Don't Shake the Flask

Because you don't know if it'll explode

Month: March, 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.

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 !

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.


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.

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”?

BacteroidesAnother 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.


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?


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.

Unconscious Mutterings

  1. I’m waiting:: For
  2. Speak:: Up
  3. Roger…:: Charlie
  4. Knock knock:: Who’s there?
  5. Hybrid:: Chicken
  6. Can’t believe my eyes:: It’s not butter!
  7. Hooked:: On
  8. Pontificate:: Fascilitate
  9. Slime:: Mold
  10. Unwelcome:: Mat


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.)

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….

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.

* * *

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.

* * *

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 An mp3 blog for electronic music fans! Plenty of interesting stuff.