One down, nine to go…

Semesters, that is…average… My last exam was today…finally…and I think it went generally alright. That last section hurt quite a bit and dropped me down from #3 to the middle of the class (of 9 people) again, but that’s cool…I’m doing alright overall, and I think I have “A’s” in my other 3 “classes” (only one of which is a real class…). Either way, glad that it’s finally over and now I get a break…until January 4th… Stoopid grad skool…

Anyway, we’re going to Hannibal tomorrow night until Christmas morning, then heading to Columbia for a few days. If you’re in the area, give the cell a buzz or something… We’re going to be here in St. Louis for New Year’s Eve, so lemme know if you’ll be in town for that, too. Otherwise, have a merry Christmas and travel safely…

Rotation #3

So, here’s Nathan’s “what’s Andy doing in his rotation this time” blog posting (i.e. he’ll be the only one to comment because no one else cares…). Regardless, I’m working in Dr. Scott Zahm’s lab in the Pharmacology and Physiology department until the end of this semester. He works with neuroanatomy in rats, generally trying to “map out” sections of the brain that are integral to motivation and, consequently, motor skills. By “motivation,” I mean a lot of things. For example, he is currently focusing on the Ventral Tegmental Area (VTA) in the rat brain, which is involved in motor function. More specifically, consider this: when we’re hungry, we have a few different competing ideas going through our brain, one of which is “where do I get food” and the other is “how do I survive while I try to get this food” (self-preservation). Our VTA works in concert with other parts of the brain to weigh each competing idea and then control our “need” for things like food, warmth, TV, drugs, whipped cream, etc.

Zahm, et al. are working to map the neurons that come in and go out of the VTA (and other structures) in the rat brain. Specifically, they want to better understand the brain “circuits” and how something that is signalled in one part of the brain can signal another part of the brain. They do this using “tracers” that can label neurons in a certain area (injected into the rat’s brain…) and then the neurons take up the tracer and transport it to other areas of the brain.

The cool pharmacological part of this is two-fold. First, his lab deals with reward systems. So, if you are taking a drug and you become addicted to it, you’ll have more motivation to try and get that drug back. The drug itself could completely rearrange different neurons in your brain as well, connecting something to the VTA that wasn’t connected before (thereby leading to addiction). This leads into the second part: we don’t know how the brain works, but perhaps more importantly, we don’t know how a lot of drugs (like Prozac) really work… The brain needs to be mapped so we know where things happen, what’s connected to what, and how a change in one area can affect transmission to another area. My interests in neuropharmacology are somewhat contingent on this fact…you can’t effectively develop new drugs unless you know how the brain is set up. We’ve found lots of drugs that have an effect…but we don’t necessarily know why… We could be prescribing drugs for ADHD that are “re-mapping” the brain of our children and not really know it… This research, and studies like it, will help us better understand how the brain is set up and how a drug can affect its organization.

As far as what I personally am doing, it’s relatively small stuff. So far, I’ve worked with putting brain sections on slides, staining brain sections with antibodies, seen the surgeries for injection of tracer into the brain and, consequently, the brain’s removal. Starting tomorrow, I’ll work on the actual mapping using light microscopes (and electron microscopes, eventually…) to take a look at the neurons and see where they go.

Nifty, eh?

Of principles and $$$…

So yeah, I got to thinking today… I use Linux and various other open-source programs instead of Windows for a variety of reasons, but one of those is that the information contained within is freely available to anyone who wants it. What does that mean? Well, it means that if you download the “source code” of the Linux kernel and other “open-source” programs, you can edit it and tweak it to your heart’s content. If you decide you don’t like the way a certain function of the program works, you can (assuming you know some programming…) change it to fit your purpose. The reason why this is cool is that it allows knowledge to travel freely between different groups; what one person starts with a program can be learned from and transferred to another application, allowing for the programming itself to improve over time.

Now, switch gears into science. My plan has been to get my Ph.D. and then work in industry for awhile, making some cash, and then maybe switch back into academia and teach for a few years to alleviate boredom around retirement time. The correlation is that academia is like “open-source,” where information is published and freely available for other scientists to learn from and take a step further, while industry is like “closed-source” where you work toward patents that can allow you to make money and prevent y our opponents from coming up with a solution to a given problem that’s better than yours.

So, the question remains: am I hypocritical in using open-source software, believing in what it stands for, and then getting a job and making a career in industry where I will work in a “closed-source” environment? I mean, I have relatively expensive hobbies (computers/electronics, etc.) and I’d like to be able to finance them, and to do so, I need a job in industry so I can afford that 1969 Shelby Mustang…but is it right to compromise principles in doing so?

I dunno…I guess there’s no simple answer to the question…but I’ve got 5 years to figure it out…

Hmmmm…well…

So yeah, had my third exam today…could have gone better, probably could have gone worse. I’m having a difficult time deciding which is worse: sitting through a 3 hour Physical Chemistry exam with under 10 questions that you have to think about a lot to get a good answer down, or a 3.5 hour exam where you have maybe 20 essay questions that you do know answers to, yet you don’t really understand what the hell the question is asking you… (i.e. you can read the question, you know information on the subject and you could easily answer a multiple-choice question, but you don’t really know what the professor is getting at…so you write down too much stuff and they count off for it…).

Anyway, I’ll get that back next week, I guess…no one was particularly happy about the test, so we’ll see what happens…

On a lighter note, Brooke and I are visiting Hannibal this weekend…haven’t been there since, like, summer…’bout time, I guess… I also start my rotation with Dr. Zahm next week, so I won’t have my afternoons off anymore…dammit… Nathan, I’ll post up a research summary when I get a chance… 😛

Not much else going on…but I’m quite ready for Thanksgiving Break, yo… Holla…

Oh, cholesterol…

So, Dr. Stephenson was talking to us in class today about something he read in the Journal of Clinical Cardiology recently, saying that they believe we should all strive for the lowest total-body cholesterol count possible. Basically, we shouldn’t try to have a count of “below 200” or “around 150″…we should just go and go until it’s as low as it can go.

Anyway, he then mentioned some studies that show up years ago on the same subject… These studies said that people who had low cholesterol were less likely to die of cardiovascular diseases. However, keep in mind, this data only reflected death by cardiovascular problems, not by other factors.

Essentially, it came out that, yes, people with cholesterol counts around 130 or a little higher did well…but people lower than that started to die off. Why’d they die off? Suicides and murders. Apparently, people who had extremely low cholesterol counts died because cholesterol is a relatively key component of cell membranes, especially those in your brain…so people would start getting either really depressed and would kill themselves, or they would get psychotic enough that someone would kill them…

Take home message: eat a lot of fatty stuff and die happy, rather than depressed or crazy.

Bank Error In Your Favor

So, I got paid today…and got an extra $600 ’cause they’ve been taking money out when they shouldn’t have been…

…now…what kind of amp should I buy? 😉

P.S. To make an already perfect day even more spectactular…I saw a 1993 Nissan Altima with a duck-shaped hood ornament…it was rather amusing…hehehehe…

Random thought…

So, sitting in class today learning about the biochemical machinery that leads to transcription via RNA Polymerase…I wondered the following: What if the world were populated by robots instead of humans? Now, these are robots with robot humanoids, robotic animals, robotic plants, etc… I mean, we know practically nothing about how or why things work in our bodies…but when we think of machines, we designed them, so we know how they work and why. So if these machines did not have knowledge of their creator, or if they simply arose on their own somehow, would they find it just as difficult to figure out how and why they work? …even though, inherently (since we designed them), they “work” on a less sophisticated level than our organic bodies? Would these robots have the same questions about their origin as we do? Would they have to learn about how they function, or would they care?

…I gotta get out of here…

…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…

…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…

…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…