Common Sense for the Biochemist

It has been extremely hot up here this weekend. No relief is in site until Friday (when the highs are supposed to be in the mid 70's). Okay, so I've grown accustomed to the normal Michigan weather, where there is snow on the ground 10% of the year. This 90 degree weather WITH humidity is killing me. I got a Flickr badge on the blog, you can check out a selection of pictures I have taken through it. The weekend was kind of slow, I did help the Farmhousers put up a new shed in their backyard (check out some pictures of the building process on my Flickr account. More later.

Here is a link to an interesting site. This site claims to be a resource for the plant made pharmaceutical industry. Also prominently displayed is the title of "International Academy of Life Sciences" (I don't really know who they are, maybe I should do a little research on them). They also have a donation link prominently displayed. Of course they have the requisite pictures of 1) A person in cleanroom garb pipetting something, 2) an old person smiling, 3) a patient with a doctor. If you have some time and are intersted in PMPs, pop on over and see what you think of their site.

Just in case you are in the Plant-Made Pharmaceutical industry and are looking for a place to locate your company. Consider Owensboro. More information about Owensboro's biotech initiatives and incentives can be found here (I know the site doesn't have much but at least it is something). Here is a brochure with a little more information. So why would I make such an advertisement? One day, I would like to end up in back in Owensboro (my hometown), and in order to do so, I've got to be employed by someone in Owensboro. So if you are a PMP company - move to Owensboro and hire me!

Just found yet another science biotech blogger (holy cow, they are coming out of the woodwork!) Peter's Weblog. In the below post, Peter comments about discussion occuring over at In The Pipeline.

Check out the interesting echange between Derek Lowe and a certain William Burke here. Look at the comments section.

I think it is fair to say with a high degree of confidence that people tend to fall into two of the following three categories (but cannot belong to all three simultaneously).

(You will have to go to his site to see what the three categories are). But it brings up a point I want to make. During these discussions between Derek Lowe and others (I would call them vitamin pushers, and very dangerous ones at that), the others have had many chances to post links to their sites. I couldn't resist, I just had to click on them. And you know, I'm probably not the only one that did that either. You may think these others are really not intelligent, repeating their unsubstantiated, rather idiotic claims (with convenient links to sites that back them up), but in reality, these guys are getting just what they want, their product in front of people.

Ever wonder what a research contract between two companies looks like? Well, here is your chance to see one. RJR and Biosource Contract Agreement I especially like the ending paragraph whereby:

Biosource will hire a PR firm to work with the company to accomplish the above listed goals. Biosource will perform the PR program at cost (non-direct PR agency charges plus direct employee costs, including travel & expenses)

RJR was trying to use Biosource's technological applications for Tobacco to create a "good" image for the Tobacco industry. More coming soon. . .

I've added Haloscan Trackbacks and Comments for my blog, feel free to leave me a comment here or on your blog. It was pretty easy to set up, although I had a few problems using the auto-install feature and had to install the features manually.

Found another one. Its called "In the Pipeline", authored by Derek Lowe. Derek works and writes about life as a scientist disocvering novel pharmaceutical compounds. A good starting (and humorous) entry is "How Not to Do It: Distilling Benzene". This entry and related comments contain some pretty humorous (at least now they are) stories.

Summer students are showing up at academic and industrial labs around the country right about now. A certain percent of them will blow something up within the next three months, and that percent will be several standard deviations above the ka-boom rate of the other lab members. I'm not trying to say mean things about summer students. I merely speak the truth.

Luckily, I have never been a subject of one of these stories (I think!!).

So as I was cruising around the "blogosphere" tonight and I did find more scientific-like minds out there blogging. First up is A Scientist's Life from an unnamed post-doc working "tirelessly" away in a lab somewhere. Well, it was late when I made this discovery. I'll have more on this later.

Like I said earlier, being able to study past business dealings in the PMP world is pretty interesting to me. As I was persusing through the Tobacco Documents, I noticed a unique relationship between RJR Reynolds and Biosource Technologies (now Large Scale Biology) unfold. Here is the short of it all. At one point in the early 90's, RJR owned 25% of Biosource (now LSBC) and was contracting with Biosource to create tobacco plants with increased levels of nicotine and other goodies. Lets begin with some initial correpsondance Here is a document from Bob Erwin (now chairman of the Board at LSBC) expressing interest in working with RJR after a visit to RJR's facilities. Basically, Biosource wanted funding to work their pharmaceutical production processes. In return, RJR could use GENEWARE for their own product development work (increasing nicotine levels, manipulating flavors, aromas, etc. . .). Here is Gary Hellmann's (RJR R&D) first impressions of Biosource (probably made in preparation of the the visit talked about above). Well, that is all for now, I'll have more of the story later. What, you didn't think you would get it all at once did you?

I have a couple of friends who keep joking around about starting an underground dairy (don't ask). Apparently, underground farming (or pharming) has caught on in the minds of several other people too. It seems that a company called Controlled Pharming Ventures has built growth chambers in an abandoned underground mine. Their reasoning is that the chambers are easily secured (armed gaurds at the entrance to the mine), there is little threat from bad weather, and there is little threat of genetic contamination of surrounding fields or native vegetation. They also claim that the climate in the chambers is easily controlled due to the static temperatures of the mine. So the next time you see your local farmer driving his brand new harvester into a cave, don't think anything about it.

For some reason, I find it interesting to follow the financial markets and all the dealings that go on between companies. I recently discovered that I can really study some of the past coroporate dealings (albeit of a slightly evil company) of the big tobacco companies thanks to the release of all of the documentation that was using during the big lawsuits that took place a few years ago. It is really interested to be able to actually discover what goes on behind the closed doors of upper management. I use the collections found at the Legacy Library at UCSF. In a few upcoming blogs I'll present some of the more interesting things I found. Some of the stuff I read really suprised me.

I am waiting for a PCR reaction to finish up so I thought I would give a little writeup about a new piece of equipment (toy) I just bought. A couple of weeks ago I purchased the 40GB version of the Creative Nomad Jukebox Zen MP3 player. My rationale for this purchase is that I can use it as a portable hard drive (which I have, and it works very well for this purpose). I still can't decide whether I like the user interface and button arrangement on the device yet or not. However, the software for interfacing with your computer is very easy to use. The only drawback I see is that to access your files or music by an interfacing computer, that computer must have Creative's software installed on it. It is also a little bulky and awkward when compared to an iPOD. I have about 800 songs on it and I have backed-up my work hard-drive and still have about 25 GB left. All-in-all, I think it was a good purchase. The fact that it was about $150 less than a similar iPOD makes it even better.

Intervexion will be relying on Medicago to supply them with quantities of their PCP addiction-beating antibody for clinical studies. Looks like Intervexion doesn't want to commit capital at this time for manufacturing. Probably not a bad move. Question is, what plant will be used as the expression host? Link to Yahoo's write-up

Alright, so I'm running a little behind on some PMP news so here goes. Icon Genetics has a paper in the June 2005 Nature Biotechnology journal. They explain their new expression system based on 'magnifection'. Basically, they insert ~12-16 introns and make a few silent mutations in their viral expression genome so that the sequence looks more "nuclear". Viral genomes usually hang out in the cytoplasm (outside the nucleus) of cells, therefore, there were problems getting the genome to be expressed when it was incorporated into a nuclear genome via Agrobacterium mediated transfection. It appears as if the insertion of introns and a few silent mutations make the genome look more nuclear and they are able to get more expression. Here is link to the paper via Icon Genetic's webpage

As I was perusing the net, I came across my blog, or should I say Brian Barnett's blog. Except, it wasn't mine. Seems that there is another Brian Barnett in Utah who blogs. Geeze, great people think alike and have the same name apparently.

I have found out one thing in my first month or so of blogging, and that is that it is a heck of a lot easier to be a critic than it is write about something funny or witty, I have even more respect for Dave Barry. Maybe it is just the fact that it has been in the 90's this week (yes, heaven forbid, it is actually hot up here and it has been for more than two days straight). I have enjoyed the blogging thing, though. I've got an interesting system down. Most of the content that I generate I write on my PDA in whatever location I choose and is then e-mailed to my blog where I do the final editing. I would eventually like to intigrate a few for pictures into my content, we'll see how that goes. Its been hard for me to keep my entries short, unfortunately, you'll have to live with that. We'll here's to a few more months of this. And now for something funny or witty: Here is a list of items that can be affixed to a concrete ceiling using caulk (from my own research of someone else's handiwork): Pens & pencils (easy) A pad of post-it notes (and the are still usuable) Business cards (these can be affixed by their edge to the ceiling. An array of these makes an interesting rolodex). Staplers Aluminum cans Glass bottles (warning: these are heavy and must be affixed with ample amounts of caulk. Do not place where a falling object (especially glass) could injure someone.) Dry-erase boards. Spoons Forks Knives What doesn't work: Remote control (not enough flat surfaces can be affixed to support the weight) Cordless phone (see above) Another warning: you are probably going to peel the paint off the ceiling when you try to take down your work. I think your beginning to get the picture, I encourage you to try this yourself.

Trying to define van Der Waals forces is a bit like defining pornography: you'll know it when you see it.

On of my most favorite episodes of South Park is the one involving the underpants gnomes. To get the uneducated up to speed: in this episode, Tweak, who we first meet, is plagued by little gnomes who continually steal his underpants. When Tweak finally follows the gnomes back to their lair, the real reason for their theivery is unocvered. It turns out that the underpants gnomes are running a business with a pretty simple business plan which is:

1) Steal Underpants

2) ?????

3) Profit

It seems as though they are having no problems with aquiring underpants, however, they are at a loss to what step two should be. They are sure, though, that step three is profit. Of course, this episode is a spoof of the glory days of the dot.com era, when businesses with no sensible business plans were being financed rightand left.

Unfortunately, there are some underpants gnomes to be found in the plant made pharmaceutical industry today. As this industry is very young, many of the leading companies are in the start-up stage. Several of these companies (and I am not going to name names because I may want to work for one of them in the near future) profess to have a great model system for production. In your research of these companies, you'll probably stumble across something along these lines:

"Company X is a leader in PMPs. Our system is based on proprietary technology using plant Y as a host system which we call the Z System. We have successfully used the Z system to produce three common, run-of-the-mill proteins that have no commercial applications.

"Well, these companies have part one down pat. And they will probably put out a few press releases like this:

"Company X has partnered with Big-Pharma A to develop products using their proprietary Z system"

Looks like they are still trying to find part two. For most of these companies, part three will probably never be realized. On the flip side, there are a couple of companies out there who have part two all worked out but need to figure out how to steal those underpants. These are the companies that have developed (or licensened) products that can be manufactured in plants but need to figure out the best way to manufacture them. There are also countless other small academic labs that have interesting products but have no idea how to manufacture it on a large scale, or the desire to. Unfortunately, there is not a single company yet who has put all three steps together. It will be interesting to see if there are some mergers or acquisitions made soon to put together a company with abetter business plan.

In my opinion, companies need to work on step two before beginning step one. A product must be found whose production in a plant system is advantageous. I think this product will probably be some form of an antibody. Large quantities must be needed, I still haven't figured out what will fit that bill, but most of the industry people seem to think it will be some form of vaccine. The protein also must be amenable to being produced in a plant system. A big hurdle in this area is the glycosylation factor (plants glycosylate proteins differently than other eukaryotic systems). As the industry stands right now, if it looks like glycosylation could cause a protein to be antigenic, I would stay away from that protein.

Once this miracle product is found, THEN the best way to go about manufacturing it (type of plant, expression system, etc ...) should beworked out. Will the underpants gnomes, I mean PMP gnomes ever make it to step three? Lets hope so.

I just finished reading a good post on the newly discovered (for me at least) BioBoom Blog. According to a story in the Boston Herald, the SBA has changed their interpretation of their rules so that companies that are backed by more than 50% venture capital can not receive small business innovative research grants. As is stated at BioBoom, this could create a few interesting opportunities.

Apologies for the long delay between blogs. As good ole J.R. Ross from the WWE would say, "bidness is about to pick up!". I read a good book this past weekend, "To Be the Man, a biography of Ric Flair." It was a pretty simple read and I got through all 300+ pages in one sitting. To those of you that don't know, back in my undergraduate days, I was a rasslin' fan. I'll still sit down every now and then and watch whatever is on but I don't follow the storylines anymore. I was a fan during the "Monday Night Wars" and to me it was just as interesting (if not more interesting) to follow what was going on behind the scenes as the two rival promotions, WWF and WCW, fought for viewers on their Monday night programs. The book chronicles Ric from his start with the Gagne's promotions in Minnesota and follows him to Charlotte, where he met with Jim Cornette. There are some pretty good anecdotes about his life outside of the ring. Most of the book seems to be historically correct, but there is some WWE propaganda in it (hey, when they are publishing the book, they are going to promote themselves).I guess the part of the book that really sticks to me is Ric Flair's portrayal of Eric Bischoff. For those of you who don't know who he is, Eric managed the WCW during its heydays, when it was beating the WWF in the promotion wars. However, Eric also managed to handly drive the promotion into the ground. If you know Ric Flair, then you know that he tried to live like his in-ring personality. The man was confident, cocky (he had every right to be), and is one of the few wrestlers that can say that he made the industry of wrestling better. Mr. Flair tells of his days in the WCW under the management of Eric Bischoff. I won't go into detail here but it is worth researching more. Basically, Eric was able to take a very talented and able wrestler and demoralize him to the point of nervous breakdowns. He was told that he was nothing to the sport. Ric was not the only one that this occured to, either. Meanwhile, Eric and his "good ole boys" made sure they had plenty of facetime on TV and made the primo money. When Ric joined the WWF after the demise of the WCW, he was not confident of himself and was really questioning what type of athlete he was. Fortunately, through good leadership at the WWF, Ric was able to gain his confidence back and was able to become a productive wrestler again. When people look back at the careers of Eric Bischoff and Ric Flair, they will realize the contributions of Ric Flair to the industry including his work attitude and ethics. All they will remember about Eric Bishcoff is how he was able to take an industry-leading company (they beat WWF 83 weeks straight on Monday night) and drive it not only into the ground, but through it. So why does this interest me? It amazes how inept some corporate managements, such as those that presided over the WCW can be when it comes to recognizing employees amongst their ranks that are so incompetent. Basically, the Erics of the corporate world, and I have to believe there are more out there, are interested in only their own self-promotion even if it is at the cost of another employee or the entire corporation. I guess they are able , through their self-promotion smoke-screens, are able to keep upper-management blind. That also gives me hope when I get back to the real world. In the long run, these guys are people in the industry that I can beat. Vince McMahan was able to pick up the leftovers from the WCW explosion for only $5 million. I'll bet Vince has already made that in profits off of the WCW tape library. If you are out there working for an Eric, just quit, as Ric Flair will tell you, life is much better somewhere else. Take 'er easy Y'all Brian "The Nature Boy" Barnett