Monday, August 25, 2008

The DNA Network

The DNA Network

Cancer Research Blog Carnival #13 Call for Submissions [Highlight HEALTH]

Posted: 25 Aug 2008 06:30 PM CDT

Highlight HEALTH will be hosting the next edition of the Cancer Research Blog Carnival, edition 13, on Friday, September 5th. As host, I invite you to send your submissions.

What is the Cancer Research Blog Carnival?

The Cancer Research Blog Carnival is a monthly blog carnival of what’s new in cancer research. Highlight HEALTH hosted the 7th edition of the Cancer Research Blog Carnival back in March 2008. Previous editions are listed at the Cancer Research Blog Carnival website.

Please note that your blog doesn't have to be about cancer or cancer research as long at the article you submit is relevant.

I'm looking for articles discussing the following topics:

  • Cancer research
  • Cancer biology
  • Cancer genetics
  • Cancer therapeutics
  • Cancer diagnostics
  • Standard of care for patients with cancer
  • Patient cancer stories

I strongly encourage submissions from bloggers who have never submitted before. Submitting to the Cancer Research Blog Carnival is a great way to meet other bloggers, make people aware of your blog and bring blog traffic your way. True to it’s name, the Cancer Research Blog Carnival is also a great way to keep abreast of new developments in cancer.

Submit your article here or email them to me using the submission format below.

Submission Format:

Subject line: Cancer Research submission
Email body:
- Post Title
- Post URL
- Post Description

Send your submissions to me using the email address on the sidebar no later than Wednesday, September 3rd at 04:00:00 UTC (12:00pm CST).

Receive e-mail notification when Cancer Research #13 is published.

Let’s make this a great edition of the best posts pertaining to cancer and cancer research. I look forward to your submissions!

Thank you for subscribing by RSS or email. I work hard to make the articles on Highlight HEALTH engaging and I truly appreciate your interest and readership!

This article was published on Highlight HEALTH.

Other Articles You May Like

"I highly recommend the book" says Sean Feder [Tomorrow's Table]

Posted: 25 Aug 2008 05:24 PM CDT

Check out the latest review of Tomorrow's Table published in Capital Press, the most comprehensive online source of daily farm and ranch news

For the Capital Press

Pamela Ronald and Raoul Adamchak say they're not proposing a seismic change in mainstream farming practices - just the next step in a long evolution.

Ronald and Adamchak are the husband-and-wife authors of the book "Tomorrow's Table: Organic Farming, Genetics and the Future of Food," published in April. Ronald is a professor of plant pathology and chair of the Plant Genomics Program at the University of California-Davis; Adamchak manages UC-Davis' organic farm.

"It's not so much replacing conventional agriculture as (altering it)," Adamchak said.

The authors advocate combining genetically engineered crops with organic growing practices as a means of feeding the world in a sustainable manner. They say they've heard criticism from both sides.

The organic-farming community tends to show a protectiveness of federal organic-certification standards, they say. Defined by federal rules in the 1990s, organic certification cannot be awarded to any crop created through genetic modification. But these authors don't want to mess with organic standards.

"One of the things we're encountering is that people are posing this false choice - conventional or organic?" Ronald said.

Those categories tend to be defined by current realities. For example, bioengineered crops are often connected with large corporations that control the distribution, pricing and use of seeds.

Observers describe such practices as counterproductive in impoverished regions of the globe. Ronald and Adamchak are not advocating any current market structures - they're describing the value of two growing systems from the perspective of agricultural science.

As organic farming gained popularity in the last 15 years, bioengineering has also ascended the market. Now, bio-engineered crops account for 50 to 90 percent of commercial crops for which they are available, the authors say - notably cotton, corn, canola and papaya.

When a virus nearly wiped out Hawaii's papaya crop in the mid-1990s, scientists responded by engineering a resistant strain. Today, that strain accounts for most of Hawaii's papaya crop, allowing for a reduction of chemical usage.

Engineered crops do have their limits. Chinese cotton growers found success with a bio-engineered crop that is resistant to caterpillars. But when they found it susceptible to other pests, they turned again to chemical pesticides.

Ronald and Adamchak say those growers might still have avoided chemicals by combining the bio-engineered plant with organic growing techniques, such as crop rotation and integrated pest management. It's that sort of combining of practices that is necessary to feed the world's population in a sustainable manner, the authors say.

Because they cannot use chemical crop applications, organic growers rely on the best-performing seeds they can get, Adamchak said. Those seeds were developed through selective breeding, a technique by which new strains have been created for centuries. The end result of that process, Ronald says, is no different from what is created by laboratory methods.

"To me it doesn't matter if it's genetically engineered or conventionally bred," she said.

Ronald has worked for years with several other researchers to modify a rice strain to tolerate consecutive weeks of submergence beneath floodwaters. The findings were published in 2006, and the rice has become popular in Bangladesh, where flooding periodically destroys rice crops.

"We have to put things in perspective, and I think people are fixated on how dangerous (genetic engineering) is, without knowledge to back it up," said Sean Feder, an agricultural professional who oversees organic-crop inspections in California.

Feder works for California Certified Organic Farmers and stressed that his opinions are not his employer's.

"I highly recommend the book," he said. "I think we can use a bit more of an open mind."

Freelance writer Wes Sander is based in Sacramento. E-mail:

Dawkins' emails... [Bayblab]

Posted: 25 Aug 2008 04:00 PM CDT

Cancer Research Blog Carnival: A New Site [Bayblab]

Posted: 25 Aug 2008 04:00 PM CDT

In honour of its first birthday, the Cancer Research Blog Carnival is moving out. For those of you who are readers of the monthly carnival, I've set up a new site that's CRBC specific. The goal was to create a centralized place to go for archives of previous editions as well as news and announcements for upcoming ones. Hopefully it will continue to grow and improve over the next year and beyond.

And don't forget to get your submissions in for the 13th edition to be hosted September 5 at Highlight HEALTH.

Webicina in the News [ScienceRoll]

Posted: 25 Aug 2008 03:58 PM CDT

Yesterday, I presented Webicina, an online service that aims to build a bridge between physicians and e-patients.

Some prominent bloggers, for my great pleasure, wrote about it:

Those who signed up for the newsletter will receive more details and a link to the FAQ page soon.

DNA sequencing as a school project: how do you get started? [Discovering Biology in a Digital World]

Posted: 25 Aug 2008 03:31 PM CDT

A few days ago, I wrote about a cool project that some high school students did where they used DNA sequencing to identify seafood.

One question that came up from one of my commenters was how a school would start a project like this. I'm totally biased, but I think DNA sequencing (well, actually the data analysis) is one of the most interesting things that a class can do as part of a research project. These days, getting started with this kind of project, wouldn't be so hard.

Here's are some ways that I would get started:

    Read the rest of this post... | Read the comments on this post...

Open Access Pioneer Award #2: R. Preston McAfee [The Tree of Life]

Posted: 25 Aug 2008 03:17 PM CDT

Great article in the LA Times on August 18 by Gale Holland about "Free digital textbooks." (see Free digital texts begin to challenge costly college textbooks in California)

The article discussed some issues in open source textbook publishing including in particular R. Preston McAfee's work on creating a free online economics textbook. McAfee is a professor at Caltech and is a self described right winger.
"I'm a right-wing economist, so they can't call me a communist," McAfee said.
And he goes on to say
"What makes us rich as a society is what we know and what we can do," he said. "Anything that stands in the way of the dissemination of knowledge is a real problem."
The article discussed other open source educational materials including:
  • Merlot, from Cal. St. Universities which is a "a searchable collection of peer-reviewed, online multimedia materials."
  • Connexions, from Rice University , which "stores free, open-licensed educational materials in fields such as music, electrical engineering and psychology.
  • OpenCourseWare from MIT which includes "virtually its entire curricula online -- video lectures, problems sets and exams for more than 1,800 courses in 33 disciplines."
  • Wikibooks, a collection of editable textbooks
  • The Digital Marketplace, from Cal. St. U. which is a "website for selecting, comparing, sharing, approving and distributing both open-source and commercial online educational materials."
Now, I am not saying here there is not a place for textbooks in the normal model (I have one).  Unlike basic science papers, for which the cost of making a presentable paper is relatively low, the cost of producing a textbook can be very very high.  Thus I think publishers are welcome to work with authors to come up with their own models for how to publish the texts.  But nevertheless, the more we can get good open source textbooks out there, the better off we will be.  And thus, for his role in promoting the release of what seems to be a high quality open source textbook, I am giving R. Preston McAfee my second "Open Access Pioneer Award.

Hat tip to Jeremy Peterson and Eilleen Hamilton for pointing this out.

Health News in Second Life: Government and Virtual Patients [ScienceRoll]

Posted: 25 Aug 2008 02:54 PM CDT

People who are obese in the real world will get the opportunity to participate in a research project conducted entirely in the virtual world to help their avatars - and hopefully their real-life selves - lose weight and get in better shape.

It’s never too late [ScienceRoll]

Posted: 25 Aug 2008 01:30 PM CDT

Is it never too late to start medical school?

(Hat tip: Prep4md)

Intronic rs833070 / rs2146323 variants in VEGF demonstrate link to hippocampal size to reinforce role in rehabilitation, resilience and medication response [biomarker-driven mental health 2.0]

Posted: 25 Aug 2008 12:54 PM CDT

The mitogenic activities of the vascular endothelial growth factor protein family are well researched. A number of findings have linked this gene to learning and memory and hippocampal-dependent response to antidepressant medication. Indeed, its reasonable to expect that a mitogen such as VEGF would regulate hippocampal cell division and the accompanying benefits of new brain cells. Using high resolution structural MRI, Blumberg and team report evidence for such in their paper, “Influence of Vascular Endothelial Growth Factor Variation on Human Hippocampus Morphology“. Individuals with the CC genotype at rs833070 and rs2146323 - located in the intron of the VEGF-A gene displayed smaller hippocampal volumes than T-allele and A-allele carriers, respectively. These 2 snps lie in a haplotype block with rs833068 which was assayed in my 23andMe profile - indicating that I happen to carry the TT genotype at rs833070 giving me slightly larger, more neurogenic & resilient hippocampus - I suppose. Now, if I could just figure out a way to put it to good use !

Update - required evolution reading/ Harmon story/ Mickey Mouse [The Tree of Life]

Posted: 25 Aug 2008 12:01 PM CDT

Yesterday I posted about Amy Harmon's excellent story in the NY Times about evolution education.  For more on it see my post - Required evolution education reading - Amy Harmon on Florida Evolution teaching

I just wanted to give an update here as I have seen a few postings out there discussing the Mickey Mouse example in the story.  In the story, Harmon described how David Campbell, the Florida high school science teacher uses the evolution of Mickey Mouse as an  example of natural selection.  

From the Times article:

He started with Mickey Mouse.

On the projector, Mr. Campbell placed slides of the cartoon icon: one at his skinny genesis in 1928; one from his 1940 turn as the impish Sorcerer's Apprentice; and another of the rounded, ingratiating charmer of Mouse Club fame.

"How," he asked his students, "has Mickey changed?"

Natives of Disney World's home state, they waved their hands and called out answers.

"His tail gets shorter," Bryce volunteered.

"Bigger eyes!" someone else shouted.

"He looks happier," one girl observed. "And cuter."

Mr. Campbell smiled. "Mickey evolved," he said. "And Mickey gets cuter because Walt Disney makes more money that way. That is 'selection.' "

Some bloggers have questioned using this example (see john hawks weblog for example as well as Bora's excellent post about this story here) because it seems more like Intelligent Design than natural selection.  I disagree and wanted to point out that this is a classic Stephen Jay Gould teaching case study which he detailed (see A BIOLOGICAL HOMAGE TO MICKEY MOUSE Stephen Jay Gould).  

In fact, when I was an undergrad at Harvard and was taking Gould's class, we played around with a cool new computer program called MacClade to track the evolution of Mickey Mouse. Little did I know I would still be using Macclade and its descendants today.

Polls closed.....Helicos is right [The Gene Sherpa: Personalized Medicine and You]

Posted: 25 Aug 2008 11:57 AM CDT

Over 56% percent of you believe that full human genomes for 1000 USD will be here within 5 years. Patrice Milos of Helicos BioSciences thinks so too. I am here to tell you that they may already be...

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Genetics of T2D among Ashkenazi Jews: Replication and predictive value of genetic information [Yann Klimentidis' Weblog]

Posted: 25 Aug 2008 10:48 AM CDT

Last year 10 loci associated with type-2 Diabetes (T2D) were identified in a WGAS (whole genome association study) and replicated in various large samples (Scott et al. 2007). Here, they assess the association between these 10 loci and T2D among Ashkenazi Jews in Israel (all four grandparents are Ashkenazi Jews). They find that most markers show similar ORs as the Scott et al. meta-analysis, and p-values lower than 0.1 for 7 out of the 10 loci. They then look at the predictive power of information on these 10 loci on the risk of developing T2D, and find that it is rather limited (at least among Ashkenazi Jews):
"Consistent with the previous findings showing that such set of SNPs may explain only a small fraction (2–3%) ofthe trait variation (Saxena et al. 2007), we have also found that the predictive value of these findings is relatively limited.
For most individuals, the genotypic information will only modestly alter their baseline risk to develop T2D. Only for a small fraction of the population (about 3%), the genetic information may indicate a decrease or increase of the baseline risk by twofold (upwards or downwards). Consequently, at present, the use of genetic information by clinicians for the identification of patients at risk to develop T2D does not seem too relevant. Nevertheless, it is important to emphasize that the value of gene discovery lies primarily in the understanding of the disease as a means to develop efficient therapies."
Type 2 diabetes susceptibility loci in the Ashkenazi Jewish population.
Bronstein M, Pisanté A, Yakir B, Darvasi A.
Human Genetics
2008 Aug;124(1):101-4.
Abstract: Until last year, type 2 diabetes (T2D) susceptibility loci have hardly been identified, despite great effort. Recently, however, several whole-genome association (WGA) studies jointly uncovered 10 robustly replicated loci. Here, we examine these loci in the Ashkenazi Jewish (AJ) population in a sample of 1,131 cases versus 1,147 controls. Genetic predisposition to T2D in the AJ population was found similar to that established in the previous studies. One SNP, rs7754840 in the CDKAL1 gene, presented a significantly stronger effect in the AJ population as compared to the general Caucasian population. This may possibly be due to the increased homogeneity of the AJ population. The use of the SNPs considered in this study, to identify individuals at high (or low) risk to develop T2D, was found of limited value. Our study, however, strongly supports the robustness of WGA studies for the identification of genes affecting complex traits in general and T2D in particular.

Getting a Research Associate Position [Epigenetics News]

Posted: 25 Aug 2008 09:03 AM CDT

I was able to secure an offer for continued employment as a Research Associate at Washington State University. I will be working in the lab of Dr. Skinner, who many know that I had also been working with during my undergraduate years. He has several NIH grants and recently secured new funding from the Department of Defense for a project that I will be closely involved in.

The job hunting was exciting early on, but quickly moved into the frustrating stage and finally the depressing stage. The fact is there are a lot of unemployed M.S. and PhD scientists around here, and they are all in need of income, which means that they had been forced to settle for research technician jobs that are normally taken by B.S. graduates like myself. My 5+ years of research experience had a favorable impact on getting into final candidate lists, but I was only able to secure two offers from a list of 8 or 9 jobs. The rest were largely taken by those with advanced degrees. I was fortunate to have an hourly position to keep the bills paid during the process, which I know from experience could have been far more than depressing.

In the lab, my “unnamed” project, which I have been working on since 2005, should be coming to the point of publication soon. For the longtime readers this is something they have probably heard before, and I should have learned my lesson long ago and just not make any predictions about it. Nonetheless, all the added data accrued during this time has been extremely productive, and should make for an interesting paper when it finally gets to that point.

As for my writing here, as you can see it hasn’t been consistent. Our family was able to take a couple trips over the summer, including one a week ago to the Newport, Oregon area, which is a spot my family regularly went to growing up. It was good to share that experience with my wife and stepson.

Hopefully now that the summer is coming to a close (classes start today here at WSU) the blog updates will be more consistent and often.

Boris Johnson, Fop or Geneticist? [Sciencebase Science Blog]

Posted: 25 Aug 2008 07:00 AM CDT

boris johnsonIt’s a UK holiday today, so just a short post. For Scousers, Londoners and fans of BBC’s Have I Got News for You satirical news quiz, the name Boris Johnson likely drums up an image of some blonde, floppy haired and confused Tory toff, who just happens to be Mayor of London.

Well, it turns out that he has quite an interesting ancestry of which he was almost totally unaware until another BBC TV show (Who Do You Think You Are?, which is all about family history and genealogy of the rich and famous) helped him dig deep into the roots of his family tree. First off, not only was his great grandfather, Ali Kemal an outspoken journalist turned politician (like Johnson) who was apparently lynched by the state in the founding years of modern Turkey but his great-great-great-great-great-great-great-great grandfather was King George II of England (illegitimately due to a “wrong-side-of-the-sheets liaison between Johnson’s great grandmother and a descendant of George II. Such ancestry means Johnson is related to all the royal families of Europe.

How’s that for a bit of name dropping? Of course, there are probably tens of thousands of people who have illegitimate links to European royals, but it’s an interesting find nevertheless.

However, for those who think Johnson is nothing more than a blithering fop, it was his final words in this episode of “Who Do You Think You Are?” that were most poignant to lineage, heredity and most of all genetics, which is why I thought they warranted a holiday mention. I just hope they were spontaneous and unscripted.

We’re all just great, our genes just pulse down the lines. We’re not the ultimate expression of our genes. We’re the temporary custodians of these things. We don’t really know where they’ve come from, where they’re going, and the whole process is incredibly democratic.

You can view a segment from the show here, unfortunately, the closing quote is not included in this Youtube segment.


Boris Johnson, Fop or Geneticist?

Tired of all the crap from the tube [The Daily Transcript]

Posted: 24 Aug 2008 11:44 PM CDT

Joe Biden. How do I feel about the pick? It's okay, nothing to get excited over. At least when Biden attacks McCain, the media will echo it.

So we spent the day packing and listening to all the "pundits" on all the MSM websites. It is amazing how vacuous all these shows are. Not one iota of useful information. All sound bites that mean nothing. Listening to all this crap can really fry your brain. Is this why after such a disastrous 8 years McSame is only 2 points behind Obama? And what's up with all this Clinton supporters who are leaning on the fence towards McCain. I know that PP and Gwen Ifill think that they'll eventually fall in line, but my wife recently found out that one of her coworkers is such a person. I just don't get it. Obama and Clinton's policy differences are so minute that this lack of support can't be based on their platforms. Obama was against the war, Hillary appeased the right before going 180 - so it can't be that either. Sure Obama voted for FISA and has expressed support for some offshore drilling, but considering that a McCain presidency would be a full continuation of GWB's current agenda, there is no way that these two should be so close in the polls. And there is no way that Clinton voters should even consider voting for McCain. No way. I just don't get it. I asked Lesley, a summer student from North Carolina. She tells me that most of the folks back home think that Obama is a Muslim. Is that it? Are people so susceptible to such childish tactics? Either people are realy dumb, or racism is still a big factor.

This all reminds me of a song that curiously appears on this blog every election cycle:

Read the comments on this post...

Genetic Passports and Code 46 [Genome Blog]

Posted: 24 Aug 2008 09:45 PM CDT

Searching for less well known Biopunk movies, I thought I’d take a peek at Code 46, a 2004 movie with Tim Robbins and Samantha Morton. It’s set in a near future, dystopian world where reproduction is only permissible between people not closely related. As a result of rampant human cloning, people have no real idea of their genealogy and thus are constantly in danger of inbreeding, so genetic screening is mandatory prior to reproduction or as the 'Code 46' dictates. Its a future of genetic travel restrictions and biological surveillance. The title is based on the fact that Humans normally have 23 pairs of chromosomes for a total of 46 and thus the Code 46.

Code 46:

Article 1

Any human being who shares the same nuclear gene set as another human being is deemed to be genetically identical. The relations of one are the relations of all. Due to IVF, embryo splitting and cloning techniques it is necessary to prevent any accidental or deliberate genetically incestuous reproduction.


I. All prospective parents should be genetically screened before conception. If they have 100%, 50% or 25% genetic identity they are not permitted to conceive

II. If the pregnancy is unplanned, the foetus must be screened. Any pregnancy resulting from 100%, 50% or 25% genetically related parents must be terminated immediately

III. If the parents were ignorant of their genetic relationship then medical intervention is authorized to prevent any further breach of Code 46

IV. If the parents knew they were genetically related prior to conception it is a criminal breach of Code 46.”

One more Olympic thought [Omics! Omics!]

Posted: 24 Aug 2008 08:52 PM CDT

One other item that was in the mental draft of yesterday's Olympic pondering, but was inadvertantly dropped. Another possible genetically-driven edge in athletic performance would not be directly on performance but on the reaction to performance. Prime athletes might have different pain or endorphin responses, less post-exercise inflammation, different injury responses. Some of these might be specific to specific events or types of sports -- joint pounding running or gymnastics puts very different stresses on the body than something like swimming or speedskating.

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