Thursday, November 27, 2008

Seasonal science: cranberry harvesting and turkey genomics – pass the stuffing

On your Thanksgiving table, consider the cranberry. Especially if you are so lucky as to have freshly prepared cranberry dressing in all its tart and tangy goodness. When you consider what went into getting those garnet jeweled fruits to your table, this unassuming side dish is remarkable.

While on vacation over the summer we stopped in Long Beach, Washington – home to the Cranberry Museum. I dragged everyone away from the carousel rides and saltwater taffy to see a modest but entertaining two-room display on the history of cranberry growing and harvesting in the coastal Washington area, alongside some working cranberry bogs. The irony of Wisconsinites learning about cranberries in Washington is that Wisconsin is far and away the leading producer of the crop.

If you grow cranberries, have patience. The berries grow on vines that have finicky soil preferences. The vines are fairly delicate and two years’ worth of growth is present at each harvest, so collecting the fruits is a careful process. The berries themselves are prone to cracking, which renders them ruined. And the harvesting? Collecting berries by hand is mind-numbingly slow and tedious, but mechanical harvesting must accommodate the fragile nature of the plant. In Wisconsin, growers typically wet-harvest the crop. Imagine the cranberry bog recessed into the ground, and with sides forming a wading pool. The bogs are flooded with water and bizarre harvesting machinery (such as a water-friendly tractor with a paddle wheel) is used to gently beat the vines. This releases the berries, which then float to the top due to their internal air chamber – like small antioxidant-packed balloons. The berries are collected on the water surface, resulting in the amazing aerial view you see in the top photo (courtesy of the Wisconsin State Cranberry Growers Association).

And now on to the main dish – the turkey that likely graces your table. Recently, poultry researchers (yes, there are scientists who focus on poultry, just as there are plant breeders, growers, and pathologists who focus on cranberries) announced a collaborative effort to sequence the turkey genome. Apparently researchers in the field take advantage of the seasonal focus on turkeys by making such announcements the week before Thanksgiving, hoping for some media pick-up; similarly, the completion of a genetic map of the domestic turkey was announced in November 2004. The media pitch appears to be working reasonably well, as they’ve gotten some good coverage.

The new genome sequencing data will allow researchers to do genomic comparison studies between domestic turkey and domestic chicken, whose genome is already available. The turkey sequence will only be a “draft sequence”, though, meaning that the quality will need to be improved in the future, and researchers are already giving warning that they will be approaching industry and federal sources for funding in 2009.

So what will knowing the full sequence of the turkey genome get you? Well, once it’s completed, look for studies analyzing genes that control muscle development, the genes that control the genes involved in muscle development, genes controlling fat formation, reproductive process genes, and likely a flock of additional papers on disease resistance genes. Domestic turkeys are not the heartiest in face of illness, as it turns out. However, at least according to one perspective, this is due to the extreme genetic homogeneity and relentless large-scale cultivation practices that the modern turkey industry relies on. Perhaps a little outbreeding is in order.

Interestingly, one of the scientists quoted in the turkey genome press release is Jerry Dodgson, a professor at Michigan State University. I took a class on eukaryotic molecular genetics from him when I was in grad school. He has worked on poultry for much of his career, mainly focusing on chickens and viruses causing chicken diseases, and is now leveraging his expertise and that of researchers in his laboratory to the domestic turkey.

Gobble, gobble indeed.

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Tuesday, November 18, 2008

The Best Things in Life are Free – Part 1

Free is favorable these days. Unless you’ve been living under a rock for the past two months, you’ve probably heard something about the economy melting down, with hyperbole about imploding real estate markets, skyrocketing unemployment, and senior citizens heading back to work as they see large chunks of their retirement savings vaporize. If the numbers are to be believed, retail spending has fallen off a cliff. In style: coupon-clipping, knitting , made-from-scratch meals. Out of style: looking at your quarterly mutual fund account statement.

In honor of the newfound frugalista mentality, I’ll be highlighting a series of resources that are both useful and 100% no-cost. Some will have a regional (Madison, Wisconsin, or Midwestern) connection. The vast majority will involve science, technology, and/or intellectual property. And all are resources I’ve personally found useful.

At the top of my list is Wisconsin Technology Network News. It’s a free news service for the life science, business, and IT sectors in Wisconsin. I started subscribing when I was a postdoc and was curious about life outside of the ivory towers, but had no meaningful connections to anything outside of .edu. Voila – generally great content, analyses, and event info updated every few days.

So there you have it. Because even in an economic downturn (and maybe especially in an economic downturn), you need information and perspective.

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Thursday, November 13, 2008

History, Plant Genetics, and Wikipedia: Remembering George Rédei

Scientists with even passing knowledge of plant biology are generally quick to recognize the foremost model plant species, Arabidopsis thaliana – a modest weed in the mustard family that goes by the common names thale-crest or mouse-ear crest. With a six-week seed-to-seed life cycle and an unusually compact genome, Arabidopsis is regarded as the best “lab rat” for plant biology. I’m dating myself, but the genome sequence of Arabidopsis was completed in 2000, while I was in graduate school. Thus, my thesis research spanned a period when you had to identify a gene of interest by old-school genetic crossing (weeks…months….years until you could confirm which gene you were working with), and a period when you could plug a bit of approximate DNA sequence into a computer database to much more rapidly identify your gene. By the time I was a postdoc it was possible to stumble upon or hypothesize about a gene you were interested in, order a mutant from the stock center, and examine its expression pattern under dozens of different conditions – all within a few mouse clicks. And these are but a few examples of the tremendous resources available.

None of this would have happened had it not been for a professor named George Rédei, who brought some Arabidopsis seeds from Hungary when he began his career at the University of Missouri in Columbia in 1957. Rédei realized that the species held tremendous promise as a genetic model for plants, but labored for nearly 20 years before others in the plant biology community recognized the true potential of the species.

Rédei died on Monday, 11/10/2008 at the age of 87. I did not know him personally, but thought it would be fitting to add some material to the sparse Wikipedia entry on him. This was my first foray into Wikipedia editing, and while I was able to update the text, I was gnashing my teeth after about 45 minutes of attempting to upload an image of George Rédei and Nobel prizewinning maize geneticist Barbara McClintock (the photo was taken in 1978 and is publicly available through the National Library of Medicine). Turns out that new Wikipedia users cannot upload images until their accounts are at least 4 days old and they’ve made 10 edits. Guess I’ll be attempting this next week. At least this got me started on learning the ins and outs of Wikipedia page creation and editing.

Rédei’s life and research are testament to the value of scholarly perseverance. Genetics, agriculture, plant biotechnology, and humanity at large are all the better for his dedication and careful studies.

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Tuesday, November 11, 2008

Innovate this

Last night I attended an “Innovation” talk presented by Accelerate Madison and WTN (Wisconsin Technology Network). The seminar was at the Fluno Center – which always provides tasty nibbles, by the way – and was given by Tom Koulopoulos, who has is on the consulting/speaking engagement/book-writing/web seminar circuit. Funny thing: the first time an e-blast went out to advertise the seminar, the Monday night seminar was simply billed as a “kickoff address and social”. After several weeks of news coverage showing Wall Street brokers sweating profusely and gripping their heads, the seminar was titled “How do You ‘Future Proof’ Yourself and Your Enterprise?”

The well-polished presentation did give some food for thought, principally on the need to accommodate – no, embrace with wild abandon – the principle of uncertainty. Within organizations, within marketplaces, within…well, everything. Koulopoulos made the assertion that 2009 will be a crucible of innovative change as small-but-mighty startups and entrepreneurs will make technological leaps that come out of nowhere and leave hand-wringing corporate CEOs in the dust. (Oddly enough, I saw another article in an issue of Forbes magazine making exactly the same point. No, I don’t subscribe to Forbes. It was in my optometrist’s waiting room.)

But the major take-home message from the speaker was his viewpoint on the difference between innovation and invention. In essence, Koulopulos defined invention as the creation of objects without regard to their usefulness or commercial value. (Think: SkyMall catalog, the Sharper Image.) Whereas innovation involves creating value, and rarely involves invention. Invention was blamed as causing an “ecological nightmare” – that is, the never-ending stream of marginally useful, short-lifecycle/long-landfill residency e-waste. He then used the iPod to illustrate his point, asserting that “there was no invention involved in creating the iPod…Apple simply licensed (X, Y, and Z) components….” (I’m paraphrasing).

No inventive concept went into the iPod? No novel intellectual property? Are you kidding me?

Let’s take a closer look.

An advanced search of published, pending patent applications at the US Patent and Trade Office with keyword iPod and assignee Apple (search query: iPod and an/apple) yields 65 pending published applications. (You get slightly different results if you search an/”apple computer” versus an/”apple inc” – apparently the filing parties have a slight identity crisis.) For issued patents, the count is 42. Not surprisingly, a fair number of the issued patents are design patents – this is Apple, after all. But a very brief survey of both issued and pending shows a wide variety of method and composition patents. US 7,312,785, for example, pertains to accelerated scrolling, a feature any iPod user with a reasonably sized music library is familiar with. 7,333,092 claims the device itself. Other patents and applications claim various iPod components or features – the touch pad, iPod-CPU interface systems, dynamic volume control systems, methods for controlling the device by defined gestures – basically, think of all the goodies that makes iPods so beloved, and they’re there. You really think Apple didn’t have any novel, non-obvious intellectual property that went into this line of market-dominant devices? Good grief. Think again. (Or, more precisely, think different.)

So three cheers for innovation. And inventiveness. And everything in between.

Let’s get cooking, folks. 2009 is just around the corner.

(Note: Royalty-free photo of child and computer by artist Chance Agrella was provided by Free Range Stock.)

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