Category: mostly unimportant

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…here we go again…

I’ve got my second exam tomorrow…and I really haven’t studied all that much for it… Honestly, I could very well get burned on this one, but it’s hard to see how…and at the same time it is… We’ve been learning about basic genetics and replication/repair mechanisms for DNA…which, again, are all things I’ve seen before (some of it as early as 10th grade…). At the same time, it isn’t necessarily the easiest stuff in the world, frequently involving somewhat complicated probability calculations. So yeah, I’m unsure as to whether I’m supposed to be really worried or not. Since it’s graded on a curve, as long as I stay where I am right now (i.e. in the middle), I’m completely golden for keeping above a “B” average. Therefore, I’m spending today in full-speed cramming mode to get all this stuff back in my head…since a great deal of it was there a few years ago already…

Other than that, I’m trying to decide whether to go to Kirksville next weekend. Brooke is working, so she can’t go…but Stu/Angela are going (it’s Homecoming…geez, I’m a dork…) and I wouldn’t mind seeing the new science building in completion…let alone a few folks that I haven’t seen in awhile (i.e. since the wedding, in some cases). Besides that, I’m looking forward to two things this week:

1). “The Colbert Report” premieres on Comedy Central this Monday after “The Daily Show“… The latter is a show of complete genius, so I’m hoping the new one lives up to the standard. Stephen Colbert is a damned funny guy, so I don’t think it can suck too much…

2). Oh, it’s baseball season again…and the NLCS/ALCS are both going on strong. I never really follow baseball at all, but it’s always fun to watch games this time of year. Going for the Astros, anyone? 😉

…I guess I’m also looking forward to this test being done…but let’s take one thing at a time, shall we?

P.S. La Russa and Edmonds have both been thrown out of game 4 in the NLCS…I’m highlyamused…

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…oh, Pastafarianism…

So, Dr. Zassenhaus is teaching right now in my lecture class about basic Mendelian genetics. He told us earlier this week that he was making a presentation today in reference to Intelligent Design and Evolution, so I’ve been looking forward to this all week because I haven’t heard much discussion amongst Ph.D. scientists that I know and the sources I’ve read through discussing the subject rarely consult pure molecular biologists and biochemists…and I came away from the presentation with a few interesting points…

First of all, Zassenhaus began the discussion talking about the Kreb’s Cycle. For those who don’t remember, this is a pathway in mitochondria (an organelle in our cells) that converts relatively simple carbon chains into other forms, generating ATP, which is the “currency” that creates energy in our bodies. Since it is a cycle, the products begin in one state, are converted to another state, and are then returned to their original state to start the cycle once again. One of the classic Intelligent Design arguments is that this process is not reducible; one cannot remove a part of this cycle and still have it function, leading them to suppose that an intelligent creator must have created this pathway. The process couldn’t have simply “appeared” on its own, already functioning.

The problem with this assumption, as Zassenhaus further enumerated, is in the fundamental argument for Intelligent Design: that life is too complex to have just happened. The argument, as he states, is the classic “Watchmaker Analogy,” such that if you are walking in a field and see a watch, you know that it didn’t simply appear, but that someone had to make it. The problem is that all of Intelligent Design arguments stem from that one analogy. There is no evidence besides it. The one scientific study he could find that tried finding true evidence was carried out by a mathmetician (Dembski) who said that the chances of such a thing appearing is something like 10^-170 (that’s one time in 1,000,000[continue to 169 “0”s…]), which is unbelievably small…bordering on impossible…

As Zassenhaus concluded, these probabilities outline a huge flaw in the thinking: where Intelligent Design advocates believe such a pathway just sprung into existence, and was created by someone else, biologists for years have viewed the formation of proteins/enzymes/etc. differently, as individual subunits that are added on and removed to provide a different function that wasn’t there originally. Therefore, those statistics don’t apply to the way we know biology to work. Sure, it says that such a thing as the Kreb’s Cycle appearing out of a soup of random amino acids is really small…but the chances of a different protein forming out of that soup is very possible, and then that protein adding on other parts of different proteins is also possible…slowly adding together to form the pathway we know as the Kreb’s Cycle.

In short (’cause I wasn’t, overall…), the moral is: Intelligent Design advocates have yet to produce true, testable, scientific evidence beyond the flawed probability studies. Is Intelligent Design still possible? Of course it is! But, as Zassenhaus said, teaching it alongside Evolution on equal footing as a viable scientific theory is, quite simply, nuts. In that room of 20+ Ph.Ds., there were none that defended Intelligent Design in the way it has been portrayed as a science. They all believe it should be relegated to a philosophy class, not the science classroom. Unfortunately, the “powers that be” refuse to listen to the scientific community on what should be taught and what shouldn’t be.

Figures…

So, in that vein, can anyone give me evidence to the contrary that isn’t based on “evidence by analogy?” I know that Andy S. already gave me information on another theory…hehehehe…

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Coldplay = Bad

Okay, seriously…Coldplay sucks…they really do…they are absolutely no good and their “music” is heavily overplayed. It makes me not want to listen to radio ever (not that I do often…but since there weren’t any good stations in Kirksville for my five years there, I’ve been trying to listen in St. Louis…).

I don’t really know why I bring this up, honestly…I guess I’m just wondering why people like them? They aren’t original, the guy sings way too high pitched for comprehension…there are various blog postings from people who hate them…some more amusing than others… Here’s even a review by the New York Times (June 5, 2005) that just trashes the album and the band…

The band plays and writes songs for the high school crowd, just like the boy bands did…songs made to make money…to make little high school girls fawn over them with their sappy, uncreative lyrics, most of which have been ripped off other, better songs… Frequently, Coldplay is considered to be a lesser, sappier, Radiohead imitator… They haven’t been innovating like the Smashing Pumpkins, Dave Matthews Band (and the other “jam bands,” like OAR, or even the Grateful Dead), or even U2…so what gives?! Coldplay is just a lighter version of Nickelback…seriously…same music, but slower and more depressing…

So…why the hell do people like them so much? Please. Answer me that. I don’t understand. I mean, I guess I don’t understand why the “boy bands” were so successful a few years back…but I can go with hearing the “Macarena” again rather than another Coldplay song…

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Of Cardinals and Random Ladies on the MetroLink…

Brooke and I went to a Cardinals game last night via the MetroLink (the above-ground “subway system” in St. Louis) since it’s way easier to right that into the downtown area rather than driving and parking down there… Brooke’s parents had 2 extra tickets to this game and decided to take us along (thanks!!). Anyway, we’re riding the thing and this lady gets on…maybe in her 40s, thin, brunette…and we’re in a huge crowd of people, most of which are heading to the game… Well, this random lady leans across 3 other people and says “you’re a very pretty girl.” Brooke, of course, replies, “thank you!”

So yeah, my wife was hit on by an older woman in a train car full of Cardinals fan…guess I should be flattered… 😛

The game itself was pretty good…hadn’t been to a game there since 1998 (maybe 2000…can’t remember), so it was good to go to “one of the last games at Busch Stadium” (even though this stadium is less than 40 years old and the new stadium will also be known as Busch Stadium…). The game went pretty well for the Cards throughout, since the Reds kept dropping the ball all over the place…literally… We left in the 8th inning after Pujols belted a grand slam out at the end of the 7th, so that was cool to see… That, and at the beginning of the game, they paraded around the 1985 Cardinals team in brand-new convertible Mustangs (w00t!)…so I got to see Ozzie Smith… They also had Mark McGuire stop by for another special appearance…

Regardless, it was a good time. I kinda wish I was more in to baseball as I used to be…not that I was ever really in to it, but I kinda kept track back when I collected baseball cards… Of course, I’m sure I would have been a bigger fan if my team, the Royals, ever WON A FRIGGIN’ GAME!!! 😛

That is all.

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…busy-ness, etc…

Yeah, school is keeping me busy, but not too busy… We got our exams back yesterday (I got a B+…not too terrible for the first exam…), so now we’ve moved on to DNA replication/repair in class…it’s been about 4 years since taking Genetics at Truman, so it isn’t quite as clear in my head as biochem was in the last unit, but it’s coming back to me…slowly… Anyway, it’s causing me to do more reading than I’d prefer…thankfully, I can do most, if not all, of it while I’m doing work at the lab in the afternoons.

That leaves me a lot of time for TV. I’m realizing how old I am since I’ve got shows to watch every weeknight…which really sucks, since I’m supposed to be studying, etc. This is mostly Brooke’s fault, of course…if she wasn’t watching these shows, then I wouldn’t have gotten “in” to them over summer… So yeah, I’ve got 3 “CSI” shows to watch during the week, “Law & Order: SVU,” “Threshold,” “Numb3rs,” etc…and the World Series of Poker is on Tuesday nights as well… I can easily sit in front of the TV for 3.5 hours almost every night of the week…which is terrible, but almost unavoidable… My VCR gets quite a workout every night, it seems…

Anyway, Brooke’s ‘rents are visiting on Friday and taking us to a Card’s game, which is cool…the 3rd-to-last regular-season game at Busch Stadium (which means absolutely nothing, truthfully…). Otherwise, I’m hopefully getting some poker played on Saturday…been a few weeks since I did that… Playing with the praise band at Webster Hills tonight, and then again on Sunday morning…looking forward to that, of course…

So, basically, life goes on. Nothing too fascinating to report…except that Brooke is this close to starting substitute teaching, which will bring in some much-needed income to a relatively poor couple…and by “poor” I don’t mean “bad”…I mean “financially lacking”… 😛

P.S. …there’s a calendar link up top…since I now have my calendar online…if you wanna know which weekends we’re in Columbia/Hannibal/etc., that’s the place to check…w00t…

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Of exams and triumph…

So, I took my first exam today…and it wasn’t terribly difficult, but the section I was most worried about was Dr. Shilati’s… It was a 10 point question (out of 80…so relatively hefty…) asking you to describe the process whereby you would assay a protein for a given function, how you would purify it, and how you would observe if it works in vivo (i.e. in a living organism). So I wrote out my answer (took 1.5 pages…) and wasn’t terribly confident, mainly on the last part of that question… After talking to other students in the class, all of us were worried about that whole question…which means that, theoretically, the curve will work out fine with all of us in the same spot… The rest of the test was generally alright…I dropped the ball on one 4 pt question, but was confident on the remainder of the exam…

…well…then I was walking back to the lab from getting a soda and Dr. Shilati stops me in the hall…and says “good job on my section of the test”…

…score one for Dr. Andy Linsenbardt, Ph.D… 😀

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It all comes down to this…

So Thursday is my first exam in BBS 501, which is our basic biomedical sciences course that all 1st year graduate students take in their first semester… Thus far, it’s really just been a review of biochem class from Truman State… The thing I’m slightly worried about is the amount of material being covered. I’ve been through 16 lecture periods at 1 hr each…which translates to over 5 weeks of MWF classes at Truman… So yeah, when you think of it that way, 5 weeks of material in any science class is a decent amount…but at least it has been mostly review…

Anyway, I don’t think I’ve described how grading is done here. It’s all graded on a curve (such that, typically, a 70% is considered a “B”…) and you’re graded with your peers from previous years, so they’ve been keeping records of how students have done over the past 7 years of the program. Therefore, if the average of all those students (~50 – 60 people) on this test was an 80% being an “A”, then that’s what this will be… So yeah, it matters how well we as a class do…but it also matters in reference to previous years, not just ourselves… I’m not sure whether to take this as a good thing or not…probably, I guess… We do get 3 hours to complete the exam, so that’s somewhat comforting.

Also, we aren’t taught by one professor. We have a rotating group that teaches each section. This time, we had 4 different professors. Each professor gets 5 points-worth of questions per lecture period so, for example, Dr. Shilatifard taught us for 2 lectures…meaning he can only write 10 pts for the exam. So if I really didn’t understand his stuff, then it’ll account for 10 points out of the 80 possible… At least I know generally how many points each day is worth going into the exam…it’s a little easier to pick out the key points of each day this way…I guess… We were also encouraged by our advisor to seek out old exams so that we know how each professor words their questions…and, supposedly, these questions don’t change much from year to year…

Therefore, this week has got me studying for my first exam of graduate school. It’s especially difficult to study knowing that a). I get a full day off on Wednesday to study for the Thursday exam, b). it’s all been review material thus far and c). lots of shows are premiering this week, so I want to watch TV instead… 😛

I’m not sure whether to be worried, though. There are a few things going for us and a few things going against us… I guess, in the end, it all comes down to how much effort I put in over the next few days…

…and how many beers I have… 😀

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…mmmm…fly paper…

So, Nathan said he wanted to know what I’m up to in my research rotation for the next few weeks… I’m working for Dr. Joel Eissenberg (who reminds me quite a bit of Dr. Buckner at Truman…) in the Department of Biochemistry. He works primarily with fruit flies, but most specifically, a protein known as dELL. This protein is known as an “RNA elongation factor.” For those who know anything about genetics, DNA is coded into mRNA by RNA Polymerase II; Pol II will sometimes pause along the transcription process, thereby causing the DNA to be transcribed more slowly. dELL prevents this “transient pausing,” allowing transcription to be carried out more efficiently. dELL has also been linked to leukemia (which is how it was discovered in the first place).

Anyway, Dr. Eissenberg is trying to get various characteristics of dELL from his research. I’m taking part in the work by using a technique known as gel electrophoresis (SDS-PAGE, to be more specific…) to isolate the protein from extracts obtained from fly cells. I then take the gel and apply it to a Western Blot analysis. The protein extracts (nuclear extracts, technically…meaning that they came from the cell’s nucleus…) are obtained by either Size-Exclusion Chromatography or Ion Exchange Chromatography, neither of which I’ll explain, but they’re both pretty cool… On the Western Blots, we use selective antibodies to detect and expose the proteins we’re interested in…one antibody binds to dELL and then a second antibody binds to the first one…but that second antibody has a luminescent “probe” (i.e. chemical) attached that allows us to see it… By carrying out this whole process, we are able to see in which cells/extracts/etc. that dELL is present and/or active.

There’s a lot more to it, honestly…most of which I don’t know. Regardless, I’m just running a bunch of SDS-PAGEs and Westerns right now…both of which are relatively time consuming…so it takes me a good two afternoons to take care of each of them… It’s relatively interesting, but not really what I want to do with the rest of my life. If anything, it’s interesting to see how proteins are isolated and such…seeing how all of this has been done in the past…

…and why everyone hates Western Blots… 😛

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…relatively amusing…

In an article posted on Yahoo! News about how poorly the box office did this summer…the following was mentioned:

“A documentary about a bunch of birds, March of the Penguins (15th place, $63.6 million), outgrossed the Ridley Scott epic Kingdom of Heaven (21st place, $47.4 million).

To this, I simply smiled… 😀

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Randomness, etc.

So yeah, a few random things:

1). Yesterday was the Biochemistry Dept. orientation for new graduate students. I’m not really considering them right now, but I am going to be rotating with a professor in that department beginning next week, so it was worth a listen, I guess… Regardless, we got free food, visited with some students in the department (I may be set up in a poker game in the next week or two as a result…heh…), and later in the day, we got to participate in a reception with more free food and about 9 varieties of beer. It is still rather odd to be on campus in a science building with free beer provided to the students. I think I could get used to this “private school” shenanigans…

2). I’m heading to Columbia this weekend briefly to visit with Jan Allmann, who was an exchange student from Germany my senior year of high school. He’s back this summer (though leaving shortly…) interning at MU for something business-related. Anyway, Brooke and I are going to Columbia Friday afternoon for some frolfing and dinner, then returning here on Saturday. My parents and Brooke’s parents are then coming into St. Louis on Monday (Labor Day) for some BBQ, so that should be fun…

3). My laptop has an obnoxious white line traveling horizontally across the entire LCD screen. I called Toshiba about it last night and they said to take it by Mobile Office Machines, here in St. Louis…who’s apparently a licensed Toshiba repair place. So I called them up this morning and I’m taking the laptop by them. They’ll need it for 24 hrs to properly diagnose the problem, then they’ll order the necessary part (while I hang on to the laptop) and they’ll call me when it arrives…and then they’ll fix it… Firstly, thank God I have that 3 year warranty on this toy…and secondly, thank God I live in a metropolitan area with a repair place close by so I don’t have to UPS this thing to China…

4). School is going alright…all still mostly review, but I’m sure it can only get harder from here. I’ve been very good about reading the material ahead of time before going to class so I know what’s going on before I get there…go me…

5). Mike Goodspeed had a very good posting on his blog a few days back…you should check it out… I still stand fast by my decision that George W. Bush is an idiot, for the record…and on a related note, the poverty rate in this country has risen to 12.7%…