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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Spliced feed for The Science Network

Spliced feed for The Science Network

Skeptics Guide #175 - November 20th, 2008 [The Skeptics' Guide to the Universe]

Posted: 29 Nov 2008 06:25 AM CST

Interview with Steven Schafersman; News Items: Kevin Trudeau Smackdown, Placebo Acupuncture, NASA Recycles Urine, Reflexology in UK Schools; Your Questions and E-mail: Flu Vaccine, NESS in Video Game; Science or Fiction

This posting includes an audio/video/photo media file: Download Now

Saturday, November 29, 2008

The DNA Network

The DNA Network

rs1815739 T/T kids dropped from sports programs everywhere - no chance for Olympic glory [Biomarker-driven mental health 2.0]

Posted: 29 Nov 2008 08:23 PM CST

nothing like hot coffee to wash down a bite of...

Image by sean dreilinger via Flickr

I was irked to see, in today’s New York Times, a picture of a young child having his cheek swabbed so that his parents could ascertain his status at the rs1815739 C/T variant .  T-alleles at this site give rise to a premature stop codon in the alpha 3 actinin (ACTN3) gene while the C-allele encodes a full-length version that contributes to the fast twitching of muscle fibers.  Not surprisingly, it was found [PubMed Central ID: PMC118068] that folks who have achieved status as Olympic caliber sprinters are more likely to carry the C-allele than ethnically matched controls. The company, Atlas Sports Genetics is now marketing the test, for $149 as a means to “predict a child's natural athletic strengths”.  Holy Crap !

Its sad to think of the myriad of ways in which genetic information can be misused and misrepresented - sadder still to think of using genetic tests to deny kids the simple joy of playing with each other.  Parents may be intersted to know that among europeans and asians, the C-allele is present at about 50%, making about 75% of the population either a C/C or a C/T … which, taken alone, explains very little of why a handful of individuals achieve athletic success. Parents considering paying the $149 might also wish to read a recent article by Dr. Jerome Kagan, a well-regarded developmental psychologist on recent trends in overparenting.

My 23andMe profile shows a middling C/T which is on par with my middling soccer skills.  Nevertheless, I had a great experience learning and building relationships with my pals on the soccer field, many who remain friends even still.

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Cyberchondria and Health 2.0 News [ScienceRoll]

Posted: 29 Nov 2008 02:51 PM CST

I should study psychiatry for my next exam, but I must share a few articles with you first:

One year ago, I discovered that I had contracted Type 1 Diabetes. I was 36 at that point and it’s relatively rare for someone of my age to suddenly get Type 1 Diabetes - indeed they used to call this form of diabetes “juvenile diabetes”, because it mostly occurs in children. So it was quite a shock to discover that I had it! Immediately I looked to the Web to find out all I could about this condition. I discovered a thriving community of ‘health 2.0′ apps and social networks, which I then wrote about in this blog.


But in the world beyond the television screen, many physicians have come to recognize the value of their patients' use of the Internet.

And, if you are like most people, you turn to the Internet for health. Eighty-four percent of adult Internet users in the U.S. go online for medical information, according to a 2007 Harris poll. Some of them, like Diana C., believe the Internet saved their life.


MyGeneticist: I want to know about my DNA [ScienceRoll]

Posted: 29 Nov 2008 02:30 PM CST

Steve Murphy, our gene sherpa, informed us about a new site, which

…is a service that empowers you to understand the information stored in your DNA, so you can use this knowledge to make healthy life choices. Founded and operated by scientists, myGeneticist’s mission is to complement existing healthcare systems and to make a positive impact on society by helping people make informed decisions. myGeneticist will be launching soon.


We need such services… I can’t wait to see how it actually works.


Genome Island in Second Life [ScienceRoll]

Posted: 29 Nov 2008 02:12 PM CST

Dangerous chemistry: explosive experiments with junk food [Discovering Biology in a Digital World]

Posted: 29 Nov 2008 01:21 PM CST

It's a long, long, weekend; perfect for going outside and doing a few loud, messy experiments. Cooking-intensive holidays always remind me how much fun it is to do a bit of chemistry, especially when it comes to food.

If you watched the video that I posted on Thanksgiving, you've probably been itching to try one of these experiments yourself.

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Parliamentary politics. [Genomicron]

Posted: 29 Nov 2008 08:19 AM CST

Ok, so Canada elected a conservative government again, meaning that the Conservative Party of Canada (a merger of the former right-centre Progressive Conservative Party and far-right Canadian Alliance) won more seats than the other parties. However, they did not win more than all other parties combined, which means that they have a minority government. In such a parliamentary system, the Prime Minister is the leader of the party who won the most seats, although his party may still be a minority in parliament.

There is now talk of a coalition government between the left-centre Liberal Party and the left New Democratic Party. Together, these two parties still would not have more seats than the Conservative Party, but with the support of the Quebec-only Bloc Québécois, they could be given the chance to govern.

There is some talk on the news and on forums that such a move would be undemocratic since the Conservative Party was elected and has a clear mandate from the people. What do Canadians want? Here are the data from the recent election (via Wikipedia).

Party Orientation Seats Votes Popular %
Conservative Party of Canada Right 143 5,208,796 37.65%
Liberal Party of Canada Left-centre 77 3,633,185 26.26%
Bloc Québécois Left-centre 49 1,379,991 9.98%
New Democratic Party Left 37 2,515,561 18.18%
Green Party Far left 0 937,613 6.78%

Conservative Right 143 5,208,796 37.65%
Liberal + NDP + Green Left 114 7,086,359 51.22%

Plants that make crystals that look like plants [Discovering Biology in a Digital World]

Posted: 28 Nov 2008 09:29 PM CST

A crystalline botanical fashion show.

Awhile back Chemical & Engineering News published a fascinating article called "The Secret Life of Plant Crystals" with some wonderful photos of calcium oxalate crystals. Special cells (called "idioblasts") produce these crystals, with shapes that are unique to each type of plant.

Reposted for the holiday.

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