Common Sense for the Biochemist

Its a Friday Ligtning Round, here we go:

The past few days have been beautiful up here in Michigan. I actually brought out the ole bike (that I bought last year and never used) and put some miles on it Wednesday.

On that note: the Lansing River Trail is a pretty neat bike ride.

I have been putting in some serious hours with a major redesign of my website. Go check it out and tell me what you think.

I think the administration at Michigan State University could improve their bureaucracy by taking a few notes from the old communist Russia (more on that later).

The Biotech world: Now is the time to be buying Biogen-Idec stock. I believe the price has absorbed all of the effects of the Tysabri incident. It is a definite buy to me but please don't just rely on me for your stock buying advice.

I still wouldn't go near Elan, though, its just too risky. At least Biogen is already profitable.

The stock price for Able labs is back up to ~$5/share from its low of $3.5/share - Why????? This company is done, stick a fork in them.

The Plant Made Pharmaceutical World: LSBC is looking at being delisted from the Nasdaq NM to the Nasdaq SC.

Hopefully this next week I can get around to compiling a list of all the field release permits that were granted to the PMPers this year.

My miscellaneous link for the day is Fold@Home. This is a distributed computing projected that uses your computers spare resources to solve protein structures.

I was looking through blogger.com today looking for other blogs that had a biotech flavor to them. Unfortunately, I did not come up with anything substantial. The majority of blogs that I have seen out there in cyberspace seems to focus only on internet stuff (search engines, computer technology, etc. . .). What sites there are that aren't filled with computer jargon is filled with the ramblings of lunatics, goths, weirdos, and "artists (painters, poets, writers, etc. . .). Question is, which of these two categories does my blog fit into. OK, fair enough, I'll take the designation as a rambling lunatic.

So whats new in the Biotech industry?

The vultures seem to be circling Able Labs, I count at least five law firms filing class action lawsuits according to their finance page at Yahoo!. I don't know what is worse, the implosion of the company or the vulture lawyers gathering over the fresh roadkill.

Well, I couldn't stand it today, I had to sell my Genentech stock. With its announcement of positive data for Lucentis (a treatment for blindness), the 5% jump in stock price officially made it overvalued. I think it'll dip back at least to $55/60 per share, I may jump back in then. I remember the analysts were screaming that it was overvalued at $50. Here we are at a price 60% above that, oh well, that just goes to show how much you should trust stock market analysts.

Well, its supper time, maybe I'll write a little more afterwards.

Holy cow! So I just got around to reading up on this fiasco. I had heard a little about it on Friday during "Mad Money" on CNBC. I just got finished reading up on the latest thanks to may daily updates from Biospace.com. From my quick research on the issue, it looks like the wheels didn't just come off, but blew-out, flew off, and killed three pedestrians. Some products produced by these guys included a generic version of Vicodin and Ritilin. I did a little snooping on their website. From their press releases, it looked like they were growing like mad last year. They had announced FDA approval of several generic drugs, they had acquired another company, and they have pictures of their new manufacturing facility on their website. All of the sudden, their CEO resigns, they withdraw their products, and shut down manufacturing operations. Browsing through the FDA warning letters, Able was cited by the FDA April of last year for not reporting some adverse side effects to several of its products. It will be interesting to see how this story unfolds. Their stock price has dropped from about $25/share to $5/share since Thursday. The question here is who is responsible for protecting the public shareholder. This is not some sort of accounting scheme that caused this collapse. This is a collapse in their accountability with the FDA. Was their any warning signs that should have been picked up on? Cramer's (from "Mad Money") advice is not to go near these small generic drug manufacturers. Unfortunately, there are many blockbuster drugs out there coming off of patent that are going to be prime candidates for generic versions and these generic drug manufacturers (the good ones at least), are going to be very profitable. Question is, how can you tell which companies are the "good ones"? I'm not done on this one yet, just done for now (its supper time).

Get over to Jeremy Ruston's site (OSMOSOFT) right NOW and check out his program called TiddlyWiki. This "program" is described as a a reusable non-linear personal web notebook. Basically, it is a single html file that resides on your computer, or memory stick, or whatever and is read by your standard web browser. It truly is a notebook as you can add entries and link them to other entries. The entries are viewable by selection from a menu, clicking on a link to it from another entry, or by a search feature. You really have to try it out to get a feel for what it does. There are several modifications for this program, including one called GTDTiddlyWiki (Get things done TiddlyWiki). Anyways, I'll be playing with this thing for a few days and see what good I can put it to use for. P.S. I first got wind of this program from Jeremy Zawodny's blog.

I've mentioned that I am an advisor for the Michigan State Farmhouse Chapter. Most of you probably don't know who or what Farmhouse is. Farmhouse is an international fraternity that is open to all majors. Most of the members come from a rural background. Many Farmhouse chapters are at the top of the grade rankings on their campus. You're first impression is that it is a bunch of uncultured rednecks sitting around discussing what brand of tractor is the best between their classes on how to grow hogs. Well, you are probably half correct. There have been many heated discussions about which brand of tractor is the best and there are several guys who are studying how to grow hogs. But there is much more going on behind the doors at 151 Bogue Street. As I am writing this entry, I am sitting in the front apartment of the chapter house, using a wireless connection to the internet. Yes, I said a wireless connection to the internet. And it was set up by one of the members in the house. There are currently three graduate students who live in or frequent Farmhouse. On of them being Nick Tipper, a Masters student in Agricultural Engineering. With his help, this house is wired with a DSL internet connection in each room and is covered by wireless internet service. Therefore, if you happen to drive by the house and see a couple of guys sitting on the front porch with their laptops in front of them, they are probably getting some serious work done while being able to enjoy the outdoors. On the whole, the use of science in agriculture has grown. Most good animals herds are bred via artificial insemination based on several selection criteria. The use of herbicides in agriculture is a major environmental issue and new technolgies are being used to selectively apply herbicides and fertilizers to those parts of the crop that need them the most. No, agriculture isn't like it used to be where you could make a decent living off the land with an eigth grade education. To be able to survive as a farmer these days, you've got to really know the science behind the things you are growing. You would think that a biochemist such as I would stick out like a sore thumb amongst this group of guys but I don't. So the next time you think of Farmhouse, or farmers in general, I hope you realize the intelligence being used to put food on your plate. And thanks again to Nick Tipper and the gang for getting the wireless internet up and going so I can publish this from by PDA sitting on the front porch of Farmhouse.

Ah the plant made pharmaceutical industry (and no, I'm not talking about that stuff grown hydroponically in someones apartment behind tin-foiled windows). PMPs (plant made pharmaceuticals) are enzymes or antibodies made by recombinantly expressing proteins in plants. Such proteins are traditionally made in cell cultures (e. coli, chinese hamster ovary, yeast, etc. . .). However, production using these cell cultures can be very expensive, scale up of production requires massive amounts of capital, and contamination with other microbes of the cell culture is a major concern. With a plant based production system, scale up does not require as much capital, you can simply plant more acreage. Contamination is not an issue as the plants native resistance strategies are used. All-in-all, it has been estimated that a plant based expression system for the production of a drug can decrease the cost for the manufacture of that compound by about tenfold. Over the course of a couple of blogs, I will delve into the details of the plant-made pharmaceutical industry and give you my opinions as to where the industry may be heading. If you want to do a little research on your own, I would suggest MolecularFarming.com. I want to now give you a little background into my qualifications to be able to give valued opinions about this industry. I was an employee at Large Scale Biology for almost three years. I chose to leave the company two years ago because I felt that my career was not advancing fast enough. For anyone that has followed LSBC, you will know that the company hasn't really gone anywhere in a couple of years although they have surprised me by being able to keep their doors open for business. I still believe I made the right choice by leaving the company as my level of understanding of biochemistry and molecular biology has increased greatly and I have been able to really study the PMP industry using my newfound knowledge for a couple of years. Well, that's about enough for this installment. If you're looking for a little lighter of a read, try Fark.com

Got to say it was a nice day up here in Michigan. Of course, I've had to spend it all day in the lab massaging some microarray data. If you ever want to see a process that vomits more data than anything I've ever seen, then analyze a few microarray slides. I guess I really need to brush up on my computer science and statistics.

Wow, its kind of been a quite day here in the lab, I've got something accomplished this week, and it looks like I'm headed for a pretty uneventful weekend. Compared to the last 7 or 8 months, this week was kind of unique.

For all of you mycological types out there, the mushrooms are beginning to appear up here and so may I suggest a link that can be conveniently found on my Website;. The site is Tom Volk's Fungi Page

In my last post, I gave you the following to chew on:

> Something to think about: > Bioinformatics - how much information will become available (number of > genomes for unique species, proteomes, etc) in the next 10 years and > how will it be processed?

Well, I'm going to let you chew on that for a while and give you another assignment. I want you to start brushing up on your knowledge of the Plant Made Pharmaceutical Industry. I'm going to fire a few salvo's that way soon so you are warned.

Well, I've got my first rant in, so now I want to write about something little different. I was perusing through the live audio archives at Archive.org the other day. I'll go into more detail about that site some other time. I had seen a listing for Hank Williams III several times and decided to give him a listen. My first impression was that he wasn't going to be that good and that he was riding on his family name. I don't remember which concert I listened to first but it started out with a couple of what I guess you could call rockabilly numbers. Hank 3 sounds eerily like his grandad, the original Hank Williams. On a side note, Hank Williams died at the age of 29 due to alcoholism, now that takes dedication. The songs where mostly about drinkin', cheatin', killin' and hell so it fit the standard of real country music accounding to the reverend John Wheeler of Hayseed Dixie. What was really "unique" is that his second set, the so-called "ass-jack" set was comprised of what I guess you would call death speed metal. It was this that has made me a true Hank Williams III fan. Now, don't go figuring me for a death metal grungy punk yet. I'm not really a fan of that type of music. What I enjoyed was Hank's ability to blend two extreme types of music into one show. The man is playing the music that he likes to play. From future blogs you will find out why this is important to me. Until then, visit Hank Williams III's website and listen to some of his music at Archive.org. You'll either love it or hate it. Something to think about: Bioinformatics - how much information will become available (number of genomes for unique species, proteomes, etc) in the next 10 years and how will it be processed?

Enough of the introductory crap. Let's get down to some real blogging business. First item up: e-mail. I ranted a little about this on my website a year or so ago. Flash back to about a year and a half ago. I have had a hotmail account for at least five years. I had to check it daily because I was at my storage limit (all of what 5 megs?) and the daily dose of spam would put me over the limit. Of course, I could pay to get more storage to alleviate that problem. Enter Google's Gmail. Holy crap! an entire gigabyte of storage space. I was able to get an invitation by promising to vote for George W. Bush in the upcoming presidential election on one of the gmail invitation websites that had popped up. You want to talk about a service that blew everyone else out of the water, that is exactly what Gmail did. These guys were offering 200 times the amount of storage compared to the other leading service, hotmail (you'll notice I am not providing a link to hotmail because I don't think it is worth visiting). Of course, hotmail got around to finally offering a whopping 250 megs (still four times less than gmail). As if the storage thing wasn't enough, gmail provides a clean interface to work from and it is extremely user friendly. Although some people have reported that Gmail can be a little slow, I have had no such problems and can say that Gmail is faster that hotmail. Okay, so you may take issue with the fact that gmail computers "read" your emails so that they can display content oriented text advertising but I am really okay with that. It sure beats the dancing snakes trying to sell mortgages that you will find on hotmail. Gmail also allows you to access your mail via POP3 (so you can access it through your favorite e-mail reading program). Skip ahead now, to this last April and Google announes that they are going to give you another gigabyte of storage space and keep giving you more (their infinity plus one program). Since this announcement, they have provided an additional 200 megs of storage space, almost as much as hotmail what a hotmail account still gives you. I am currently in the process "archiving" all of my e-mails that I have collected through the years into a Gmail account. It is very intersting digging through your old e-mails and seeing what kind of story they can tell about your life. You'll notice through all of this I have not mentioned Yahoo!'s e-mail service. I have an account through them and I get 2 gigabytes of storage (because I had DSL through them), but I don't use it. Gmail, also caused them to up their storage space and they responded better than hotmail, but Gmail still blows them out of the water. I would like to know what kind of economic impact they have had on these two services by offering for free something you had to pay to get with the other services (extra storage). I guess what really ticks me off about this is that it took Google shaking things up for the other e-mail providers to expand their services (and they still haven't caught up). As long as noone was rocking the boat, these guys were going to sit on their current level of tehcnology and milk it for what it was worth. I'm going to be writing more about Google later and I will have more to say then. Alright, that's enough, its only an e-mail account. If you want to try out gmail, leave your e-mail address in a comment to this post and I will send you an invitation.

Well, I guess I've named my blog. What is common sense to a biochemist? I may attempt to answer that question someday but not today. Think it over for yourself. Anyways, if you want to find out more about me, please visit my website. It's a little out of date but now with summertime rolling around maybe I can get back to fixing it up. I don't know if you could call me a "biochemist" by trade, I like to think of myself more as a "protein scientist" (alright, so that's probably just some asinine symantics there). I am currently a graduate student at Michigan State University working towards a Ph.D. in Biochemistry and Molecular Biology. As far as this blog goes, I really don't know to much of the direction it will take. I'll probably throw in my thoughts on such things as the Plant Made Pharmaceuticals Industry and the Pharmaceutical industry in general since that is what I know. I can be pretty opinionated so expect some rants on various current issues. I might even throw in a few war stories from my time involved as a member and advisor for a couple of Farmhouse fraternity chapters. This blog is syndicated so you can read it via your newsreader or however that works. I don't know much about syndication yet, but it is on my list of things to get around to learning about. -- Brian Barnett Graduate Assistant Michigan State University

Just testing out the e-mail capabilities of this blog. -- Brian Barnett Graduate Assistant Michigan State University