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Saturday, September 30, 2006 More Blog Stuff Speaking of the Technorati Top 100... John Scalzi points out that very few of the popular blogs, according to Technorati, are personal blogs. The blog world, he says, is becoming ever more corporate and political and he laments the apparent imminent demise of personal blogs. Well, Technorati is not a very good resource to go to when trying to find blogs that people are actually reading. All it tracks are links. I suspect that there are probably more people reading personal blogs than political blogs but the readership is split between thousands of personal blogs rather than just a handful of political blogs. Blogmatcher, Blogmatcher. Neil Kramer fixes up bloggers with other bloggers they've never read before in a yenta-like fashion. I am somewhat skeptical with all the glowing endorsements in the comments. I figure people are more excited about getting matched in the first place than in any new blogs they are being introduced to. The strong, silent types. A commenter over at Dustbury says he will stop visiting his site if it starts getting a lot of comments. Stop visiting a site when it becomes popular? Hm. I'd say it depends. If the blogger's style changes with the increase in visitors, I'd say yes, I'd probably stop reading too. Otherwise, I can't really see myself being influenced by what other people choose to read. I personally do not comment very often on other people's blogs because I do not feel like the blogger will pay any attention to what I have to say. (Well, most of my visitors never pay any attention to what I write in here--zero seconds spent on one page view, anyone?--but it's a different matter when I'm just scribbling on my own web space.) [posted by S. Y. Affolee on 8:12 PM : Friday, September 29, 2006 Blogging About A Book About Blogs Blogosphere: Best of Blogs by Peter Kuhns and Adrienne Crew. What the heck am I doing reading a book on blogs? This must be the ultimate in navel gazing or something. I mean, I've been doing this for years so I must know what I'm doing, right? Anyways, I was curious so I picked it up. There are basically three sections to the book. The first part is a short history of the blog, the second is the most lengthy which reads more like an abbreviated yellow pages of representative blogs in different topics, and the third part is on how to make your own blog. The authors also added that they had bonus chapters (13 and 14) up on their website (blogsbestof.com) but I got an error when I last tried accessing it. I tried looking it up on Google's cache but I don't see any links up on the cached page either. All I found was a bonus section of chapter 9 which was just an extended list of environmental blogs. I find this sort of silly--why write a book about blogs when the blog about the book on blogs isn't even working properly? As for the meat of the book, I was not surprised by the listings of entertainment, hobby, or political blogs. But parenting blogs? Sports blogs? How popular are those topics in the blogosphere anyway? I'm sorry, but I don't see how you can justify filling up about one-fourth of all the listings with parenting and sports blogs even if a lot of people are interested in parenting and sports. There are tons of other subjects out there. And then there is this section about "faking it", i.e. pretending to read blogs to seem cool. I am not impressed. I couldn't believe that they left out some essential topics. Okay, so these are geeky topics and perhaps the authors thought that only non-geeks would pick up the book--but dang it, blogs wouldn't be possible without geeks. Where are the technology blogs--especially the ones that started it all? The linklogs? The science blogs? (No, sticking a chemist blogger in the middle of a list of medical doctors does not count.) How about the blog carnivals that highlight the best posts in the blogosphere? Photoblogs? Group blogs? But judging from one of the book's blog entries about hoping to include an extra section about bloggers getting married in the next edition--I am not sure whether the authors really quite get it or they're pandering to the clueless (and decidedly dull) crowd. [posted by S. Y. Affolee on 6:46 AM : Thursday, September 28, 2006 Notice Arg. I've just realized that some of these blog comments are being marked as spam by Gmail. You'd think that it wouldn't since Blogger is also owned by Google, but noooo. So if you've sent me a comment and are thinking that I purposefully deleted it--I didn't! So send the comment again and I guess I'll just go rooting through the spam instead of blissfully consigning the whole thing to oblivion. [posted by S. Y. Affolee on 12:00 PM : The Thursday Threesome: Clean Air Act Onesome: Clean-- as a whistle? Can you whistle? When did you learn? ...and with pursed lips or with that finger thing? I can whistle. I taught myself around the age of nine or ten. However, I do not know how to do the finger thing. Twosome: Air-- quality: an issue where you live or not? ...enough to move? It's only bad when there is a wild fire nearby. Then it can get worse than L.A. You can smell the smoke even when you're inside a building. See the smoke. The nearby hills/mountains are virtually invisible. Otherwise, it's fine. Threesome: Act-- Hey, do you 'act your age'? Sure, that's subjective, but what do you think? ...or better yet: what do your friends think? Er, I don't know. I'm a rather reserved person so I suppose it would be difficult for most people to tell. How are you supposed to act like when you're twenty-five? People say that they've been pretty angsty at that age since they were having their "quarter life crisis." But I don't do angsty. [posted by S. Y. Affolee on 7:26 AM : Wednesday, September 27, 2006 Tangled Bank #63 Go read some science-y goodness over at OK So I'm Not Really A Cowboy that has the latest edition of Tangled Bank. (Unlike the commenters, I am glad he did not put up a country music theme. I'm subjected to the stuff far too often as it is anyway.) [posted by S. Y. Affolee on 6:38 AM : Tuesday, September 26, 2006 Fight! Fight! Fight! Boy, this brought a happy giggle to my week. Forget about chicken fights. Fly fighting is in! While I was fiddling with literature searches, I stumbled upon this paper by Dierick and Greenspan which is attempting to get into the molecular basis for aggression, specifically in Drosophila melanogaster. The experiments sounded fun. In order to select for aggression, the investigators watched two flies fight in what was called "the two-male arena assay." Each fighting pair was graded on how long it took to start a fight, frequency of fights, duration of fights, and intensity of fights. See the video. (Also The Fruit Fly Fight Club for those of you who missed it when I posted it previously.) There was one observation in the paper that I found sort of interesting. Without a territory, aggressive flies actually had less success competing for mates than the neutral flies. This must certainly give hope to "beta" and "gamma" males if everything else is equal... [posted by S. Y. Affolee on 9:47 PM : Friday, September 22, 2006 My Neighbor Sang The Empire Strikes Back Last Night Links: MeepToys. Cute hand-stitched toys for sale! (Disclosure: This is my sister's site.) The Leaky Science Pipeline--and Why a Science Web is Better. Leslie Brooks doesn't like the pipeline metaphor that's been bandied about the blogosphere concerning the recent discussion of why women do not go into science. She argues that science should be more accepting of people who want to go into the field later in life and to emphasize that it does not only involve research. Interesting take--but research is still the aspect of science that gets high profile coverage. 2006 Fall Warmup. Write 25,000 words in two weeks! Starting Sunday! I signed up for it, but I have absolutely no idea what I'm going to write. I have no plot, no characters, no setting. As for those of you who want to participate in National Novel Writing Month this year, sign-ups begin on October 1. [posted by S. Y. Affolee on 6:41 AM : Thursday, September 21, 2006 The Thursday Threesome: Ice Cream Social Onesome: Ice-- skating? Yes? No? Rinks? Ponds? No way? No. Twosome: Cream-- soda? The work of evil scientists or a true pleasure in life? Somewhere in between, I think. Threesome: Social-- Are you considered to be a social person? ...or are you more likely to not be comfortable with a bunch of people around you? ...and wait a moment: how about in a classroom situation? Is that different for you? I consider myself a loner. Which is not necessarily a good thing. The world revolves around social networking and if you don't make some sort of effort to communicate with someone, you pretty much get left in the cold. As for the classroom--I will admit that I am intimidated with more than 15-20 students. The likelihood of me speaking up when there is a loud-mouthed know-it-all in the midst pretty much drops to nil. [posted by S. Y. Affolee on 6:58 AM : Wednesday, September 20, 2006 Nuttier Than Pistachios I stepped out of class this afternoon to find that a huge crowd had gathered on the Commons. People were holding signs that read, "Fear God!" I passed them, long enough to hear a old guy rant, "It doesn't matter if you do good works your entire life! If you don't believe in God, you'll be eternally damned!" What a bunch of crock. Religious zealots are always trying to convert people, be they saints or criminals. It doesn't matter if you killed a bunch of people. If you convert, you'll be saved. If you single-handedly created world peace and eliminated world hunger, but you don't believe in their God, you'd be damned. Why are people so obsessed with the afterlife, if indeed there is one? We're living life now, and on a practical standpoint, I find it a freakin' waste of time to worry about where souls go after brain activity flat-lines when there are more pressing problems in the world. [posted by S. Y. Affolee on 2:14 PM : Tuesday, September 19, 2006 Yar(g)! Some crazy wench on the other side of the library lounge has just doused herself with some foul smellin' stuff. Some perfume and body sprays are better'n cannon balls and sabers. I'm dyin' here, mateys. (Or at least my nose is.) [posted by S. Y. Affolee on 7:49 AM : Monday, September 18, 2006 Rabid Med Students Will Be All Over Me I have heard that medical students get multiple choice tests. WTF?!!! Multiple choice tests only for the ability to choose a correct answer among all the possibilities given. It does not test your knowledge base at all. Yes, I have a poor opinion of multiple choice tests. And yes, maybe it's because the only tests I've taken had been essay-type exams, and I'm a little bitter at the fact that biology grad students (often stereotyped as med school rejects) have to really learn the material while med students (who knows, maybe one of them will be your future surgeon) can skate by with guessing at the answers. Also: Fill-in-the-blank is not much better. [posted by S. Y. Affolee on 6:48 PM : Sunday, September 17, 2006 Ack! The End. (via Dustbury) The blogosphere's original carnival is closing down? Yikes. Does this mean that carnivals are now just another blog fad? Most likely. But I don't want others to take this as a cue to pull up the stakes and leave. Because then where would I find the good stuff to read? [posted by S. Y. Affolee on 10:34 AM : Animalcules 1.12 The latest edition of Animalcules, a blog carnival dedicated to our favorite microbes, is up at ˇViva La Evolución! There's stuff from the latest O157:H7 scare to microbial hydrogen factories. So go, read! [posted by S. Y. Affolee on 8:15 AM : Saturday, September 16, 2006 No Mad Skillz Here Gah! The Blogger SAT Challenge! (via A Blog Around The Clock) Can you write as well or better than a high school student taking the written portion of the SAT? I'm thinking of taking it--for my own edification. I wonder if my recent spat of kamikaze novel writing will help me any? [posted by S. Y. Affolee on 6:56 PM : In Other Blogs Five Questions. The brief e-mail interview on blogging and books I had with John Baker is now up on his blog. The Story Behind The Killer Spinach. Carl Zimmer has a really interesting article up on The Loom about the recent outbreak of E. coli O157:H7 and its evolution. Lonelyguy15million. (via 2Blowhards) Never trust a picture on the internet. If people kept in mind this The New Yorker cartoon, guys wouldn't have to worry about falling for beautiful girls who turn out to be dweebs blogging in their underwear. As for Sailer's hypothetical take on what goes on in an Asian girl's mind--heh. I don't know what other Asian girls think about this, but all that internal dialogue gives me a headache. Besides, I don't feel it's very honest to fake being interested. (As for whether or not I would fake an interest in physics, see the paragraph below.) Getting along vs. fixing the problem. Janet Stemwedel has a good deconstruction of the discussion involving the physics "pipeline problem" I mentioned in a previous post. One of the commenters asked: "Has anyone actually talked to women who were considering physics but ended up choosing a different discipline instead?" I had once considered double majoring in physics and biology. In my first semester as an undergrad, I even chose to take a physics elective rather than the biology one. All I can say is, I realized at the end of the term that I was a lot more fired up about biology than physics--i.e. my degree of interest--which had nothing to do with class difficulty or skewed ratios. Or even the professors--I've met some really nice physics professors and some really temperamental biology profs as an undergrad. As for math--three words: creepy teaching assistants. Addendum: Now that I'm on the subject of teaching assistants, that brings up one particular incident involving a class on quantum chemistry. A couple of other female students and I went to the TAs (who were all male) for help but all they told us was to "figure it out yourself." So we ended up camping outside the prof's office door until the next morning in protest. Needless to say, those TAs were chewed out for being unhelpful. [posted by S. Y. Affolee on 5:08 PM : Friday, September 15, 2006 Random-o-rama How to Dissuade Yourself from Becoming a Blogger. (via Modulator) "If attention and validation are what you're looking for, know that you will get neither from blogging." Dare to Be Bad! I so need some motivation to write. I've got to carve out another weekend some time (not this weekend, though) to get some rough drafts done. But wait--maybe there's this. 25k in two weeks? Heck, yeah! If I can do 30k in 3 days, hopefully this will be a piece of cake. Peter Jackson enters dragons' den. Napoleon and dragons--who can beat that combination? Actually, I've heard good things about Naomi Novik's books and the first three novels in the series have been sitting on my shelf for the past summer, waiting to be read (along with all the other books I've heard good things about). And if Peter Jackson is going to make some movies about this series--well, all the more to get crackin'. Stains on Paper. "A community art project involving stamps and spots." Now I am tempted to send some wacky stain in the mail. [posted by S. Y. Affolee on 6:33 AM : Thursday, September 14, 2006 The Thursday Threesome: Common Household Products Onesome: Common-- Quick and easy: the most common name you can think of! Okay, let's make it a first (given) name... John Twosome: Household-- cleaners? What is your "go to" cleanser when you have to clean the place up? Are you a Lysol Junkie, an Orange Blossom Special or maybe a Bleach it to Death type? Come on, come clean! It's called 409, right? Threesome: Products-- come and products go. What's on your list as a "wanna' have" for this Fall (no, not for Christmas; we'll save that for later). It's not a product, but if I could get more of it: time. [posted by S. Y. Affolee on 5:43 AM : Wednesday, September 13, 2006 The Navelsphere In the order that I read them: Mark Evans | Nicholas Carr | Shelley Powers. All of them are talking about the inequalities of the blogosphere--how A-listers hog the traffic and fail to link to "tail-end" bloggers unless they link to them first (and most of the time, not even then). I'm not sure I really want to be linked to by the A-listers--especially since they tend to specialize in tech or politics, subjects in which I am not an expert in or have chosen to remain mum about. Although Shelley Powers had pointed out that Technorati now has a search on "authority." That is such a big misnomer that it's not even funny. Popularity is more like it. Everyone may love the mutt that goes begging around for treats, but it is no surgeon. [posted by S. Y. Affolee on 8:44 AM : Web Bingo Tangled Bank #62. It's the Travel Bingo Edition at the Hairy Museum of Natural History so go read some cool science posts around the web. (On another note: I am not sure why the link to me is the same link from the last Tangled Bank. I am positive I submitted a different article. Ah well, such is life. These things are out of my hands.) [posted by S. Y. Affolee on 7:37 AM : Tuesday, September 12, 2006 The ARG! of Science There's something I totally don't get. Why do some bloggers just post quotes from news sources and then get tons of comments from readers? Even more galling: how come they post quotes of science stories from mainstream news sources about recent science papers and get tons of comments whereas I (or other science bloggers) read the science paper directly and write about it but get absolutely zilch feedback? The (Former) Life of a Microbiology Grad Student. Evidence that even graduate students can get dooced. And of course this makes me paranoid. Or rather, more paranoid than I already am. I'm semi-anonymous here, but that doesn't guarantee that no one will find me. In fact, people I know in real life have found me here online. That is why I hardly blog about any real life problems. Loud and obnoxious next door neighbors? Yes. Weird lab/school stuff? No. Although if you went through my archives with a fine tooth comb (and no, I am not suggesting that anyone really do so), you could probably figure out who I worked for and who I'm working for now. Anyways, back to the link--I really do feel for him. I went through Grad Student Hell (perhaps I should continue to refer to that period in my life in those terms) not so long ago and to my relief and amusement found that my love of science is about as hard to kill as a cockroach. [posted by S. Y. Affolee on 8:02 PM : The Unbalanced Ratio Lately, I've been following an interesting conversation over at ScienceBlogs. In The Pipeline Problem, Chad Orzel, a college physics professor, argues that the lack of women in the sciences is not his fault. Sure, there are sexist pigs in every field, but he implies that the problem lies primarily in the grade school years where girls are discouraged from going into the sciences by disinterested teachers and peer pressure. Suzanne Franks posts a rebuttal: one cannot pin all the blame on elementary and high schools. Even university professors must shoulder some of the responsibility--their lectures may be turning young women off or their faculty ratio may not be so great. More subtly, they may not even realize that they've only invited male speakers to a seminar or show only pictures of guys on their recruiting website. Although Orzel is a bit naive in his views (how can he be really sure his colleagues are not doing any harassment?), both do bring up good points. Science on a university level can be intimidating even if all the male professors are Very Nice People. Being a minority is both alienating and lonely and many people, whoever they are, cannot handle that kind of isolation for very long. I went to a science-oriented university as an undergraduate--less than 30% of my graduating class was female. It was not due to the admissions process, which was fifty-fifty, but the critical point when prospective students visited campus that severely skewed the ratio. Elementary, middle, and high school weren't better--although, I wouldn't say the problem was with male teachers as much as with female teachers with low expectations and an ill-hidden distaste for the sciences. Physics teacher? She didn't think we could do the math. Biology teacher? She didn't believe in evolution. Chemistry teacher? She blabbed about how great her sons were instead of teaching orbital theory. With all that negative stimuli during my formative years, one could wonder how I retained any shred of love for science at all. I'm pretty sure none of my female classmates from high school have. They all wanted to become lawyers or psychiatrists or political activists or artists. [posted by S. Y. Affolee on 12:13 AM : Monday, September 11, 2006 Linky-Dink Tiny Animals on Fingers. Depressing blog posts today getting you down? Here's some cuteness to brighten up your Monday. Time to weep for the state of the bookstore. Although I have met bookstore employees who have been fairly knowledgeable, I generally have a low opinion of anyone who wants to "help" me find a book. I guess it's just part of my personality to go at things alone--and the fact that I once worked at a library. (I even organize my bookmarks by Dewey Decimal. I'm currently considering putting them in LCC instead. Does this qualify me as a nerd? At any rate...) If I don't find a book where I would intuitively shelve it, I poke around in the other sections. It's not like I actually waste any time--I mean, what kind of book lover just grabs a book and high-tails it out of the store anyway? Added later: Sculptures of Cartoon Skeletons. (via Drawn!) Both morbid and cool, they look like they should belong to the freakshow exhibit in a natural history museum. [posted by S. Y. Affolee on 9:27 AM : Sunday, September 10, 2006 Endosymbionts Do The Horizontal Most people will be familiar with aphids as pests in their gardens or as the insect version of a cow--that ants "farm" in return for secreted honeydew--in nature documentaries. But an aphid's association with the ant isn't its only mutualistic relationship. This other relationship is microscopic and so vital that an aphid cannot survive or reproduce without it.  About 200 to 250 million years ago, a free-living bacterium infected an aphid ancestor. Over time, the bacteria established themselves within aphid cells. Once inside this comfortable and safe niche, the bacteria began shedding some of the essential genes required for free-living. And in return for its new home, the bacteria began producing essential nutrients like amino acids for its host. In this way, the aphid and its endosymbiont--such as a Buchnera species--became dependent on each other. But aside from ecological reasons for studying Buchnera, endosymbionts are excellent examples of bacterial evolution from free-living to intracellular. Buchnera may even be a snapshot of what a mitochondrion or chloroplast might have looked like before they were relegated to the status of organelles.Aphids also have a very strange life cycle. Most aphids are parthenogenetic and some act like real-life tribbles--female aphids will be pregnant with daughters who are already pregnant before they are born. During the spring and summer, aphids continue to reproduce parthenogenetically, but in the autumn, males and sexual females are produced. After mating, eggs are left to overwinter until the next growing season when the parthenogenetic cycle begins anew. Meanwhile, Buchnera live happily within vesicles called symbiosomes that are inside specialized cells called bacteriocytes. These endosymbionts are maternally transmitted. When the aphid reproduces, bacteriocytes migrate to the embryo and enter it. So during a parthenogenetic generation--not only are mother and daughter aphids genetically the same but also their endosymbionts. But is this the only way an endosymbiont can be transferred from host to host? Moran and Dunbar in a recent paper in PNAS wondered about this very question: there must be another mechanism for endosymbiont transfer. Observations from the field indicate that horizontal transfer of endosymbionts--that is, the transfer of endosymbionts between different maternal lines--was fairly frequent. But aside from artificial transfers like microinjecting an uninfected aphid with the hemolymph from an infected one or feeding aphids an artificial diet composed of symbionts--there was no known natural way known for this type of endosymbionts transfer. One possibility for horizontal transfer is during the autumn when the aphids are sexually reproducing. Moran and Dunbar hypothesized that endosymbionts might be transferred at the same time as sperm and other proteins during mating. To test this, they used the pea aphid, Acyrthosiphon pisum. In addition to Buchnera, the pea aphid can also be infected with a secondary endosymbiont which can be any number of three kinds of enterobacteria--Hamiltonella defensa, Serratia symbiotica, or Regiella insecticola. The researchers conducted aphid crosses by mating uninfected mothers with fathers infected with one of these secondary endosymbionts. In the case of R. insecticola, after monitoring the progeny for several generations, aphids in later generations still retained the paternally acquired endosymbiont. Using fluorescent in situ hybridization, the researchers were also able to locate these endosymbionts inside the male reproductive organs but not inside the sperm cells themselves. So what possible benefit could the host aphid have for acquiring endosymbionts via horizontal transfer? One possibility is that the symbionts confer some survival advantages for the aphid--such as resistance to environmental stresses or to aphid pathogens. And what of the endosymbionts themselves? What do they get out of this transfer other than hopping from host to host? Well, there's one major implication in symbiont evolution, especially considering a situation involving coinfection. Symbionts can replicate themselves with genetic fidelity via host parthenogenesis, but when a different strain is introduced through host sexual reproduction, symbionts have the opportunity to swap genes, compete with each other for a favored niche, and influence the life cycle of their hosts. [posted by S. Y. Affolee on 12:44 PM : Friday, September 08, 2006 I Am So Easily Amused I've gotten to the point where my eyes just gloss over the targeted text ads in Gmail. But this morning, it was amusing to note what types of ads were splashed on the page. Nope, not your usual dating sites or online movie rentals. I have ads for: Glutathione assays! Antimicrobial products! and Superoxide dismutase! Scientific Communication. (via A Blog Around The Clock--who also has some very cool bacterial clock posts currently up) Oh man, ordinary citizens mostly inform themselves about science with little input from anything else, even by the mainstream media that tends to garble things up. No wonder the public's image of science is so screwed up. [posted by S. Y. Affolee on 8:05 AM : Thursday, September 07, 2006 Meme-ish It's been a while since I've visited the TTLB Ecosystem (was it last year or before then?) so I was kind of surprised at the change in layout. I was not surprised, though, that I've dropped from fish to insect. Is it safe to say that my blogger heyday has already come and gone? Nerd-off. A challenge to science bloggers to reveal their uber-nerdiness. I personally think most science bloggers are more well-adjusted than they let on. As for myself: I'm sort of like Nabokov and his butterflies. Does dressing up as part of a molecule for Halloween count? Reading science books for fun? Owning a complete set of YBFH? Writing a novel in three days? Or maybe I'm just crazy and not nerdy. The Thursday Threesome: How High is Up? Onesome: How-- many Apples in your orchard? Didn't we just ask this one? Are you a Mac-o-phile, a Windows user, or one of those penguin people (Linux users)? I use Windows, as everyone who has figured out who I am from their referral stats knows. Twosome: High is-- what in height for your family? Are you a tall group? ...a short stack? ...or a mixed lot? I assume my family is shorter than the American average. Threesome: Up-- ...and down and all around: Labor Day marked the end of Summer for those of us in the US (regardless of how the plants felt what with the temperatures out West and hurricanes in the East). How about you: what signals the change of seasons this time of year for you? When it gets colder. [posted by S. Y. Affolee on 6:40 AM : Wednesday, September 06, 2006 Survival of the Competent  Why do bacteria need to take up DNA in the first place? And how do they do it? There are three ideas about why a bacterium might want to acquire DNA in the first place: for genetic exchange, for use as a template to repair its own DNA, and even for food. But a bacterium can't take up DNA at just any time. It must physiologically ready itself for a state called competence.Competence has been studied in gram-positive bacteria--notably using the pathogen Streptococcus pneumoniae and the soil bacterium Bacillus subtilis as models. The ability to be transformed, or to uptake DNA, was originally observed in S. pneumoniae by Oswald Avery and his colleagues in 1944. It was then documented that the bacteria's competence phase only occurred during a certain window during the growth phase, but it wasn't until 1965 that Alexander Tomasz discovered that competence was, in fact, the product of cell-to-cell communication. In both S. pneumoniae and B. subtilis, the regulatory cascade that leads to competence begins with a small pheromone peptide called an alarmone because it conveys a stress signal. As the bacteria grow to exponential phase, more alarmone is produced. This is sensed by a receptor on the bacterium's surface which activates the cascade that turns on transcription of genes that will make a DNA-uptake apparatus. Interestingly enough, competence also triggers bacterial fratricide in non-competent cells. In a July 2006 Science report by Prudhomme et al., an additional idea was proposed as a reason for competence. Not only is extracellular DNA taken up to help repair DNA in times of stress, but it may even be a fitness-enhancing strategy helping to drive bacterial evolution. To test this idea, Prudhomme et al. stressed S. pneumoniae by adding mitomycin C, a chemical that damages DNA. Competence was monitored by hooking a luciferase gene to one of the competence genes and by assaying photon emission. So increased light production from the bacteria meant that they were becoming competent. The researchers' experiments showed that not only mitomycin C but also several other antibiotics such as kanamycin and streptomycin induced competence in S. pneumoniae. The ability to gain competence in a stressful environment--such as the sudden introduction of antibiotics--has some obvious benefits for the bacteria. When a bacterium senses the antibiotic in its surroundings, the competence genes are switched on. It begins producing and exporting alarmone which is sensed by neighboring bacteria. They too begin producing alarmone, increasing the number of competent cells in the population. At the same time, the competence genes produce lytic enzymes and the proteins that will make up the DNA-uptake apparatus. The enzymes are the death knell to any bacteria that do not or cannot become competent--once the non-competent bacteria are lysed, in effect spilling their guts, the other bacteria take up in a Donner-party-like fashion the released nutrients and DNA. Taking up other bacteria's DNA is particularly useful if the population of bacteria is diverse. In turn, the competent bacteria will be more genetically diverse. After all, some of that DNA might contain a useful gene for antibiotic resistance or conferring an advantage for the bacteria in another challenging environment to allow it to persist in places where it originally couldn't before. Competence, particularly in gram-positive bacteria like S. pneumoniae, probably plays a major role in how strains acquire antibiotic resistance over time. And perhaps, this observation is an "alarmone" for us not to overuse antibiotics as these bacteria fully have the ability to out maneuver us with this particular evolutionary trick. [posted by S. Y. Affolee on 2:14 PM : Tuesday, September 05, 2006 Links Scavenged From Other Blogs Mendel's Garden #5. It's a blog carnival dedicated to all things genetics. There are a ton of neat links here from coffee and diabetes to red panda classification. What a Professor Learned as an Undercover Freshman. (via Gully Brook Press) I'm not sure what I would have felt as an undergrad if there was somebody around studying me. Weirded out, probably. For one thing, I don't think there's anything sociologically interesting about college kids. (I was an undergrad a couple years ago and I didn't think I was all that interesting.) I mean sure--culture differs from school to school--but basically they're just a bunch of post-adolescent kids who are semi-on-their-own for the first time in their lives. Just think of the triple mantra: sleep, study, or socialize--pick two. And that's it in a nutshell. Almond Pizzelles. Those are so yummy. I'm going to start saving up for a pizzelle iron. Scienceblogger Hot or Not. (via Pharyngula) Heh. You know something crazy is going on when a stuffed monkey ranks higher than pictures of guys. [posted by S. Y. Affolee on 7:37 AM : Monday, September 04, 2006 Update #4 on Insanity! This is the final update on this craziness on a 3-day novel (or rather novelette). I finished with a little more than an hour to spare at 32,010 words. It's just pure craziness. (Tentacle monsters! Pirates! Plot holes the size of the Grand Canyon!) It's been a while since I've done any writing without prior planning and I've realized how much I do depend on it to have things go smoothly. As it is, the draft I've just created over Labor Day Weekend is way too rough for me to show it to anybody although I suppose there are bits and pieces of it I could probably cobble together later to make a decent short story. [posted by S. Y. Affolee on 11:03 PM : Sunday, September 03, 2006 Update #3 on Insanity! 25K! A showdown with Cthulhu and the pirates is imminent. But first, some sleep... [posted by S. Y. Affolee on 10:26 PM : Update #2 on Insanity! I don't think there is any way I can finish this today. Currently, I'm up to 20K. I suppose I could have been further along if I didn't do my laundry or go grocery shopping. I might try to finish this tomorrow--either early morning or in snatches during lab when things are incubating. So far, I had some ninjas make an appearance as well as having Cthulhu crashing a cephalopod convention. The pirates have been plotting about a takeover. Cthulhu might make another appearance, but I'm not sure yet. And dang it, I still don't have any idea where my plot is going. [posted by S. Y. Affolee on 5:16 PM : Saturday, September 02, 2006 Update #1 on Insanity! At the moment, I'm up to about 9.3K worth of words and I have absolutely no idea where the plot is going. I probably wasted a lot of time today sleeping and eating regular meals and going on bathroom breaks and surfing on the internet for inspiration. I probably wasted more time staring at the screen not knowing what to type. That's the bane of writing a novel without any sort of plan. What I have so far: my main character is the Eater of Souls (from Egyptian mythology) and she's going on a cruise. Her companion is a neurotic cat with an obsession for shiny objects and her love interest is a surly folklorist who's on an enforced vacation. I'm definitely going to fit some pirates into the plot somehow. Currently, I'm contemplating ninjas as well. You can obviously tell that I'm getting desperate. [posted by S. Y. Affolee on 8:41 PM : Friday, September 01, 2006 Insanity! I just found out something called The 3-Day Novel Contest. And I thought I was crazy writing a novel in one month during November for the past five years. This contest has you writing 30,000 words in 3 days. And it starts tomorrow! I'm thinking about doing it. (Without registering, of course. I don't have fifty bucks to throw away on doing something this impulsive.) But I don't have any plans or outlines or ideas on the plot. And more importantly, I only have two days to do this because I plan on being in the lab on Monday. We'll see. By Tuesday, you'll know if I survived or crashed and burned. [posted by S. Y. Affolee on 6:25 PM : |
