Blog of Bermanism

Rachel, Kerrie, Dave and I went to see the Hitchhiker’s Guide to the Galaxy last night. We were all a little reluctant to go since any movie made from a well written book with a large following, could seriously suck. Also, after reading the movie’s reviews on Rotten Tomato, you got the impression that the movie could either be brilliant or terrible. Bravely, we ventured to the movie.

This movie was great! We laughed most of the way through it, the special effects were dazzling, the cinematography was stunning, the acting was mostly fantastic (I love Alan Rickman), and the story held mostly true to the book, from what I remember (I was in 7th grade when I last read it). The book had an extremely sarcastic tone to it, and they managed to duplicate that effect in the movie. We felt like we were watching a high-tech, futuristic Monty Python movie. The movie was wrought with British humor while maintaining an interesting story line. Hollywood did manage to plant a love interest into the screenplay that wasn’t there originally, likely in order to appeal to a wider audience who just can’t stand to see any movie that doesn’t have a love interest. Thankfully, the love interest was minimized to save the content of the movie.

The movie was put together like a series of short skits that all fed into the main story line, which, as improbable as it is, is the search for the question to the answer for all things in the universe (the answer being, of course, 42). Also, the guide, as it was represented in the movie, was perfectly done. I couldn’t have imagined it any other way. The creative genius of Douglas Adams, his uncanny wit and vision of the universe, and the placating aura of the film leave you with the warm happy feeling that you’ve just laughed your ass off for 1.5 hours. This movie was really fun and I definitely recommend it to any audience. You don’t have to be a fan of the book to enjoy this one.

This past Saturday night, the 23 of April, marked the beginning of the Jewish holiday Passover, which commemorates the Hebrews’ exodus from slavery in Egypt. Passover begins at sundown on the 14th of Nisan (first month of the Jewish calendar, corresponding to March-April) and lasts seven days in Israel, eight days in the Diaspora (although Reform Jews observe a seven-day period). The holiday begins with a ceremonial feast, called a Seder, which is part of a home-based service that is read from a 2,000 year old text called a Hagadah. The meal consists of traditional Jewish fare that is considered Kosher for Passover. It is always good, and it is usually spent with family and friends.

This year was a little different for Rachel and I. Since I’m so close to graduation and still have so much work to do toward that end, I chose to stay in Austin for this Passover so that I could write and relax. Both sets of parents requested our presence at their homes for Passover, but I chose not to go to either house. Rachel chose to stay with me in Austin, mainly because she’d been traveling for the previous two weekends, the first to a conference in Dallas, and the second to Hawaii with her friends (yeah, I’m really feeling for her too). Anyway, our families were disappointed that we wouldn’t be joining them for the holiday, but they understood the reasoning behind us staying home. We missed them for sure.

Anyway, as I mentioned above, Passover lasts for eight days. These days are spent eating specialized foods which help us constantly remember why we are celebrating Passover. Mainly, we do not eat anything leavened, like bread. The reason is that when the Jews were exiled from Egypt, they had to leave so quickly that they didn’t have time to let their bread rise, so they baked it and ventured out into the desert. This was the birth of flat bread, or Matzoh. Matzoh tastes a little like a mixture of cardboard and dirt with a stale crunch to it. Basically, it isn’t very good. I always need to put something else on it to make it good, like cream cheese or jelly or something like it. It makes a nice crunch when used as a sandwich and you almost don’t notice that the Matzoh is soaking up every bit of water in your body because it is so dry.

If you clicked on the Kosher for Passover link above, you saw that our diet essentially excludes anything that can be used to make bread. Mainly grains and legumes (beans). Wheat, corn, rice, rye, barley, oats, and legumes. You’d be surprised how many things in the American diet this excludes. It definitely cans bread, tortillas, cookies, pitas, pizza, and pasta, and other things that you might not expect like sodas, fruit snacks, granola bars, and cereals. These foods are excluded due to the presence of things like high-fructose corn syrup and wheat and barley. Speaking of barley, the diet also excludes things like beer (since it is brewed from grains like barley) and things like vodka and rum since they are distilled from a mash of grains that can include wheat, corn, rye, and usually potatoes. While potatoes are fine, it is rare to find a liquor made with only potatoes. Thus, the only alcohol left to us is wine, which suits most of us just fine. The other aspect of maintaining kosher for passover, is that all of the foods eaten have to have been prepared under the supervision of a Rabbi. The Rabbi monitors the entire production process to make sure that the food does not come in contact with any of the forbidden foods and that the food is processed by the guidelines of standard koshrut law, mainly that dairy, grains, and meats are not processed on the same machinery, or even in the same facility. So, we usually look for foods that carry the Kosher for Passover symbol on it:

The hebrew reads “kosher l’pesach”, which translates to kosher for passover as the text reads in English. No idea what all that Hebrew at the top means. You can imagine that all of this specialized processing, supervision, and care ends up taking it out of your pocketbook, and it does. Maintaining kosher is an expensive proposition, which is why most modern day Jews only keep kosher during passover. Remember also that kosher for passover is much more strict than common kosher practices.

In addition to eating kosher, we are supposed to go through all of our food before passover begins and remove all non-kosher foods. Traditionally, we are supposed to take it all out on the lawn and burn it, but since Jews hate to waste anything, the powers that be decided that it was ok to sell or donate the extra food. Also, we are supposed to remove all dishes and silver used for every day eating and cooking and replace it with special passover china, that is only used during passover. We’re also supposed to scrub all of the shelves and drawers that held the contaminated eatery. Rachel and I don’t practice this, and neither did my parents growing up, but Rachel’s parent did, and still do adhere to this practice. It seems a little extreme, but it does force a very nice spring cleaning to occur. Maybe Rach and I should try it, we need to clean up a little around here.

Anyway, that is a brief explanation of Passover and the rules and reasons that we do the things we do. Most of us really enjoy the holiday, despite the eating restrictions and we usually enjoy the company of family. One might equate Passover with Christmas when compared on a family level. It is certainly one of the most important holidays to the Jewish people and one of the most revered. Rachel and I had our own little Seder this year, complete with her famous chicken and honey, noodle koogle (a sort of noodle casserole with sugar, cinnamon, rasins, and noodles that are made with potato, of course), matzoh ball soup (which is way yummy), and specialized Passover desserts like macaroons, which are like soft cookies made from coconut. Hopefully, we’ll be able to spend next year in the company of our families, but for this year, we are content. Please feel free to comment if you have any Passover questions.

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We are all periodically faced with a responsibility to experience something that ellicits thoughts of gouging your eyes out with writing implements, simply because it would be far more enjoyable than what you are currently doing. Thus was my latest experience with a defensive driving course.

Those who know me know that I’m an insufferable lead foot. I am simply not happy in a vehicle if I’m driving less than 10 mph over the speed limit. It is also a universal fact that my car works better when the speedometer is pointing up (90mph in my car). So, one sunny January day, I was heading to a dentist appointment on the other end of town. I was naturally running quite late. So, I was going 85mph southbound on the MoPac expressway. I happened to pass a brown, highly tinted Mercury coupe of some kind and it just happened to be an unmarked police vehicle, a trick that APD has been pulling a lot recently. Well, I had ol’ smokey on my tail before I knew it, and I was getting pulled over. This was an odd experience since the officer walked up to me and exclaimed, “Hey man! How you been?” Being the typical embarrased-guy-who-just-got-pulled-over, I just sat there looking blankly at him. He went on to explain that he swore he knew me from somewhere. At this point, any reasonable person would have begun to milk this opportunity for getting out of a ticket, but I was my typical honest self and told him that I didn’t recognize him. Well, he was still pretty cool because he gave me a ticket for going 75 in and 65, instead of 85, which would have meant that he could have arrested me. Not fun! So, then I went on to the dentist apparently free of all of my bad karma for the day since I didn’t have any cavities.

About a week ago, I found the court documents that I received to be able to take defensive driving. It was, of course, buried under one of the many time-dilating piles of paper on my desk. With a start, I realized that I needed to have my course completed by April 20th, which at the time was less than 6 days away. So, I elected to go to comedy defensive driving at the Cap City Comedy Club. A lot of people told me that I should take the course online, but I thought this would be more painless. Wow, was I wrong!! The teacher guy, named John, was a hispanic guy around 5′6″, probably in his late 20’s, and he had a pretty serious case of ADD. He was actually pretty funny, but defensive driving is a tough room since no one wants to be there.

The class was scheduled to take 6 hours, four minutes repentance for every mile per hour that you were going at the time you were speeding. As is typical of any government activity, the class was required to take exactly six times as much time as it should take to complete the course. This could have been done in an hour, easily! But, instead we got to hear the same rules repeated over and over again, watch these really scarily fake early 80’s style training videos that showed you how you’re supposed to drive, and ultimately take the ridiculously easy test to get out and get your ticket dismissed. Among my favorite videos was Paths of Thunder II. This was a late 70’s-style 1993 classic that was supposed to teach you how to deal with dangerous situations involving trains. It featured a horrible actor who was wearing glasses so thick that they could probably see the future. This guy was an endless source of amusement while we watched trains hit cars stopped on railways, which of course instantly caused the cars to burst into flames. Anyway, after about 3 hours of this, the tip of my ball point pen was looking rather inviting to my right eye. I kept thinking, if I’m blind, will have to finish this course? I wonder if they actually have a rule for that; ticket dismissal due to accidental blindness while taking defensive driving. I’d look it up and put it here, but I’m too lazy today. Anyway, our 6 hours were finally up. I came home and was in a horrible mood for the rest of the day because I seriously felt like my soul had been raped or something. I will never get those six hours back, that is for sure. So, the moral of the story: be more careful not to get caught speeding, you don’t want to do defensive driving!

I just got back from a fantastic lunch with a bunch of my friends from a place in Austin called Hoover’s. Man, this place is great. It is in East Austin, right near The University of Texas, and it serves traditional down-home style southern cookin’. Ummm, this stuff is heart attack on a plate with a side of crack. It is so good, but so amazingly bad for you. It is one of those restaurants that is neatly nestled into a strip mall, but has grown to encompass the majority of the building, there’s only one other tenant and I couldn’t tell you who it is. You walk into this relatively plain foyer area where the hostess (who looks like she eats the food regularly) abjectly greets you and marvels briefly at the power she holds over you by telling you she’ll call you when your table is ready. You just know that she sees that you’re shaking with hunger/bad-for-you-food-withdrawal.

The rest of the place is divided into two rooms, one very large room with a full bar in the front and a smaller room through the alternate doorway from the foyer. There is a gamesh of tables from picnic type tables to booths. It feels like you’re just hanging out in the mess house of some large ranch in south-central Texas.

Once you’ve sat down, your eyes neatly skip right over the salad section to the solid arteries section. Naturally, I ordered the Chicken Fried Chicken Platter with fries and macaroni and cheese today. You should have seen this plate. It was a deep-fried monument to high cholesterol and type II diabetes. Just looking at this dish made you full and want to crawl into bed and take your food coma nap for the afternoon. Oh, but I dug in anyway. The chicken is amazing, it is so well fried that the meat literally melts under your knife. The fries aren’t the best, but they still satisfy that fry craving that all true-blooded Americans feel. Ah, now the macaroni and cheese is a delight like few others. I think that they put a double dose of crack into this dish. It is narcotic and you can feel each macaroni noodle quietly lodging itself into your coronary artery. Ah, the life of an American eater.

Anyway, this place is heaven on a plate for sure, but a tribute to the downfall of American health. It’s a good thing that I work out 6 days a week or else I’d be even fatter than I am already. Sadly, I know exactly how bad these things are for me to eat, but it doesn’t stop me from doing it. I suppose food is my addiction. Time to start a support group!

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A great many people have asked me over the years to repeatedly explain to them what it is that I study for my research. It seems that every time I tell someone, they forget inside of 10 minutes and need to be told again. This is all very understandable and I appreciate that people care enough to want to know what I do, even if they can’t remember long enough to tell someone else. So, for my second ever post to this blog, I will describe what I have been up to during graduate school for the past few years in a simple form so that everyone can understand it. Please note that I am intentionally leaving out a lot of the details of how things are done and why you’d want to do them from a biological standpoint. This explanation is for the general person who is interested in being able to amaze their friends with the fact that they know this guy who is doing this thing that is cool.

Basically, I am studying how long-term intoxication by alcohol affects brain gene expression. Ok, what does that mean? Well, for all you alcoholics out there, it turns out that addiction is genetic and you probably inherited the predisposition for alcoholism from your parents! Weird right? Between 40-60% of one’s risk for becoming an alcoholic is genetic, and the rest is usually influenced by the environment you grew up in and how it affected you. So, even if you have inherited as much of a risk for alcoholism as you can, if you don’t ever drink alcohol, you won’t become an alcoholic.

So, when most people think of something as being genetic, they think that there is a gene for the trait. Thus, based on my statement above, one would conclude that there is an alcoholism gene. Sorry, but it turns out that alcoholism is an incredibly complex behavior, and there isn’t a single alcoholic gene that will make you an alcoholic. The disease is likely caused by the combination of hundreds of genes that contribute to your risk for alcoholism. Up until now, researchers have been trying to discover which genes to study out of the ~40,000 genes in the human genome. A lot of research has already been done on certain genes and we know that they react in some small or large way to the presence of alcohol in the system, but the research has been limited to a few obvious targets for alcohol. So, we needed a way to find as many of these candidate genes as possible in order to begin to crack the code of inherited addiction.

So, some really brilliant scientists at Stanford University decided to design a method of research that takes advantage of what we know about how genes work. Genes are stored in every cell in your body as deoxyribonucleic acid, or DNA. DNA is stored in the nucleus of the cell. When the cell needs to make more of what a gene encodes, it transcribes the appropriate DNA sequence into ribonucleic acid, or RNA. This particular type of RNA is called messenger RNA (mRNA), and it is exported out of the nucleus into the cell. The cell then reads the new message with tiny organelles called ribosomes which translate the mRNA into a sequence of polypeptides which ultimately become a protein or enzyme. These proteins or enzymes are then taken to whatever part of the cell that their function is needed. The compliment of proteins that are active in your body at any time make you who and what you are. Proteins are the primary functional molecular machinery that drive all of the actions in your body. These actions include everything from getting salt into or out of your cells to muscles contracting or relaxing. With this in mind, you can imagine that any change that happens in your body is likely going to be the result of a change in the amounts or types of proteins that are active in your body at that time. Since the presence of alcohol in your system can ultimately cause a disease like alcoholism, it is likely that alcohol can change some aspect of the way your body functions, which means changing the protein complement that your body has. If your body, for instance, needs to make more of a protein that helps break down sugar into energy that your body can use, it tells the cell machinery to make more of it. The immediate response is for the cell to make more mRNA for that protein. The amount of mRNA in the cell at any time is called the gene expression level. The gene expression level can go up or down, or even turn off completely if necessary. The scientists at Stanford took all of this into account and developed a research tool called the microarray. This innovative tool allows researchers to scan tens of thousands of mRNA sequences simultaneously from a complex sample like a mouse brain. Individual genes are “printed” onto a microscope slide and the samples are washed over the slide in a manner that allows the same gene in the mouse sample to bind to the gene printed on the microarray. This process is called hybridization. At UT, we have a microarray facility that allows us to put up to 50,000 genes on a single microarray slide. Ultimately, we would like to be able to represent the entire genome at once on the arrays, but that is a little ways off.

So, in order for me to discover new genes that are being affected by alcohol, I needed to use microarrays. I also needed a model system to work with, since humans don’t generally like having their brains cut out at the end of an experiment. Plus, they take so damn long to grow! So, I used mice. Cute little gray buggers that are called DBA/2J mice. These particular mice have a strong aversion to drinking alcohol and go through a severe withdrawal when they are forced to take it. Since withdrawal only occurs once a subject is dependent upon a substance, it is an important part of an addiction of any kind. We chose this mouse and a study of withdrawal as our model system. So, this study is looking for the effects of long-term exposure to alcohol. We chose a long-term (chronic) exposure so that we could more accurately approximate the condition of alcoholism.

Well, now we were stuck with a mouse strain that didn’t drink alcohol, so we had to find another way to give them all alcohol in a controlled and predictible fashion. So, we made them breathe alcohol. We built this nice chamber that vaporizes alcohol holds it at a certain level. The mice were all put in the chamber and made quite drunk for three days. Oh, they were having fun in there, let me tell you! Once the three days were up, we took their brains, pulled out the mRNA, and put the extracted samples onto the microarrays. The result was 1.5 million data points!! This is a lot of data. We had gene expression data for 17,000 genes in six different brain regions, at three different time points beginning after we stopped giving them alcohol, and there were five mice in each group!! Now we had to make sense of it. So, we put the data through very rigorous statistical tests, mathematical routines, and visualization algorithms. The end result was a subset of the original data that we are confident represent the major portion of the effects that alcohol has on brain gene expression. This is where we are now. The trick now is to take all this data and find some sort of meaning to it all. It is great that we have 3,000+ new candidate genes to study for alcoholism, but there is more there. The data contains some biological insight into the development of dependence on alcohol. Now, we must find that story and tell it. Once I’ve written the story up into a paper, I’ll be able to graduate. (*cheer*)

Well campers, that, in a nutshell, is what I’ve been doing for five years. I am very near to the end of my long journey and have only to write it all up and I’ll be finished. I hope this post is useful to you and that you feel like you learned something from it. Please feel free to post comments on what I’ve written if you have questions or find anything confusing and I’ll answer them for you.

Ok, Ok! Back to work!!

Well, I’ve joined the masses. The endless sea of faceless entities that ubiquitously fling their thoughts, opinions and desires out to the public eye for all to see. It is a madness, an obsession, a tribute to entropy, and a fairly profound insight into the human consciousness. Opinions are what drive the fabric of human society. Very little fact or logic rules in the realm of what is socially acceptable or desireable. The fact that reality television, for all its scripted and coerced nature, is now the favorite type of entertainment for the vast majority of TV watchers in the US is a tribute to the ideal that, if it isn’t happening to me, it must be interesting! I find myself being dragged unwittingly into the greedy grasp of shows like The Amazing Race, The Contender, and American Idol (The first two are worthy of my attention, American Idol is probably not). I always feel just a little dirty for being caught up in the drama that unfolds in these poor souls’ lives, then I remember that they are willingly putting themselves through that experience and I feel a little better.

Blogs are the new thumb on the pulse of the American opinion. It has been proven to be a viable and necessary alternative to the media giants and one that has said giants trembling at the thought of losing control over what the public views as reality. But, you must remember to take what blogs say with a grain of salt, as Edward Schrock recently learned. Some bloggers do their homework and have a determination to present the news as truth in an unbiased fashion, while others are just trying to get people to believe in their conspiracy theories, whether they be about our subversive goverment, or the hidden messages of the popular Harry Potter Series. Still, some bloggers simply want to illicit insight into their very interesting and unusual lives, like Wil Wheaton (child actor in Stand By Me and Star Trek: The Next Generation). His blog is filled with interesting insights into who he is and what kind of life he is leading, I am an avid reader. Recently he wrote a very touching biography of his cat Felix that you should check out if you get a chance. It made most people I know who read it cry. Anyway, the reason that I quote this particular blog out of all other blogs is that I hope to emulate the purity of the content that Wil keeps on his blog. I want this to be like a live journal that spans everything from my opinions to reports on our lives as they get turned upside down by our impending move to San Francisco. I hope that everyone enjoys the content. Please feel free to register and tell me exactly how much you love or hate what is here. See you, out there….