genes. The most obvious benefit that these microbes have for their hosts is that of nutrition--they help break down food. But in order to stay in the nice comfortable niche of the GI tract, these microbes must develop some sort of strategy to evade the immune response in which the primarily response is to recognize self from non-self. So how to overcome this "immunological paradox"?  Another article in Science by Coyne et al. examines the gut bacterium Bacteroides fragilis and its particular strategy for immune evasion. A large percentage of our gut microflora consists of Bacteroides species--up to 30-50% of the feces--which are important energy sources for our colon cells by producing butyrate, acetate, and propionate. They're also important for creating a nonhospitable environment for pathogens like Salmonella although occasionally, B. fragilis can get out of control too and cause abdominal absesses and diarrhea.But what does B. fragilis get out of the whole deal? One can think of the bacteria as tiny herds of herbivores snipping off the sugar residues (fucose) on the surface of host cells and using those sugars for food. But how to evade those immune cells scouting for rogue bacteria? Coyne et al. teased apart the fucose metabolic pathway in B. fragilis and discovered that not only does the bacterium use the sugar as an energy source, but it also incorporates the sugar into the polysaccharides making up the bacterial capsule. So these bugs are not just eating the "grass" but are sticking clumps of vegetation onto their hides to escape the notice of the host's police force. This type of camouflage on the molecular scale is called molecular mimicry or "crypsis". This hypothesis proposes that molecular structures such as amino acid sequences and proteins with a specific conformation may be similar in two different organisms (like a microbe and its host), but the origin of those similar molecules are different. In 1964, R.T. Damian coined the term "molecular mimicry" to describe the idea that microbes evolved similar antigens to the host to evade immune response. But what happens when molecular mimicry "fails"? In the early 1980s researchers were attempting to generate monoclonal antibodies to the measles and herpes simplex viruses. When these antibodies were tested, some of them not only interacted with the virus proteins but also host "self" proteins such as the ones found on the surface of T cells. Later experiments with animal models proved that this phenomenon wasn't just a fluke and analysis of amino acid sequences showed that some viral proteins and self proteins have significant homology. This failure of molecular mimicry can spell disaster for ourselves, especially for people with hypervigilant immune systems (such as lacking T cell Robin Hoods). A major problem that molecular mimicry poses to our health is autoimmune disease. If a microbe cloaks itself in proteins or molecules that are similar to the ones host cells, the immune system can get confused and not only attack the microbes but also our own cells. But for our commensal microbes it's business as usual as they dispense nutrients in our guts with disguises intact. [posted by S. Y. Affolee on 3:53 AM : Monday, March 28, 2005 Sigh I am so very, very tired of once again getting lectured for something that I didn't do. It's not my fault that other people aren't responsible and they don't fess up. Or maybe some people are just more prone to lecturing whenever they open their mouths than others. Lately, I've been thinking (although I probably mentioned this numerous times before)--if an infinite number of universes exist, there must be at least one where I'm happier than the one I'm in now. But if I'm happier, will I be the same person? Will I be a better person? [posted by S. Y. Affolee on 6:22 AM : Interesting Brazil opens microbe bank for bioprospectors. (via Boing Boing) "Hundreds of bacteria, fungi and yeast species, mostly collected from the wilds of Brazil, have been made available to researchers looking for new chemicals with scientific or industrial applications." Cool. [posted by S. Y. Affolee on 3:45 AM : Sunday, March 27, 2005 Unconscious Mutterings
[posted by S. Y. Affolee on 5:36 AM : Saturday, March 26, 2005 Arg! Dang it, the neighbors have started up that rapping "music" again. But this time, I've realized that this really isn't something on infinite replay--they're practicing. Is there some rapping contest somewhere that I don't know about? Except I think this is worse than having an amateur garage band next door. (Or is something more sinister happening, like in that movie The Ladykillers? They're not trying to cover up their tracks for robbing a casino, are they? Wait a minute. There aren't any casinos here in the boondocks. Only the lotto stuff at the local gas stations.) [posted by S. Y. Affolee on 5:54 PM : So What's Up? Some would argue that people dislike certain types of music because they haven't listened enough to it to grow to like it. Well I can say this: After being forced to listen to a profanity-ladden rap song on infinite looping from last night to this afternoon (played by no other than my annoying neighbors), my opinion of the genre has gone from extremely strong dislike to utter and complete loathing. Like going from -10 to -10^10^10^10. As for my neighbors, I wish someone would implant some earphones in their ears so they'd be forced to listen to a certain singing purple dinosaur for 24/7. On a completely different note, I'm currently reading Jared Diamond's Guns, Germs, and Steel which I find really fascinating. I first heard about the book a couple years ago when a professor recommended it out of the blue during a class. Looking back on it, I have no idea why the book was recommended--it had nothing to do with the class's subject matter. Maybe the prof just finished reading it and he couldn't wait to make other people read it too. (Not that I'm complaining, mind you. I think it's really good so far.) I am also attempting to finish several fiction books that I've been in the middle of for ages, but we'll see how it goes. I haven't been feeling in the mood for fiction lately. Perhaps of interest to a few people, I've obtained copies of The Red Queen by Matt Ridley and Human Natures by Paul Ehrlich today. I have no idea when I'll get around to reading them--hopefully sometime soon. Also, I have not forgotten the Margaret Atwood recommendations from Gully Brook Press. I just haven't obtained copies of those yet. Current reading queue: Waking the Moon - Elizabeth Hand (I swear I'm going to finish this one before the end of April) Snow Crash - Neal Stephenson A Few Short Notes on Tropical Butterflies - John Murray The Mismeasure of Man - Stephen Jay Gould Those aren't the only books in my queue, but if I were to list it all out, you'd probably think I need at least a decade to finish them. Of course, this doesn't mean that I'll turn down any suggestions.... [posted by S. Y. Affolee on 1:57 PM : Friday, March 25, 2005 I Stole a Link Hoard from a Dragon That is, if dragons were real and they hoarded links. Anyways, never fear, this isn't turning into an uberlinklog any time soon. I just have the habit of bookmarking stuff to read later and then thinking it would be such a waste if I simply deleted them after I'm done. Blogger-Centric Where Are All The Women? One blogger thinks the whole argument of female vs. male blogs is blown out of proportion and that feminist bloggers should chill out. I'm thinking I really should stop linking to all this blather about whether or not female bloggers are ignored, but I can't help reading this stuff--it's like being morbidly drawn to watch car wrecks. Where are the women bloggers overload. A Pandagon article quoting women op-ed journalists on the reasons for the dearth of female opinion writers. The Blog Cycle. Anil Dash writes about how blogger communities rehash the same things over and over again. I think musing about the blog cycle is part of the blog cycle itself. How to grow your (blogging) audience. I think you can do all those things and still have no audience. Blogsnow. Another link aggregator. Science Classic maths puzzle cracked at last. A graduate student finally figured out the pattern for primes and partitioning--which will undoubtedly have applications in encryption technologies. Chewing gum can 'enhance breasts'. This is a BBC article, not spam. Utensils divulge dinner date's feelings. "Although it may never reach the market, a new type of dating tool could give inspiration to the romantically challenged. By attaching electrodes to regular eating utensils, inventor James Larsson has created knives and forks that can pick up on whether the person across the table feels uncomfortable or pleased." Women get extra dose of X-chromosome genes. "However, it seems that the inactive X doesn't just sit down and shut up. The first of two research papers on the human X chromosome, both published in Nature, analyses the complete sequence of the chromosome. The second shows that women still express many genes from their inactive X chromosomes. What's more, different women express different genes from the inactive X." Time Wasters Moodcatcher. It says I'm experiencing an existential crisis and that I'm having a "long dark night of the soul." I suppose that's true enough. Also it gave me Eel-grass, a poem by Edna St. Vincent Millay. Is that a spreadsheet on your screen - or solitaire? Companies want to pose restrictions on employees for playing computer games. Well, I don't play solitare (or any other computer games for that matter, except for IF)--but I do read weblogs. Actually, sex doesn't sell. "Sex sells, but not serious sex. Films can be sexy, but they can't portray the sexual intimacy most people crave. In the movies, you have to have safe sex palatable to a younger audience. The portrayal has to be violent or funny." How to really confuse your party guests. Pictures of a gravity-defying room. The Periodic Table of Rock. Split into metals and non-metals as well as a bunch of false metals. And why did Lenny Kravitz get his own column? Medieval and Renaissance Illuminated Manuscripts from Western Europe. I am such a sucker for old books. 'Satanic' turtle survives inferno. I don't see any devil faces. It's just a case of a bunch of crazy pet shop owners trying to make a quick buck off of gullible, superstitious people. Knobtweakers. (via Podcast.net) An mp3 blog for electronic music fans! Plenty of interesting stuff. [posted by S. Y. Affolee on 3:39 AM : Thursday, March 24, 2005 The Thursday Threesome: Wine, women and song Onesome: Wine- or beer? Or do you prefer your beverages non-alcoholic? Non-alcoholic, usually. Twosome: Women- and men. We're entirely different creatures. What do you think makes the opposite sex tick? Or do you consider their behaviour a complete mystery? It's too early in the morning to speculate. Threesome: and Song- What's your favorite song? Your favorite band/ musician? I don't have a favorite song, band, or musician. I typically listen to a variety of music--if I stuck to one, not only would it be boring, but I'd get sick of it after a while. Yesterday, I found myself on a shuttle full of old people--more specifically, of the near-retirement set. They complained about silly college students and their own kids and their video-gaming grandchildren. Kids these days! And all that blather. Some old people think they know everything. I'm positive those biddies and geezers will just lump me into a group called "empty-headed twenty-somethings." I won't argue the fact that they have more experience living than I do. But that doesn't automatically mean that they're wiser too. [posted by S. Y. Affolee on 3:26 AM : Wednesday, March 23, 2005 Tangled Bank #24 Welcome to the twenty-fourth edition of Tangled Bank and boy, do we have a live one! There's everything from visual perception to DNA repair and evolution to salamanders. The sheer variety of science articles and links surely live up to this weblog carnival's title. As I was contemplating on how to order the submitted entries, it struck me how boundary-less science really is. Aristotle, the "father of biology," may have been fond of categorizing everything, but disciplines don't exist separately in a vacuum. Things meld and mix to become something that is both like the previous things as well as something completely new. I suppose one could put things up in neat little rows like an unimaginative librarian, but subjects are more like moldable forms than cubbyholes. So I submit the following four forms to help navigate this week's entries: Many of the entries are interdisciplinary in nature and could fit in more than one subject, but I have taken the liberty to group what I saw as similar. I recommend all of these links, but I also realize that it's not so easy to digest everything in one sitting. So feel free to use those four internal links to bookmark your reading. Living Do you remember one book that you loved as a child? Bora at Science and Politics reminisces about an early 1900 children's book called "The Prince and His Ants" and points out The Mighty Ant-Lion which has the curious habit of digging holes during the full moon. At Creek Running North, Chris photographs and muses about a creature that you might run across on a nature walk or in your own living room (!), Aneides lugubris, the lungless salamander. In A Tale of Two Teals, Mike of 10,000 Birds and his Core Team go "twitching" for teals and discuss the two subspecies of duck, the American and Eurasian Green-winged Teals. Lauren at Feministe is fascinated that scientists have found evidence that some herrings communicate via flatulence and On Herrings: An Honest Question muses about the similarities between that and male blogging practices. John Forth submits Fear-No-More Zoo, a place in California that provides "people with the opportunity to appreciate non-humans in their natural state of Contemplation." Jennifer Forman Orth at the Invasive Species Weblog took a picture of Knotweed and Tulips as two cultivated plants with very different temperaments. Geoffrey Palmer, a New Zealand official, announced that the international moratorium on commercial whaling may be dumped spelling Bad News for the ocean's ecosystem. Josh at Thoughts from Kansas explains that whaling will deprive ocean bottom communities, such as the ones at ocean vents, of valuable influxes of organic material. At RoguePundit, some people are playing a strange kind of Exotics Politics by claiming that introduced exotic species in Oregon such as the turkey shouldn't be called exotic because scientists found 7,000 to 13,000 year old turkey fossils in the region. Dharma Bums takes A Walk on the Beach after it's been pounded by winter storms and discovers some wonderful invertebrate fossils along the Californian coast. Following the mini-theme of fossils, Wolverine Tom is doing some cool Trilobite blogging in which he has compiled some vivid images of the extinct marine arthropods. Over at The Frontier Channel, Richard Leis does An Interview with Geologist Jay Quade, a University of Arizona professor who is looking for hominid fossils in Ethiopia. The interview is in four parts: Part I | Part II | Part III: Tools of Time | Part IV: Geology, Famine and War. For the tech-savvy, the entire interview is also on podcast. The Evolution Project points out the discovery of a new predatory shrimp in New Fairy Shrimp Species and remarks on the diversity of species and the need to catalogue new species. Changing Evolgen writes an essay on the origin life. It's one of biology's "great unsolved mysteries" and most of today's research is dedicated toward cracking the origins of RNA and the genetic code. Gird your loins and take a deep breath as we plunge into some math in The Recipe for Complexity: A Pinch of Simplicity. DarkSyd at Unscrewing the Inscrutable illustrates how creationists are wrong to assume that complex systems can't be reduced to a couple of rules by pointing out that simplicity can lead to complexity. In Less than the sum of the parts, the author of Frankenstein Journal takes exception to a New Scientist article in which Paul Davies argues that it is impossible to make a reductionist model of the universe. Pat Hayes posts Darwin and Hitler: An Exchange With Richard Weikart over at Red State Rabble. Are scientists really at the root of evil, as Weikart seems to think, or is he just really mixed up about science and politics? On a lighter note, R.J. Riggins submits Things Creationists Hate which includes (among numerous things), cute little bunny rabbits, male nipples, snowflakes, and pi. Lots of DNA doesn't necessarily mean increase in complexity. In Fugu!, David of Science and sensibility describes the usefulness of the puffer fish genome which is more than seven times smaller than the human genome yet is able to produce a perfectly functioning (as well as tasty and deadly) fish. All about Steinsky explains how memes are more like genes than you think. Just as bad genes detrimental to the survival of an organism are selected out leaving the good genes, human ideas also go through the process of selection--theoretically leaving the good ideas to be passed down. Chromosomal Evidence for Human Evolution is another rebuttal to creationist claims. Cogito, Ergo Sum...Atheos describes experiments which show one piece of the story in the evolution of the human Y chromosome. On the other side, in the Evolution of the X chromosome, Pharyngula notes a recent Nature article summarizing the X chromosome sequence and comments on the interesting evolutionary history of the X and Y chromosomes which have traveled a decidedly different path than the rest of the autosomes. How did vertebrates get the ability to generate receptors that can recognize any protein or similarly sized molecule? Dr. Andy explains in Evolution of Adaptive Immune Response that the RAG genes, which are critical for recombination to create antibodies and receptors in B and T cells, may have derived from parasitic "jumping DNA" called transposons. At Keats' telescope, Gaw3 is "Alu" about translocations. Recent research show how a type of repetitive DNA called Alu sequences can influence whether DNA is repaired by non-homologous end joining (simply sticking the DNA break points together) or single-strand annealing (using one strand of DNA as a template to fix the new junction). Healing Orac at Respectful Insolence continues his thoughts about wearing two hats. Unlike basic research scientists, the clinician researcher must somehow find a balance between running a laboratory and a medical practice. Who do you trust, a young or an old doctor? Conventional wisdom says that an older doctor would have better skills and more experience, but the Hospice Blog indicates a Medscape article and cites anecdotes that younger doctors may in fact provide higher quality of care because older doctors are more entrenched in the more "traditional" methods. Living the Scientific Life has an excellent three parter on avian flu. First off, Is Avian Influenza THAT deadly? A Nature publication claims that H5N1 is more widespread than previously thought, but that also means that mortality rates would be lower. However, this might only add to the Public Confusion Surrounding Influenza due to widespread misunderstandings of the cause, mechanism, and symptoms of disease. Here's also a primer on influenza and How Its Biology Affects Vaccine Production. Speaking of vaccines, with avian influenza a high priority in public health what sort of antiviral drugs to we have now in our medical arsenal that can help combat the disease? Effect Measure describes a neuraminidase inhibitor and asks how oseltamivir (Tamiflu) works (and does it?) Trish Wilson writes about an ebola-like hemorrhagic fever outbreak in Angola. Unlike Ebola, this disease is striking a significant number of children. Thinking At the Tales of a MD/PhD student, the author muses about a New York Times article and the possible therapeutic uses of the brain scan in Neuroimaging in Psychiatry. Dr. Charles has a conversation with one of his patients in The Color of One's Life. A color-blind person may not perceive colors the way the rest of us do, but that doesn't mean that they completely lose out in the visual world. Over at Musical Perceptions, Scott Spiegelberg tells how those Catchy Tunes (or more annoyingly, those tunes that get stuck in your head) is evidence of auditory imagery--that we can imagine music without an outside stimulus. Synaesthesia is the nifty ability to associate something with one of the senses such as associating numbers with colors or sounds with taste. Mind Hacks proposes to Test Your Synaesthesia through some easy do-it-yourself tasks. Cognitive Daily explains some experiments appearing in Nature that visual skills can be improved by playing video games. But those same violent video games may be linked to aggression. Finally, (but definitely not the least!), She Flies With Her Own Wings submits a marvelously detailed abstract, The SCN acts as an ensemble of individual oscillators. Neurons in an area called the suprachiasmatic nucleus act as a biological clock in the mammalian system which leads to all sorts of circadian activity. I would like to thank all the contributors--both new and returning--for making this a most fantastic edition. The next Tangled Bank will be held on April 6 over at Respectful Insolence. You can submit your science related posts to Orac, PZ Myers, or host@tangledbank.net. [posted by S. Y. Affolee on 3:00 AM : Tuesday, March 22, 2005 Revealing Genetic Ancestry Because of mitochondria's unique properties of possessing a genome and maternal inheritance, we can all trace our matrilineal ancestry all the way back to one woman--"Mitochondrial Eve." (This is somewhat of a misnomer though. The name "Eve" has too many cultural and religious connotations which makes understanding exactly who she is confusing. See Krishna Kunchithapadam's essay on the topic.) Bryan Sykes discusses this idea in The Seven Daughters of Eve, a popular science book ranging from the expository to the imaginary. The first two-thirds of the book is grounded in the research. The story itself begins with Sykes' scientific coup of extracting mitochondrial DNA from the Iceman, a frozen perhistoric corpse found in the Italian Alps. From there, the author jumps into an explanation of DNA and genes. Because genes resulting in relatively straightforward traits like the ABO blood group are terrible clues for trying to determine human ancestry, Sykes settled on the mitochondrial genome. But can mitochondrial DNA (mtDNA) be used as a gold standard to determine descent? One possible problem is that mtDNA might mutate too quickly, which would render any attempt to peer into the past useless. Sykes and his colleagues sequenced mtDNA from the fast breeding hamsters and proved that mtDNA didn't hypermutate since they were able to trace all pet hamsters back to a founding matron. From there, the author was able to undertake other applications of mtDNA technology--identifying the last Tsar of Russia, tracing the descent of Polynesians to East Asian ancestors, proving that the Neanderthals did not contribute to the genomic makeup of modern humans, and discounting an earlier theory that all Europeans are descended from invading farmers who displaced the local hunter-gatherers ten thousand years ago. From his research on European ancestry, Sykes and his colleagues discovered seven different "clans"--which meant that virtually all Europeans can trace their matrilineal descent to just one of seven women. There are, of course, other "clans" for the populations throughout the world and in turn, all of these clans can be traced back to the "Mitochondrial Eve." But Sykes doesn't dwell too much on that conclusion. The last third of the book is devoted to the imaginary lives of the seven daughters of Eve and reads more like prehistorical fiction than science. There's an obvious disconnect between the first two-thirds and the last third of the book which I found both odd and disconcerting. But as Sykes observed at people's reactions to finding out that they were descended from the remains of prehistoric humans, people want to feel connected. This may seem irrational, but if you want to popularize science, a certain bit of sensationalism must be allowed. I might still read the book if all it consisted of was a rehash of Science papers, but non-scientists want all the involved human drama. So even if some critics might decry Sykes for being a bit egomaniacal in his book--we wouldn't know how human the search for the seven daughters was without Sykes' petty rivalries, angsty waiting for results, and almost-arrogance of vindication. That part of the book was interesting. However the last third of the book was pure fantasy and probably should have been axed. I'm sure that some people might enjoy envisioning their prehistoric ancestors, but this is one of those times where the author should have left the imagining as an exercise for the reader. [posted by S. Y. Affolee on 3:23 AM : Monday, March 21, 2005 Yet Another Reminder! Tangled Bank is coming up in two days and it's definitely shaping up nicely. But there's always room for more entries--so if you haven't submitted that biology/science/nature/medicine/just some random musing about cockroaches taking over the world post--do it now! You can send submissions to syaffolee@gmail.com, host@tangledbank.net, or pzmyers@pharyngula.org by March 22 (at midnight EST you'll definitely make it, midnight PST at the latest) with the words "Tangled Bank" somewhere on the subject line. For those of you who have already submitted--thanks!--but if you haven't received an e-mail reply from me, please send your submission again. Addendum: I edited the times because the AM/PM thing can get confusing. [posted by S. Y. Affolee on 8:04 AM : Bits Yesterday, I finished The Seven Daughters of Eve by Bryan Sykes. I suppose one could say it's terribly old news (it was published in 2001)--but it's non-fiction for the masses and different rules apply. I will probably babble about what I thought about the book tomorrow. Grid Game. (via Monkeyfilter) I find that you can move more tiles if the initial tile you move will touch two other tiles. Lately, I've been listening to Enigma's 2003 album Voyageur. Yeah, call me a sucker, but I like electronica bordering on New Age. The song "Boum-Boum" is definitely catchy though. Reminds me of the Venga Boys single "Boom Boom Boom Boom!" [posted by S. Y. Affolee on 3:24 AM : Sunday, March 20, 2005 Housekeeping, Of Various Sorts Ah, bread baking. The overly analytical would perhaps delight in explaining the biology and chemistry of rising yeast dough, but sometimes it's just nice to do something. Stirring a tablepoon of yeast into warm sugar water, watching it rise, mixing in the flour. Manual work can have a bit of zen too. Today I'm making chocolate and hazelnut bread without use of any written recipes. Cooking and baking are strange alchemies--I experiment never knowing how things will turn out. (Experimenting with socks and now with food--what will she experiment with next? you might wonder.) I cook out of necessity. Most of the time. But I always feel somewhat uncomfortable with this sort of domestic chore because I tell myself, often, that I'm not domestic. Cooking is like a slippery slope--people will start to think that I have the proclivities of a housewife. I have no temperament to be a housewife. I'm a loner and I brood too much. I do housework wishing I was doing anything but. There's a saying--women are cooks but men are chefs. I'm not a cook or a chef. I'm just an impulsive and unpredicatble mixer-upper using myself as a guinea pig. Yesterday, I fiddled with some minor stuff on the site. The most noticeable change is the link to a list of science articles that I've written previously. This is primarily an aid for all those people googling science-related terms and then ending up in my archives with no clue to which entry to look for. It's also a list for anyone who just wants to skip all my personal kvetching and get to the science posts. I've also updated my geek and blogger codes on the about page (sorry, I'm not ready to update anything in the "real life" department). GS/O is probably more appropriate than GFA/S/TW as previously, I hadn't figured out how to indicate my writing hobby with the codes available. Anyways, I think the geek code is far too oriented toward computer-related stuff. Why just concentrate on the computer sciences when there are a multitude of other disciplines? For the blogger code, B7 became B9--a definite indication that I should have updated it sooner. There's no code after B9 so does this make me a blogging geezer? Unconscious Mutterings
[posted by S. Y. Affolee on 4:30 AM : Saturday, March 19, 2005 Cold Feet For the past week, I've been experimenting with not wearing socks at home. My conclusion--I don't like it. My toes get cold and I just feel colder in general. Maybe it's the weather. (Although it has been getting warmer--warm enough for some people to break out the shorts.) A post-doc and a graduate student have started a television show where they play "cupids" trying to match up lonely single people. It sounds like a dating game type show with interviews and the like. But knowing those two, I wonder if they're really sincere about matchmaking or if this is just a big set-up for a hilarious prank. I remember seeing a couple episodes of the Love Connection with Chuck Woolery when I was younger. Tacky sets. Sappy host. Those really strange video clips of the three contestants vying for the bachelor or bachelorette. I wasn't sure if any of these people were serious or just acting--although I have to say that the big highlight for me was when a contestant turned out to be a real looney on the video clip. I didn't really care if a connection was made or not--I watched the show for the giggle-inducing weirdness. (Why am I even talking about TV shows? I've sworn off TV shows. I don't know anything about TV shows, especially for the past couple of years. I don't even own a TV.) Lately I've been taking the morning shuttle (some people who work at the medical center and say that 9 AM is extremely early would think that my schedule is absolutely insane) and there are two very loud and talkative ladies who are also passengers. Of course, one could not help but overhear them complaining about men who only ask "skinny sexy girls" to dance rather than the "fat wallflowers." And I'm thinking, well what do you expect? Guys do not act like roulette wheels and pick up girls at random. (There is the option of asking a guy to dance, but I think most women avoid that for fear of rejection.) For some reason, this is reminding me of the time I visited a French discothèque. I can't remember what the heck I did there though. [posted by S. Y. Affolee on 3:25 AM : Friday, March 18, 2005 An Assortment of Stuff Science Fiction Author Andre Norton Dies. Wow. I did not know she was living a little over thirty miles from where I grew up. RIP. Batman: New Times. A Batman animation--with legos. It's just...weird. How emotional and naunced can you get with legos anyhow? Fifth Annual Weblog Awards. As usual, the big names won again. But despite that--some of the prizes are better than others, which I find somewhat unfair. Registry of Standard Biological Parts. Hehe. I can't help but say this is like legos for molecular biologists. Flowers in Ultraviolet. Flowering plants display different markings under UV light--but that's because they want to attract pollinating insects that can see in that light range. This nifty site lists the ultraviolet features (as well as pictures!) of a whole bunch of flowers. No Word for Sex. Language Log takes exception for novelist Frank Delaney's remarks that the Irish have no terms for sex. In fact, there are a lot of words. 13 things that do not make sense. Eh, I think everything will be explained rationally, eventually. The list includes stuff like the placebo effect, homeopathy, and a bunch of physics puzzles like dark matter and cold fusion. We're Not Worthy! We're Not Worthy! Hm, interesting comment--that if women bloggers want to get noticed, they should blog about politics, technology, and business--and that the subject matters, not the quality of the posts. So I guess no one will take me seriously since I don't blog on those subjects. Venetian Grinds. (via Reflections in d minor) Discovering that Venetian paint also consists of glass may explain the paint's unique optical properties. A rare screening reveals the hidden Dr. Seuss. The children's author famous for Green Eggs and Ham and other silly rhymes also made "racy and suggestive" animated films. [posted by S. Y. Affolee on 3:23 AM : Thursday, March 17, 2005 A Reminder The next edition of Tangled Bank is coming up in less than a week so if you have a great science-related post you'd like to share, don't hesitate to submit! You can send submissions to syaffolee@gmail.com or host@tangledbank.net or even pzmyers@pharyngula.org by March 22 with the words "Tangled Bank" somewhere on the subject line. [posted by S. Y. Affolee on 3:47 AM : The Thursday Threesome: Happy St. Patrick's Day Onesome: Happy-- No matter what's going on in your life, what always makes you smile? I don't want to be a stick in the mud, but there is nothing that will reliably make me smile, especially when things are going badly. Cheery things are liable to make me feel worse. Twosome: St. Patrick's-- St. Patrick's Day is March 17th. Do you celebrate and wear green? Drink Green Beer? Ignore it? Aside from forced grade school hoopla, no I don't celebrate it. Seems somewhat appropriate as I'm not Irish and I don't know any Irish people well enough to get invited to their parties. Threesome: Day-- What day of the week is your busiest? Tell us about your schedule... The weekdays are busier than the weekends. As to which weekday is busiest, I can't tell you. It varies. [posted by S. Y. Affolee on 3:44 AM : Wednesday, March 16, 2005 Linkage Carnival of the Vanities #130. An interesting compendium of links from the oldest carnival with the loose theme that the blogosphere is a "men's club". The host observed that there were a dearth of female bloggers who submitted posts but that the diversity of viewpoints made up for the diversity of bloggers. I'm not sure I quite agree with that, but I do know that for a lot of people, they don't want to look beyond their little blog cliques. Bloghercon conference proposed. Huh. I find the comments interesting--that women prefer to express themselves rather than seeking status like all those top (male) bloggers. Blogging Beyond the Men's Club. A rumination from Steven Levy on why the blogosphere is dominated by all those white guys. Burningbird (via Insiteview) replies that this is the fault of all those ranking tools and blogrolls. Ten Reasons Why Blogging Doesn't Matter. Ah! Finally an article to downplay all this weblog pontificating. You Call That Art? In some respects, I don't agree with this article. Their notion of art is elitist. My notion of art coincides with "creation". If you created something, then it can be called art. Whether it's bad art or good art is completely subjective. Brain of the Blogger. They say weblogs promote critical thinking. Depends on how you use it. Kiddies who use weblogs as a new-fangled tool for diary writing (with all caps, misspellings, and internet slang galore) aren't helping themselves. Did Black Death boost HIV immunity in Europe? Conceptually, it makes some sense. If both diseases exploit the same thing in the immune system, the Black Death may have created a genetic bottleneck during the Middle Ages so that now there's a prevalence of certain alleles in the European population that confer resistance to HIV. [posted by S. Y. Affolee on 3:22 PM : The Deadly Wall When we usually think of immune defenses, we turn our minds to the B cells and T cells, the macrophages and neutrophils, and those antibodies and antigens. Too often, we get mired in the details and we forget our biggest ally in the fight against nasty microbes--the skin. But what's so great about the skin besides being the thing separating us and the outside world? Well, think of it this way: the skin isn't just a passive barrier keeping things out--it's an active player of the immune system. The skin is like the Great Wall that's been booby-trapped like nobody's business. Characterization of these booby-traps began in the late 1980s when Michael Zasloff discovered that the skin of Xenopus laevis, the African clawed frog, produced antimicrobial peptides called magainins. Due to their unique biochemical properties, magainins are able to insert themselves in the microbe membrane to form a pore. The pores alter the permeability of the membrane, like punching holes in a dam, and cause bacteria to lyse. The mammalian skin produces two kinds of antimicrobial peptides, cathelicidins and defensins. Cathelicidins were originally found in analyses of skin wounds. In humans, the peptide is produced by skin cells (keratinocytes) and found in sweat and saliva. At the site of inflammation, cathelicidins not only kills microbes but also acts as a signal to recruit immune cells to the site of infection. Defensins act similarly to cathelicidins and are known to be produced by the gut's Paneth cells (previously discussed here) and skin cells as well. A third class of antimicrobial peptide is granulysin which is made by T cells and brought to the skin. Aside from killing bacteria and fungi, granulysin has the interesting property of killing tumor cells. Exactly how important are these naturally produced antimicrobials? Very important. Mice deficient in cathelicidin production are susceptible to bacterial infection. In clinical studies, patients with chronic inflammatory skin disease were found to produce significantly less cathelicidin and defensin. In Nature Immunology, Glaser et al. discovered yet another protein that contributes to our skin's antimicrobial activity. These researchers observed that when they innoculated E. coli on the fingertips of healthy volunteers, these bacteria rapidly died. The obvious question was--what in our skin is specifically killing off these bacteria? They took skin fluid and skin samples from these volunteers, separated out fractions with E. coli-killing activity, and analyzed these samples. Glaser et al. isolated psoriasin, a protein that was originally found in the skin lesions of people with the skin disease psoriasis. The investigators tested psoriasin against a variety of bacteria but found that the protein had specific antimicrobial activity for E. coli. Keratinocytes are stimulated to produce psoriasin when they come into contact with E. coli compounds. The psoriasin itself kills E. coli because it sequesters zinc, an essential nutrient for bacterial growth. One curious observation is that people suffering from psoriasis have far fewer skin infections than one would expect. This is backed up by the fact that they produce psoriasin and other antimicrobial peptides which act like a "chemical shield" that protects them from infection. So our skin is far from defenseless in the war against pathogenic microbes and it will be interesting to see what other "booby-traps" scientists will dig up from the skin. [posted by S. Y. Affolee on 3:29 AM : Tuesday, March 15, 2005 Rowing Towards Headache Oh, how perfectly lovely. My neighbors are such bad examples of domestic bliss. If I weren't already extremely cynical about soulmates and all that gibberish, I'd be throwing up my hands in exasperation now. [posted by S. Y. Affolee on 3:30 AM : Monday, March 14, 2005 No, I'm Not Going to the North Pole Urg. Today is just one of those days when you're running around doing stuff and you don't have any time to just sit and breathe, but at the end of it all, you don't feel like you've accomplished anything. It's really weird being the only passenger on the bus with a driver that looks like Santa Claus. I'm primarily a short story kind of person since I don't have much time and all, but for the past couple of weeks, I've been seriously contemplating writing a novel, editing it, and submitting it to a publisher. I figure if I start writing now, I might have a 100,000-150,000 word rough draft by the end of the year. But first, I must get an idea. [posted by S. Y. Affolee on 3:36 PM : Sunday, March 13, 2005 Some Links and a Meme Moving the Axum Obelisk (via Boing Boing) An interesting article detailing the moving of the Ethiopia's Axum Obelisk from Ethiopia to Italy and back again. Gender bias in IKEA instructions? This is silly, although I think anyone who is offended that a woman is depicted assembling furniture is even sillier. Colorization Using Optimization. Some interesting techniques used to colorize black and white images. Unconscious Mutterings
[posted by S. Y. Affolee on 5:02 AM : Saturday, March 12, 2005 Mucking About Mexican officers brought to book. "Police in Mexico City, one of the most crime-ridden capitals in the world, have been told they must read at least one book a month or forfeit promotion." What an odd, although amusing, project. It would certainly be a change to have cops who can quote Shakespeare and Proust. Snowcat. (via Drawn!) A cute cartoon even though I can't read Korean. Need Some New Luster? Try Rosie O'Donnell's Method: Create It by the Blogful. (via Kottke) This former talk show host really does have a blog. Everyone and their dog has a blog these days but I am somewhat surprised that she decided to use the ol' blogger template. Thiomargarita namibiensis. (via Modulator) Also known as the "Sulfur pearl of Namibia." Ooo, so pretty. Can I please take it home with me? [posted by S. Y. Affolee on 5:27 AM : Friday, March 11, 2005 The Male-Killers There is a certain genre of post-apocalyptic sci-fi which considers the following senario: something catastrophic happens and all the males in the world are killed off. It sounds like a feminist fairy tale or a prurient male dream (that is, if you're the last man left alive). But is this just a wild, impossible fantasy or is there any basis in reality? It all starts out with the humble fruit fly, Drosophila, known to biology students as the workhorse for genetics studies. One species of the fly, Drosophila willistoni, is found in a variety of tropical places in the new world. Due to this species' adaptability and possession of the greatest chromosomal polymorphism among Drosophila, it is an ideal candidate for studying population genetics and evolution. In the 1950s, some female D. willistoni caught in the wild exhibited a very strange trait--all of these flies' progeny were female. Virtually no male flies were born. Donald F. Poulson, an important Drosophila embryologist since the 1930s, worked with these flies that had progeny with skewed sex ratios. It was first thought that this strange trait was hereditary. However, Poulson showed in the late 1950s that this wasn't the case--a skewed sex ratio was due to an infectious agent and not a genetic trait. When material from dying eggs that originated from flies with the skewed sex ratio condition was introduced to female flies without the condition, those female flies were converted to that condition. In 1960, Bungo Sakaguchi in collaboration with Poulson observed that the haemolymph of D. willistoni females producing only female progeny was teeming with microorganisms that were identified as spirochetes. Later, the bacteria was correctly identified as a member of the spiroplasmas.  Spiroplasmas are helical microbes originally discovered as plant pathogens, particularly for corn and citrus plants. For the periwinkle plant, it is known that spiroplasmas are transmitted through an insect vector, the leafhopper. Many spiroplasmas reside harmlessly in the insect gut, but some are outright insect pathogens. S. melliferum and S. apis are honeybee killers. The spiroplasmas found in D. willistoni, later named Spiroplasma poulsonii after the original discoverer, are also killers--although they kill in an extremely peculiar way.But why would male-killing bacteria, well, kill only males? For these bacteria, it would be a great opportunity for them to propagate themselves by also infecting the host's offspring. They can easily do this by simply "hitching a ride" in the egg--so a mother can infect a daughter who can in turn infect her daughter and so on down the line. But what happens with the male? He's a dead end. Sperm, compared to eggs, contain very little cytoplasm so the bacteria cannot hitch a ride to the next generation. In this case, the bacteria kills the male so he becomes extra fodder for his female siblings that can infect future progeny. The male-killing bacteria aren't just confined to S. poulsonii. Rickettsia are male-killers in ladybird beetles. More famously are the male-killing Wolbachia bacteria which are distributed among many insect species. In some cases, the bacteria's effect on the host is so extreme that the insect cannot reproduce sexually any more. In the imagination, this has led to fantasies of female-dominated worlds as mentioned in a recent New York Times article, but for humans, this may as well be fiction. It may be normal for 5%-50% of female insect hosts to be infected with male-killing bacteria, but these bacteria have not been found in other animals. And why not? You might not realize it, but insects have a primitive immune system and most of the time, it's quite effective at clearing bacterial infections. However, male-killing bacteria try to exploit any weakness of the insect immune system. Wolbachia, for example, simply evades the immune system by staying in an intracellular niche which the immune system has no access to. Spiroplasma, however, can infect all parts of the host with impunity. The insect immune system works by detecting components unique to a bacterial cell wall, but Spiroplasma lacks those components, thus rendering them invisible to the immune system. One question that has been largely unanswered is, how do the bacteria know they're in a male embryo or a female embryo? A recent Science paper by Veneti et al. tries to answer it. In Drosophila, the sex of the fly is determined by the ratio of X chromosomes to autosomes. There are several "signals" or proteins which help count the chromosomes (thus leading to correct sexual development) by binding to the X chromosome. The researchers decided to generate fly strains with mutations in the genes for these proteins, infect them with Spiroplasma, and count the surviving male progeny. In mutants for the dosage compensation complex (DCC), there was a significant increase in male survival. This means that Spiroplasma must be targeting males via this DCC protein. So should we start wearing t-shirts with the slogan, "Save the Males"? Well, maybe--if you're an entomologist. [posted by S. Y. Affolee on 3:42 AM : Thursday, March 10, 2005 The Thursday Threesome: A Somewhat Aimless Hodgepodge (apparently inspired by one of my previous post titles) Onesome: A Somewhat-- We're in somewhat of a lull between holidays. Are you decorating for St. Patrick's Day or going right for the Easter season. ...or are you just hanging on for margaritas by the pool? Despite it being around 6:30 in the morning, I think the margaritas would be better than the whole holiday regalia. So yeah, I suppose for the next couple of months, one could say I'm in a lull. A lull in which I'm just hanging by my shoestrings. Twosome: Aimless-- Aimlessly waiting for Spring? What are you just waiting to do once the weather clears up? I am not sure. At this point, I don't want to speculate needlessly. Definitely something that will let me keep some sanity. Threesome: Hodgepodge-- Where's the hodge podge collection at your place? You know, that drawer or shelf or cabinet where 'all the other stuff' ends up when there's no place assigned to it. Yeah, that one < g >! A closet. Seven Mistakes Superheroines Make. I think the main point is that people only like their superheroines to be super. They don't want these fantasy women to display any weakness--they don't want them to have human foibles. I guess it's because people don't want reality. There are already too many whiney women in the real world already. How To Get Rich & Famous By Blogging At Work. More like a primer to get fired. Happiness is back. "Growing incomes in western societies no longer make us happier, and more individualistic, competitive societies make some of us positively unhappy." There's another bit in the article about how ranking and happiness goes hand in hand. I've known people who were obsessed with ranking, but I wonder, what the is the point of it all? Even if you were the best of something, it isn't going to make people respect you more as a person. Living Jewels. "Evolutionary design photography." Wonderfully vivid photographs of exotic beetles and moths. Generation Debt: The New Economics of Being Young. All about the depressing job prospects for humanities graduate students in academia. [posted by S. Y. Affolee on 3:27 AM : Wednesday, March 09, 2005 Tangled Bank #23 Ah! Another Tangled Bank is upon us, this week hosted by Living the Scientific Life. So go on, click that title link and spend the rest of the day reading some excellent science blogging. And least we forget, this is an extra special edition because it also happens to be the birthday of Tangled Bank's founder. So don't forget to hop on over to Pharyngula and wish the ol' coot a happy birthday. As for the next edition of Tangled Bank, I'm hosting it in two weeks. So if you have a post about biology, medicine, science in general, or just the general workings of the natural world that you want to share with the rest of us, send it to syaffolee@gmail.com or host@tangledbank.net by March 22 with the words "Tangled Bank" somewhere on the subject line. And I assure you, no Ph.D.s or big words are necessary to get accepted. [posted by S. Y. Affolee on 7:44 AM : A Dream Last night, I dreamed that Maggie Smith gave me a package wrapped in brown paper. I opened the package and found a scrap book filled with bloggers' secrets and I thought, "Oh, this is good. I hope this will still be here when I wake up from this dream." The package also contained Hello Kitty post-it notes from a pen pal I've never even heard of. Imagine my disappointment when I woke up and there was no book to be found. [posted by S. Y. Affolee on 3:44 AM : Tuesday, March 08, 2005 Road To Somewhere, Part A: 3 Down, 0 To Go This morning, it rained. And then the rain turned into a snow storm. To be honest, I don't really pay attention to the weather any more. I just prepare for the worst and try to ignore all the howling and screaming--both literal and metaphorical. I only knew there was a snow storm because I had to go out to the post office around lunch time. The last time there was a blizzard, it was the end of a very horrible week and I nearly got my car towed by a bunch of anal-retentive people. Did I not tell you about how I saved my car from tow-truck driving burly men? Oh I didn't? Must have slipped my mind. I originally wanted to title the post "Road to Happiness, Part A: 3 Down, 0 to Go" but I realized quickly enough that I'm not sure the road I'm currently digging out of the snowdrift is really the road to happiness. No one really knows what the road to happiness is and if someone does, well, that doesn't mean I should just merrily skip down the same path. Different individuals and circumstances require different directions. But I do know the new path leads somewhere--I'm just not sure where yet. As for the old road, I've had more than one person point out to me that the possibility is high that I'd end up an eternal drudge. In Part A, three is a very significant number. For certain people, they'd understand immediately why I am referring to the number three. For everyone else, I'll just say that in my case, this particular number has nothing to do with religion. I would have been glad if I didn't have to do Part A and just skipped to Part B. Some people might think that Part A is a piece of cake--I think it's quite hard. Part A requires a balancing act between tact and agressiveness that I know I'm not that good at. But that is over with and I'll try not to think about it too much (my subconscious, however, might make an exception), and it is onward to Part B. I finally started paying attention to the Site Meter statistics. I've had the counter on the site for quite a while, but I never really looked at it before because for some reason, the privacy option was on and I had forgotten my password. It turns out that Extreme Tracking is seriously undercounting the number of visitors that this site gets. And didn't I read somewhere else that Site Meter itself undercounts? I'm more popular than I thought I was--and that's a bit scary. So for all those extra people I didn't know who are reading this site, uh, hi. [posted by S. Y. Affolee on 1:11 PM : But I Want A Golden Ticket I was reading this article and it got me thinking about how foreigners and immigrants view opportunity and America. My parents had recently visited Vietnam to celebrate my paternal grandmother's birthday. I've only met my grandmother once--a diminutive, but tough old lady who enjoys chain-smoking. I couldn't communicate with her since I don't speak Vietnamese and I can only imagine what she thinks of me. Anyways, my Mom shared some "village gossip" with me, so to speak. I didn't really care for the gossip, but one particular tidbit did stick in my mind. She recounted the story of a couple who had a daughter with a rare type of throat tumor. An American doctor happened to be doing a stint in the area and fortunately, he offered treatment to cure the girl. The doctor also offered the couple to bring the girl to America where other doctors could study the rare disease. The couple refused the second option. In response to the story, one of my Dad's cousins said that if the doctor had offered to take one of his daughters to America, he would let her go because there would be more opportunity for her there than the rural and mostly poverty-stricken backwoods of Vietnam. My Dad's brother, however, said that he agreed with the couple's decision. Exactly how much does background or personality influence one's decision about that particular problem? My Dad's cousin has never left Vietnam so perhaps he views other places as a "greener pasture." My Dad's brother, however, left Vietnam for college and eventually settled in the United States. Perhaps my uncle still harbors some nostalgia for the "motherland" or maybe he just likes to keep a close eye on his kids (I don't think he let my cousins apply to college out-of-state), but I am not privy to his thoughts. And what of my Dad? If I lived in Vietnam and got a chance to go to America, would he let me go? I think yes--in some ways, he's much more of an optimist and is willing to let his children go off. Even now, when I can't seem to see past my shuffling feet, he tells me I have so much opportunity to start anew. Yale psychologist designs test, a challenger to the SAT. Also see a response to the article at Number 2 Pencil. Personally, I would not want to be assigned a test score for making up cartoon captions. Guys Don't Link. (via Pharyngula) Burningbird has an epiphany--the current bruhaha over autolinking has a very Freudian explanation. [posted by S. Y. Affolee on 3:28 AM : Monday, March 07, 2005 A Somewhat Aimless Hodgepodge I've got to find a different time to do my laundry. Before 8 AM on a Sunday, the laundromat is filled with too many people. One would think that most people would be sleeping in. Is Batman Nuts? Whoa. This could be a whole thesis or something. Adventures of an Occult Investigator. And I thought this particular occupation was mostly confined to fiction. So I was glancing through a bunch of microbiology journals and this title caught my eye: Molecular detection of Bartonella spp. in the dental pulp of stray cats buried for a year. Way weird. Actually, it isn't so weird if you think about it. Bartonella henselae is the bacteria that causes cat scratch disease or CSD in people. The researchers were just trying to see if they could amplify Bartonella DNA from dead cat teeth. But why teeth from dead cats and not teeth scrappings from live cats? Well, the researchers wanted to develop a method that they could use to detect bacterial DNA in cats that have died centuries ago so they could trace Bartonella as it evolved with its feline host. Snack Food Chinese Zodiac. (via Monkeyfilter) I am Cheese Puff, Taker of Souls and Destroyer of Dreams. Fear me. What's Special About This Number? I had to look up 1111, but all it said was that it was a repdigit. Man, I feel gipped. The Eggcorn Database. Arg! If I was a grammar nazi, all those misused words would make my head implode. [posted by S. Y. Affolee on 3:24 AM : Sunday, March 06, 2005 The Evolution of Powerhouses The endosymbiont theory, originally proposed by Lynn Margulis, says that mitochondria are the decaying remenants of an aerobic bacteria that lived inside one of our eukaryotic ancestors. Some evidence for this theory include the facts that mitochondria synthesizes its own proteins, contains its own genome, and replicates independently of the host cell. But surely, this sort of thing couldn't have just happened once. One would think that with all the symbiotic relationships in the natural world, eukaryotic cells would have a bunch of different organelles derived from long ago endosymbionts.  In 1973, two Trichromonas researchers--Donald Lindmark and Miklós Müller--were studying the cattle pathogen Trichromonas foetus (the human version, Trichromonas vaginalis, is an STD). Trichromonas species are parasitic flagellate anaerobes and at the time not much was known about this microbe's metabolism aside from the production of waste products, acetate and hydrogen. Lindmark and Müller were characterizing the enzymes in the hydrogen production pathway when they noticed that these enzymes were concentrated in a "subcellular particle" that did not resemble any of the other organelles in the cell. They named this new organelle the "hydrogenosome."The hydrogenosome is a special organelle found in eukaryotic microbes as well as some fungi that like to live in poor oxygen environments. In order to generate energy for the cell, it oxidizes pyruvate and releases hydrogen and produces ATP. Sound familiar? In fact, hydrogenosomes have an uncanny likeness to mitochondria--not only do both organelles produce ATP, but morphologically they are similar--they are both surrounded by a double membrane and they both compartmentalize their different metabolic functions. The only big difference between the two is that hydrogenosomes use the anaerobic (fermentative) pathway while mitochondria use the aerobic pathway (Krebs cycle). So is it possible that hydrogenosomes and mitochondria are related? Both of these organelles multiply independently of the host cell and anaylses of hydrogenosome associated proteins and mitochondria associated proteins show that both have similar functions. But while mitochondria have their own genomes, the hydrogenosomal genome has been quite elusive. Experiments aimed at Trichomonas or anaerobic fungi have failed to turn up significant amounts of hydrogenosomal DNA which, understandably, has made it hard to determine what sort of evolutionary relationship exists between the two organelles. A recent paper in Nature by Boxma et al. reports success in finally isolating a hydrogenosomal genome. The researchers turned to a different anaerobic microbe, Nyctotherus ovalis--a resident of the termite hindgut. Analysis of the hydrogenosomal genome of N. ovalis showed that it had significant homology to that of mitochondrial genes. Further examination of organelle associated proteins revealed that the hydrogenosome had many of the proteins that were associated with mitochondria except for the ones involved in aerobic respiration. From this data, perhaps the hydrogenosome is an evolutionary precursor to mitochondria. Right now, it's still too hard to really tell if mitochondria and hydrogenosomes are related or the descendants of two different endosymbionts. There are plenty of hypotheses floating about though. The Hydrogen hypothesis says that the host cell engulfed a hydrogen-producing bacterium because it needed hydrogen. The Syntrophy theory says that a hydrogen-producing bacterium and a second bacterium that was the precursor to the mitochondria were engulfed together. Another theory, the detoxification hypothesis, proposes that aerobic bacteria were engulfed by the anaerobic host cell when there was a sudden increase in oxygen levels, or "oxygen spike", around two billion years ago. However, the Boxma et al. paper lends credence to another possibility--that mitochondria and hydrogenosomes have a common ancestor. In this hypothesis, a hydrogen-producing bacteria would be associated as endosymbionts of a eukaryotic host before the oxygen spike. During the oxygen spike, the eukaryotes would be forced to associate with aerobic bacteria for detoxification and instead of forming a new organelle, the hydrogen-producing endosymbiont would fuse with the second aerobic endosymbiont to create a hybrid that would later give rise to mitochondria and hydrogenosomes. [posted by S. Y. Affolee on 3:50 AM : Links and a Meme I really like the local Co-op's chicken terragon salad and I was thinking: when I leave the Upper Valley, that's going to be one of the things I'll miss about this place. They don't make chicken salad like that elsewhere. The Modulator has a meme where you can indicate which states you've visited and lived in. Honestly, I'm sort of fuzzy as to which states I've visited. Maybe one of these days, I'll do a road trip across the U.S. but right now, I have no time. I'm pretty sure I've been to California, Florida, Georgia, Indiana, Kentucky, Maryland, Massachusetts, Nevada, New Hampshire, New York, Ohio, South Carolina, Tennessee, Texas, Vermont, Virginia, and Washington D.C. Obviously, that's not a lot, but then I've visited other countries too, so I am not a total homebody. While searching for pictures of Trichomonas, I came across this wonderful microbe microscopy site which has all the pictures and illustrations listed in handy-dandy A to Z format. It's one of those sites where you say, "D'oh! Why didn't I notice this before?" Here's a nifty blog that I found because they inadvertently linked to me: 3quarksdaily. If you haven't heard of it before, this is a linkfilter with lots of science/art/intellectual goodies. Essential Fonts For Designers and critiques of weblog design on someone's IRC. Who isn't in the middle of a blog template overhaul these days anyway? Unconscious Mutterings
[posted by S. Y. Affolee on 3:45 AM : Saturday, March 05, 2005 Somewhere Else For a couple of minutes, I just want to pretend that I'm sleeping on a beach in the south Pacific under the shade of a ridiculously large umbrella. No one will dare bother me because I'll be surrounded by a small army of trained komodo dragons that will dismember any unruly trespasser. More strange dreams: I dreamed that a famous basketball player was riding at the head of an Olympic parade, but the car spun out of control and the car crashed. I saw the basketball player's head impact a fence and there were blood and brains everywhere. An ambulance carted him off, but in the dream, I knew he had no hope. In a second scene, I was marching with my mother and my sister in a crowd that was all dressed in black. Eventually, we stopped by a cafe to have lunch and my sister ran up the bill with a very expensive sandwich that contained violets. Finally, I was walking alone on a street in some city. I heard voices coming from the ground. I opened a grate and asked someone from below if I could borrow a ladder so I could climb down. They said no. [posted by S. Y. Affolee on 3:46 AM : Friday, March 04, 2005 All Over the Place The old ladies on the shuttle were being mean again. They were making fun of someone's roof which was made of tiles consisting of recycled tires. Some people really need to stop being so snobby. So I was going through the blogroll (mine this time), and I happened upon a post where the author asks why women flirt more with married men. And I had to laugh. Well, I laugh at most angst about social interactions between the sexes because as an outside observer, it all seems so silly. A short while back, I was wondering about online fiction markets, but of course no one replied because I don't have any readers who also happen to be professional fiction writers. John Scalzi talks about the virtue of smaller markets which is more about e-mail submissions than online fiction markets, but hey, close enough. E-mail is certainly easier, but personally, it somehow feels like I'm doing less by sending an e-mail than sending something by snail mail. I also discovered a list of cliched story plots. And I'm thinking, "Are there really lots of writers who write about writers having writer's block?" Instant Messaging is Surprisingly Formal. But they only surveyed college students. What about those high school kiddies? The Commonly Confused Words Test. Woohoo! I'm an English genius (or at least that's what the results said) and I scored higher than everyone else in my age group who has taken the test before. However, fifty-something year olds have hogged most of the high scores. [posted by S. Y. Affolee on 3:25 AM : Thursday, March 03, 2005 Old Ladies and Zombies, Same Difference Why do some people insist on writing "sandwiches" as "sammiches"? Are they trying to be cute or something? "Sammiches" sound like some sort of "delicacy" consisting of pureed roadkill which has been colored pinkish-gray and slopped on a stale bun. On another note, old ladies who ride the shuttle are plain mean. And I don't mean mean as in hitting you over the head with umbrellas or shoving you out of your seat. Old ladies (well, maybe I should clarify--fifty to sixty-something year olds) are almost never physical, but they can give you whiplash with their scathing tongues. Perhaps this is the nature of ladies of a certain age. Amidst the jabbering about their enthusiasm for books that are tear-jerkers, they gossip and complain and put-down people, particularly other women. I don't really care if they gossip and complain--they can say whatever they wish--but what I don't approve of is saying all of these things loudly so that everyone, including the party that is being maligned, can hear it. You would think that women should be better at social etiquette, but really, they're just as bad as men only in a different way. Via Blog Sisters, I found out that March is Estrogen Month and that there is some sort of contest for female blogger of the month. For one reason or other, I simply can't get worked up about any of this. This is just another blogging award thingee where the winners get to pat themselves on the back. And because there are so many of these self-congratulatory things around--I make it a point to never vote in them, even if one of the nominees happens to be someone I like. Yeah, yeah. You might start accusing me of apathy for not voting, but I also think there's a big difference between voting for something important and voting for something stupid. If this were some hot-or-not contest, you'd immediately forgive me for declining to vote. Besides, the winners to blog contests rarely deserve the title "Best of [Anything]." A more accurate description would be "Blog with the Most Hits." Pharyngula had a post on bad teachers in which he talks about this one kid who got arrested for writing about zombies in his creative writing class. This reminded me of some of my not-so-great high school teachers, including a physics teacher who forbade all the students from solving problems with calculus and a biology teacher who thought evolution was a bunch of hooey. Maybe growing up in the Bible Belt had something to do with it, but I suspect I would have encountered crazy teachers regardless of geography. It also reminded me of middle school when I was on this monster streak. Whenever class had a creative writing assignment, I would always manage to sneak in an alien or a sea monster into the story. Now that I think about it, those early efforts were rather Lovecraftian although at the time, I didn't even know who Lovecraft was. I guess I was lucky the teachers just thought me odd and not delinquent. I've never written a story about zombies before though. Maybe I should start one. The zombies would be victims of a weird infectious disease and the outbreak would happen in a thinly disguised New England college in the midst of a snowstorm.... The Thursday Threesome: Routine Scheduled Maintenance Onesome: Routine- Tell us about your morning routine. Do you get up at the same time every day, or do you sometimes hit the snooze button on your alarm clock more often than you should? Do you head straight for the coffee or into the shower? I get up at approximately the same time every day, including the weekends. Lately, one of the things I have been doing in the morning is posting to the blog, but that's after I've gotten dressed, had breakfast, etc. Twosome: Scheduled- What’s on your schedule for the day? Do you schedule every minute or go with the flow? I don't schedule every minute, but I schedule every hour or so to try to get things done. Threesome: Maintenance- What do you do to maintain your sanity each day in this hectic world? Do you find a little time to yourself each day and meditate, or wait until everyone’s tucked in for the night and log on to the computer or settle down with a book? Or do you run off to the gym and maintain your body while maintaining your mind? I try to keep myself busy. [posted by S. Y. Affolee on 3:55 AM : Wednesday, March 02, 2005 More Navigating in Unknown Blog Territory Despite my surly mood yesterday (actually, when have I not been surly? I certainly don't remember the last time I was feeling pleasant), I did appreciate how the snowstorm made the landscape all white and pretty. However, I did not appreciate the shuttle driver (it was a substitute shuttle driver) zooming about on the roads as if it were a balmy summer day. I swear he barely missed a minivan or two along with a handful of pedestrians. It made me reconsider just driving about myself, but I am not so arrogant as to assume that I would be able to navigate the snowy roads any better. Continuing on my blogroll meanderings (other people's blogrolls, not my own, if you remember), I went through a couple of media/culture blogs. They were beautifully designed but talked about subjects way over my head--well, I shouldn't say that since I understand it well enough. I just don't usually pay attention to all that modernist and post-modernist gabble. What I need is something simple but not dumb either. So I'd like to point out Kelly Jane Torrance who occasionally puts up the "Thought for the Day" which are interesting quotes from various culture personnages. After that, another culture blog, a philosophy blog (Yikes, and a really high-brow one too! Or are they just pulling words out of their butt?), a bunch more political blogs (I'm beginning to think some people are right about the blogosphere being made up of mostly obnoxious conservative wingnuts), a dead blog in which the last entry was about the author going to Iceland (I hope he got back from his trip okay--if he got back at all), and more political blogs (and by this time, I'm noticing that they all have really disturbing ads on their sidebars). Another interesting blog--Thrasymachus, which is written by a doctoral student in physics, has bits of science and culture. He has an interview with Gregory Cochran in which he blathers about his "gay germ theory" which states that homosexuality is caused by a virus. I personally think the theory is absolute bull and that physicists should stop mucking about in biology unless they actually plan to do some experiments to test the theory. Besides, the "gay germ theory" sounds like something someone would make up to justify their own homophobia. Then I passed by a blog trying to make money off its audience and then, lo and behold, a blog by a Dartmouth alumnus, Turnabout. What are the chances of that happening? And from there, I discovered an odd site called The Japery--the design aesthetic which for some reason reminded me of Tanith Lee's website--it's like a culture blog with religious overtones. It is also hosted on some sort of religious magazine. I am always leery about religious magazines--is it tongue-in-cheek sarcastic or maniacally serious? I am never sure so I always read such things in such a way that a xenobiologist might look at an alien microbe under the scope. Odd Books. Well, they seem odd, but I'm sure that at the time they were published, they were probably as normal as self-help books are today (not that self-help books are all that normal). New retroviruses jump from monkeys to humans. "Two new retroviruses - the type of virus which causes AIDS - have jumped from non-human primates to people, a new study reveals." Cultured bone offers novel wedding rings. The weird thing is, I'd rather wear a bone ring made out of my own bone rather than someone else's. I suppose you could say this is not that different from an organ transplant, but I'd like to point out one crucial point that makes organ transplants okay and bone rings strangely gruesome. The organs you get from a transplant are still alive. The bone tissue, once it's made into a ring, is dead. (You could also argue that a bone ring is just like keeping locks of hair from your loved one, but I also find that equally odd. Then again, I'm not a particularly sentimental person who likes keepsakes.) [posted by S. Y. Affolee on 3:34 AM : Tuesday, March 01, 2005 Around What a vivid and disturbing dream I had last night. I was in a seven floor library making copies on the ground floor. Then I stepped into the elevator and pressed the button to go to the seventh floor. Instead, the elevator went down to the basement and really weird people started filtering in. Every time the elevator would start to close its doors, someone would force the door open. Soon, the whole scene resembled a nightmarish Hieronymus Bosch painting. It ended with me throwing out somebody's pulverized brains. Anyways, I visited a bunch of blogs by clicking on people's blogrolls semi-randomly (i.e., I delibrately ignored blogs I've heard of before). First I ended up flipping through a string of political blogs. I don't know how people can survive on a reading diet solely about politics--everyone has something to say, but they're all rehashing the same subject as if they're news channels on virtual replay. Then I stumbled upon a couple of mommy blogs, blogs by twenty-something hipster wannabes, southern blogs, and more political blogs. I didn't really see the appeal of those particular blogs, but they all had more visitors than I do, so they must be doing something right. The only exception to all that blogosphere dreck (no offense to political bloggers, mothers, twenty-something hipsters, or southern bloggers--I'm sure there are excellent examples of each but I did not find any yesterday), was the last blog I found Old Hag via a referral from the blog's old Blogspot site which was listed on the blogroll of Daily Gusto. Old Hag is a pithy, but amusing, website filled with snippets about books and culture. I've almost forgotten how fun it is to poke around on random blogs, even if some of them are bad. How to Read and Digest a Book. The only part I really disagree with is the "Read Actively" part where the author advocates scribbling in your textbooks. I'm fine with post-it notes and inserted notecards, but highlighting and underlining and making notes in the margins? Arg. Underwater bike ride to launch students' eight-week crime spree. I say good luck. I hope they don't encounter any deranged maniacs with a puritanical streak who get it into their heads to make a citizen's arrest. Engineers devise invisibility shield. The idea so far says that it can only work on microscopic objects, but still, cool. [posted by S. Y. Affolee on 3:54 AM : |
