January 27, 2006
All systems go... Houston, we have achieved travel fundingconference. Ben and I are planning to work in a vacation around this, too. With this trip, I'll achieve one of my graduate school goals: do interesting research and get the opportunity to share my work with premiere scientists in far-away places. Life is good.
(By the way, this is a photo by et1 I found on flickr. It's one of the coolest pictures of Paris I've seen.)
January 25, 2006
Buying organic; BSE in the news
Consumer Reports recently produced a review of organic foods: Organic products: When buying organic pays (and doesn't). The investigators group foods according to how likely it is that a fruit, vegetable, or meat product contains pesticides and other additives. They also consider the price difference between organically- and conventionally-grown foods.
For example, CR suggests purchasing organic varieties of what the Environmental Working Group calls the "dirty dozen": apples, bell peppers, celery, cherries, imported grapes, nectarines, peaches, pears, potatoes, red raspberries, spinach, and strawberries. This is because these foods "consistently carry much higher levels of pesticide residue than others," based on USDA testing.
On the other hand, CR determined that purchasing organic seafood isn't worth it. The USDA has not established organic certification standards for seafood. And organically-produced fish can still contain mercury and PCBs.
It is important to point out that these evaluations are based solely on a comparison of certain contaminants -- what is typically seen on organic foods versus what is typically seen on non-organic foods. There is no consideration of environmental impact, animal production and handling practices, or other conditions that characterize organic farming. But CR does a good job of explaining why a certain organic food is deemed 'worth it' or not in their opinion. It's a good starting point for consumers to assess their own beliefs and value judgements in deciding whether to buy organic or not.
There was one part of the report that popped out at me as especially intriguing. For the most part, all the comparisons were an assessment of chemicals: pesticides, heavy metals, etc. There was no assessment of risks from infectious agents save one: BSE. CR suggests buying organic meat in part because of the reduced "risk of exposure to the agent believed to cause mad cow disease." They also mention that buying organic meat, poultry, and eggs is a good idea because of the antibiotics used in conventional farming and the greater potential for toxins in non-organic feed. I must say that worrying about contracting the human form of BSE, variant CJD, doesn't keep me up at night. But BSE and other prion diseases are definate health concerns.
The BSE point is especially interesting in light of Japan's recent re-instatement of U.S. beef ban just a month after it lifted its initial ban; and the continuing discovery of BSE in Canada, and suspected BSE in UK cattle born after the 1996 feed regulations.
There is interesting debate between Japan and the U.S. over what is considered risky for BSE. The risk of a cow getting BSE increases with age. This is because the BSE infectious agent, the prions, need time to become established in the brain and nervous system tissues and time to replicate and cause damage. (Find out more about BSE here.)
The U.S. argues that there is little or no risk of BSE in very young cows (less than 30 months old). Furthermore, the very small levels that would exist in these young cows would be too small to detect using the clinical tests that are presently available. These beliefs have resulted in two U.S. policy decisions: first, it is not useful to test any cows younger than 30 months old, and second, brain and other risky tissues pose no risk for transmitting BSE. Japan, on the other hand, tests all ages of cattle and prohibits risky tissues (also called specified risk materials or SRMs) from cows of any age to be included in any food product. This last difference is what prompted the ban reinstatement, and the difference is summarized nicely in this posting to ProMed-mail.
Personally, I tend to agree that testing of symptom-less cows less than 30 months old is futile with current technology. But I also think that the current feed bans for cattle in the U.S. are too permissive. I think they should read as the USDA organic standards do: "The producer of an organic operation must not feed mammalian or poultry slaughter by-products to mammals or poultry" (see National Organic Program regulation Â§ 205.237 Livestock feed). I just don't want to eat meat from a herbivore animal that has been fed animal products. The organic rules aren't perfect, but they are a step in the right direction.
January 20, 2006
Tools of the trade
While I'm doing a lot of analysis now, I'm also trying to keep up with the writing so I won't be swamped with it all at once as I get closer to the end of the semester. To me, writing is its own special agony. Nothing helps alleviate this--I just have to force myself to plow ahead. But there are tools that help me prepare and get organized. They don't make the writing any easier, per se, but make what is a 'tough row to hoe' at least a straight row and let's me know where I'm going. (Keep in mind that many of these are offered at discounted prices for students and that FreeMind is free!)
Useful tools of thesis-writing trade:
|â€¢||EndNote - reference manager|
|â€¢||Adobe Acrobat - not just the Reader but the fully-functional program|
|â€¢||Freemind - mind-mapping software|
|â€¢||Adobe Photoshop Elements - digital image editor|
|â€¢||MS Word - yeah, I know, but I have my reasons (see below)|
These software programs can be used in a wonderfully synergistic way. For example, I use EndNote to store all of my references. But it also stores files! I can store one file per reference. Almost all of the references I have are journal articles and reports, and most of these are available in PDF format. So I just insert the Adobe PDF file right into EndNote which adds a unique ID to the file and copies it into the EndNote library folder on your computer.
And I can launch the file right from EndNote. I'm not limited to PDF files. I also store Word files of manuscripts and reports, and JPG files of pictures, tables, and figures I've stored as their own reference entry.
I've already mentioned how useful Adobe Acrobat is for viewing publications, and this can be done with the free Reader version. But there are some nice features of the full Standard version that enticed me to purchase it. For one thing, I can manipulate files a bit more. I can select text for copying, highlight and make comments to the document as I read it, and take screen clippings. Some of these features do not work if the document is locked, but most of the documents I've come across are not locked. Another nice feature is that I can delete pages or add/combine pages in a document. This is handy with really big documents that are offered only in segments--I can combine them into one document on my machine.
An additional feature I've used quite a bit is the web capture. I can open a web page in Acrobat and save it as a PDF. This is a handy way to save web pages as references in my EndNote database. I use this a lot for press releases and federal reports from sites like the USDA or CDC when PDF versions aren't available.
A final feature I've grown to love is the Adobe Acrobat Organizer. This is a place to manage and store PDF files in an organized way. The Organizer keeps a history of recently-viewed files as well as a file manager system. In a way, this overlaps with the EndNote feature as a way of keeping track of PDF files, but sometimes it's easier to find files in the Acrobat Organizer since it keeps a screen shot of the document. It's also a quick way to save something I want to look at later (notice the "To be read" folder).
Now that I've got my references all organized, I actually have to start synthesizing that knowledge into my thesis, i.e., I have to start writing. How to begin? I've got all of this stuff swirling around in my head and it never seems to come out in a clear, orderly manner. That's where FreeMind comes in. Wonderful, wonderful FreeMind. I've talked a bit about the program before. It's a way to outline your ideas--to get them down--without having to worry about order right off the bat. That's what I hate about traditional outlines: whether it's bullets or numbers, I'm still fixated with order because I type things one after another. With FreeMind, just jot down your ideas as a bunch of blobs (nodes) around a central blob. I keep the central node something stupidly vague and short, like "methods chapter." Once I've done my first 'mind dump,' I go back and arrange things. I usually keep FreeMind open in the background to add things as they come to me. I've even used FreeMind to take notes as I'm reading a book or journal article.
One of the great features about FreeMind is that I can insert images and links. When I come across a key table or figure I want to discuss, I just insert it so it's right there for me to take notes on. (I'll create a screen clip and open it into Adobe Photoshop to tweak it, if need be, and save it as a JPG.) The links work well for referencing larger things or to serve as place holders for coming back to. These links can be internal to other nodes in the mind map, external, like links to files on my computer, or hypertext links.
After I've got a good map down, I export it as HTML and bring it in to Word so I can flesh it out into a finished document. It exports as a hierarchical outline. I take each piece of the outline and fill it into a complete paragraph. It helps a lot if I write my FreeMind nodes as paragraph topic sentences to begin with. For more on this, see my previous post or go directly to John Carlis' "Design: The Key to Writing (and Advising) a One-Draft Thesis" (under Selected Papers on his personal web page). I highly recommend it!
The reason I use Word is that it supports EndNote's "Cite While You Write" feature. As I'm writing, I can just plop the necessary citation into my document and EndNote does all the formatting, and even creates a reference list at the end of the document. I've looked into the open source word processors like Open Office Writer. The Writer is very good, but without the easy citation feature, I went back to using Word.
Well, there you have it. It may sound like a cumbersome Rube Goldberg system, but I've found it helpful. Now, back to writing...
January 19, 2006
I just had a poster abstract accepted for the I3S Symposium this May in Saint-Malo, France. It's not a sure thing yet, primarily because I have to secure funding (registration itself is €300--and that's the student price). But I'm very excited at the idea of sharing my dissertation work with Salmonella researchers from all over the world, particularly since I'm using a fairly new methodological approach. This would be the first time I presented in a foreign country. (Thankfully, the official language of the conference is English.)
Here's hoping we'll be in Brittany in four months!
January 17, 2006
Winter break pix
A few quick pix from Winter Break. We had a really nice Christmas spent visiting family and friends on the East Coast. Amidst our traveling, Ben and I made a quick trip into New York City. We did some tourist-y sight-seeing, like visiting the Christmas tree at Rockefeller Center.
Neither of us had been to an opera before and we thought seeing a performance at the Metropolitan Opera House would be a great New York experience. As fate would have it, our first taste of opera would be a light operetta -- something to get our feet wet, so to speak. The Metropolitan Opera was performing Johann Strauss' Die Fledermaus. A comedic story of drink, dance, frolic, and pranks.
Lincoln Center was beautiful. They had their own Christmas tree -- this one decorated with the shapes of various musical instruments.
The inside of the Opera House was very beautiful as well. There's a grant atrium decorated with crystal chandeliers and plush red fabrics. Here's the view from our seats. You can see there is a railing in front of each row of seats. Embedded in the railings are small display screens that show English subtitles for the performances (you are given the option of disabling the subtitles). Die Fledermaus was performed with the traditional German songs, but with English dialogue. I was at first surprised when the subtitles displayed during the dialogue as well as the songs, but that turned out to be useful since some of the singers/actors had thick accents.
Saving the best for last, we were delighted to be able to visit my sister and her husband and their new baby, Henry.
January 11, 2006
A little winter exercise...
I'm a little sore this morning. Got back on the bike for the first time since before winter break. But I wasn't riding, I was spinning. And I wasn't alone. It was me and Ben and 198 riders from the 2003 Tour de France.
Ben and I got a new bike trainer just before Christmas, since the old one bit the dust. At some point over the summer its fluid must have leaked out because when we set it up this winter there was no resistance--we were just spinning a hollow tube. The new one is much better and it is designed to handle the wider real wheel we have on our tandem. (The old one Ben had to jury-rig with some stiff wire.)
Spinning on a tandem works out pretty well. We can both exercise at the same time, like when we get home from work, or one of us can exercise alone. Ben did some solo spinning over the weekend when I was away, so I'm sure he's not as sore as I am this morning.
But what really makes spinning fun--or at least more enjoyable--is keeping your mind engaged during the workout. We're not interested in training videos, and most of what's on television won't cut it either. Last year we started buying DVDs of old cycling races and those are perfect. The races keep us engaged and motivated and set the right pace.
This year for Christmas, Ben gave me the awesome 12-hour 6-disc set of the 2003 Tour de France. (By the way, the DVD producer, World Cycling Productions, has its home right here in St. Paul, Minnesota.) We popped it in for the first time last night. Ah, it's a classic, right? The chases, the crashes, the suspense. It was great to see big Jan Ulrich in the Team Bianchi colors, now-defunct teams like ONCE, and Tyler Hamilton riding for the Danish CSC team. We just finished the Prologue--bad luck for David Millar whose chain slipped off and cost him the win--and the 1st stage that saw a horrific crash in sight of the finish line, one that broke Hamilton's collar bone and portended a wild and woolly Tour.
I can't wait to get back on the bike and see what happens next...
January 9, 2006
I've been doing lots of traveling lately and haven't posted in a while. I hope to post some pictures by the end of the week, and also comment a bit on my writing progress, but in the meantime, a quick mention of a useful bundle from Google.
The Official Google Blog had an item last Friday announcing a convenient bundling of PC software they're calling Google Pack. It contains a lot of basic software all in one place, all bundled in an updater that will periodically scan for updates.
Most of the software is Google's own products: Google Earth, Talk, and Desktop; but also Firefox, Ad-Aware, Adobe Reader, and the like. I had most of these installed already, but there were a few that I didn't. Google Pack lets you select only the pieces you want to download. But a nice feature is that Google Updater (which is part of the Pack) recognizes the existing software on my machine and includes it in it's check for updates.
That's all for now, but here's wishing you a healthy and happy start to your new year!