Sunday, November 30, 2008

The DNA Network

The DNA Network

Community-based science, an introduction to finding opportunity [Discovering Biology in a Digital World]

Posted: 30 Nov 2008 05:48 PM CST

Getting kids involved in science, outside of the classroom.

A conversation with a friend last night reminded me of some posts I wrote earlier about helping scientists connect to programs for helping students.

My friend, as a parent, approached this idea, of connecting scientists with students, from a different angle.

She wanted to know how you go about connecting students with science?

  • What do you do if the science program at your kid's high school seems a little, well, uninspiring?
  • If the teachers aren't interested, how do you help?
  • How do you create opportunities for kids to get involved in doing some kind of science?

As I talked to her, despite all the difficulties flashing before me eyes, I realized that I do know some things about finding science opportunities, at least in my community, and I could help by writing about them. I've written a few things about ways that scientists can connect, now, it's time to write about ideas for students.

Here are some of the different ways that high school kids can participate in science:

  • School science clubs or other kinds of school clubs with a service component, or other organizations like Girl Scouts, Cub Scouts, or Campfire.

  • Participate in some kind of outreach program

  • Volunteer somewhere

  • Contests and fairs

  • Paid internships

I'll write about each topic, in no particular order. If you have ideas, questions, or suggestions, I'd be glad to hear them.

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Useful paper for GA users (Sanger's process improvements) []

Posted: 30 Nov 2008 04:30 PM CST

Here's a paper from the Sanger, talking about their experiences and process improvements with the genome analysers: Quail ME, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ Nature Methods 2008; 5(12): 1005-10 The Wellcome Trust Sanger Institute is one of the world's largest genome centers, and a substantial amount of our sequencing is performed with 'next-generation' massively parallel sequencing technologies: in June 2008 the...

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NY Times article on testing kids for ACTN3 gene [Yann Klimentidis' Weblog]

Posted: 30 Nov 2008 02:15 PM CST

It was only a matter of time, but there is now a company in the US that is offering a test to determine a person's ACTN3 genotype. This is a locus for which there is some evidence of an association with muscle fiber composition (fast vs. slow twitch) and whether an elite athlete competes in sprint or endurance events.
This article in the New York Times describes the test, some of the evidence concerning the association, and some of the issues surrounding its costs/benefits.
My favorite line:
Dr. Foster suggested another way to determine if a child will be good at sprint and power sports. "Just line them up with their classmates for a race and see which ones are the fastest," he said.
Dan MacArthur has done some of the primary work on this locus and its association with athletic performance. I'm surprised his name didn't show up in the article. Actually, I just noticed that he has also written a blog post about this article.
He discusses the tests' limitations and mentions that this test has been commercially offered in several countries for some time and is available through the personal genomics companies in the US.

There are indeed many limitations to this test. Given what goes into making a great athlete, I see no use for it whatsoever, except for giving some solace to a person wondering why, after years of training, he/she didn't become the great athlete he/she hoped to become. Given the predictive power of this test, I think that the costs (mostly psychological) of doing this test to see what you would be good at greatly outweigh the benefits.

More election data. [Genomicron]

Posted: 30 Nov 2008 10:25 AM CST

As indicated by the popular vote totals, there is little support for the claim that a coalition government between the Liberal and NDP parties in Canada would be undemocratic. However, this represents a very rough analysis because the Canadian system, like many others, is a first-past-the-post process in which the candidate with the most votes is elected regardless of the margin.

In order to reveal the desire of the electorate more realistically, it is necessary to consider the total votes in each riding rather than at the national scale. I decided to see what would have happened in the latest election had the Liberal and NDP candidates run jointly in each riding from the outset by summing their respective votes on a riding by riding level. I compared only the major parties, meaning that I did not include any votes from the Green Party, independents, or fringe parties in the new totals. Data were acquired from Elections Canada and only verified final results were analyzed.

The actual election results were (number of seats):
  • Conservative: 143
  • Liberal: 77
  • Bloc Qubecois: 49
  • NDP: 37
  • Independent: 2
Now, taking each riding individually and adding the Liberal and NDP votes received, we note the following changes:
  • Conservatives would have lost 30 ridings to Liberal+NDP and retained 113.
  • Bloc Quebecois would have lost 9 ridings to Liberal+NDP and retained 40.
The new election results, if we count each riding by itself but combine the voters who chose either Liberal or NDP, are then:
  • Liberal+NDP: 153
  • Conservative: 113
  • Bloc Quebecois: 40
  • Independent: 2
We can't assume that the election would have turned out exactly like this with combined parties (it would depend on the candidate, party leader, etc.). Nevertheless, this gives a reasonable estimate of what voters wanted in terms of representation. In other words, the election results, whether analyzed by popular vote nationally or riding by riding, clearly refute the claim that a coalition of the Liberal and NDP would contradict the expressed will of voters.

Poor sports []

Posted: 30 Nov 2008 09:45 AM CST

The New York Times treads familiar ground this morning with a front-page account of testing kids for the ACTN3 gene, variants of which can predispose one to excelling at speed or endurance sports. Never mind that we have known about this for more than five years or that 23andMe has been doing it for a year or that it’s been available via Australia for four years. Whatever: it’s always fun to revisit the tired memes of genetic determinism, designer babies, ambitious parents living vicariously through their children,  and unscrupulous biotechnology companies. Yawn.

The ACTN3 sports gene test: what can it really tell you? [Genetic Future]

Posted: 30 Nov 2008 09:40 AM CST

Disclaimer: I was one of the authors on a 2003 study reporting a link between ACTN3 and athletic performance, but I have no financial interest in ACTN3 gene testing. The opinions expressed in this post are purely my own.

baby-athlete_small.jpgAn article in the NY Times yesterday describes the launch of the grandiosely named Athletic Talent Laboratory Analysis System (ATLAS). The ATLAS test looks at a common genetic variation within the ACTN3 gene, which has been associated in numerous studies with elite athlete status and with variation in muscle strength and sprint ability in the general population. The company claims that this variation "may determine the type of athlete you were born to be".

In the NY Times article ATLAS explicitly describes its target audience - the parents of young children:

Atlas executives acknowledge that their test has limitations but say that it could provide guidelines for placing youngsters in sports. The company is focused on testing children from infancy to about 8 years old because physical tests to gauge future sports performance at that age are, at best, unreliable.

Setting aside the unsettling ethical issues associated with recreational genetic testing of children, how useful will the test be to parents looking to find out whether or not their kids will be future track superstars? Here are the facts:

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Make a merry molecule mug! [Discovering Biology in a Digital World]

Posted: 30 Nov 2008 08:05 AM CST

The grocery store magazine covers all say that home made gifts are big this year. So I thought, some of you might like to channel your inner Martha Stewart and make gifts with a science theme.

Reposted in honor of the holiday and the economy.

caff3.gifI'm here to help to you make a merry mug with one of our favorite molecules. Yep, we're talking caffeine.

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Farewell! Thou art too dear for my possessing* [Tomorrow's Table]

Posted: 27 Nov 2008 02:53 PM CST

"A thing of beauty is a joy for ever;
Its loveliness increases: it will never
Pass into nothingness; but still will keep
A bower quiet for us, and a sleep
Full of sweet dreams, and health, and quiet breathing."

(Keats, "A thing of beauty")

Imagine the choices. You have successfully had two children using in vitro fertilization (mixing eggs and sperm in the laboratory), but there are 10 embryos left over. When faced with such an overabundance, what would you do? Do you attempt to have more children, discard the embryos, or donate them to embryonic stem cell research?

This choice is faced by thousands of parents every year, because, for every successful in vitro fertilization, more embryos are created than can be implanted into a womb.

If you choose research, scientists will harvest the inner mass of cells from your embryos and transfer them into a plastic laboratory culture dish. After six months or more, the original 30 cells of the inner cell mass will proliferate, yielding millions of embryonic stem cells.

Future experiments with your embryonic stem cells could lead to partial or complete cures for Parkinson's disease, Lou Gehrig's Disease, and type I diabetes. They may even be useful for repairing heart muscle damaged from a heart attack.

If you choose to implant the embryos into your womb (or into that of your wife or a stranger's) they will most likely grow into a child that will be loved.

If you choose to discard the embryos, they will pass into nothingness-- no research will be carried out and no additional children will be created.

I think about the donors of these gametes. Some of these couples may have wanted a child for years. Some may have lost pregnancies through repeated miscarriages. I know one woman who lost her only child to a sudden heart attack on the high school football field; a weak heart that had gone undetected. These parents are beyond ecstatic when the in vitro approach is successful. I expect that it cannot be an easy decision for them to discard "surplus" embryos. After all, can one separate the concept of a child from that of an embryo?

What would I do? Would I donate the embryos to stem cell research so people like my father-in-law could one day have new bone marrow cells that would mitigate his leukemia? Or would it be too difficult to give up the idea of more children.

I think of the physical characteristics of my own boy and girl: the dimples of my son that he shares with his father and grandfather; the blue eyes that I envied in my handsome brothers, now his. My daughter's dark, thick lashes that have no precedent in recent family history. And then the complex behaviors- the calm, easygoing son who asks, puzzled, "mommy why do some people get mad so easily?" The daughter who does. The picture-perfect handwriting of one, the illegible scrawl of the other that is so closely related to my own. The team player and the rebel. I cannot help but wonder what our other children would have been like if we had had more.

And I would want more. After all, I was never was one to stop with one cookie. So sweet, so satisfying, seemingly simple. But I also know reaching for too many can bring indigestion. Before deciding to have more children, I would need to consider the possible stress it would bring. Would more children disrupt the delicate balance of family harmony we have occasionally achieved?

President-elect Obama has indicated that he will lift the current administration's ban on the federal funding of research on embryonic stem cell lines created after August 9,2001. That means that parents who donate their embryos will enhance the ability of some of the best scientists in the nation to develop cures to some of the most dreadful diseases. And they may be successful in our lifetime.

I imagine that faced with the choices of donate, discard or raise more children, that I would choose donation. A simple act of generosity, perhaps, but one made with regret and sadness for the children that I would never embrace.

* from Shakepeare's Sonnet 87

The Health Thing to Do This Thanksgiving [The Gene Sherpa: Personalized Medicine and You]

Posted: 27 Nov 2008 12:32 PM CST

In the US, today is Thanksgiving. A day where family and friends come together and appreciate what we have. We consume massive amounts of food, drink, some smoke, and not surprisingly get admitted to...

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