Monday, October 16, 2006

Getting This American Life

It took me a bit of searching, but finally I found it. A way to get archived versions of This American Life onto the ol iPod.

wget http://wbez-tal.streamguys.us:8000/content/314.mp3

It will start downloading. Look in your home directory and you see the file 314.mp3

Friday, June 09, 2006

Words of Deep Sadness

I've been reading from "Sophie's Choice" by William Styron, and can honestly say it's the best book I've read in some time. I can only read for a bit at a time, so it's a slow go of reading, but I came across a passage I felt I had to post. To me it underlines the importance of standing up for what is right and call for something that is wrong to be brought to a halt.

"One of the things I cannot grasp, though I have often written about them, to get them into some kind of bearable perspective," Steiner writes, "is the time relation." Steiner has just qouted descriptions of the brutal deaths of two Jews at the Treblinka extermination camp. "Precisely at the same hour in which Mehring and Langner were being done to death, the overwhelming plurality of human beings, two miles away on the Polish farms, five thousand miles away in New York, were sleeping or wating or going to a film or making love or worrying about the dentist. This is where my imagination balks. The two orders of simultaneous experience are so different, so irreconcilable to any common norm of human values, their coexistance is so hideous a paradox - Treblinka is both because some men have built it and almost all other men let it be - that I puzzle over time. Are there, as science fiction and Gnostic speculation imply, different species of time in the same world, 'good time' and enveloping folds of inhuman time, in which men fall into the slow hands of the living damnation?"

Wednesday, May 17, 2006

The Results Are Back

I found out yesterday afternoon that I passed my comprehensive exam! Wow, that was a little nerve racking for a while when I figured out a couple of little things I did wrong. I did not pass every single question, that's the only disappointment. I was one point shy on a question about the action of drugs that control seizure. Oh well. The total score was a passing one, and that's all that counts for this test.

Wednesday, May 10, 2006

One thing behind me...

Yesterday I finished taking my comprehensive exams/qualifying exams. It's basically a long test that is given after two years of working on a PhD that tests the knowledge you've acquired over time. Think of an essay exam that is designed to cover four or five classes. 12 questions, pick eight and answer them. Pass or fail. That's it. You fail it you get another shot in one year. You fail again and you get the boot from the program. It's a bit scary.

On each day I felt like I was able to write decent answers for three out of the four questions that I chose (you get six questions per day). I'll find out next Tuesday if I passed or not. This week is kind of a limbo status week.

Now that I've got the exam out of the way it will be full steam ahead on the lab research front. I got some disappointing results last week. I've been working for over a month trying to get a cell line to express two genes simultaneously which are not normally expressed in them. One gene makes the cells resistant to a drug, the other is a receptor I want them to express. So after a month it looked good. The cells were resistant to the drug, so chances were good that the receptor was also being expressed.

I tested the expression of the gene for the receptor I wanted. Nothing. Big bummer. All hope is not lost, because I have a second set of cells going that are resistant to the drug and might express the receptor. I'm going to try to make that determination this week. Otherwise it will be back to the drawing board to make a different expression plasmid (DNA which I'll put into the cells that contains the genes I want expressed) and start over again. I'll work on some side projects at the same time though, so it's not like I'll just be twiddling my thumbs.

Saturday, April 08, 2006

Another Couple of Months, Another Update

My blog is probably starting to feel like an unloved stepchild. Since Simone's arrival it's definitely been a slower process of writing. I suppose this is just something that goes with blogging. The initial excitement, followed by drudgery posting, and finally neglect. My hope though is that even though I may not post frequently, perhaps years or decades from now I can look back at it and recall what was going on in my life.

Ellie and Simone are getting back today from their trip to Williamsburg. It's been two weeks I've been on my own at home, other than a short visit from my mom and brother Dave for his birthday. I've been studying for my comprehensive exams that are on May 8th and 9th, where I'll be tested on knowledge I should have from two (or in my case three) years of coursework. After that I think I've only got one more class to take, a Genomics course, and then it's full time lab research until the end. I've done a bit of baking too. I've made a couple of loaves of bread and learned each time I've done it. Too bad home baked bread doesn't stay fresh very long. It only seems good for day or two.

My research continues to limp along. I'm trying to get a gene expressed stably in a B cell line where it's not present. If I can get it to work then I'll have something to write a proposal on. It's been almost a month now the cells have been growing in with their selection drug and I'm getting close to the point of testing them to see if the gene is expressed and works as expected. I'll cross my fingers when I do that test.

Made a couple of DVDs from video I had recorded on the camcorder we've got. I used one of the new Macs in the lab to do the editing, and I'll say, iMovie is a vastly superior product compared to Windows Movie Maker. It's a joke. And once I got the hang of iDVD, that was easy too.

The laptop somehow got a Trojan on it. It may have been a false positive (the only test that showed it with TrendMicro's Housecall, and I scanned with 4 different anti-virus maker's products), but there was also some odd behaviors that suggested to me it wasn't. IE would crash when I tried to access TrendMicro Housecall, it was sending emails to strange addresses in foreign countries when I didn't have an email program open, and some of the rootkit detectors I used were turning up hooked DLLs.

Problem is, I can't find the system restore disks anywhere. Ack. I tried using nLite to generate a new copy of WinXP Home from the files on the computer, but when I used it to try to reinstall Windows (after formating the drive) the install failed because it was missing some system file. Argghh. Now that's bad. I've got some other things I can try, but for now I'm frustrated because for one thing I can't find the system restore CDs that would make this an easy process. Oh well. I'll figure something out.

Sunday, March 05, 2006

Movies Ellie and I Want To Watch

So we're watching the Oscars, and there are a few movies that we're both thinking we'd like to see:

Walk the Line
Hustle & Flow
Brokeback Mountain
Syriana
Transamerica
Pride & Prejudice
North Country
Hotel Rwanda

And there are a few that I'd probably want to watch with or without her:
Crash
The Constant Gardener
Munich
A History of Violence
Batman Begins
Enron: Smartest Guys in the Room
The Squid and the Whale

Thursday, March 02, 2006

Actual Research about Teflon (You can FWD if you like)

I don't know why people are so willing to quickly believe what they hear on the radio/tv, but a lot of the scare stories you hear on the news are crap. If people don't want to use Teflon because it scares them, they are free to make that choice (I love choice, that's why I'm a Liberterian). I just don't think they should make it based on flawed information. We're exposed everyday to compounds that can cause cancer (acrylamide in French Fries anyone), yet we're living longer, healthier lives. Something is wrong with the picture. Let's stop worrying ourselves to death, and live the how we want without anxiety about cancers and heart disease (because we all die at some point). Live while the living is good!


This is an abstract for a paper that demonstrates there is NO DETECTABLE PFOA released into water (a common solvent) or water/ethanol (a solvent that can better pick up fat soluble materials) when they were placed in consumer cookware and heated to boiling or higher temperature. I think this statement from the paper also provides useful insight:
"The absence of PFOA from the coated cookware was not surprising. Fluoropolymers are typically manufactured near ambient temperature. Fabrication processes, such as those used to coat cookware, require temperatures of greater than 300 °C (typically 350 to 450 °C). These temperatures, and the large surface area of the coating material, would easily vaporize any PFOA (boiling point 189 °C 17) that may have originally been present. Also, Krusic and Roe 18 conducted gas-phase NMR studies where the ammonium salt of PFOA was observed to completely decompose within minutes at 234 °C."

Analyst. 2005 Sep;130(9):1299-302. Epub 2005 Jul 28. Related Articles, Links
Click here to read  
Determination of perfluorooctanoic acid (PFOA) extractable from the surface of commercial cookware under simulated cooking conditions by LC/MS/MS.

Powley CR, Michalczyk MJ, Kaiser MA, Buxton LW.

Haskell Laboratory, E.I. du Pont de Nemours and Company, P. O. Box 50, Newark, DE 19714-0050, USA. Chuck.Powley@usa.dupont.com

Salts of pentadecafluorooctanoic acid (PFOA) are polymerization aids used in the manufacture of fluoropolymers; one of the applications of fluoropolymers is the coating of metal cookware products. A method was developed to determine if PFOA might be present in and extracted from the surface of commercial frying pans coated with a DuPont fluoropolymer under simulated cooking conditions. Commercial grade cookware was obtained, then extracted with water and ethanol/water mixtures at 100 and 125 degrees C, and the resulting extracts were analyzed by liquid chromatography tandem mass spectrometry (LC/MS/MS). Detection and quantification limits as low as 100 pg cm(-2) were demonstrated. None of the fluoropolymer treated cookware samples analyzed showed detectable levels of PFOA when extracted under simulated cooking conditions.



This abstract is for a paper that indicates PFOA is not likely to be a risk either.
Environ Sci Technol. 2005 Jun 1;39(11):3904-10. Related Articles, Links

Exposure assessment and risk characterization for perfluorooctanoate in selected consumer articles.

Washburn ST, Bingman TS, Braithwaite SK, Buck RC, Buxton LW, Clewell HJ, Haroun LA, Kester JE , Rickard RW , Shipp AM .

ENVIRON International Corporation, 6001 Shellmound Street, Suite 700, Emeryville, California 94608, USA. swashburn@environcorp.com

An exposure assessment and risk characterization was conducted to better understand the potential human health significance of trace levels of perfluorooctanoate (PFO) detected in certain consumer articles. PFO is the anion of perfluorooctanoic acid (PFOA). Concentrations of PFO in the consumer articles were determined from extraction tests and product formulation information. Potential exposures during consumer use of the articles were quantified based on an assessment of behavior patterns and regulatory guidance. Health benchmarks were developed and then compared to the exposure estimates to yield margins of exposure (MOEs). A simple one-compartment model was also developed to estimate contributions of potential consumer exposures to PFO concentrations in serum. While there are considerable uncertainties in this assessment, it indicates that exposures to PFO during consumer use of the articles evaluated in this study are not expected to cause adverse human health effects in infants, children, adolescents, adult residents, or professionals nor result in quantifiable levels of PFO in human serum.

Tuesday, February 28, 2006

Comings and Goings

It's been a busy couple of weeks in the lab lately.

Up to this point I've worked on several projects. Over and over it seems they go nowhere for me. Over time I came to doubt my abilities, though I know the process of science is filled with failure. Despite knowing that, it can still be tremendously discouraging.

Things have been cooking along a little better lately though. I'm trying to make a cell line that expresses a gene that it previously didn't do (a gene for a receptor I'd like to activate). Things are moving along slowly, but I'm keeping my fingers crossed. I've had a little bit of sucess lately, and I hope I can keep it coming.

Monday, February 20, 2006

Short Thought Stream

I've been neglecting this blog for some time now. Not that there weren't things equally interesting going on that I used to write about, but I just haven't found the time to write about the goings on. Work has been a real drag for the last three months or so, but things are starting to look up again.

It seemed like every time I was doing something in the lab the result would not be good enough. Maybe I would have a measurable effect, but then I'd have some problem with the controls for the experiment. It's been like that for a while, very discouraging. The last two weeks have been marginally better. I've been trying to generate a copy of a gene so that I can put a gene that wasn't previously expressed into a cell line and get expression of the protein it encodes. It will be a project which I could turn into a thesis if it works, so I'm crossing my fingers.

As far as family life goes I'm learning every day how important communication is. Most people have heard it hundreds of times before, but practice is much more difficult I'm learning. I think our marriage keeps getting better though as we learn to read each other and talk more effectively.

What seems to have made a particular difference for my self and my marriage is my growing spirituality. I think it's given me a much more positive outlook on many things, and I hope when RCIA comes around again next year to begin to learn what it takes to become a Catholic. I used to wonder how people could be religious, without solid evidence of God. Then I came to understand a little better what the word "faith" means, finding the ability to believe in something even without clear proof. Evidence supports fact, but faith needs no evidence to exist and do good.

One last thing I've been thinking of that I should finally get down is how I feel guilty I've not been in touch with my friend AJ. I had sent him an email saying Ellie and I would like to visit he and Jaime while they were in Grand Haven for the holidays. In the end Ellie and I spent all the holidays either in Detroit or at home, so we never go to see them. That wouldn't have been as bad had I contacted him, but he called and emailed me and I never got back to him. I'm awful about that kind of stuff, even with my brothers and parents. I guess the thing to do is email him and tell him all that, the sooner the better.

Wednesday, January 04, 2006

NIEHS Abstract

One of the most potent suppressors of the anti-sheep erythrocyte antibody forming cell (AFC) response is 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The mechanism of TCDD-mediated suppression of the AFC response is known to be dependent on the aryl hydrocarbon receptor (AHR) and involves a disruption of B cell differentiation into plasma cells. Previous studies have shown that addition of Interferon gamma (IFNg) to in-vitro cultured mouse splenocytes prevented the suppression of AFC response caused by TCDD. To further characterize the effect of IFN on TCDD-mediated suppression of the AFC response other IFN forms were used in culture (IFN alpha or beta). To evaluate downstream AHR effects quantification of mRNA for Cyp1A1 and IgM heavy (IgH), kappa (IgK), and J (IgJ-chain) component chains was performed. Addition of 30nM TCDD to cultures caused Cyp1A1 mRNA increases as much as 38-fold over control, as well as significant decreases in the AFC response (58%), and decreased mRNA levels of IgH (37%), IgK (36%), and IgJ-chain (68%). Co-treatment of splenocytes with TCDD and 100U/mL IFNg prevented suppression of the AFC response. mRNA levels of Igh, Igk, and Igj from splenocytes cocultured with TCDD and IFNg returned to near control values. TCDD-mediated induction of CYP1A1 was attenuated by as much as 50% with IFNg. Treatment with IFNa or IFNb did not alter the effect of TCDD on the AFC response. Additionally, for IFNg to reverse the effect of TCDD on the AFC response it must be added to the culture within two hours of TCDD and antigen.

Friday, December 23, 2005

 
 Posted by Picasa


So we got a new camera with the Christmas money by dad and susan gave us (Canon Powershot A520), and I've been testing it out. It can even take low resolution movies WITH audio. Cool! Posted by Picasa

Friday, December 16, 2005

Implications of Dedritic Cell Antigen Presentation to B cells

When it comes to Nature magazine, I enjoy it. When my brother got me a subscription I really started to appreciate it. One of the best sections in it is the "Research Highlights", which points out papers that the editors thought where significant but appeared in other journals.

I get the Nature table of contents by email every week, and while I don't always find an interesting article, I always read the research highlights, and that's where this paper came up.
[blockqoute]Cell surface recycling of internalized antigen permits dendritic cell priming of B cells.

Bergtold A, Desai DD, Gavhane A, Clynes R.

Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA.

Dendritic cells process internalized antigens to present degradative products on MHC for TCR recognition. Because antigen-exposed DCs also induce humoral immunity, DCs must also retain antigen in its native state for the engagement of BCR on B cells. Here, we demonstrate that antigen endocytosed by the inhibitory Fc receptor, FcgammaRIIB, accesses a non-degradative intracellular vesicular compartment that recycles to the cell surface, enabling interaction of native antigen with BCR on B cells. Immunization with IgG-opsonized, T independent antigens leads to enhanced humoral responses in a FcgammaRIIB and complement dependent manner. IC-loaded DCs trafficking to the splenic marginal zone can prime a T independent response in an FcgammaRIIB-dependent manner. Thus dendritic cells are equipped with both non-degradative and degradative antigen uptake pathways to facilitate antigen presentation to both B and T cells.[/blockqoute]

Why is this important? Previously it was thought that B cells had to be exposed to free, native antigen. This changes the picture, showing that dendritic cells can stimulate both T cells and B cells to activate a robust antibody response. Very cool, and it even has some implications on immunotoxicology (agents that selectively affect dendritic cells may cause significant interference in an antibody response). It remains to be seen how important or widely occuring this phenomenon is, but I think it's pretty cool.

Friday, December 09, 2005

I Love the GPL

So I've got a 700Mb mp3 (an audiobook), and the iPod chokes on big files. What do I do: google search for "split mp3 gpl", and what comes up, but this sweet little free utility that does exactly what I'm looking for, it's called Mp3Splt. That goodness for the GPL (there were plenty of programs in the $20-$30 range that could do that, but who wants to pay for that kind of stuff when I might only use it a single time!).

Tuesday, December 06, 2005

Friends In Far Places

I've been thinking about my friend AJ and his wife Jamie this past weekend. They're teaching elementary children in Honduras right now (they've got a nice website for their adventure), a long way from family. While I'm sure things are a bit warmer there (though I'm not jealous as I look out my office window to see several inches of snow on the ground), I'm thankful that I've got my family around even if it is cold. I'm pretty sure they're ready to see their own families. I know they'll be back for a while over the holidays, and I hope Ellie and I get to see them.

I registered to officiate MHSAA wrestling this year, quite a bit late. Fortunately I didn't have to pay the late fees, as I wasn't registered last year. I just hope I'll be able to pick up some events. Ellie and I are going to need the money to pay for the holidays I think. I'm even thinking about becoming an official for some other sports, but I don't know. I wonder what they pay freestyle/greco roman officals now a days.