A funny thing happened today. I turned on the PS3 and logged in to play a bit of Ratchet & Clank. Actually, Ratchet & Clank downloadable content. My husband played the game when it was new, and downloaded the extra content after he finished the game. I've been playing and enjoying it for the past few days.

But when I tried to load my saved game, it said there was no data. I restarted the system (because that fixes a great deal of computer-based problems) and most of the downloaded games were gone! Including, of course, the one I've been playing.

Thirty minutes on the phone with PlayStation support flushed out the root of the problem: apparently, I was never supposed to have access to that content in the first place. System maintenance that was run today has found these "problems" and addressed them.

And therein lies the real problem. Why wasn't I supposed to have access to my husband's downloadable content? Yes, he bought it on his account, but it's our system. The full game, Ratchet & Clank Future: Tools of Destruction, is on a disc and thus we can each play it on our own accounts any time we like. The downloadable content, however, does not exist on physical media, and is therefore susceptible to "copyright infringement protection".

All this protection of digital media is supposed to deter piracy, but I think it probably has the opposite effect. After all, analog media isn't protected in the same manner, and when's the last time you heard of a bootleg copy of Gone With the Wind? If I buy a book, I can read it anytime I like. I can loan it to a friend. I can read it out loud to a group of friends. I can donate it to a library. I can even sell it to a bookstore, if they're in the market for used books.

So why can't I do the same thing with my downloaded films, songs, and video games? I paid for it, after all. If I like it, I'm likely to want to be able to enjoy it in many different places (after all, who limits themselves to reading their favorite books, say, only in their bedroom?). I'm likely to want to loan it to my friends, so they can enjoy it too.

But the companies that produce this media think maybe, just maybe, I'm going to share it with the entire world and they're not going to make any money. So, rather than have faith that people will continue to buy video games, just as they continue to buy books, they make it so that, even if my family has paid for a copy, we have to buy another one so each of us can enjoy it.

And this is why this "protection" encourages piracy. What I am absolutely NOT going to do is buy a second goddam copy of a game we already own just so I can play it under my account. What I might do is play on my husband's account, which unfortunately erases all his saved data and means we'll have to each play all the way through if we want to share. But what I might do is crack the content we already own, or obtain some cracked content from someone else. The companies who set up these ridiculous "anti-theft" devices make it so impossible for those of us who aren't pirates to actually enjoy the media that we have no alternative (other than amply lining the pockets of the media execs by purchasing multiple copies of digital files). By attempting to protect their media, these idiots are actually creating a market for bootleg material.

So here's a message for the people in digital media: learn to work for your consumers, not against them. There are more pirates than there are of you, and, on probability alone, they're likely smarter. You imagine we're all greedy enough that we'll refuse to pay for your products. Keep up your miserly tactics, and you'll find you're quite right.

I recently finished Diana Wynne Jones's Hexwood, and was astonished by its format. When you think of young adult sci-fi/fantasy, you probably think of Harry Potter, right? I did too.

But Hexwood threw me a real curve ball. The story isn't just non-linear, it's multi-linear. The main character, Ann, experiences four separate events more or less simultaneously, and we're right there with her, repeatedly passing the pretzel bag in the tree on her way to meet Mordion. Ann's friends in Hexwood forest might be any age when she meets them, but, judging by the cut on Mordion's wrist, only a few days pass for them as well as for Ann. Then, suddenly, we discover Ann isn't 15-year-old Ann, but 21-year-old Vierran, who we are introduced to about halfway through the book. To be honest, it's a bit hard to keep up.

But that's sort of the fun of it, isn't it? Trying to keep pace with a book that throws convention to the wind. The postmodernists discovered this decades ago, and changed the face of fiction. It seems sci-fi/fantasy is catching up, and it's the authors who write for children who are leading the way.

Even C.S. Lewis dabbled with this sort of format in his Narnian chronicles. Although the Pevensies grow into adulthood in Narnia, they emerge from the wardrobe only moments after entering it at the end of The Lion, the Witch, and the Wardrobe. When they return not long after in Prince Caspian thousands of years have passed in Narnia, and they find their castle lies in ruins and their names are the stuff of legend, much like our King Arthur.

Ursula K. LeGuin employed this sort of device in her short A Fisherman of the Inland Sea, in which Hideo devotes his entire life to the study of time travel just so he can rewrite his own biography. Granted, not all of LeGuin's work is for children, but a great deal of it is, and I think this story is one children can easily enjoy.

Upon reflection, it seems sci-fi/fantasy authors are the logical choice to begin to play with the structure of a story. The genre lends itself well to manipulations of time, perception, and reality. It does seem surprising, though, for the children's authors to be the trailblazers in this respect. Perhaps children are more receptive to their notions of reality being smudged? Perhaps the things that inspire authors to write for children inspire them to bend the rules?

At any rate, I couldn't be happier.

Stumbled across this post from my OKCupid journal from about a year ago, and decided it was still fascinating. What do you guys think?

After I've been drinking on a Friday is not the best time to blog about major scientific paradigm shifts. However, this is what I'm doing.

So, here's the thing: ever since DNA was discovered to contain heritable material, scientists began to endeavor to discover what mechanism translated genes into phenotypes (characteristics, for you laymen). Years ago the scientific community coined the phrase "central dogma" to describe the process, and it states, simply: DNA -> RNA -> Protein. And this is largely still true.


However, this has been interpreted as DNA -> mRNA -> Protein, with structural changes in proteins providing feedback and thus regulation of DNA. Now, this interpretation is true in most prokaryotes, but in eukaryotes it breaks down. Eukaryotes are incredibly complex, and yet contain hardly more (if as many) protein-coding genes as prokaryotes. The question becomes, if these organisms are so much more complex without containing a larger number of protein-coding regions, what accounts for this complexity?


As these questions were being pondered, the race to decode the human genome reached its end. We sequenced the entire genome, only to find that most of it is "junk". So much genetic material, but only 2% of it makes proteins! What's going on with that other 98%?


Perhaps it's structural, providing the scaffolding to hold the coding sequences in place while they are transcribed or regulated. Perhaps it's evolutionary leftovers, remnants from our ancestors who no longer needed certain genes, or who contracted non-lethal viral infections that took up residence in the genome. Or could it serve some other purpose?


Evidence points to the last of these hypotheses. It has long been known that few genes exist as one long, sequential element, transcribed perfectly in a neat strand. Most initial transcripts are spliced, modified, and edited in numerous ways, leaving only bits of the original sequence to go on to be translated into protein. Many of the bits that are cut out of these regions are, in fact, opposite to the regions themselves, or to other regions nearby on the DNA strand. Would junk be so specific? It's unlikely.


Furthermore, this junk isn't just sitting around. In vivo and in vitro studies have shown that this genetic material is ubiquitous in all eukaryotic cells, and that certain material localizes in a predictable manner in many types of cells. Much of these non-coding RNAs are developmentally regulated, highlighting the fact that they are not discarded by the cell as "junk" material.


Possibly most interestingly of all, the regions of the human body where these ncRNAs are most evolutionarily active are the brain and testes. What have humans prided themselves on as long as they've recognized it? Their brain, and its enormous capacity that far outstrips that of less complex animals. It's our most recent adaptation, and our most complex. Thus, it's not surprising that it's undergoing the fastest change.


And here's something fun for you network nuts: a functionally integrated network requires that the number of connectors increases as a square function of the number of nodes ([R] = aN^2). In fact, this is the exact pattern of increasing proportion of ncRNAs to coding RNAs that is observed in living things.


What all this points to is that ncRNAs are serving quite a specific regulatory function in the cell. In order for organisms to obtain high degrees of complexity they must evolve a regulatory system that can handle a lot of inputs and connections. Eukaryotes have done just this, utilizing the specificity built into the DNA strand. Rather than rely on cumbersome proteins and structural changes to provide feedback about the environment, eukaryotic cells create specific RNA sequences that can form RNA-RNA, RNA-DNA, and RNA-protein interactions. This provides potential for a very high degree of regulation within the cell without relying on an analog system like structural changes.


I learned about the regulatory functions of ncRNAs from Dr. John Mattick of the University of Queensland, who recently gave a phenomenal presentation at my work. Check out his publications for more eloquent explanations of my ramblings here. In fact, if you're really interested, he'll probably share his slides with you. Send him an email!

For the past 11 days, I’ve had a physical disability. I had a torn meniscus, and had arthroscopic surgery to remove it. While I recover, I have limited strength and range of motion in my knee, but it is recovering quickly.

But my days of walking with a cane, and slowly working my way to unassisted mobility, have shown me some surprising (and frequently disappointing) facets of the people I encounter day to day.

My first surprise came early last week when I decided to go to Best Buy. I had spent most of my time on my couch since the surgery, and was running out of entertainment. For my first solo venture out of the apartment since surgery, I went to buy some DVDs and a burger for lunch.

I was in the checkout, having my purchases rung up by a kid no older than 20. I paid with a credit card, using one of those swipe machines that are in nearly every store. Now, I’m no stranger to Best Buy, nor was it my first time to use such a machine, but this kid felt the need to give me instructions every step of the way. It seems my physical impairment, to him, implied a mental deficiency as well. Why? It’s anybody’s guess.

Not to say that everyone was insulting that day. The folks at Fuddruckers treated me as just another customer, which I sincerely appreciated. They clearly understood that I was a fully functioning human being, and that I knew what I could do and would ask for assistance if I needed it. I appreciated that.

But the next day it was time for me to return to work. In some ways, I’m grateful for this experience, because it has shown me something about the true nature of a few of the people I work with. My immediate coworkers, as well as my boss, are all quite easygoing about my knee. I have asked some of them for help when I needed it, which they gave uncomplaining, and they in turn have inundated me with questions about what it feels like and how long my doctor thinks my recovery will take. In short, we treat each other as the friends we are.

But the people I pass in the hallway are frequently nearly intolerable. I accepted that I would be explaining my condition to ten or twenty people a day, and I don’t mind. People are curious. What I didn’t expect was the interaction I get when walking down the hallway.

There is one girl, who I know to be an otherwise good person, who makes a pouty face at me every time we pass. All she can see is what I can’t do, never how far I’ve come. Today was my first day walking unassisted, which, admittedly, makes me slow and laborious. However, it’s a major step toward walking normally again, and I’m quite proud to have achieved it. Every time she makes that face at me, she shows me that she has no idea what I’m going through, nor how much she belittles my accomplishments.

Then there’s the guy who asked how I can drive (a question I’ve frequently encountered). I responded as I always do, telling him that it’s my left knee that is healing, and I drive an automatic, so my driving is unaffected. His response? “Well, that’s one thing at least.” Indeed, that is one thing, which we can add to the dozens of positive things that have come about as a result of the surgery, which actually have affected my daily life. I mean, if we’re going to look on the bright side, let’s start with the fact that I no longer have debris floating in my knee joint causing me pain and difficulty walking. How about the fact that I have made significant improvements in my range of motion in the past week by working with my physical therapist?

The truth is that these people truly don’t understand the challenges I face and the hurdles I have overcome. Their misplaced sympathy is, to me, worse than apathy. I don’t need them to feel bad for me; I don’t feel bad for myself. In fact, I’m quite pleased with my progress, even if the road is difficult.

And this has enlightened me about how I imagine people who are permanently handicapped might feel. I will never understand what they have endured, and what they face every day. They don’t need my sympathy. Sometimes, they might need my help. They can certainly use my respect. But what they really need is to be treated as people, the same as anyone else. They’re not less, nor are they more. Some of them are nice, and some are them are, I’m sure, quite rude. There’s no need for me to be overly friendly or accommodating. As I knew how to ask for help when I needed it, I’m sure they know also.

So here’s my message for you: if you encounter someone you don’t know who has a disability, it’s probably best for you to just treat them as you would anyone. If you don’t regularly make conversation with strangers, leave them alone. If you’re the type to engage the person next to you in conversation, then go ahead and strike one up with them. If you spit at everyone you meet, well, spit right on them. The more you treat them as special, the more they will resent your highlighting the differences between you. The more you treat them as humans, the more they will appreciate you for it.

I had my knee surgery yesterday. It was over quickly and I didn't have any nausea from the anesthesia (a huge improvement over my last surgery, which left me puking for the whole first day).

Yesterday I wasn't in any pain, but this morning it's starting to hurt. That's probably why I'm up right now, at 4:30. I hope it's not swelling. I "iced" it all day yesterday, but it was hard to actually get it cold under the several layers of bandages I'm not supposed to remove. Oh well.

The doc ended up taking out my entire meniscus. That was a surprise. I thought he was just going to carve away the middle part. Maybe it was a mess once he got in there, so there was nothing to be done. I dunno. But it looks like I'm guaranteed some arthritis in the joint later, since I don't have a cushion between the bones anymore. That sucks.

On the other hand, it's better than a torn up cushion and a giant cyst under my kneecap. So I guess I'll take what I can get.

John has been an absolute doll. I feel bad calling for him every half hour or so, but getting up and moving around wears me out like you wouldn't believe. He even brought me a box of chocolates when he went to pick up my pain meds. He calls them my "feel better treats". Aw!

Congress is hard at work making the BCS ranking illegal.

The country is in the depths of a recession that is putting families out of their homes. Businesses are failing left and right. War continues to rage in Iraq. And what are our legislators deciding? Whether the BCS is fair.

What the hell, congress? Is this seriously a good use of your time and our money? I mean, I understand some people think the BCS ranking and decisions about championship games are unfair. Sure. Maybe they are. But is it such a threat to peace and order in society that we must pass laws about it?

Sports are dumb. Our government is dumb. No wonder the rest of the world thinks we're a bunch of idiotic, fast-food eating, consumer-driven morons. We kind of are.

I saw another tampon commercial today in which the company proclaimed that their tampon "opens outward like a flower".

I'm about to get graphic, so if you're not up for a tampon discussion, stop now.

( Menstruation this way. )

You know... I've heard a lot of Twilight fans styling themselves "nerds". I take issue with this. Twilight is one of those lowest common denominator sorts of things. I skimmed through one at the bookstore recently, and it's about the same quality as Ann Rice fanfic written by an eighth-grader. I'm not convinced it's not actually Ann Rice fanfic written by an eighth-grader, come to think of it.

At any rate, I protest that Twilight fandom does NOT count as nerdy. Princess Leia hairdo at the prom? Nerd. Fluent in Klingon? Nerd. Proud owner of an original copy of the first Superman comic, in the package and everything? Nerd. Big fan of trashy, badly-written vampire romance drivel? NOT NERD. Just adolescent.

I have an extra ticket to the Michael Jackson Thriller Sing-Along next Thursday. It includes learning the Thriller dance at a nearby club in preparation for the Thrill The World event next Saturday. Anybody wanna join me? I only have one extra ticket, but if you want to bring friends, there are still tickets available.

So, any takers? I don't want to go by myself.

Today I got a promotion and a 15% raise. It's been a long time coming. I'm glad I finally got it. :)

I recently read a story in Oliver Sacks's The Man Who Mistook His Wife For A Hat which was the most horrific thing I have heard of in a long time.

There is a condition known as Korsakov's Disease which is a type of amnesia usually caused by alcoholism. This amnesia is both retrograde and anterograde: the patient cannot form new memories, and the past has been wiped out back to a specific point in time.

In the postscript of the story entitled The Lost Mariner Sacks speaks of a man who suffered from this type of disease. He was a permanent resident at a psychiatric hospital, due mostly to a seizure disorder which made at-home care impossible. On occasion he would be allowed to spend a weekend at home with his wife, in the house they had shared prior to the onset of his amnesia. During these weekends, although he was sometimes surprised by small changes (the color of the curtains or there being a supermarket on the corner instead of a cinema) he managed quite well and seemed completely normal. However, his amnesia prevented him from having any knowledge of his illness or any memory of living in the hospital, so when the time came for his wife to drop him off again at the hospital he would launch into fits of terror, screaming, "Why are you leaving me here? Why can't I go home with you? Who are these people you're leaving me with?" After a few minutes, of course, he would forget his terror, and forget that he had visited his wife at all.

However, during those brief, horrible moments I can only imagine how fearful he must have felt. I could equate it to waking up on a Sunday after spending a relaxing weekend at home, and getting in the car with John to go somewhere, only to find him dropping me off at a strange building and driving away. It would seem as though he was a co-conspirator with the staff of that place and, indeed, possibly a much larger group, as though they shared some secret about my fate that they refused to tell me. And for this to be done by the person you love and trust above all others.... I can't even imagine the torment that must bring.

Sacks described this man as having "a gaping time wound", but I think it's far more than that. It's a wound of every sort. Eventually the man would become perplexed that his young and beautiful wife looked old and feeble. He was not only losing time, he was losing the family he loved. I guess we can only be thankful that he will never be aware of these things for longer than a few moments, but that is a small comfort. What a terrible way to live.

Miya, our new kitty, came home today! She is a 7-pound, 1-year-old cat who is recovering from her first time giving birth (she has since been fixed). She is VERY affectionate, very curious, and extremely playful. She became the vet's new favorite the moment he laid eyes on her.

( Adorable! )

She came to us from Town Lake Animal Shelter. If you are in need of a new buddy, I definitely recommend them. They don't have much space, but they do a lot with what they have. Very friendly staff as well.

Ling is not too thrilled about a new cat in her house, but she doesn't seem as bad as she could be. They growled at each other while keeping a respectable distance between themselves for the few moments we let them meet each other, and Ling sat and watched later as Miya explored her new home. John and I have our fingers crossed that they will take to each other in time.

Got my letter from UT today. I didn't get in. At this point, it wasn't all that surprising. I figured I would have heard before now if I got in, and I was right.

I'll spread out my applications next year. Maybe something even better will work out.

I'm not really upset. A big change at work means I'll probably be enjoying the daily job more, so another year there isn't a big deal. Even so, I'm not giving up on grad school. Eventually I'll get there.

Went to Laredo over the weekend to meet our new nephew! He's adorable, and fabulously well-behaved. There was a rather tense few hours when Ave, his mom, got lightheaded and had some pains, but a trip to the ER showed that everything was fine, it's just a mild infection that some antibiotics will clear up.

Unfortunately, we forgot our cameras, but the Laredo family had some, so hopefully they'll send the photos.

Also, my mother-in-law gave me a huge stash of yarn! She got it from her mother-in-law and hadn't been using it, so she sent it to a better home. There's a lot of it. ( Here's a photo. )

So I'm working on my third knitting project, a hat for Justin, a friend of mine at work. I also joined Ravelry, an online knitting community.

And now I want to knit everything in the universe.

I want to finish this hat for Justin, and make a similar one for myself.

I want to make a toy owl from a pattern I make up.

I want to make a teddy bear and matching booties for my nephew who is due at the end of this month. Maybe a hat too.

I'd love to knit Ron Weasley's sweater from Harry Potter and the Prisoner of Azkaban if I could find a pattern, or figure out how to do it myself (told you I'm a Potterfag).

I have an idea for a sweater I'd like to try when I'm a bit more accomplished.

I'd like to do some socks, but I have absolutely no idea what style to make.

Oh, and I have a ton of sparkly yarn that I got on sale, and I think it would make a nice set of gloves and a hat, maybe a scarf too.

This is going to take up way too much time.

Okay, I admit, I'm a Potterfag. Whatever. Secretly, you probably are too.

Here's my beef with other Potterfags: you can't all be in goddam Ravenclaw. You're not all the smart, bookish type. Most of you are just dorks. Just like the rest of us.

That is all.

As a couple of you may know, I recently took up knitting. It's fun, though slow, but overall very satisfying. Especially when a project finally comes together. Here's my first finished piece!

( Photo behind the cut. )
I'll be sending this to my friend Vinay in NYC. It's a gift for him, because he needs a way to keep warm during this awful winter storm they're having. I hope he doesn't mind the lumps!

I don't know why I was thinking of this today, I guess it's just one of those days.

You know how some stuff from your childhood sticks with you for your whole life? When I was a kid we didn't have a TV. I sometimes got to watch TV when I was at one of my grandparents' houses. I don't recall taking a particular interest, as I was a highly energetic kid and greatly preferred swimming in a creek to catching the latest Thundercats episode.

I did, however, see my fair share of Sesame Street. Now, there's no escaping the fact that nearly every American child born since the sixties grew up on Big Bird and Bert & Ernie. I certainly had my favorite characters (Mom tells me of the day she came into the kitchen to find me sitting in the garbage can, trash strewn across the floor, declaring that I was Oscar), but I think none intrigued me as much as The Count.

The Count, you might remember, is a Romanian vampire who lives with bats and spiders in a dusty, dark castle which is forever in the middle of a storm. And The Count, you might guess, loves to count.

In fact, he has a song about how he loves to count.

Now, I've forgotten most of what I saw of Sesame Street in the years since my childhood. I remember a few characters, and one or two of the skits, but I don't recall specifics, for the most part. Except for The Count's song. All these years I've remembered the whole thing, melody, lyrics, all of it. Granted, it's not complicated, but you tend to lose these things over time. I certainly don't remember the other songs from the show, aside from the theme song.

And the funny thing is, The Count's song doesn't even suck. The theme song is a bit grating to me, and I probably wouldn't enjoy listening to it these days. The Count's song, however, is just fun, and I find myself making up new words to the tune just because I like it.

I think that's very interesting.

So, for no apparent reason, I've decided to learn to knit. I bought some yarn and some needles yesterday and started on a scarf. So far, so good, but it's definitely going to help increase my patience, cuz this is slow work!

Any of you guys knit? Wanna share patterns/secrets? Not that I have any patterns yet, but hopefully, one day...

Oh, and the scarf I'm knitting is purple, knit stitch. I'll post pictures once I've finished.