Wednesday, November 19, 2008

The DNA Network

The DNA Network

Gary Marchant: Legal pressures and incentives for personalized medicine [Think Gene]

Posted: 19 Nov 2008 08:13 PM CST

Gary Marchant, Robert Milligan, and Brian Wilhelmi of the Sandra Day O’Connor College of Law at ASU write an excellent paper regarding the nature of American law and the nascent genomics industry: “Legal pressures and incentives for personalized medicine

As individual plaintiffs [of personal injury from medical malpractice or product liability cases] usually cannot afford to finance the litigation, their attorneys must fund the case using their own resources on a contingency fee basis. One implication of this financial relationship is that plaintiffs’ attorneys are generally reluctant to litigate and fund novel claims based on new scientific evidence. However, once a However, once a new claim has proven to be successful by one or more favorable verdicts and ‘blood is in the water’, there will be a swarm of lawyers willing to file and finance similar ‘copycat’ suits. For a new field such as pharmacogenomics, this litigation dynamic means that there will likely be an initial calm until there has been a breakthrough case, and then there will be a sudden storm of litigation that will have immediate and enormous implications for defendants, including manufacturers, providers and payors.

The organic approach is as old as dirt [Tomorrow's Table]

Posted: 19 Nov 2008 06:27 PM CST

"The organic approach is as old as dirt (literally), but it is not mired in the past. Our methods are built on the wisdom farmers and gardeners have gleaned from centuries of experience observing nature and using their resources efficiently. Researchers, however, continually uncover the scientific basis for how and why the organic approach works. And organic farmers and gardeners are benefiting from new tools and technologies that help us build healthy soil and protect plants from destructive pests without disrupting the balance of nature....

As you read each issue of Organic Gardening, notice that nearly every article is built with input from scientists. We don't rely soley on personal anecdotes- they can be interesting and useful, but also flawed and misleading. You also will see in this issue an excerpt from a provocative new book written by a scientist and an organic farmer, who assert that the tools of bitoechnnolgy could be useful to sustainable agriculture.

This premise may be viewed as heresy by many in the organic movement. But when I read the book, I was reminded of the words of our visionary editor, Robert Rodale, from our January 1989 issue. 'Biotech will have to be part of that environmental solution,' Rodal stated. 'And it will have to blend into a whole landscape of farm and garden methods that will be asked to regenerate instead of degrade the environment. What I call the tricky biotech of today- the search for ways to fool plants and animals to do more - will evolved into a much more sensible and high-quality way to improve plants in the more distant future.'

Why give these advocates for GE a chance to state their case in the pages of OG? Because a scientific approach demands a reasoned, informed debate, not dogmatic rejection. Because if our organic principles are sound, they can hold up to debate. You dont stand up for centuries if you don't have sturdy legs."

- An excerpt from Scott Meyer's editorial entitled "Looking Forward" from the Nov -Jan 2008-2009 issue of Organic Gardening magzine that featured "Tomorrow's Table".

Embryo screening for common diseases: coming soon? [Genetic Future]

Posted: 19 Nov 2008 05:49 PM CST

A Nature News article describes the growing availability of technology that allows the screening of human embryos for hundreds of different genetic disorders prior to implantation. The technology is based on the same type of chips used by personal genomics companies like 23andMe, but the chips used for embryo screening would initially be used to target known rare disease-causing mutations or large chromosomal abnormalities rather than performing a genome-wide scan for common variants (in the article, a screening company director describes the targeted diseases as "nasty, early-onset and ethically uncomplicated"). Such testing is generally accepted by Western society, as witnessed by the extremely high rate of termination of trisomy 21 embryos.

However, the article also notes that there's currently nothing to stop companies from including variants on the chips that provide information about adult-onset diseases like diabetes or Alzheimers - indeed, in the UK there have already been embryos screened for breast cancer risk variants. This type of screening currently raises some serious ethical eyebrows, but perhaps not for long: the article argues that "as the technology advances, consumer demand is likely to overwhelm societal ethical qualms" - and I'd tend to agree, in general.

However, before we get too carried away by visions of a Gattaca-style future, it's worth noting a couple of serious obstacles in the path of widespread adoption of the use of this technology to screen for common disease genes.

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

New Applications Forums []

Posted: 19 Nov 2008 03:41 PM CST

In an effort to increase the organization of the discussions and make things easier to find...I've created a new set of "Applications" forums: My intent is to segment the purely scientific/biology discussions away from the previously instrument provider-focused areas. I think this organization offers more opportunity for people with different instruments to cross-pollinate, as regardless of what chemistry/instrument produces the data, the biology remains (roughly!) the same. I...

Read more and join the community...

Nobel Prize: Look to the Stars [Bayblab]

Posted: 19 Nov 2008 01:03 PM CST

If you have your eyes on the Nobel Prize, you may want to think again if you were born in the midsummer months. A study published in the Canadian Medical Association Journal (CMAJ) compared the birthdates of 171 Nobel laureates with 375 scientists who had not won the prize and shows that people born under the star sign Leo are the least likely to win the prestigious prize for Medicine or Physiology, while Geminis have the best odds. This is just common sense for any astrologer
Selective retrieval from the multitudinous traits attributed to particular astrological signs showed that "Gemini produces persons of greater intellect and more powerful invention and genius than any other sign of the zodiac" and that Gemini are "thirsty for knowledge and eager to study."
But don't worry Leos, you still have the "natural creativeness and magnetism" that attracts others to you.

The Evolution of Writing [ScienceRoll]

Posted: 19 Nov 2008 12:27 PM CST

Robert Scoble left a message on Friendfeed yesterday:

"I invested a lot of time this year in FriendFeed and Twitter instead of my blog. Was that the right decision?"
I replied to him:
No question about that. In the past, websites were static compared to blogs. Now blogs are static compared to microblogging services.

This image shows something like that:


A Very Brief History of Micro-Media. Credit: David Armano.

(Hat tip:


Gene Genie #40 at Human Genetics Disorders [ScienceRoll]

Posted: 19 Nov 2008 12:12 PM CST

The  40th edition is up at Human Genetics Disorders. A great compilation of articles and blogposts about human genetics and personalized medicine. Thank you, Chavonne Jones, for hosting Gene Genie.

Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). We accept articles on the news of genomics and clinical genetics. The news and articles of personalized genetics are also included. Check out Gene Genie for more about this unique field of medicine.

Many thanks to Ricardo Vidal for the logo!

Don't forget to submit your articles via the official page.

Let me know if you would like to host an edition.

Here are all the issues of Gene genie:


What you have to know about Twitter [ScienceRoll]

Posted: 19 Nov 2008 12:09 PM CST

I thought I should collect and share all the things I’ve learnt or found about Twitter as this is one of my favourite web 2.0 services these days. Twitter is a microblogging service that allows us to send 140 character-long messages to our followers. There is a huge health 2.0 community out there. Follow me and let’s keep in touch.

First, a few posts I’ve dedicated to this subject:

And other posts from great bloggers:


Generic genome sequence press release (by Andy). [Genomicron]

Posted: 19 Nov 2008 11:25 AM CST

This comment by Andy was too good not to repost.
Generic press release for genome sequencing

Scientists map genome of (insert name).

A team of researchers from (insert university/institute/lockup garage) has completed mapping the genome of (animal/plant/squashy deep-sea thing).

"We were amazed how (strike one) similar/dissimilar it is to the human genome," said (insert name of lead scientist/grad student/custodian who happened to answer the phone).

The discovery should help scientists (strike all but one) cure cancer/end world hunger/prevent hair loss).

Modern eugenics and genetic sins [Mary Meets Dolly]

Posted: 19 Nov 2008 10:29 AM CST

Bill Muehlenberg has written a tremendous piece at called "Towards a coercive utopia" where he argues against modern eugenics that uses genetic testing in the worst way possible: to discard humans that are "genetic defective."  The whole piece is an amazing read, but I would like to point out a couple of important points.  Muehlenberg quotes Julian Savulescu, a bioethicist who argues for using genetic testing along with IVF to create the "most genetically fit" children.  Savulescu wrote:

The AU$3,440 test, called karyomapping, which should be available as early as next year, will allow couples at risk of passing on gene defects to conceive healthy children using IVF treatment. [My emphasis]

This statement is such a subtle slight of hand, that even I almost missed it.  The karomapping that Savulescu discusses would test embryos created with IVF for genetic disorders, among other things, and then the couple can chose which embryos to implant.  The embryos that do not make the cut are discarded, donated to research or kept in the deep freeze indefinitely.  So Savulescu is very wrong.  Couples will conceive both "healthy" and "defective" embryos.  The defective ones just don't get a chance to finish their lives because they are deemed inferior to their siblings. 

This procedure, a more sophisticated version of preimplantation genetic diagnosis or PGD, does not cure disease.  It just gets rid of those humans that have the disease.  Muehlenberg writes:

But as Australian ethicist Anthony Fisher reminds us, scientists should
focus on curing such diseases rather than eliminating people with the
condition. Genetic screening can easily lead to selective breeding and
selective abortion. It can easily lead us to a return to eugenics

Which brings me to a quote from Leon Kass that Muehlenberg rightly highlights:

One of the most worrisome but least appreciated aspects of the godlike power of the new genetics is its tendency to 'redefine' a human being in terms of his genes. Once a person is decisively characterized by his genotype, it is but a short step to justifying death solely for genetic sins.

Anyone who was awake during this election cycle could not escape the vitriol spewed at Sarah Palin.  The irrationality of it made me conclude that her transgression was not just being a conservative.  Her real sin was to give birth to Trig, her Down syndrome son. Open your eyes and you will see that in the eyes of many, including some of the most influential bioethicists in the world, "genetic sins" are already walking among us.

Review paper on the importance of considering sex for genotype-phenotype relationships [Yann Klimentidis' Weblog]

Posted: 19 Nov 2008 09:22 AM CST

Sex-specific genetic architecture of human disease
Carole Ober, Dagan A. Loisel & Yoav Gilad
Nature Reviews Genetics 9, 911-922 (December 2008)
Abstract: Sexual dimorphism in anatomical, physiological and behavioural traits are characteristics of many vertebrate species. In humans, sexual dimorphism is also observed in the prevalence, course and severity of many common diseases, including cardiovascular diseases, autoimmune diseases and asthma. Although sex differences in the endocrine and immune systems probably contribute to these observations, recent studies suggest that sex-specific genetic architecture also influences human phenotypes, including reproductive, physiological and disease traits. It is likely that an underlying mechanism is differential gene regulation in males and females, particularly in sex steroid-responsive genes. Genetic studies that ignore sex-specific effects in their design and interpretation could fail to identify a significant proportion of the genes that contribute to risk for complex diseases.

Epigenetics & Chromatin: Epigenetics Goes Open Access [Epigenetics News]

Posted: 19 Nov 2008 08:02 AM CST

While Landes Bioscience made headway by debuting a journal devoted solely to epigenetics (Epigenetics), BMC has really opened the door to epigenetics research by debuting the first open-access journal devoted to epigenetics. Epigenetics & Chromatin is a new open-access option for researchers wanting to make their research available to a wider audience. The co-editors, Steven Henikoff and Frank Grosveld, are open to a wide range of topic areas:

Epigenetics & Chromatin will publish articles aimed at understanding how gene and chromosomal elements are regulated and their activities maintained during cell division, self-renewal, differentiation and environmental alteration. Epigenetic research encompasses studies that use model systems to discover and investigate epigenetic mechanisms, as well as studies aimed at combating diseases that involve epigenetic processes. Topics include, but are not limited to, gene activation, silencing and imprinting, cellular reprogramming, nucleosome modification, assembly and remodeling, DNA methylation, chromatin structure and dynamics, chromosomal maintenance elements, dosage compensation, intra- and inter-chromosomal interactions and prion inheritance. Approaches that apply cutting-edge technologies to problems in the field are especially welcome.>

A publication fee of US$1800 is pretty standard fare for an open-access journal, and I’ve heard that many scientists are willing to pay the fee if it means increased awareness (and citations) of their work. I have to believe that with an increased focus on the field from a diverse arrange of disciplines, Epigenetics & Chromatin will be a popular and high impact journal. Link

Genome Sequenced, Published via Press Release [evolgen]

Posted: 19 Nov 2008 07:30 AM CST

Back in the day, you could sequence a genome and get a Nature paper out of it. Pretty soon, the sexiness of genome sequencing wore off, and it took a bit more to get into a vanity journal. You had to sequence something cute and cuddly, something extinct, or a lot of genomes at once. Any other genome sequencing projects were relegated to lower tier journals.

Now, it appears that even sequencing the genome of charismatic megafauna only gets you a press release. As TR Gregory points out, the sequencing of the Kangaroo genome was announced in such a manner (Science by press release). But check out the title on the press release:

Australian First: Kangaroo Genome Mapped

They report that the genome was "mapped". Not sequenced. This is the incorrect terminology. One the positive side, at least they didn't say the genome was decoded.

Read the comments on this post...

Polymer, Nanotech, Vitamins [Sciencebase Science Blog]

Posted: 19 Nov 2008 07:00 AM CST

This week the Alchemist hears how polymer chemists are turning to supramolecular chemistry (or is it supramolecular chemists turning to polymers?) to create novel flexible and elastic materials. In nanotechnology, a British consumer activist organization is calling for more safety data on nano materials used in cosmetics, and French scientists have demonstrated how nitrogen oxides released by snow melt in the Arctic could have a global impact.

In biological research, US scientists are suggesting that a specific active form of vitamin D could be useful as a protective agent against nuclear incidents. And, in interplanetary chemistry, Johns Hopkins researchers have found spectroscopic evidence that water-bearing opal formed on Mars much more recently than previously thought.

Finally, we’re going Dutch with this week’s award in which technology transfer in the area of solar energy conversion brings a financial reward and prestige to a graduate student and his colleagues. Get the full skinny and the links in current issue of The Alchemist

Polymer, Nanotech, Vitamins

Consumer Genetics Show 2009 in Boston [Eye on DNA]

Posted: 19 Nov 2008 05:30 AM CST

dna string Here’s where most of my fellow DNA Network members would surely like to be next summer - the First Annual Consumer Genetics Show at the Hynes Convention Center from June 9-11, 2009.

Speakers include:

Show objectives include:

  • Regulatory issues
  • Intellectual property considerations
  • Interaction between biotechnology, molecular diagnostic, and pharmaceutical markets
  • Role of physicians in helping patients interpret results from direct-to-consumer (DTC) genetic tests
  • Effect of DTC market on molecular diagnostic laboratories
  • Patient and consumer security (Blaine at The Genetic Genealogist recently wrote about security at Navigenics and 23andMe)
  • Public relations and business strategies to optimize public perceptions of DTC genetic testing (given persistent negative opinions issued by various experts and professional societies)

Are you planning to attend?

Photo credit: Pieter Musterd

Genomicron on Science by press release. [The Tree of Life]

Posted: 18 Nov 2008 09:02 PM CST

Just a quick one here. Ryan Gregory is going on against science by press release - one of my biggest pet peeves. Check it out at:

Genomicron: Science by press release.

I see PLoS in everything IV: PLoS at Metagenomics 2008 meeting [The Tree of Life]

Posted: 18 Nov 2008 08:44 PM CST

I may see PLoS even when it is not there, but in this picture, which was the group photo for the Metagenomics 2008 meeting at CalIT2, I weaseled my way to the front hoping to get my PLoS bag and PLoS shirt into the picture. And looky there - it worked.

Not Intended to Diagnose or Treat [The Gene Sherpa: Personalized Medicine and You]

Posted: 18 Nov 2008 08:45 AM CST

Andrew Yates at ThinkGene comments on something that I have not been able to effectively explain. We trust health assets like "medical advice" to exist. That is, we trust that public medical...

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