Don't Live Like a Lab Rat!

Earlier this week, Terry blogged about a Princeton study showing that All sweeteners are not created Equal. (Thanks, Terry!) The press release she cited begins:

A Princeton University research team has demonstrated that all sweeteners are not equal when it comes to weight gain: Rats with access to high-fructose corn syrup gained significantly more weight than those with access to table sugar, even when their overall caloric intake was the same.

In addition to causing significant weight gain in lab animals, long-term consumption of high-fructose corn syrup also led to abnormal increases in body fat, especially in the abdomen, and a rise in circulating blood fats called triglycerides. The researchers say the work sheds light on the factors contributing to obesity trends in the United States.

I was rather excited about this--I sometimes teach simultaneous biochemistry and statistics courses for nursing students, and a paper like this would be ideal--combining carbohydrate chemistry, data analysis, and dieting. It would be bound to pique their interest.

Unfortunately for my purposes, the press release veered into diet-guru pseudoscience right away, speculating that

as a result of the manufacturing process for high-fructose corn syrup, the fructose molecules in the sweetener are free and unbound, ready for absorption and utilization. In contrast, every fructose molecule in sucrose that comes from cane sugar or beet sugar is bound to a corresponding glucose molecule and must go through an extra metabolic step before it can be utilized.

Really, that's their explanation? Hydrolysis is an extra metabolic step here? I suspected that the researchers were not responsible for the flaky press release, so the next step should be the actual article. The press release said the article was published online Feb. 26, but it provided no link. Still, search engines soon took me to the abstract: High-fructose corn syrup causes characteristics of obesity in rats: Increased body weight, body fat and triglyceride levels. The abstract seems reasonable enough--no speculation about metabolic pathways, no suggestions that fructose calories are qualitatively different than sucrose calories. Unfortunately, the abstract is all you get from the publisher, unless you wish to purchase the full text for $31.50 USD. My adjunct professor status doesn't cover such costs.

Meanwhile, everywhere I looked, there were blog posts and science news articles concluding that if we switch to soda pop sweetened with sucrose, it will keep us from getting fat. Much as I would like to eat more sugar and lose weight, I'm pretty sure that's not going to happen.

As I went about trying to sort out this puzzle without spending $31.50, I found some helpful and interesting discussions of the article (listed in the links below), and this afternoon a Slashdot commenter provided a pre-print of the actual paper.

The press release conflated the two experiments described in the article, overstated the differences in weight gain, left out the data from female rats (which seemed to contradict the male rat results) and didn't mention how small (eight rats per group) the treatment groups were in the long term study. If you look at the table of final weights for the short-term study, the rats that had sucrose to drink 12 hours a day had the same mean final weight as the 24-hour-a-day corn-syrup drinkers. The group with a statistically significant difference was the 12-hour-a-day corn syrup drinkers, and their standard error bars came very close to overlap. Given that there were only 10 rats per treatment, I'd hardly call this a definitive finding.

The graph on the right shows the inconclusive results in female rats in the 6-month study. Over all, I'd say this is an interesting little study over-hyped by Princeton's PR department. If it's now true in science, as in Hollywood, that there is no such thing as bad publicity, these researchers can look forward to some more funding.

Here are some of the links I found informative or interesting.

• High-fructose corn syrup causes characteristics of obesity in rats: Increased body weight, body fat and triglyceride levels. by Miriam E. Bocarsly, Elyse S. Powell, Nicole M. Avena, and Bartley G. Hoebel. Also available: pre-print of the actual paper.
• The press release: A sweet problem: Princeton researchers find that high-fructose corn syrup prompts considerably more weight gain
• The Industry Response: Gross Errors in Princeton Animal Study on Obesity and High Fructose Corn Syrup Research in Humans Discredits Princeton Study from the Corn Refiners Association. The "gross errors" they mention are in the press release, not the study, but hey, it's PR--who cares if it's true?
• High Fructose Corn Syrup Causes Bigger Weight Gain In Rats at Slashdot. The comments were very helpful. Here's where I found links to the full text of the article (without paying $31.50) and also the Ars Technica and LA Times critiques. There were some nice technical discussions of the enzymatic pathways involved in fructose vs. glucose metabolism, some pseudo-scientific rants, and some funny comments as well. Slashdot can be so great.
• Does high-fructose corn syrup make you fatter? Ars Technica is more harshly critical of the original article than I am. Really, it's a fine line between convincing editors to publish and overstating your results.
• A not-so-convincing case that high fructose corn syrup is worse for you than sugar. The LA Times also finds fault with the study.

Shopping, Crochet, and Spring Wildflowers

I believe I stated a while ago that I had plenty of crochet patterns and books on hand, that there was no need for me to spend any money on this new pursuit, or to acquire more stuff to clutter the new house. When I found a big gap in my collection of crochet hook sizes, it didn't seem outrageous to buy a set of large-ish steel crochet hooks at Wal-Mart. They wouldn't take up much space, and they only cost seven dollars--not as much as many new hobbies require, surely?

A few weeks later, shopping online for a replacement flashlight, we found what we wanted on Amazon. Just a few dollars short of the free shipping minimum, I dipped into my "Wishlist" and added on Beyond-the-Square Crochet Motifs: 144 circles, hexagons, triangles, squares, and other unexpected shapes by Edie Eckman.

Although I'm nickle-and-diming my way out of my frugality promises, I am very pleased with this book. It's hardback and spiral bound, and the colorful example motifs fulfill my yen for new eye-candy. I'm pleased to have both text directions and diagrams, and I've learned some new-to-me techniques. There's also a section at the back on how to design your own unique motifs. That's something I'd never even thought about before, but that is one of the truly cool things about crochet--you can go wild and just try things. (With knitting and the sort of sewing I usually do, you need to plan ahead more.) I'm really pleased with this book, and here are some of the motifs I've made so far.

Eckman's book shows all the motifs in colorful sport-weight yarn, so of course I'm trying them in some rather coarse crochet cotton thread (using my new Wal-Mart steel hooks). A couple dozen of the ecru squares at the top of this post would make a handsome table runner, I think. I like how open this square is, compared to the granny squares we're used to seeing sewn into afghans and blankets.

These motifs remind me of dogwood blossoms. I think I'll sew them onto my next pair of slippers, with some little gold buttons in their centers.

These white motifs are two variations on a theme. I think they both look floral in crochet thread, like some small spring ephemeral--perhaps wood anemones?

Long-Deferred Socks Complete At Last

I started knitting these socks as part of Sharon B's fiber arts community Take It Further Challenge, February 2008. My participation in her inspirational project fell by the wayside due to an unexpected work opportunity and the building of our new house, and the socks also stalled.

Originally, I planned to knit a dainty texture pattern on my smallest steel needles, with this machine knitting wool held double.

Unfortunately, fine yarn held double played the devil with all the twist-stitch patterns I tried. I couldn't keep from splitting the yarn, so I fell back to knitting this sort of wide, plain rib pattern:

It was slow going at this gauge, but after I'd knitted about four inches of the top, I knew something wasn't working well. It looked nice enough:

However, the stockingette stitch was rather loose, even with my tiniest needles, and I've found that loose-knitted socks are very uncomfortable inside shoes. You end up with a mesh pattern embedded in the soles of your feet. So, I unraveled again, and this time I knitted with four strands of yarn held together. This was bulkier than fingering weight, but finer than sport weight, and it produced a nice fabric. I chose a knit-purl design to make these fancy ribs, and I used a strand of wooly nylon to reinforce the heels and toes.

Wearing of the Green, 1909

Although my grandmother, Florence Williamson was the daughter of a Scotsman and a Bohemian, her St. Patrick's Day postcard collection is quite extensive. This one was sent from Des Moines March 17, 1909, and reports a foot of snow still on the ground. Much like this year, I'd guess.

Crochet in Plaid, My Favorite Color

Here's another crochet-skills-building exercise I've worked through. These place mats are rectangles of crochet mesh, and my big accomplishment is that I have the same number of stitches on each row. At least in the case of mesh stitches worked in yarn, I'm now able to create actual rectangles, sporting lovely parallel sides.

I changed color several times in the mesh pattern, to make stripes, and then I took advantage of the "holes" in the mesh to slip stitch perpendicular stripes over the top of the mats. I've been fascinated by crochet faux-plaid patterns, and it happens to be a simple design to make, one that doesn't require much advance planning. It's perfect for using left-over bits and pieces from other projects.

Pleasures of E-Books

I always love an event that features free stuff and sales, so I took notice of Read an E-Book Week (March 7-13). Their website features a list of authors, publishers, and ebook stores giving away free ebooks or slashing prices. The E-book promotion site says of their event:

Read an E-Book Week educates and informs the public about the pleasures and advantages of reading electronically. Authors, publishers, vendors, the media and readers world-wide are welcome to join in the effort. We encourage you to promote electronic reading with any event....

This week, I'm reading Anthony Trollope's Can You Forgive Her?, which I got from my beloved Project Gutenberg. I'm reading it on my Astak Reader, where I've also downloaded all 69 files they have of his, including 47 novels, some short writings, and his Autobiography.

If I were reading my first Trollope novel in the usual way, either from a library or from a second-hand book dealer, I'd be reading whichever novel I happened to find. This way, I was able to pick the one that seemed the most engaging for me, and I am able to read the Autobiography alongside it. In fact, my local library has none of his books, and my second-hand paperback copy of Barchester Towers is falling apart and features type too small to read except in very good light.

I'm not saying that ebooks have no drawbacks. So far, I haven't been able to find a well-formatted poetry book. (I'm using Tennyson and Whitman as my test cases.) Also, I have no truck with Digital Rights Management (DRM), so that means I won't be buying many ebooks in the near future. Still, access to "The Complete Works of" so many out-of-copyright authors is a real treat for me. When I enjoy a work of fiction, I immediately want to know what else that author has done.

Drupal Updates, the Afterword

I've updated At Home on Spice Ridge and Pocahontas County History on the Web, and I've been asking myself, "What was all the fuss about, Boots?" It was much more trouble to set up test sites on localhost than it was to run the update processes on the live web sites. Of course, I see the point of having a test site, and I'm going to keep localhost up-to-date and backed up, so that next time I have a hardware disaster, I won't be starting from scratch.

I never got the Drupal image gallery modules and the enable clean urls functioning on localhost, but they never stopped working on the live sites, so there's not much pressure to fix the issue locally.

It seems that it's best to update modules one at a time, so that if there's a problem, you'll know which module caused it. Because I had both module updates and core updates, I updated the modules first, one at a time, and then did the core last.

Here's a list of the resources I used in the update process, with short descriptions.

• How to Upgrade Drupal from the O'Reilly Web site. This was much more helpful than the equivalent Drupal.org explanations, mostly because it was better written and edited. This is the link to go back to.
• HowTo: Updating Drupal 6.x to newer minor version. From the title, you'd think this Drupal.org guide would be exactly what you want when you're ready to update, but that's not the deal. It's a discussion of different tools that expedite the updating process, but you need to fuss with these long before you need to update. Frankly, I'm wondering whether these are worth the trouble...given how painless updating was. Of course, painless updates may be a fluke....
• Introduction to Upgrading. This seems to be Drupal.org's canonical upgrade instruction. It seemed pretty complete, but I didn't hit any snags, so I don't know whether it will help when one really needs help.
• update modules best practice--This is a nice discussion on a Drupal forum. I found it helpful in figuring out the sequence of my updates--that is, what to update first, second, third...

Openoffice Crashes in Kubuntu Thanks to openoffice-kde

Since I involuntarily switched from Debian to Kubuntu a month ago, I've run into some new and unfamiliar problems with Openoffice.org. (I teach courses in Microsoft Office, and some of the organizations I work with are Windows shops, and Open Office meshes better with that stuff than anything else I've tried.)

Basically, every time I used Open Office under Kubuntu 9.10, it would hang or crash. I couldn't identify what procedure precipitated the crash, so it was hard to find solutions via search engines. Eventually, I found this, (while looking for something else).

Title: OpenOffice 3.1.1 crash from the Kubuntu Forums

Title: Re: OpenOffice 3.1.1 crash
Post by: CH~ on November 07, 2009, 09:24:19 am
I had diffrent problem with it. You can see it here http://kubuntuforums.net/forums/index.php?topic=3107536.0

Resolution:

Remove openoffice.org-kde and install openoffice.org-gtk. ::)

So, that's precisely what I did. I uninstalled the package openoffice.org-kde and I installed openoffice.org-gtk and it has worked just fine for several days now. I'm posting this in the hopes that the search engines will find the terms "openoffice" "kubuntu" "kde" and "crash" together in one place.

New Crochet from Old Thread

Rather than posting yet another "tinkering with computers and software" saga, I'll show you some more of my crochet projects. Like the wobbly potholder, the goal here is to improve skills, while making a potentially useful object.

After completing the potholder, my next thought was to crochet some slippers from my cheap acrylic yarn collection. Acrylic yarn has gone steadily downhill in quality in the years I've been knitting, but this yarn was given to me during someone's spring cleaning, and had been purchased new in 1970--in other words, a blast from the past. I actually crocheted three different slipper patterns, found them unsatisfactory, and unraveled them. At this point, I decided that the best slippers are the garter-stitch rectangles that you sew up and adorn with pompoms, so I put aside my crochet hook and knitted the black acrylic yarn, sewed them into slippers decorated with two-tone pink crocheted "roses." They're washable house slippers, and the "roses" don't look so oversized when the slippers are stretched over my feet.

Having practiced a bit with stretchy yarns, I believed I was ready to move on to crochet thread, which is reputedly more difficult to work with. I pulled out my Quick Crochet thread, purchased at American Thread's "Yarn Barn" in Willimantic, CT around 1980. (For me, fiber crafts are always a walk down memory lane.) I'm really pleased to finally use this stuff, after hauling it up and down the Eastern Seaboard over all these years.

First, I made a simple pinwheel motif out of white thread. This stuff is a little coarser than the thread sold as "Bedspread Cotton," it's polyester, and it came from the factory seconds bin at American Thread. I was pleased to have it turn out relatively pinwheel-shaped, although there are a number of mistakes. Washed and starched, it doesn't look too bad, and it is currently sitting on the kitchen table under the sugar bowl.

I've been intrigued by two-color crochet, so my next move was to mix the red and the white thread in a project. I just followed the instructions I found on Carol Ventura's web pages (see links below), and made up the pattern as I went along. It's crocheted very tightly, and because the unworked thread is carried along in the pattern, it's quite thick, and works as a potholder.

Some of Carol Ventura's Tapestry Crochet links:

• Tapestry Crochet, a website by Carol Ventura, features her own approach to colorwork and beading in crochet. She has text instruction, free video tutorials, links to her books for sale, and examples of her own work. The work in her Gallery is just amazing.
• Tapestry Crochet...the rest of the story is Carol Ventura's blog where she profiles tapestry crochet artists. More examples of beautiful colorwork crochet.

More Fun With My Local Drupal Laboratory

I was very happy yesterday when I edited my settings.php file and a normal-looking copy of my Spice Ridge home page appeared at http://localhost/spiceridge. I posted my step-by-step directions here, and marveled that I had completed my cloning project before the wee small hours of the morning, and without weeping or cussing. Then, I sat down to tweak, modify, and update the local installation, and discovered to my dismay that the only thing that worked as intended was the front page, the page generated by index.php

The course of true upgrades never did run smooth....So I turned to Community Plumbing for Drupal advice:

• Copy your live site to a test site (GUI). OK, that's what I'm trying to do...but these things aren't working.
• How to copy a Drupal site from server to local? Here's a forum question from someone who's having the same problems I am, and who has tried a bunch of the same things I have. One helpful person points to this:
• How do I unset the clean URLs? There were three things to try, and I tried them all. when I tried logging in by adding ?q=user to the end of the localhost URL, I got a 404 error as usual; while the msql commands to clear the cache files in the database had syntax errors that I couldn't work out. However, when I added $conf['clean_url'] = 0; to the end of the settings.php file I was back in business.
• But only for a minute. This lets me log in, but I still can't find my image files, and I get "Fatal error: Allowed memory size of 16777216 bytes exhausted (tried to allocate 40961 bytes) in /var/www/spiceridge/projects/includes/theme.inc on line 1010" when I try to navigate to the admin page. The Drupal.org advice was quite confusing and probably not applicable to my situation: Increase PHP memory limit.
• It seemed to me that the thing I should do (since the installation on my hosting provider's server runs like a top) is to fiddle with my newly-installed PHP stuff.
• Ubuntu Documentation--Drupal has this to say:

  You should increase the default PHP memory limit value (the amount of memory dedicated to running scripts), since the default 8 Mb is not sufficient. Use 96 Mb (or even 160M) if you intend to use graphics (although for simple uses 32 Mb may be sufficient).

  In newer versions of Drupal6, you can simply edit the settings.php file and add the line:

  ini_set('memory_limit', '96M');

  In older versions of Drupal5, or if using PHP for many different uses, it is best to increase the amount of PHP memory using this method:

  Edit the /etc/php5/apache2/php.ini file and increase the memory_limit value to 96M (or another value of your choice).

  Of course, you have to do all this as root, and then you restart apache2: /etc/init.d/apache2 restart (also as root).

• All right! now I can log in and access my Administration page, and start playing with the core and module updates. However, I notice that all my pictures are missing. What's an image gallery with no photos? Well, I know where they're supposed to be:

  rebecca@hecate:/var/www/spiceridge/projects/sites$ ls default/files/images
  ls: cannot access default/files/images: Permission denied

  Permission problems? This is really weird...I can't navigate into the default/files directory, even after I chmod the files as root. So I delete them, and ftp the originals from http://spiceridge.com, where the permissions are normal. OK, these are fine; let's see if the browser can get to them now....

• OK, I'm seeing some images, but I'm also getting lots of copies of this error: warning: unlink(sites/default/files/images/1908Xmas001.preview.jpg) [function.unlink]: Permission denied in /var/www/spiceridge/projects/includes/file.inc on line 435. OK, I read in the comments in includes/file.inc that directory permissions might be the problem....I chmod a+w for the involved directories, and this brings in some, but not all of my images. About half of the thumbnails are gone.

Well, I never liked that image gallery anyway....This permissions issue is the inelegant and rather haphazard way Drupal handles an aspect of security. That's the down-side of having an automated installation, I guess. They say all this will be much improved in Drupal 7.x, but of course, that will be its own "learning experience."

I'm going to say, "Good enough for government work," and start messing around with the updates now.