Monday, December 31, 2007

Game Review: Orcs and Elves

Holiday blogging . . . ugh.  I'm waiting for the people I'm going to spend New Year's eve with to finish sleeping off their drinks last night, so I thought I'd throw a quick post up while I had the chance.
I received Orcs and Elves for Christmas for the DS.  It's a fairly interesting game.  Made by id software, the game is a first-person RPG, the likes of which I haven't seen in ages.  Think Doom, but with swords and a magic wand instead of guns and a chainsaw.

Like most RPGs, the main character doesn't speak . . . ever.  You're guided around by your talking magic wand, who speaks to the ghosts of dwarves for you.  If that sounds strange, then you may not enjoy the story.  It's pretty simple, but the draw is the gameplay, not the tale.  

The game mechanics are decent.  It seemed a tad easy, but I played it on the easiest setting to get a feel for it.  Like the older games by id, you can only look straight ahead, in one of four directions.  Each time you perform an action, either moving, attacking, opening a door, or drinking a potion, you use a turn.  Then all the monsters in the vicinity get to take a turn.  It's an interesting way of dealing with the awkward movement scheme, although it can prove frustrating when some monsters get more turns than you.

It's fun to play in a "throw-away" kind of way, but the game is short.  I'd say I put it to rest after somewhere around 5 hours of play.  I guess that's not terrible for a portable game, but I've come to expect a longer lifespan out of my RPGs.  

Gamespot didn't give it an official review, despite all their hype leading to its release.  If you wanted my opinion, I would give the game a 6.5/10.  There's no music during the game, the graphics don't take advantage of the DS (which is saying something), and the game is far too short.  However, it is redeemed by being fun and accessible, so I'd recommend it to anyone who enjoys a good adventure game.

Thursday, December 13, 2007

Game Review: Phoenix Wright, Ace Attorney: Trials and Tribulations

I really don't play enough games on my DS. Then again, most of the library is pet simulators and Brain Age wannabes. For this reason, I was very, very excited when I found out that they were releasing a third entry in the Phoenix Wright series.

If you've played either of the first two, then you need no convincing to buy the third one. For the rest of you, let's recap:

In these games, you play as Phoenix Wright (the guy in the blue suit and red tie), a defense attorney who always seems to be taking on clients with desperate cases. You'll spend your time talking to witnesses, examining the scene of the crime, and gathering clues and evidence. Finally, you'll end up at trial, pressing those who testify and using the evidence to either expose their lies or to convince them to reveal more information. In the end, it's pretty much like a game of interactive Matlock; you always prove the innocence of your client by proving that one of his accusers is the real culprit.

If that sounds like a wacky justice system, that your client isn't innocent until you've proven someone else to be guilty, well, just roll with it. Despite the silliness evident in the system, the game is still incredibly fun and quite amusing.

The games were initially released for the Gameboy Advance, but were later adapted for the DS. In the first entry in the series, there was a special case which you unlocked which was made specifically for the DS version. It incorporated a lot of DS specific features and was the longest, most intriguing adventure to have shown up, period. Sadly, neither the second nor third games included any of these features, but the games were still fun all the same.

The third game is still loads of fun, but I have two criticisms about it. First, it's too short: In the previous games, you had to spend three days solving all of the crimes. In this entry, most of them take place in one day, two at the most. It's just gone too fast. Second, Phoenix Wright feels like a bit player in his own game. There are five adventures, and you don't even play as Phoenix for two and a half of them! How can it be his game if you only control him for half the game? Bizarre!

Don't let my criticisms stop you from playing it, however. These games are worth every penny. If you're new to the series, you should definitely find a copy of the first one, as there is no excuse for not having these games in your library. If you've already played the first two, then stop reading this and go buy the third!

Friday, December 07, 2007

Wednesday, December 05, 2007

The Great Porn Debate

Last Wednesday, that legend of the not-so-silver screen, Ron Jeremy, came to UMSL for a debate on pornography with XXXChurch co-founder Craig Gross. For those not familiar with those names, Ron Jeremy is a porn star with thousands of "movies" to his name, while XXXChurch is an organization devoted to porn, either helping men to break their addiction to it or helping those in the industry leave it.

I'd wanted to go, but sadly it took place entirely during the class I teach on Wednesday nights. So, just as you'll have to, I had to suffice for The Current's article about it.

I wouldn't have thought Jeremy to be the philosophical type, so I wasn't expecting much. I don't think my expectations were entirely inaccurate; while he seems to have offered up some interesting arguments, it doesn't seem like anything new or particularly compelling. But then, I'm already fairly biased, and most articles of this nature tend not to do justice to the debates.

Something interesting has been brewing in my mind regarding porn and proof that it harms the participants ever since I heard about the debate. One of the most easily quantifiable proofs of harm to participants would be from STDs. I know California requires anybody participating in pornography to use a condom and be tested for STDs regularly, and I imagine that it's fairly standard for the industry either way. Still, there's a curveball in there I've been mulling over lately.

HPV.

Not the traditional "cauliflower penis" variety, but the cervical cancer-causing strains. I'm sure I'm misinformed somewhere in here, but here's what I think I know about the disease:
  • It can be transmitted without showing symptoms
  • It can only be tested for after symptoms have appeared in women
  • There is no test for it in men, currently
In addition, I would add that condoms are of questionable efficacy in preventing transmission, but I'm uncertain about that mark. A lot of the articles I've seen on HPV lump the wart and cancer causing strains in together, and it seems like they would behave slightly differently when it comes to transmission. Can condoms prevent transmission? Can it be spread via oral sex? I'm uncertain, but so far as I've seen, the answers seem to be "maybe not" and "yes."

Anyhow, the point of this is to point out a big danger such a disease poses to people in pornography. Ron Jeremy probably has it, but he'll never be able to know for certain. For the women he gives it to, they'll never know they have it until it's too late to do anything about it, and in the meantime they are capable of spreading it around to others. On top of that, if condoms don't effectively protect against it, then there's no safe way to be in porn and avoid it.

Which, if you've read my paper on pornography and the First Amendment, this seems like causus belli (is that right?) for making pornography illegal; speech that causes direct harm is not protected by the First Amendment.

Of course, I welcome comments on this. I more than likely have things wrong on some count here, but I'm curious where people think I actually did go wrong.

Game Review: Super Mario Galaxy

One complaint about the Wii that hasn't changed is that the number of quality games has not increased at a very fast pace. While the Wii library of games is growing, most new games are made by third parties, and those third party games tend to be poorly made, or at least poorly take advantage of the Wii's capabilities.

The upshot to this criticism is that when Nintendo makes a game for its own system, it does a bang-up job of it. With Super Mario Galaxy, they really hit the mark.

Of course, the plot really needs no introduction. Peach is kidnapped, save her from Bowser, blah blah blah. Okay, you don't play Mario games for their innovative stories. You play them because they're typically platformers of phenomenal quality.

Where do I start? I guess the control scheme deserves a mention. It's a bit difficult to get used to in the beginning; it's unusual to be controlling characters on a spherical surface, and the lack of camera control can be frustrating in rare occasions. However, after you get the feel for the controls? Man, does this game feel right. Smooth, accessible play that anybody could pick up and go with. The new features are integrated in nicely, too, like Bee Suit Mario and Boo Suit Mario. They're fun, though they do feel a little gimmicky.

Every level feels like it was crafted just right. The graphics are simply stunning, and the music evokes something while you're playing that you just don't get from most games. I really couldn't praise this game more.

There are two features I should mention, though. One is the two-player mode. Throughout the game, you can use the wii-mote to pick up "Star Bits" on the screen, and then fire them off at enemies. Since this can be a bit distracting while playing, a second player can take up a wii-mote and take over this function for the guy playing as Mario. While this seems like I nice feature, I can't help but think that it's not very fair to the second player. There just aren't enough enemies affected by the Star Bits to make it a very fruitful role, and otherwise all player two will do is wave the cursor around the screen trying to pick up Star Bits. Wee!

The other feature involves stat tracking. Each level keeps track of how many stars you've found and the highest number of coins and Star Bits you picked up in each level. You have the option of posting this information to an online message board, which other players can view, though I haven't looked at it yet myself. I wouldn't complain about this kind of feature, as it's one of the things that people seem to like about the XBox, but these things always leave me feeling so pressure. I don't play these games to unlock every last nook and cranny hidden feature, so the idea of having other people's scores as such staring me in the face does not strike me as being too appealing. Yes, you completed the game in a perfect manner. Good for you.

Those things aside, this game is bound to become a classic. If you own a Wii, there is no reason to not own it. It's fun to play, it's a joy to watch, and it's accessible to gamers of many levels without being too simple for more advanced players.

Monday, December 03, 2007

Advertising Corn

Sorry about the quiet around here. One more exam and I should have a master's degree. Awesome, huh?

Random thought from watching television: Why do crop companies advertise on television?

During The Simpsons' normal premier slot last night, I saw an advertisement by DeKalb about their corn, how superior it was, and how farmers should plant it. I can't help but wonder if this is an effective use of advertising dollars. A commercial during this primetime slot seems like it would be expensive, and how many farmers would be watching? They're not exactly a huge chunk of the population, so they're going to be a proportionally small chunk of The Simpsons' audience. At least, I assume they would be.

Then again, I have no idea what the most "efficient" way of advertising to farmers would be. Any ideas?

Friday, November 30, 2007

I fought the law

. . . And I won.

For those of you who haven't heard the story yet, I was in a car accident back in September.

I live out in the country, so I typically take a two-lane country highway home. September being harvest season, there's a lot of farm equipment that travels on the highway. One Sunday, on my way home from church, I was stuck behind a combine. I wanted to pass, but the traffic in the other direction was too thick. It finally came to the point that I was so close to my turn that I was better off waiting rather than passing. I waited for the combine to get far enough ahead of me so I could see the traffic coming from the other direction was clear.

Unfortunately, when I went to make my left turn, someone further back in the line of traffic decided to pass, and, well, an unstoppable force met an unmoveable object, so to speak.


Pretty nasty looking, huh? I'm glad that driver wasn't going any faster, or I'd be roadkill. Of course, the crazy driver gets out and starts yelling at me. Apparently I shouldn't have let her hit me. My bad.

Long story short, the cop who showed up gave us both tickets. Mine was for "failure to signal." Which was bogus, since the officer took the word of a witness who wavered on that fact and of the other driver, who has a vested interest in saying I didn't signal, over mine.

Anyhow, the ticket was just thrown out, and I'm pretty excited. Take that, state of Illinois!

Wednesday, November 21, 2007

No wonder they lost

Is it just me, or has the entire nation of England lost their sanity?

We've been hearing lots of "war on Christmas" stories out of that country for a few years now. This year is no different. This Daily Mail article talks about a school replacing the normal, red-suited Santa with a green suited . . . something, because traditional Santa is "too commercial." Whatever. I'm not sure what they replaced him with, though. They say they're using the Eastern European Santa, who wears green, but the article mentions something about a green-suited gnome in an "elemental grotto," whatever the heck that is.

This, however, is the part that just boggles my mind:
School spokesman Sarah James said: "The red-suited Santa was created as a marketing tool by Coca-Cola, it is a symbol of commercialism."
Are . . . are you serious? Really? Is there actually someone in England who is that dumb? Seriously?

Stupid Blogosphere

Sometimes I hate being a small fish in the big pond that is the blogosphere. Why's that? Everyone is jumping at the bit because a "recent" study just reported turning fibroblasts into stem cells, which could make ESCR obsolete as we know it.

I'm bitter because I actually reported on the exact same thing . . . in June.

I guess if you're not "in the circle," no one cares what you have to say about anything.

*Grumble*

Monday, November 19, 2007

I'll take a democracy, please

Sometimes my fellow citizens scare me. I'm generally not belligerent about my countrymen's political decisions (or lack thereof), but this scares me: A survey amongst NYU college students found many of them willing to sell their right to vote.

What's the asking price? Apparently 20% of these students will give up their right for an iPod Touch, 66% will give it up for a year's worth of tuition, and 50% will give it up forever for the low price of $1 million.

I find the concept somewhat scary. We take a very dim view of those who would buy an election, either by stuffing the ballot boxes with scurrilous votes or by bribing people at any stage of the process to act unethically. While I can appreciate sentiments such as, "New York will always be a blue state, no matter how I vote," (Hooray for Illinois!) it still doesn't excuse such indifference towards such a right.

Here's a better way to think about it. Due to the shenanigans in Florida in 2000, Bush won the state, and thus the election, by something like 500 votes. Let's consider how much these students would cost to sway the election.

An iPod Touch costs $300. I don't know how much a year of tuition at NYU costs, but let's average it out to $20k. So, for someone to have changed the course of the 2000 election, either for Bush to have bought it or for Gore to reverse it, would be anywhere from $150k to $6 million. Considering how much political campaigns manage to raise during the course of an election . . . doesn't that seem a bit low to you?

Even if you want to quibble on the numbers, that 20% came of a survey of 3000 NYU students . . . so 600 would sell their vote for an iPod. That's still enough to sway the outcome of the 2000 election.

As I said, I tend not to begrudge people their politics, but this is just scary.

Saturday, November 10, 2007

Theoretical Biology

Earlier this year, I did a round-up on what I thought could conceivably be a biological explanation for vampires. I think such thought experiments are neat. I'm going to make you endure another.

This past week in my seminar course, we talked about this worm that has no digestive tract, no mouth, and no anus. It obtains all of its metabolic needs from bacteria which live just under its skin. The worm absorbs minor nutrients from the environment, mainly dissolved gases, and the bacteria use them to create metabolites which they share between themselves as well as with the worm. Sometimes the worm directly absorbs the bacteria for fuel as well. The worm's waste products are absorbed by the bacteria for fuel as well.

I find this to be fascinating, and we spent a good while wondering how situation would evolve. Since we were all molecular biologists, nobody had an answer. Still, I was left with one intriguing question:

What if people had turned out like this?

Think about it . . . no digestive tract at all, coming or going. What would this mean?

For starters, any joke using the punchline, "Wrecked 'im? It nearly killed 'im!" would never be known. Uranus would no longer be a funny planet name. No one could make fun of Preparation H or use "stomach problems" as an excuse to get out of work.

On a more serious note, many things would be radically different about people. You wouldn't have obesity, as all of our energy would be self-sustaining. Consequently, you wouldn't really have body-builders, either, as you couldn't get the additional energy that would need. Agriculture would never have developed, nor would hunting. What would have been the premise for the beginning of human civilization?

Of course, though we would have no mouths, we'd have to breathe a lot more, as those bacteria need the CO2 to build sugars with. Perhaps many more nostrils? Of course, with no mouth and no tongue, this leaves open the question of how communication develops. Perhaps vocal cords still exist in whatever airways we'd use, so there would still be some form of vocal communication, but it wouldn't resemble anything we call language.

And, well, reproduction is a whole other case entirely. Without a waste tract coexisting with the reproductive parts, would those parts have turned out the same? Or would they be entirely different as well?

Go ahead and add in your $0.02. I'm curious what the thoughts are on this one.

Sunday, November 04, 2007

Flash Portal

I haven't gotten to play Portal yet . . . silly me for not buying the Orange Box. Still, this seems to be a suitable (and ridiculously fun) alternative: Flash Portal.

Go. Enjoy.

Why is it a guessing game?

I'm sure I've posted about this at some point before. Let me be very specific about my point.

Perhaps I'm just a crank. I'm starting to suspect it's the case. Still, I heard a song today that riles me every time I hear it. The lyrics are below:
Draw me close to you
Never let me go
I lay it all down again
To hear you say that I'm your friend

You are my desire
No one else will do
'Cause nothing else could take your place
To feel the warmth of your embrace
Help me find the way
Bring me back to you

You're all I want
You're all I've ever needed
You're all I want
Help me know you are near
Who is this song about?

Tuesday, October 30, 2007

Science Shmience

I had the privilege of listening to a guest lecture by a rather distinguished researcher in plant viruses (viri?) Monday, and I'll get to hear him again on Wednesday. He seems like a smart guy, but I'm starting to wonder how we're ever able to tell the difference between people who are genuine geniuses (geniui?) and those who can throw up a screen of BS like you wouldn't believe.

I'm not necessarily saying this guy was the latter. But we spent the better portion of an hour listening to him talk about research . . . sort of. Imagine a class that spends about half of its time telling you what is known about a subject, while the other half is a lengthy explanation of what is not known. You might walk away wondering whether you learned anything. Now imagine that you've spent the last year of your life researching a subject, and you have to justify your time and money to someone. How would you feel if that entire presentation was, "Okay, here's everything we now know we don't know about the subject that we didn't know we didn't know before."

This, to me, is the problem with the fine line between the people typically dubbed "smart" and those dubbed "geniuses." The label comes only as part of perception. If someone seems to have a lot of knowledge about a subject we find complicated and confusing, we tend to label them as some form of smart, depending on how much they seem to know. Other times, we might understand the subject to a similar degree, but we'll call someone smart because they agree with us about it and/or can talk about it very well.

I'd clump a lot of theoretical physicists in the first category. My grades in quantum mechanics were always hit or miss, so I'm just barely able to grasp what they talk about when it comes to things like string theory or the behavior of particles inside black holes or . . . or . . . zzzzzzzzz. When they throw around their fancy terms and their complicated mathematical processes, I have to admit that they're probably first class geniuses.

On the other hand, how much theoretical science has been tossed out the window umpteen years later because experimental science showed that the previous ideas were just science fiction run wild? That's the red light that flashes in my brain when I hear those guys talk, and I'm not sure how to tell the difference between the geniuses and the guys who wish they could write for Star Trek.

The other category can fall into the political, but the basic idea is that we tend to imagine someone as a genius if they can talk about a subject in "smart," flowery language that expends a lot of $10 words without really saying much. This was the worst part about being a philosophy minor; I was always listening to these people rambling on and on in vague, showy terms trying to show off how smart they are. Half the time it's ridiculous terminology that people hide behind, but other times access to a dictionary and a thesaurus reveals just how little they just accomplished.

Again, the real question here is how do you tell the difference between people who are smart and people who have just learned how to look smart?

I guess that's something we all have to deal with. With the primaries coming up soon, I guess we better get our act together, too.

Friday, October 26, 2007

What a drag

While I was at ISU, I dreaded the issue of The Daily Vidette that came out every year after PRIDE, the campus GLBT group, held their drag show. I dreaded it because it always meant the front page was going to be a man in a dress, and not in that hilarious, "somebody just came up with a last minute Halloween costume" way.

I never complained to the Vidette, though, which suprises me considering how many other things I complained to them about. I guess I was just due, however, because UMSL has a similar group (PRIZM) who just held their 4th annual drag show. And wouldn't you know it, the cover of The Current, UMSL's student newspaper, was devoted to the drag show.

As it turns out, so was the back page. Full page photo spread, even. I wasn't very pleased when I saw one of those photos included a guy and a queen dry humping. Normally, I'd just ignore it, but I usually read the paper on the train. The night I grabbed this paper and started reading, I realized I'd been waving the picture around in front of some kids in the next seat. Beautiful.

I decided to do what any cranky prude does and complained on The Current's website. Hoo boy, did that earn me some wrath. It was like a siren song to the angry gay men, because I received a virtual earful from some guy named Mike.

You're welcome to examine the exchange. I think at times he's either cutting/pasting from a bunch of form letters or material that they use to deal with "homophobes" on the webernets, but I could be wrong. It just seems like he's having a completely different discussion at times, throwing in a couple of remarks directed at me just to keep things on track. Meh. I'm done with it. One can only read 10 page screeds about why you're a terrible person for so long before one walks away. I guess I'm not cut out to be POTUS.

Wednesday, October 24, 2007

*Grumble*

I'm not a big fan of the days when I'm stuck in my office studying or grading. I get hungry and have nothing to snack on. Today, I decided to do something about that and actually remembered the dollar sitting in my pocket.

I thought my luck was grand when I saw that a package of peanuts was a dollar. I fed in my money, plugged in my order and . . . watched as my peanuts spun on the spindle and held on from dropping by a hair.

Right now I'm amazed that this even happens outside of television. What a day.

Monday, October 22, 2007

An Accurate Description

Sadly, I'm still under a deluge of grading I have to do for the class for which I am a TA. My poor neglected, blog . . . oh, and the readers, too.

To tide you over, an anecdote from a conversation I overheard today:

Two other people (grad students? professors? post-docs?) were having a conversation in the bio department galley while I heated my lunch. I'm guessing their research involves ecology or zoology in some form because they were discussing tramping through forests that had bamboo across the path, so it sounded neat.

Well, that was until they revealed their goal. They were looking for signs of bushdog habitats. The best signifier of this? Scat. Feces. Poo. They flew off to some exotic location just to traipse through the forest looking for animal turds.

Isn't that exactly what you imagine for your life? Spend however many years earning a bachelor's degree, then umpteen more for that PhD, all to figure out whether or not some animal took a dump in the woods?

On the other hand, this doesn't seem like an inaccurate description of being a TA, so perhaps I should not judge.

Sunday, October 14, 2007

Is God responsible for natural disasters?

The other day I complained that I hadn't written about religious topics in a while. I guess God was thinking the same thing, because the very next day who should show up at my door but a pair of Jehovah Witnesses. Of course, it was slightly awkward, as I actually went to high school with one of them. I think at that point we both realized nothing productive would happen, as we'd played out a lot of arguments and discussions years ago. Granted, we were both high school kids then, so our ability to debate has probably improved, but there's no changing history.

In any case, the ladies wanted to discuss with me whether or not God was responsible for natural disasters, especially because some people argue that events like hurricane Katrina were God's judgment upon those people.

Reading their literature, there isn't much to the discussion they added. I agree with them that many of the fatalities that can result from natural disasters are the fault of people, not God. There was plenty of warning that Katrina would be incoming, and yet there was still a failure, both personal and governmental, in evacuating the city. Humans were responsible for levies and maintenance, not God. Humans neglect to enforce building codes or move to areas with high risk weather (tornadoes, hurricanes, earthquakes, etc.).

Still, there is some room for God in this. Nothing happens without his permission in this world. So he at least allows natural disasters to occur. Why is this? Is it judgment upon people?

I think it is next to impossible to find answers when we look at any of God's actions and ask, "Why?" Sometimes this is because we may never be able to understand God's perspective on the matter. Sometimes things only become clear in hindsight, and that could take years or even centuries to become apparent. Sometimes there might be so many consequences of an event that it is impossible to consider everything that happened and all of the events which follow as a result.

In the end, nothing really new. But then, the conclusion to the JW article was answerless as well, so I don't feel so bad on the matter.

Tuesday, October 09, 2007

The stupidest monsters ever

Actually, I think Douglas Adams (Hitchhiker's Guide to the Galaxy) had the best one. I forget the name of the creature, but it was apparently a flesh-rending horror. However, it was so stupid that it would think that if you couldn't see it, it couldn't see you. The key to escaping a horrible death was to cover your eyes if you made spotted it.

Anyhow, that theme brings us to an article about some of the dumbest monsters in Dungeons and Dragons. I'm inclined to agree, although I'm thinking that having a room of death with just the floor, ceiling, and walls is not enough.

Hat tip to Shamus, who generated a great discussion, including the guy who made one of the stupid monsters. Fantastic.

The Minimal Bacterial Genome

Hey folks, grad school is tough business. So, in lieu of a real post (not yet, anyhow), I thought I'd share my project for the last few weeks or so. Enjoy!
_______________

Introduction
The minimal genome is a concept that has garnered significant scientific interest in recent years, for a variety of reasons. It is defined as the core, essential genes that an organism requires to sustain life. This is typically a greatly reduced gene set from the organism’s natural genome, although this will vary by conditions. A sulfur-reducing bacterium will have a different minimal genome than one which reduces oxygen, and these will be exceedingly different from any multi-cellular organism. Growth conditions such as nutrients provided by the medium may also play a role. The addition of amino acids to a bacterial medium would render said synthetic genes unnecessary, while providing one type of sugar would render transporters or metabolic genes for other sugars unnecessary. Thus, while the concept of a minimal genome can be generalized for total life processes, it is still dependent on the defined experimental conditions under which the list of essential genes is determined.

Various species of bacteria have been examined for their minimal genome, though some other organisms have been the subject of such studies as well, such as S. cerevisiae and C. elegans. Bacteria remain the simplest organisms to study, as their genomes are usually in a state of reduction already. Many will have less than 8,000 protein coding genes, though those with less than 1,000 genes already have a metabolically simplistic lifestyle, making them ideal candidates for minimal genome studies. Examination of such organisms has led to tentative estimates of minimal gene sets, ranging between 200-500 genes.1

Why the minimal genome?
There is much information that can be derived from an understanding of the minimal genome. With an understanding of what essential enzymatic functions are necessary for life to take place, progress towards understanding pre-biotic existence and the first bacterial organisms can be made. Additionally, species specific experiments in deriving the minimal genome can grant further clues as to the developmental path a given species has taken.1,2

A more specific use for the minimal genome, however, is the Mycoplasma laboratorium envisioned by Craig Venter. Venter hopes to use the determination of a minimal genome to synthesize a minimal bacterial organism. By utilizing a “blank slate” bacterium, researchers could introduce genes of their choosing with, purportedly, minimal systems interactions. This would allow for the efficient production of materials through a biological system, according to Venter. Biofuels such as ethanol are the most popular possibility at the moment, but other potential M. laboratorium inserts include genes for plastics or pharmaceutical drugs. It is quite possible that the next generation of biologically synthesized materials will come from plugging genes into a minimal organism.3

Venter recently reported an interesting step towards the creation of a synthetic organism. Researchers extracted the genome of M. mycoides, with little accompanying protein, and utilized PEG-mediated insertion to transplant it within M. capricolum cells. Antibiotic resistance coded in the donor genome selected for successful transformants. The result was recipient microbes with both the phenotype and genotype of the donor organism. This is a promising result, showing that a complete genome can be inserted into an organism and can still functionally express its own genes.4

Researching the minimal genome
There are many potential ways to study and understand the minimal genome. Some would start by defining the categories of either essential functions or essential genes. At the most basic level, cellular processes can be broken down into metabolism, compartmentalization, and information transfer. Whether the groupings are defined by specific functional categories (Figure 1) or more generalized categories of function (Figure 2), proper division of the genes is essential for understanding what properly contributes to life, as different categories may shape our understanding of what constitutes an “essential” function or gene.2,5

In general, two different approaches may be taken towards establishing a minimal genome. The first of these is a bioinformatics approach. Researchers have compared the genomes of various organisms, particularly bacteria, and examined which genes, or at least gene functions, are conserved across a wide variety of species. Those functions which are nearly universal could be considered essential, as nearly every form of life retains them in some form. Some researchers distinguish between “persistent” genes, those present in a select number of genomes, and “conserved” genes, those seen everywhere. This is usually an attempt to minimize the possibility of missing an essential function because it is not structurally conserved.1,2

A different approach to this is to attempt to use computational models of cellular pathways to determine a minimal genome. Though a system-wide approach is thought to be unfeasible, combining models of individual systems, especially metabolic networks, has seen some success. However, one method of approach at a system-wide calculation uses a minimal model and then derives the genetic pathways backwards, looking at biochemical “modules” as they interact with the components of the model. As with any computational approach, however, experimental verification of any data is necessary.1

The other approach to determining the minimal genome is experimental, by reducing the genome of existing organisms. Knock out a gene, and the survival of the clone will verify a non-essential gene, while knockouts of essential genes will be fatal. The method of distinguishing transformants is important, as extra gene copies may allow a normally fatal knockout to be survivable. For example, if a protein is secreted from the bacteria, a knockout of that gene may not be fatal as long as there is another bacterium in the population that has a wild-type copy of the gene.1

There are three general approaches to gene knockout, all of which are somewhat similar.

Suicide Plasmids
In this method of deletion, a plasmid is introduced to the cell with two homologous “arms” whose sequences flank the sequence to be deleted in the genome. After the plasmid is integrated into the host genome, intramolecular recombination can occur between either pair of homologous arms, resulting in either the expulsion of the plasmid DNA or the “scarless” deletion of the sequence of interest (Figure 3). Suitable screening for the appropriate event is dependent upon the deleted gene and the original marker used for clonal selection.1

Linear DNA
This method of deletion utilizes linear DNA fragments rather than plasmids. The principle remains the same, with flanking homology arms allowing recombination events to excise genomic DNA in favor of the insert. There are a variety of methods which follow from that in order to remove the sequences between the homology arms in the inserted fragment. Regardless, the end result is a knockout with little to no “junk DNA” left over from the insertion, leaving a clean knockout (Figure 4). One attraction to this method is that large fragments of DNA can be excised by this method, eliminating multiple genes at the same time if desired.1

Transposon insertion
The final deletion method utilizes transposons, DNA sequences which can excise themselves from a plasmid or genome and reinsert into another location by using a specialized set of enzymes. This method is random, lacking the possibility of a targeted knockout. In addition, it adds new DNA to the genome, precluding multiple knockouts in one transformant due to the undesirability of introducing large amounts of new material into the genome. However, this method is likely the simplest of the three, not requiring specially designed plasmids or PCR products for each gene to be tested.1

Essential genes of a minimal bacterium
In their 2006 paper, Venter et al examined Mycoplasma genitalium for a minimal genome experiment. M. genitalium is a pathogen of the human urogenital tract, a living arrangement mild enough to be conducive to a reduced lifestyle. It has a genome 580kb in size, coding for 482 proteins, giving it one of the smallest genomes discovered. This already reduced set-up, along with the low genetic redundancy characterized by few of the genes being found in paralogous families (6%), makes M. genitalium a suitable candidate for minimal genome studies.5,6

The study in question is a follow-up of a 1999 study attempting to examine the same question. Having determined that their previous results were not reliable due to the labeling as non-essential of genes known to perform essential functions, the group sought to correct the mistakes of the 1999 methods and analyses.5

Procedure
The researchers introduced a plasmid containing a transposon (Tn4001) via electroporation in the M. genitalium liquid cultures. These transformants would then be spread on a plate and monitored for colony growth, with allowances of up to four weeks for colonies to develop so as to catch slow-growing clones. Antibacterial resistance coded by the plasmid allowed for selection of successful transformations.5

To verify insertions, a single-primer PCR strategy was utilized. After isolating the genomic DNA of a colony, a primer of the sequence in the transposon was elongated and then sequenced. By BLASTing the sequence found, the researchers were able to verify successful transposon insertions and determine which gene, and the location within the gene, the transposon disrupted.5

If there was any genetic redundancy, such as multiple copies of a gene within the colony, an essential gene knockout could be non-fatal. To verify that no extra copies of the knockout genes were present, the researchers performed PCR with primers for the gene found to be knocked out in the BLAST searches. If there is only one copy of the gene, there would be no PCR product. The group found, unfortunately, that each colony tested seemed to display wild-type genotype.5

To analyze this occurrence, the group performed quantitative PCR on the colony DNA using one primer for the knockout gene and one for the transposon. This led to the discovery that most of the colonies contained at least two different knockouts. The researchers concluded that the M. genitalium, coming from the liquid culture, had both a high transformation rate and a tendency to aggregate when spread to solid media.5

To correct for this, the group performed “filter cloning,” running the colonies through a 0.22μm filter and then replating the clones. This successfully led to the isolation of clones from the original colony into subcolonies. Transposon insertion was then verified as with the primary colonies. Colonies that were considered useful for analysis contained <1%>5

Results
The researchers examined 3,321 colonies and subcolonies, with 62% of the primary and 82% of the secondary colonies providing sequence data allowing them to map a transposon insertion. From these colonies, 2,462 insertion sites were mapped to the genome. In order for an in order for an insertion to be considered a knockout, it had to appear between the first three codons of the 5’ end of the gene and before the last 20% of the 3’ end of the coding sequence. This was to minimize the identification of a gene as non-essential which was merely tolerant to the insertion.5,6

As the researchers continued to examine colonies and subcolonies, the number of new insertion sites and successful knockouts reached a plateau, indicating that they were reaching a “saturation” point of non-lethal inserts (Figure 5). Of the 2,462 insertion sites identified, 84% were mapped to protein coding genes. No RNA coding sequence (rRNA, tRNA, etc.) insertions were found. From this, an initial estimate of 100 non-essential genes, out of 482 protein-coding genes, was determined.5

Discussion
Several sites of transposon insertion were encountered much more frequently than others (Figure 6). Though the original authors examine this amongst all colonies as well as with only primary or secondary colonies, the data still shows a very high rate of insertion within very specific genes. Four of the genes listed in figure 6 (MG339, 414, 415, 428) represent nearly 31% of the total clonal pool. Correlation of these genetic “hot spots” to figure 1 shows that the size of the genes is not an issue.5

The authors do not offer much in terms of an explanation for this phenomenon. They suggest that the clones for those insertions grow fast enough that they are discovered often. They also suggest that the transposons preferentially jump to the locations in question, though without any explanation as to why that might occur. Is there some sequential or structural feature of the loci in question that makes them attractive to the transposons? It is an area for possible further work.5

While the authors did find 100 non-fatal knockouts, they bring adjustments to this list because of uncertainties in their findings, preferring to offer a conservative estimate of the minimal genome. Several factors went into ruling out genes from the list. Since they did not verify that a knockout created no transcript or protein product, they relied on their insertion criteria listed above. However, if a knockout appeared in a primary colony as part of a mixed population but did not appear in a secondary colony after filter cloning, the authors ruled it to be an essential gene. It is likely that the knockout, in those situations, was due to a gene acting in trans, either from an excreted metabolite or an excreted protein.5

Additionally, three proteins deemed critical for cell survival were listed as essential even though successful knockouts were achieved. Knockouts for three genes encoding phosphate transporters were discovered, though this is an unusual result. A cell must import phosphate, so it would be unlikely that all three genes could together be unessential. Knockouts were also found for three genes which putatively encode phosphonate transporters. The authors surmise that the various transporters might take on the role of the knockout due to relaxed substrate specificity. Another possibility they suggest is a pathway where phosphate and phosphonate are freely converted, though they do not assign a gene to this function. However, because of this they discrepancy the authors assign all three phosphate transporter genes essential status.5

The final measure used in ruling out knockouts was limited redundancy. Though M. genitalium does have few genes shared across paralogous families, two paralogous families were completely knocked out. This included families for lipoproteins (MG185, 260) and glycerophosphoryl diester phosphodiesterases (MG293, 385). Again, the successful knockouts might be due to the ability of the remaining family member to fill the role of the knockout. Still, the authors included one protein from each family as a conservative estimate of the essential genome. This increases their count of essential genes to 387 out of 482.5

In the 1999 study, the researchers found around 130 non-essential genes. Only 67 of those genes were part of the list of knockouts found in the 2006 study. This is a significant difference, one which the authors attempt to explain. Previously, they found knockouts for seemingly essential genes such as tRNA synthetases (MG345, 455) or DNA polymerase III subunit α (MG261). The difference in procedure for the current study seems to account for this discrepancy, however. In the 1999 study, the authors did not plate their transformants on solid media but grew them solely in liquid pools. This would allow for genes to work in trans and show essential genes to be survivable knockouts, and is thought to be the case for a group of lipoproteins, as well as an extracellular nuclease. While this is the most significant change, a few other minor alterations to the previous experimental set-up are thought to have factored into the different list. The use of a different medium, as well as a different antibiotic used for selection, could have led to the requirement of a few genes such as lipoprotein MG395 or lipase/esterase MG310.5,6

On the other hand, the current study also found “non-essential” genes which would seem to be crucial to the metabolism of the genome. The genes in question are related to DNA recombination and repair, and their absence should be detrimental to the bacteria over time. It is thought that the colonies were not examined over a long enough period of time for these missing genes to become critical, or that another enzyme was able to fulfill the role of each individual knockout.5

Several other strange results arose as well. No insertions were found for any of the cytoskeletal proteins, which is at odds with previously reported work. Another group apparently used a recombination method to excise a cytoskeletal protein HMW2 (MG218), and did not find the deletion to be fatal. The authors of the current study do not have an explanation for the discrepancy. The size of the gene is not the issue, as it is relatively large compared to most other M. genitalium genes. The authors guess that the knockout could hamper growth speed enough that it was not found in their mutant screens. This seems unlikely, as their protocol involved watching for colony growth for a period of four weeks. There is no mention of unusual replication time for the transformant in the previous work as well.5,7

There were several mutations which did affect growth speed of the colonies, though the authors are unable to explain the reasons for these. Knockouts for dihydrolipoyl dehydrogenase (MG271), a component of the pyruvate dehydrogenase complex, grew ~20% more slowly than wild-type M. genitalium. The enzyme normally oxidizes dihydrolipoamide to lipoamide, a redox component for the generation of acetyl-CoA. It seems unlikely that a cell would be able to function if this portion of the TCA cycle were to be absent. Since the knockouts are not verified by gene products, it is possible that the insertion results in an enzyme of reduced function rather than a total knockout. It is also possible that, once again, reduced substrate specificity allows another dehydrogenase to fill the role of the knockout.5

Other insertions resulted in growth speeds ~20% faster than wild-type. These included lactate/malate dehydrogenase and two conserved, hypothetical proteins (MG460, 414, 415). The authors do not suggest any sort of function for the hypothetical proteins. They do mention that there are enzymatic functions known to be performed by the bacteria which have not be assigned to specific genes yet, although it would be difficult to assign any function on the basis of altered growth speed alone. The lactate/malate dehydrogenase is an unusual case. There is nothing outstanding about the reaction catalyzed by the enzyme which suggests that it would slow down the growth of the organism so severely. It also seems unlikely that these reactions are redundant or unnecessary for cellular proliferation. The authors suggest that the gene acts as a metabolic “brake” on bacterial growth. Such a mechanism may have evolved to protect the organism, as fast growth would attract the attention of the host immune system and destroy the bacteria.5

Based on the listings of essential and non-essential genes, it would seem that there is still much to be discovered and understood about cellular life at the molecular level. The authors list all of the genes found in each list as supplemental data, but they provide a summarizing figure (Figure 7) for several metabolic pathways, indicating with black boxes those that were non-essential in this study. Many proteins end up in this category when a cursory analysis might indicate otherwise. For example, a subunit of ATPase (F0F1-ε) was found to be non-essential, while conventional wisdom would say that all the subunits of such a critical enzymatic complex would be necessary for cell survival. In the figure, several pathways are listed with purported functions that ought to be present but have not been assigned to specific genes or proteins. From the 100 non-essential genes, 48 were from hypothetical or unknown genes. It is possible that those genes represent non-existent products and thus would be unnecessary for the cell. However, 110 of the 382 essential genes came from unassigned or hypothetical proteins. Though it is possible that many of these are simply proteins with known but unassigned function, it is also possible that many of these perform functions that have yet to be characterized. When nearly a third of the minimal gene set has unknown function, the question naturally arises as to how much is actually known about the fundamental metabolic functions of a cell. Further study into this, as well as the other metabolic phenomena, could greatly enhance our understanding of the biochemical lifestyle of the cell.5

Conclusions
The authors produced a list of 382 essential genes not found in insertion knockouts. This list is increased to 387 through conservative estimate of gene necessity. This brings the group much closer to the minimal genome than previous studies have, by means of the stringency of the knockout criteria and the saturation of their mutations. Unfortunately, the list is merely putative. A thorough examination would examine each knockout for the presence or absence of protein product or enzymatic activity. Additionally, sequential knockouts would be more helpful in identifying the actual list of essential genes. As seen above, many of these knockouts may be tolerable when only one is gone, but if a second “non-essential” gene takes up the role of an absent protein, the two do not belong on the list together. A cell may not actually function in the absence of all 95 proteins designated non-essential in this study.5

Venter’s goal of a synthetic organism is brought closer with this, as his next logical step would be to synthesize a genome containing the list of essential genes found in this study. Venter’s group actually accomplished this goal, announcing it to media sources in early October. Combined with the successful demonstration of the ability to transplant a genome into a recipient bacterium, it would seem that the creation of Mycoplasma laboratorium is imminent.8 It remains to be seen, however, whether or not it will become the industrial powerhouse Venter purports it to be.

References
1. Fehér, T., Papp, B., Pál, C., & Pósfai, G. (2007) Chem. Rev. 107, 3498-3513.

2. Danchin, A., Fang, G., & Noria, S. (2007) Proteomics 7, 875-889.

3. Highfield, R. “Man-made microbe ‘to create endless bio-fuel.’” Telegraph.co.uk. August 6, 2007. October 9, 2007. http://www.telegraph.co.uk/news/main.jhtml?xml=/news/2007/06/08/nbiofuel108.xml

4. Lartigue, C., Glass, J.I., Alperovich, N., Pieper, R., Parmar, P.P., Hutchison III, C.A., Smith, H.O., & Venter, J.C. (2007) Science 317, 632-638.

5. Glass, J.I., Assad-Garcia, N., Alperovich, N., Yooseph, S., Lewis, M.R., Maruf, M., Hutchison III, C.A., Smith, H.O., & Venter, J.C. (2006) Proc. Natl. Acad. Sci. USA 103, 425-430.

6. Hutchison III, C.A., Peterson, S.N., Gill, S.R., Cline, R.T., White, O., Fraser, C.M., Smith, H.O., & Venter, J.C. (1999) Science 286, 2165-2169.

7. Dhandayuthapani, S., Rasmussen, W.G., & Baseman, J.B. (1999) Proc. Natl. Acad. Sci. USA 96, 5227-5232.

8. Pilkington, E. “I am creating artificial life, declares US gene pioneer.” The Guardian October 6, 2007. October 9, 2007. http://www.guardian.co.uk/science/2007/oct/06/genetics.climatechange

Figures
Figure 1.5 Physical map of insertions found within the M. genitalium genome. Genes are colored by the designated key. Arrows pointing down indicate an insertion from the 1999 study, while arrows pointing up indicate an insertion from the 2006 study. Red, filled arrows indicate a location where 10 or more insertions were found.

Figure 2.2 An alternative system for classification of basic life functions.


Figure 3.1 Suicide plasmid-mediated gene deletion. See Reference 1 for more details.


Figure 4.1 Linear DNA-mediated gene deletion. There are several different means of achieving complete deletion depending on the nature of the flanking sequences used. See Reference 1 for more details.

Figure 5.5 Graph showing the number of insertion sites and disrupted genes versus total acquired sequences. The data indicates a saturation point for the insertions.

Figure 6.5 The frequency of insertions (y-axis) at physical locations within the genome for both colonies and subcolonies. Genes with a particularly high frequency of insertion are labeled.


Figure 7.5 A summary of metabolic pathways utilized by M. genitalium. Black boxes indicate non-essential genes. Orange names are known proteins, while green names are known functions not yet assigned to a gene. Transporters are color-coded by system. See Reference 5 for more details.

Wednesday, October 03, 2007

Distractions Abound

Y'know, a responsible blogger might have followed up his post, and its consequent linking to by a much larger blogger, with further posts to convince new readers to stay. Then there's me, the guy who disappears for days at a time.

So, what's my excuse this time? Well, crazy school stuff. Busy, busy, busy.

Also, in much nerdier news, I've been preparing for my new Thursday night activity. I'm starting a D&D game with some buddies, and yours truly is the GM. I'm probably cementing my single status for the next 10 years, but my glass is still half-full. I'm looking forward to it.

My other time drain has been this: The Order of the Stick. It's another webcomic about, about a bunch of D&D players. Also, they're stick-figures. It's hilarious, in an incredibly dorky kind of way. I recommend it, if that's your kind of thing.

Friday, September 28, 2007

What makes a great RPG?

I feel kinda guilty for talking about either science, politics, or video games lately. I just haven't had a lot of truly interesting religious thoughts. At least, not interesting enough to share here.

In any event, over at Twenty Sided, Shamus asked what made a great RPG. I gave my answer there, but I thought I'd share my thoughts and ask for yours.

Part of the trouble everyone had in answering this question was that there are two very different conceptions of an RPG. Western RPGs tend to let you pick a role and then set you loose to play in the sandbox. Japanese RPGs tend to give you a role and then let you play it out. The characteristic that connects them both is that you typically don't engage in a lot of fast, frenetic gameplay (although that is allowable). The games aren't based on fast fingers and great keyboard skills alone, but the time and progress you're willing to put in. You'll have a character who will grow more powerful over time, with in-game statistics that evolve as the game advances, and sometimes options for acquiring better equipment as well.

So, what makes a great RPG to me? The same thing that makes any game great: It's fun to play.

That being said, I should address some rather specific issues.

A lot of people in Shamus's comments harped about freedom and story. They wanted a story that was strong and compelling while being free to make some/any decision in the world they've been planted in. I think both are overrated. Story is necessary to a degree, yes, but
not every game requires a story that is novel or ultra-compelling. The Paper Mario series, for example, was ridiculously fun, yet had a story that most would characterize as shallow. Freedom comes out either way. The Elder Scrolls games were a very open-ended, while any Final Fantasy game will put you on a very specific path ("railroading"). Both are great fun, though.

Three issues that I see as necessary for a great RPG: Advancement, Variety, and Pay-off.

If you're playing a game where the core mechanic revolves around statistics, it should be both reasonable and worthwhile to raise those stats. It shouldn't take 200+ hours to become powerful, but you shouldn't spend a long time playing just to earn increases that are nearly irrelevant. Players like to think that if they start off knowing the magical equivalent of a cigarette lighter, they'll eventually be able to detonate nuclear warheads from their fingertips.

Variety is necessary in any game, but RPGs can be won or lost on this issue. If all the enemies are just palette swaps as you progress ("Oh look, now the soldiers are wearing green instead of blue! Scary!"), there's very little sense of advancement. If you're stuck in some city for half the game, you're going to start feeling wanderlust and boredom. And this ties directly into advancement, too. Every rookie Jedi plans on taking out the dark lord of the Sith, every 1st level adventurer wants to go toe to toe with a dragon. That kind of variety gives a game a meatiness that a good story just can't account for. After all, if the story is great but the game play isn't any fun, why not just turn it into a novel?

Finally, I should note the pay-off. If you play the game for 40+ hours, you ought to be a monster-crushing legend. You ought to be rewarded for sticking it through for so long. An epic boss battle? A tear-jerking wrap-up to the story? Whatever your prize is, the pay-off should be satisfying. Too many games offer up 30 seconds of video as a denouement and expect players to be happy with it. Such a decision can make the difference between an okay game and a legendary game.

If you've stuck with me for this long, good. I just have a few more notes to make, as the original question also asked what mistakes can make a good RPG bad.

My first example is "The Bad-Guy-Bait-and-Switch." I'm sure you'll recognize this. You've spent the game chasing after the Bad Guy, just waiting to get your hands on him and dispense some sharp, stabby justice. Suddenly, you're told he's not the real Bad Guy. Maybe he was being controlled by the Big Bad Guy. Maybe he was just a flunky for the Big Bad Guy. Maybe you just misunderstood his actions for the last 20 hours and didn't realize he was trying to fight against the Big Bad Guy. Either way, your emotional attachment to this villain is now gone, and you're left to fight some Big Bad Guy for reasons that are fuzzy at best.

Wee.

My next example is the deus ex machina. This involves somebody rescuing you from defeat, rather than allowing you to achieve victory alone. Perhaps the BBG is just too powerful for you, and some guy finishes the job when all seems lost, or weakens him enough for you to strike the final blow. Perhaps your dead parents/friends/lover comes to your side and saves you from the BBG's devastating attack. Either way, you are not a hero, just an "almost-victim." You're forced to watch the end of the game as a spectator, not a participant.

Pass.

Almost as bad is the touchy-feely story. Your characters bicker and whine a lot and ultimately get in touch with some very sensitive issues and feelings. This can be touching if done right, but almost always ends up trying your patience. When I want to listen to whiny emo kids, I'll just go on MySpace, m'kay?

Finally, I should mention a non-story related faux pas, especially since I didn't feel like ruining any plot devices by naming names. While the game mechanics should be satisfying, an overly-complicated system can make the game too intimidating and ultimately drive away all but the hard-core players. As Final Fantasy games evolved, this started to become a problem. In VI, it was "espers," which allowed every character to learn every spell, ultimately leaving the characters with only superficial differences. In VII, it was a goofy system of "materia" which granted abilities in complicated mixing and matching schemes. In VIII, you had "guardian forces" which bonded to the characters, as well as magic that was siphoned off of enemies and turned into stat boosts. Ten was the worst, with its gargantuan grid of spheres offering skills and spells and stat boosts to whoever would dare probe its vastness. If none of that made any sense to you, then you're already aware of the problem I'm describing. If you have to study to understand the system, fun gets lost somewhere in there.

Well, thanks for sticking around to the end of this lengthy, rambling post. Maybe in the future I should blog about what makes a great blog post. Not that I'd know anything about that.

This day in history

Most significant of all: I was born. Awesome. Since some of you might not care as much, I need to make the day relevant to you. So what else happened?

1066 - William the Conqueror invades England . . . interesting.

1867 - Toronto becomes the capital of Canada. Meh.

2003 - Final game played at Veterans Stadium in Philadelphia. I guess if you're a Pirates fan (all three of you), this is interesting.

Hm . . . apparently if I were Catholic, I'd know that I share feast days with Saints Leoba, Wencenslas, Lorenzo Ruiz, and Aaron of Auxerre. The more you know.

Any other famous birthdays? Hm . . . Confucius in 4BC. Interesting. Let's see, sports star I've never heard of . . . actors I've never heard of . . . oooh. Apparently I share birthdays with Janeane Garofolo (1964), Moon Unit Zappa (1967), Gwyneth Paltrow (1972), and Hilary Duff (1987). Neat.

Okay, maybe it's not that exciting of a day. I find it to be an important day.

Monday, September 24, 2007

Propaganda on campus

If you haven't been paying attention, then you may not have heard that Mahmoud Ahmadinejad, President of Iran, will be speaking at Columbia University in NY this week.

I've seen all kinds of snarky comments floating around. Some like to point out that ROTC isn't allowed at Columbia due to the military's "Don't ask, don't tell" policy, but the President of a country where homosexuality warrants the death penalty is okay. Others have noted that since Ahmadinejad was involved in the hostage crisis involving our embassy in Tehran so many years ago, it would be fitting for Columbia students to hold him hostage for a year or so.

All clever quips aside, I'm just baffled by the level of intellectual denial, on so many levels, that has to take place for Columbia administrators to think that this is a good idea.

First is the absurdity of asking the President of Iran to speak at an American university. Do they forget his repeated calls for the utter destruction of Israel and the US? Have they ignored our government's repeated warnings that Iran is actively waging war against us in Iraq? What possible "dialogue" could fruitfully result from allowing this guy a platform?

Additionally, do these people not understand the value of such propaganda? If this is a country that thinks we're a "paper tiger," what is going to be the result of letting their President just walk onto our soil and lecture us? Have they ignored the usual pattern from his letter to President Bush several months ago?

I'm left in utter disbelief that there are people who think there is something valuable to be gained here. Nothing good can come of this.

Update
Looks like I'm not the only one who thinks so. Captain Ed scolded Columbia for the results of this debacle.

Sunday, September 23, 2007

Fantasy Science

I have a bunch of friends who take part in fantasy football leagues. I'm not much of a football buff, so their prolonged conversations about the matter tend to make my mind wander. Still, it gave me a humorous idea.

Why not have fantasy science? Each participant assembles his "research team" of scientists. You can have them work on any project you want, but they'd have to be working together. You couldn't get a psychologist to work on a physics project unless his involvement made at least remote sense.

Then, you assign points to the players over the "season" based on the number of publications members of your team co-author, research funding they pull in, or any special recognitions or awards (departmental chairs, ACS/AAAS recognition, etc.).

Hard to pull off? Oh yeah, especially because you'd be hard-pressed to even find scientists who care that much. On the other hand, how hilarious would this be if someone actually made it happen?

Saturday, September 22, 2007

Super Happy Weekend Fun Poll

I'm working on a presentation this weekend, so no political rantings, scientific drudgeries, or philosophical musings. Instead, I thought I might get the rest of you to participate (all 3 of you, or however many actually manage to return).

The new season of Heroes starts Monday, so I thought it might be a good time to break out the question that was asked of me: If you could have any of the Heroes powers, which one would it be?

I think it's a better question than usual. Most other superheroes tend to be overpowered (Spiderman, Superman, etc.), so you usually ask for a package deal. The Heroes cast seem to be one-shot characters.

Your choices:
  • Self-healing (Claire)
  • Healing others (Linderman)
  • Remove memories/block powers (Haitian guy)
  • Create illusions (That one lady)
  • Pass through solid objects (DL)
  • Super strength (Nikki/Jessica)
  • Manipulate electronics (Micah)
  • Communicate with electronics (That Israeli soldier-lady)
  • Manipulate space-time (Hiro)
  • See the future (Isaac)
  • Telepathy (Matt)
  • Manipulate people (Eve)
  • Radioactivity (Ted)
  • See how things are "broken" (Sylar)
  • Invisibility (Australian guy)
  • Appear in people's dreams (That Indian kid)
  • Locate any other hero (Molly)
  • Fly (Nathan)
  • Absorb powers (Peter)
Did I leave anyone out? Vote in the comments, I don't know how to make a poll. Also, feel free to discuss predictions for the new season.

I think I might go with flight. I'd enjoy it more than any of the others without the risk of abusing it, and it comes with far fewer drawbacks than some of the "cool" powers. Linderman's ability to heal others would be nice, but he's right that the weight of only being able to heal the world's wounds one at a time would be taxing.

On the other hand . . . if I had Hiro's powers, I could finally go back and meet Jesus.

After further thought . . . I couldn't be trusted with invisibility. Who could?

By the way . . . yes, I know Blogger allows you to add a poll to the blog. The problem is, it adds it to the sidebar, not in the post, which really screws up the formatting on the page. I really ought to hire a professional to deal with this stuff for me. And when I say "hire," what I really mean is "wheedle into working for free."

Wednesday, September 19, 2007

More humor in science

As I mentioned before, I'm taking a plant biotech class, and we've been talking about making transgenic plants (genetically modified organisms, GMOs). Of course, this brings up a classic paper where RNAi (RNA interference) was discovered. Sometimes overexpressing a transgene in a plant can cause the plant to use the transgene against the same copy of the natural gene and eliminate both of them, effectively causing the opposite effect of what the researcher may have intended in the first place.

Of course, when discussing a sample scenario in trying to avoid this, I asked my professor a question about this and her response made me laugh:
Co-suppression occurs as a result of overexpression with the 35S promoter – it’s possible if you used a different promoter, the plant wouldn’t be so pissed off and turn off all gene production.
I had to laugh. How often do your professors talk about a plant getting "pissed off" by overexpressed genes?

Tuesday, September 18, 2007

The longer you work here, diverse it gets

Okay, maybe there's time for one news article. The Current is UMSL's weekly student newspaper, and this week's issue is a doozy. I've been critical of campus papers for being sophomoric, uninformative, or (in the opinions) downright nonsensical. This is an actual news article, but I'd challenge you to tell me what it's actually about.
"We live in a global society," said Malaika Horne, chair of the Chancellor's Diversity Initiative. "How can you interact with different nations if you can't interact with different ethnic groups in your own country?"

The Chancellor's Diversity Initiative, previously known as the Task Force on Diversity calls itself "cultural diversity in action."

According to Horne, they want to first enhance diversity on campus. Then, identify what is already occurring, find the gaps that exist, then take diversity to the next level.

The initiative is actively taking a role in shaping the acceptance of a diverse population at UM-St. Louis.

"We're walking the walk," said Gerda Ray, Associate Professor of History. "We make sure the initiative is diverse, including faculty, staff and students." Ray has been a member of the initiative since it was started in 2004, when it was started as a task force.
Okay, so what is this "diversity initiative?" No idea. The article does little to say, beyond quoting lots of diversity claptrap from members of the task force (or whatever it is). What does this group do? Sit around and talk about the diversity on campus and its diverse groups. What does that mean? They never say. It's probably the standard, "ethnic/minority/sexuality student groups" and so forth. I always feel a little left out when people go on about diversity without mentioning me. When do I get my White Student Union or the Straight Student Alliance? (By the way, if you can't read sarcasm, you're best bet is to go up to that "back" button on your browser and start clicking for all you're worth)

But why on earth was this article, with about 12 paragraphs of sloppy boot-licking, even written? Well, from what I can tell, the "initiative" wants to change the photographs representing the school, so that more "diversity" is represented therein. In other words, there's too many white people in the pictures. They don't say it, but I'm willing to bet that's the end result. Is it a legitimate grievance? No idea.

My main gripe here is the utter incomprehensibility of the article, the density and silliness of the quotes, and the paucity of actual news to be reported. What was the point of all of this? And why do these people get paid to sit around and slaver about diversity? Remember when universities were actually concerned with educating students?

Science in lieu of news

Oh, there's so much happening in the news lately, and so little time to blog about it right now. I'll get around to it before week's end, I suppose, but in the meantime I shall thrill you all with some scientific geekery. I'm supposed to be giving a presentation next week on microbial bioenergetics, and my initial paper topic fell through. So, since it won't be my presentation, I thought I might share my thoughts with you suckers interested readers.

Recently, the genome for an exotic microbe known as syntrophus aciditrophicus was sequenced. The link goes to the PDF of the news article. I'd originally read it as an HTML story, but I'm not sure if that's open access. You may need access to Science to read these things anymore.

Anyhow, the microbe is already interesting because it's a syntroph. This means that it can't exist on its own but relies on a symbiotic relationship with another microbe, typically a methanogen. S. aciditrophicus creates H2 in the course of its metabolism. However, build-up of the gas shuts down its metabolic processes, making them energetically unfavorable. Thus it partners with another microbe which can utilize the H2 and thus survives.

This diagram take from the article linked above
There's quite a few syntrophs out there, and they have similar metabolic situations. What makes the genomic sequence of S. aciditrophicus so interesting is that it's missing all kinds of genes that they would expect to be there for the metabolism it seems to perform. Many of the genes found have only limited homology to known genes with appropriate functions, but many are just simply not there.

This leads to all kinds of questions about how the thing actually survives. Does it utilize its partner for these missing steps? Does it do the steps with some protein which simply hasn't been identified? Or does it use some novel pathway for accomplishing these processes?

It's an exciting mystery as far as I'm concerned. Your mileage may vary.

Sunday, September 16, 2007

There are worse things than death, unless you can't find a save point

Why does MSNBC have a top five list of the worst ways to die in a video game? Seems like soft news to me. Not that it matters . . . they have it all wrong.

5. Death by camera. Whether it's an accidental step off of a cliff you were trying to sidle up to or being shot in the head by an enemy just off screen, there's no more frustrating or rage-inducing way to die than to be killed by something the "real" character would never have to worry about.

4. Death by blue screen. Well, this isn't really a "death," per se, but losing your progress because the game crashes is maddening. Power outages count on this one, too.

3. Death by zombie. Seriously, who wants to be eaten by, and subsequently drafted into, an army of the rotting undead?

2. Death by blue shell. If you play Mario Kart, then you know. Even worse than the lightning bolt, nothing strikes dread into the heart like the tell-tale buzz of impending doom and last place.

1. Death by stupidity. Oh, if I had a dime for everytime I planted a motion-sensing bomb, only to walk past it later because I forgot that I placed it. Or fired a grenade off and watched it bounce back at my face. Let's face it, nothing is more embarrassing than inadvertently causing your own demise while trying to hasten someone else's.

Thursday, September 13, 2007

GMOpinions

I've been taking a plant biotech course this semester, and it's been incredibly interesting. I've learned enough that I could probably create my own transgenic plants, given the right materials (and maybe a few good instructions as well). It's neat stuff, but not the right material for blogging. Well, that was until we started talking about the controversies surrounding genetically modified plants.

When I hear about the riots and protests that take place all over Europe regarding transgenic food crops, it strikes me as being a bit anti-science, with a hint of thinly-veiled agricultural protectionism. Still, we discussed some of the complaints in class, and I thought I'd share my thoughts on the matter. Feel free to contribute your own.
  • "Superweeds" will devastate us all!
This isn't an unrealistic fear. Several species (~12) of Round-Up resistant weeds have been documented, and given its widespread use, there are probably more on the way. This can be curbed, by the use of a variety of herbicides, whether through cycling or through mixes, but we may still be in the situation of an ever-escalating arms race with the weeds.

Partially included in this is the risk that ultra-hardy crops might become weed-like and spread to areas where they'll choke out natural vegetation. This seems unlikely to me, at least anytime soon. After all, if we had a food crop that was anywhere near that robust, we wouldn't be worrying about insect resistance, drought resistance, and so forth.
  • "Superbacteria" will become antibiotic-resistant
This is a bit of an offshoot from the first point. Some crops use genes encoding antibiotic resistance as a selectable marker, and the fear is that bacteria in your gut may pick up the gene and become resistant.

I'm not sure why this is a fear. The bacteria in your gut don't make you sick as it is, and you don't need antibiotics to fight them off. Additionally, the "antibiotics" used as selectable markers usually aren't used therapeutically for people anyhow, as some of them will hurt humans just as easily as plants or bacteria. They're more like general poisons than antibiotics, really.
  • "I'm not eating that!"
The idea here is that unknown toxins or allergens may crop up in food and cause illness. This could be a conscious objection, or just a sub-conscious reaction that people may have, similar to the suggestion of eating insects or chilled monkey brains (the "yuck factor").

I'd say that the only good way to move past this one is education for the public. Transgenic foods undergo incredible amounts of testing before they're deemed safe for public consumption. They are tested to ensure that the chemical composition is identical to natural varieties. Should anything be different, it is tested to determine toxicity or allergenicity. Despite people's fears about heartless corporations, they won't risk billions of dollars trying to sell you food that will kill you. How do dead people buy more food?
  • Monoculture will lead to large-scale crop losses
This is another somewhat valid fear. If a variety of transgenic plants is planted very, very widely, but suddenly becomes vulnerable to some epidemic problem (herbicide-resistant weed, insecticide-resistant pest, a mutant virus, etc.), then a famine and economic fiasco could result. This problem could be more probable if there is little genetic diversity amongst a country's crops.

The fact is, this is a problem for natural plants as well. Hawaii's papaya industry was nearly wiped out by disease ~15 years ago, and it was transgenic papaya plants that saved it. While tinkering may open the door for a problem, those same tools can be used to solve those problems when they arrive.
  • Ecological damage
This is a difficult argument. The idea is that your transgenic crops may harm the environment, whether by leeching something harmful into the soil, or by killing beneficial insects through plants which produce their own pesticides.

There's been very little evidence for either of these happening, and I doubt the first would occur, again because these plants are tested for toxicity. However, it is possible that you could kill good insects. Discovering that fault would take longer than other indications or an unusable transgenic crop.

Still, it doesn't seem like a reason not to genetically modify crops. It seems like more of a "deal with it when we get there" kind of problem. In fact, transgenic crops allow for more environmentally farming practices, including no-till planting and less use of sprays.
  • BigAg wants all your monies!!!
Okay, it's not quite that hysteric, but there are people who argue that a lot of this is just a grab by corporations to get rich off the backs of farmers. Since most transgenic plants are male sterile, the crops can't produce seeds to be used the next year. Instead, the farmer must purchase new seeds each planting season.

This complaint runs head-first into worries that transgenic crops might cross-pollinate with natural fields of said crop and produce something either unknown or unhealthy. The example might be from corn engineered to maximize ethanol production, or to produce an antibiotic or some other industrial compound.

This is solved slightly by using plants which aren't used for food crops as "biorefineries." As for the other problem . . . I'm not sure there's an easy solution to that. There's probably an argument to be made, from the corporation's perspective, that only being able to sell seeds to someone once would be fiscally dangerous. You could even argue that by forcing the buying of seeds each year, you can limit the potential for the development of superweeds/bugs by "updating" the crop.

(Heh. "Yes, I'd like to buy some corn 2.1." "Oh, I'm sorry, but you're going to have to move on to the next version, corn 3.0. We've added lots of great new features!")

Again, this doesn't seem like a reason to not make GMOs to me. Which rather sums up my thoughts on all of these issues. I don't think any of them are deal-breakers, because a lot of them can be avoided through prudent scientific/farming practices, while others are more "what if" types of problems, which could again be solved through the same technologies. Transgenic plants might make it possible to end world hunger some day. Why not take a stab at it?

Surviving the Inevitable

Some people worry endlessly about what they'll do when the zombie uprising comes.

Yeah, that's all well and good, but perhaps a bit unrealistic.

Surviving the robot uprising, on the other hand, will probably be on your to-do list sometime in the next century. That's why you should memorize this handy guide on how to flee from a robot or snoop out one disguised as a human. Although I guess if you watch Battlestar Galactica you already know all of this.

Friday, September 07, 2007

Flashy entrance, you say?

I've previously mused on things I'd like to see at my ideal wedding reception. Some people consider limos to be the best way to say, "I'm coming and going in style." More recently, people have opted for the SUV-limo.

Amateurs.

If you're having your big day in London, and you want to show people that you are living la dolce vida, then perhaps you ought to consider this. Nothing will accentuate that blessed day like rolling up in an APC.

And hey, if that drunken relative of yours happens to make a scene at the reception, you can always lay a couple of mines behind his car. Or just crush it. Y'know, whichever is more convenient.

Thursday, September 06, 2007

UMSL Student to leave Russia

In case you didn't hear, that UMSL student who was being held in Russia is now free to leave.

Apparently, the judge asked her to pay a $600 fine and sent her on her way. Happy ending, yes?

Friday, August 31, 2007

When Anecdotes = Data

I realize the title above is never true, but I never enjoy hearing the horror stories that come from places like Canada or Britain, detailing the terrible failures resulting from the socialized medical systems there. The frequency with which I hear them is what makes them so tragic. Again, the plural of anecdote is not data, but they make great illustrations about the shortcomings of such systems.

Anyhow, Captain Ed has a post illustrating yet another disaster to be laid at the doorstep of socialized medicine, this time in Japan. It details the story of a woman who went into labor and was turned away by eight different hospitals. There was a ninth which was going to admit her, but the ambulance crashed on the way there and she miscarried. At that point, the hospital refused to admit her.

Be sure to read the entire thing. Ed rightly asks why, after seeing so many stories like these, anyone would still think that putting the government in sole command of the health care system would be beneficial to anyone. I wonder the same thing myself.

Thursday, August 30, 2007

Is 45% a consensus?

I'm not sure what to do with this.

According to this article, a researcher examining 528 papers published from 1993-2003 in the ISI Web of Science database show that only 45% of the papers give at least implicit support of the "consensus" view that humans were having an effect on global climate change.

Feel free to read the article. The numbers are as surprising as they seem at first glance. My own question is whether or not this is a good measure. ISI Web of Science? Is Science included? Nature? I just don't know whether or not this is a decent standard of comparison.

Interesting if it is, and somewhat interesting even if it isn't.

Tuesday, August 28, 2007

UMSL Student in Russia

I saw this on the local news a few nights ago, but they stated the student was a SLU student. I guess you can't win 'em all.

In any case, an UMSL student is being held in Russia on some rather strange charges. A Chilean national studying in the US, she was living in Russia for a year and bought some Soviet era medals as souvenirs, only to find out at customs on the way out that such was a crime. Since then, she's had a bit of a crazy ride on the way to charges actually being brought against her. Her trial is supposed to begin today.

Want to support her? I'm not entirely certain how. There's a couple of facebook groups/petitions, but I can't imagine what that will accomplish. I'd recommend calling the state department, or perhaps one of Missouri's senators, or even the governor, if you're feeling so inclined.

I'm wishing her the best outcome in this.