Wednesday, April 30, 2008

The DNA Network

The DNA Network

My 23andMe profile: no genomic guide to sports cheating [biomarker-driven mental health 2.0]

Posted: 30 Apr 2008 07:08 PM CDT


Just checked for my status at UGT2B17 - locus of a 150kb deletion variant covered here in the Economist - to see whether I might have missed my chance to inject ‘roids and claim international sports glory without getting busted by the World Anti-Doping Agency. Unfortunately, the 23andMe profile provides data for the flanking genes YTHDC1 and UGT2A3 on chromosome 4, but not this specific gene. Doesn’t quite seem to validate my choice to couch-potato-dom though.

Predictive Health: Best Ethics Blogs - April, 2008 [PredictER Blog]

Posted: 30 Apr 2008 06:09 PM CDT

This issue of the "best" predictive health ethics blogs includes entries on education, eugenics, genetic counseling, genetic testing, personal genomes and privacy.


More on the need for science education. Sue Trinidad, Women's Bioethics Blog. 11 April 2008.
How will tomorrow's voters make informed decisions about the predictive health research and medicine. Sue Trinidad looks at the results of a recent evaluation (see: PMID: 18245328) of submissions to the DNA Day essay contest for high school students; the forecast is not good. After reading comments like:

Genetics create a perfect being. Change the genes. Make that child perfect. There's no better solution to an impending health care crisis. … What we can have is a sea of people who all look brilliant, who are all smart and who all have perfect eyes, nose and lips. It's a perfect society, what more could we want?

Trinidad calls for improved K-12 science education:

[T]hese are the responses of students who were willing to participate in an essay contest about genetics. What must be the level of understanding among those who wouldn't bother? Clearly, CLEARLY, we need to do a better job of K-12 science education.


Genetic DisEnhancement -- Does reproductive autonomy extend to choosing a disability? Linda MacDonald Glenn, Women's Bioethics Blog. 13 April 2008.
Following the recent news from the UK that the government will remove references to deafness from the proposed Human Fertilisation and Embryology Bill, a decision that will permit couples to use preimplantation genetic diagnosis to select a child with congenital deafness, Glenn questions the broader implications of the decision:

My concern about removing the clause banning the creation of disabled children entirely, is why stop at deafness? Aren't the primary purposes of medicine to heal, to cure diseases, restore, and alleviate suffering? … So the question is how far does reproductive autonomy go? Nobody wants to see a fellow human being struggle or suffer, especially in the name of 'reproductive autonomy.'

Whose Normality? D. Joy Riley, 17 April 2008.
After reading that a economically disadvantaged couple in India accepted a child with Craniofacial Duplication as potentially a reincarnated deity, Riley wonders about Western notions of "normal" in the context of prenatal genetic diagnosis. Riley is alarmed by the concept that prenatal screening for Huntington's Disease "could eliminate this entire population!" The author asks:

Who defines 'normal'? Is normal equal to "without disease or abnormality"? If so, when? Is normal to be born without disease, or to be born with no disease or disorder present at birth, AND no genes for known disorders that will develop later in life, like breast cancer, familial polyposis of the colon, or Huntington's Disease?

Genetic Counseling

Now this is why we need genetic counselors. SciPhu. 25 April 2008.
After writing (in an earlier post) that reliable predictive testing may render the job the genetic counselor obsolete, the author of SciPhu reads a paper by lead author Kimberly Quaid (a PredictER team member). SciPhu calls the experience "eye-opening". When it comes to "high risk tests", such as a test for Huntington's Disease, SciPhu concludes:

The final take home message must be that not testing for a condition has significant value, especially when treatment options are scarce or non-existent. … Hope is sometimes a life saver. Knowledge on the other hand, can put peoples lives in ruins.

Genetic Testing

Over-regulation. Steve Murphy, Gene Sherpas: Personalized Medicine and You. 8 April 2008.
In this "follow-the-money" assessment of genomic medicine, Murphy points to the disproportionate influence of the business sector: "Genomic Medicine is being driven by business. Why? Because academia has failed to take the bull by the horns. Why? They are comfortable in their own realm. This is a stretch for them." In Murphy's view, while business sees potential money in testing, less emphasis is placed on genetic counseling and other genetic services. In the long run, however, this lop-sided approach may hurt the life sciences industry. Murphy cautions that the direct-to-consumer genetic testing push may be annoying all the wrong people—some of the big names on the beltway: "AMA, ACP, SACGHS, FDA, CMS, GAO, US Senate, Department of HHS, FTC, ACMG, NHGRI..." In other words, "over regulation" may be on the way.

The gap is widening on genetic testing, too. Ricki Lewis, 14 April 2008.
Following a post on the widening gap between public perceptions and the reality of the current state of the art in stem cell science, Ricki Lewis writes on a similar gap in the genetic testing industry. Lewis warns that whole-genome association tests may not be ready for the consumer market:

The truth is, and the direct-to-consumer company websites actually say so in the fine print ... Consumers may not be aware of these limitations, nor realize that "link," "marker," and "association," have precise scientific meanings.

After reciting the disclaimers, Lewis doubts the services provided by 23andMe, Navigenics, and deCODEme are legitimately non-medical and asserts:

It isn't ethical to market DNA tests based on whole genome population-based studies without randomized, controlled clinical trials, replication, and validation. ... Whether considering stem cells or DNA tests, that's simply the way that good medical science is done.

The Ethics of Genetic Testing. William Martin, Free and Wandering Thought. 18 April 2008.
After reporting his less than stellar performance on a recent "biopsych test", Martin shares a few free thoughts on the ethics of genetic testing for diseases like Huntington's and Bipolar disorder. Martin worries about where our society will draw the lines for the appropriate use of genetic information. Like many, he anticipates that trouble in the insurance industry and asks:
"What happens when insurance companies find out you are XX% likely to develop a disease?"
With this in mind, Martin applauds Paul Wellstone's drafted "Mental Health and Addiction Equity Act", which, as Martin reports, might have some impact on how insurance companies will (or will not) use genetic information to determine coverage for mental health disorders.

Personal Genomes and the Bioscience Industry

The Personal Genome discussion. Sandra Porter, Discovering Biology in a Digital World. 24 April 2008.
Porter provides a summary of panel discussion at the University of Washington. At the event Bill Gates, Eric Lander, Maynard Olson, Leena Peltonen, and George Church fielded questions from the audience about the personal genomics revolution. Porter summarizes responses to some really interesting questions, including:

Should people be given information about genes that are related to diseases if there's nothing that can be done?
What are options for the personal genome to benefit third world populations?
How will personal genomics affect privacy?
Are we going to make designer babies?

Also see Deepak Singh's thoughts on the discussion at bbgm.

Personal Genomics Takes a Bashing on Physician Oversight, Financial Backing, and Privacy. Hsien-Hsien Lei, Eye on DNA. 21 April 2008.
Lei reviews the "snarky" news coverage of the consumer genomics industry published in Forbes and BusinessWeek. While Forbes reports that New York's State Department of Health has sent threatening letters to some direct-to-consumer genetic testing companies ("jail-time"!), BusinessWeek focuses on Google's role in supporting the industry. Lei concludes: "If anyone ever organizes a biosciences startup school, they need to put regulatory affairs, investment choices, and privacy concerns on the syllabus!"


A new model for genetic privacy: you don't have any. Daniel MacArthur, Genetic Future. 20 April 2008.
After perusing a perspective piece in Nature Reviews Genetics, MacArthur notes that the authors call for a paradigm shift in the approach to research subject privacy, he comments: "Essentially, they argue that 'the reality of the new genetics and genomics urges us to abandon the traditional concept of medical confidentiality …'." In MacArthur's assessment, the authors:

[A]rgue for a strategy of "maximizing data protection while informing people about its limits". In other words, doing your best to limit disclosure of individual health data, while clearly informing participants of the fact that their privacy can't be guaranteed.

Although he sees the value to the science and acknowledges the risk to privacy, MacArthur wonders how these changes might influence the future of human subjects research:

[W]ill such a policy discourage people with a clear family history of genetic disease from participating in large-scale cohort studies (for insurance reasons), thus reducing the power of such studies to detect disease-associated variants? Will it create a generation gap in research participation, with conservative older people shunning studies while the children of the Facebook era - who engage in public disclosure of information with a willfulness that seems shocking to their elders - embrace participation?

The New BRCA and SubSegments of a Segment [The Gene Sherpa: Personalized Medicine and You]

Posted: 30 Apr 2008 12:45 PM CDT

First and Foremost, To all women who have hereditary patterns of Breast Cancer, but have a negative BRCA work up....there is new information which deCode has released in Nature Genetics. I was very...

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America must rebuild, not destroy, agricultural research programs [Tomorrow's Table]

Posted: 30 Apr 2008 12:01 PM CDT

In an op-ed piece today, Nobel Peace Prize winner, Norman Borlaug, describes a new strain of stem rust fungus that could reduce world wheat production by 60 million tons, or 10% of the world's wheat harvest. "If millions of small-scale farmers see their wheat crops wiped out for want of new disease-resistant varieties, the problem will not be confined to any one country. Widespread failures in global wheat production will push the prices of all foods higher, causing new misery for the world's poor."

Is there anything we can do to avoid a global crop failure of this magnitude? Yes. Borlaug argues that it is critical to continue American support for the international agricultural research centers (The State Department is recommending ending this support as well as support for important research centers, including the Department of Agriculture's essential rust research laboratory). If publicly financed international researchers move together aggressively and systematically, high-yielding replacement wheat varieties can be developed and made available to farmers before stem rust disease becomes a global epidemic.

The story of papaya provides an excellent example of how plant biologists can thwart such a disease.In the 1950's, the entire papaya production on the Island of Oahu was decimated by papaya ringspot virus.

Because there was no way to control the disease, the papaya farms moved to the island of Hawaii where the virus was not yet present. At the same time, Dennis Gonsalves, and coworkers initiated research to develop strategies to control the disease.

In 1992, the virus was discovered in the papaya orchards and by 1995 the disease was widespread, creating a crisis for Hawaiian papaya farmers. By 1998 papaya production had dropped to 26 million pounds.

Fortunately, Gonsalves' group was able to develop papayas resistant to the virus by using genetic engineering. Gonsalves' group spliced a small snippet of DNA from a mild strain into the papaya genome. Similar to human vaccinations against polio or small pox, this treatment immunized the papaya plant against further infection. The GE papaya were highly resistant to the viral strain.

After release of GE papaya to farmers in May 1998, production rapidly increased with a peak of 40 million pounds in 2001.

The story of the Hawaiian papaya is an example where GE was the most appropriate technology to address a specific agricultural problem. There was no other technology then to protect the papaya from this devastating disease, nor is there today.

This brings us to the question, what if genetic engineering, the most promising method for controlling stem rust, is used to develop new high-yielding resistant wheat varieties? Will the public's anxiety about the process of GE, a technology that has been used in agriculture for 15 years (and in medicine even longer) without a single negative environmental or human health affect, paralyze us and prevent release of life-saving wheat varieties?

Just as the public's embrace of the political strategy of "manufactured uncertainty" about global warming delayed much needed action, so can whispers of uncertainty about GE delay our focus on helping feed the poor and malnourished.

Whose genome? [T Ryan Gregory's column]

Posted: 30 Apr 2008 07:31 AM CDT

The term "genome" is oft-heard but seldom defined, and indeed has more than one meaning. Little wonder, then, that discussions about genome sequences and comparisons thereof can leave otherwise interested audiences more frustrated than enlightened. "What is a genome?" and "whose genome was sequenced?" are legitimate questions, and what follows is an attempt at clarification that is, by necessity, as much philosophical as scientific.

Definition #1: In a broad sense, a genome can be considered as the collective set of genes, non-coding DNA sequences, and all their variants that are located within the chromosomes of members of a given species. This definition does not consider variation among individuals within a species, and instead relates to distinctions between species.

read more

Spicy Nanogoo [Sciencebase Science Blog]

Posted: 30 Apr 2008 07:00 AM CDT

Nano Car (Photo by Y. Shirai/Rice University)Nanopaprika could be the key ingredient for spicing up the nanoscience and nanotechnologies communities. Site editor Andras Paszternak asked me to join just before the scientific social networking site passed the hot point of 500 members. Whether or not that nice round figure really is key to online science remains to be seen but there is certainly a buzz about the place.

I had rather hoped to kick off a lively debate on nanogoo and the media hype and parallel scare stories that have emerged since K Eric Drexler’s first proclamations about nanobots following on from Feynman’s famous room at the bottom lecture.

We’ve all read the grey goo headlines but we’ve also seen the hype regarding what nano has to offer. I often tell people it’s nothing special, just stuff that happens to be a few billionths of a metre in scale. If it’s not grey goo and it’s not the Drexlerian promise of a decade since, then where is modern nanoscience and when will it truly beecome nanotechnology?

I also asked the same question, in time-honoured fashion, of my LinkedIn contacts and have summarised responses here.

Liam Sutton, a Business Research Fellow at the University of Sheffield’s Polymer Centre and Technical Consultant at FaraPack Polymers had this to say: “Well, ‘nanoscience’ is such a broad area. After all, the term encompasses (as far as I understand it) anything physical with a characteristic length scale in the order of nanometres. So there are unpleasant stories to tell, like the discovery of penetration of the blood-brain barrier in rats by diesel smoke particles and, equally, there are billion-dollar nanotechnologies already out there like hard disk drives based on the giant magnetoresistance of synthetic nanoparticles.”

Suttons adds that the Sheffield answer to this sort of question is to direct people towards the Soft Machines blog of Richard Jones, who is Senior Strategic Advisor for Nanotechnology for the UK’s Engineering and Physical Sciences Research Council. “It’s a very well written and authoritative source on the place and direction of nanoscience and technology,” Sutton says.

Tim Harper, a (nano)Technologies Entrepreneur, says that, “Most of the hype seems to have shifted to Cleanteach (along with most of the hypers) so the picture is becoming a lot clearer. The technology is now emerging in a number of areas although the majority of ‘nano’ is still nanoscience.” He points readers to a couple of white papers dealing with this on the Cientifica website. Harper is VP Business Development at PlayGen, Contributing Editor at The Real Nanotech Investor, and an Editorial Board member on NANO, published by World Scientific.

Philippe Bradley (no relation), an Oxford Uni student and founder of, which is currently in development said: “Nanobiotechnology seems to be a very exciting field at the moment - because, behind the opaque name, it’s basically the science of beating nature at its own game. The body is full of amazing machines, nanoscience seeks to modify or emulate them - or create completely new machines that perform similar functions.”

“Nanotechnology, as far as theory goes for technology in the nano domain, exists very much today,” adds Santanu Ganguly, at Network Engineer at Swisscom. He points to quantum dots, electron spin dynamics, atomic clusters etc, which all lie under the nanoscience banner. “In terms of actually seeing the basic science become a ‘true’ technology, certain challenges still remain,” he adds, “most of which has to do with quantum interactions. The most promising part so far, from the point of view of applications and control over quantum interactions, seems to be quantum optics and manipulation of DNA.”

You can read other responses and follow additional resources via the LinkedIn answers page. What are your thoughts on nano hype and nano fears? Are we set to drown in nanogoo at some point in the future or will nano save the world? Surely, with all this paprika around it’s time for a pep talk…

A post from David Bradley Science Writer

Spicy Nanogoo

Eye on DNA Headlines for 30 April 2008 [Eye on DNA]

Posted: 30 Apr 2008 06:21 AM CDT

  • Scienceblogs Gene Expression hosts Gene Genie #30.
  • Thank you to the Missouri State Genealogical Association (MoSGA) Messenger for sharing Eye on DNA with its readers!
  • dna-blue-skyDNA inspires not just scientists but artists too. Check out Digital 3d Art created by a “quantum theoretician involved in studying life at a molecular particle level.”
  • Are we in for another Myriad genetic test ad uproar? Identigene (more from Eye on DNA), sellers of over-the-counter paternity tests, have hired STG Media Corp to create TV, print, and radio ads that will “not only inform consumers that the product is out there, but that will also demonstrate that the product actually works.”
  • A “major television network” (I can vouch for their authenticity) is looking for people to interview. Here’s what they sent me:

    For an upcoming series on genetic testing, a major television network would like to interview a person who has ordered an online gene test to assess their future risk of getting certain diseases. Twelve complaints have been filed with the california Dept of Health and the New York State Dept of Health has sent letters explaining the legal ramifications of testing New York residents without the proper clinical laboratory permit. Most of these complaints are anonymous. Would anyone speak on-camera to their issues and share their personal experience ordering one of these tests and getting the results? Please call 917 991 3689 or write to

Bio-IT World Day 3 - Linda Avey Keynote [business|bytes|genes|molecules]

Posted: 30 Apr 2008 06:10 AM CDT

Bio-IT World day 2 - iPhones, Virtualization, EC2 and the Semantic Web [business|bytes|genes|molecules]

Posted: 30 Apr 2008 05:43 AM CDT

Cropped version of :Image:IPhone_Release_-_Seattle_(keyboard).A quick report on Day 2 of Bio-IT World.

The day started with a keynote by Josh Boger, founder and CEO of Vertex. His talk spanned several real world examples and some food for thought. Highlights

  • Vertex has made active use of a MedChem ELN, which has been extended to their entire MedChem community, including external partners. In his own words the goal was “enabling the virtual research organization”
  • Metric of success was user adoption and there were some good analytics supporting uptake
  • He spoke at length about the HCV program, where they have used extensive predictive modeling and simulation
  • Clinical data has backed up their predictive modeling (they’re in Phase III now)
  • They have avoided some experiments (carried out by competitors in one case) that their models suggested they avoid
  • He ended by talking a lot about communication and how technology can impact the healthcare system. Much of this section of his talk was around the iPhone. For example how the iPhone can be used to track RFID tagged pill bottles, patient exercise regimens, carry patient records, monitor weight, etc. They’re actually implementing some of these ideas

There were many other talks to attend, and I won’t bore you with some of the details, but I will talk about one talk, a talk by Chris Dagdigian of The BioTeam, a small boutique consulting shop, which readers of this blog will know via mentions of Michael Cariaso. Chris spent a lot his talk discussing the economics of storage and the kinds of storage, etc available these days and trends in storage and computing. Perhaps it shows how much of a geek I am, but this was a dream talk, one full of hardware specs, pictures of data centers, etc. It is clear that virtualization is big; Chris’ preference being Xen. There was a cool slide on meta-virtualization (a virtual machine inside a virtual machine inside a virtual machine). Two thoughts really resonated with me; first was his distaste for classical Grid Computing, which I have long considered impractical for most companies. The second was his strong support for Amazon Web Services, especially EC2. Apparently, every single BioTeam consultant has independently deployed an EC2 solution, i.e. they’ve all come to the same conclusion. Can’t wait to see this talk next year to find out where they’ve gone with AWS. One thing he said which also resonated was to talk about the death of the small cluster. Today and in the future, we will either have multicore (8-16 cores) on our desktops or dial up cloud resources. His slides will be available somewhere. Can’t wait to get my hands on them. This was a GREAT talk.

One of the highlights for me was attending the W3C Semantic Web HCLSIG lunch. I got to meet people I know (Eric Neumann), people I have interacted with online (Vipul Kashyap) and followed (John Wilbanks from Science Commons). And I got to say hello to Sir Tim Berners-Lee, who needs no introduction.

Another highlight for me. I got to finally meet Joe Landman, whose JackRabbit got a good plug in the BioTeam talk as well. It was great to meet Joe with whom I’ve been having a conversation via our respective blogs for quite a while now.

Met several former colleagues and customers as well. Bio-IT World has definitely been one of the better conferences I have had a chance to attend in terms of interest and people.

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Search for Life Science: NextBio launches for the public! [Think Gene]

Posted: 30 Apr 2008 04:22 AM CDT

Cupertino, CA, April 28, 2008 - NextBio today announced the next step in making Open Biology a reality: a free version of the NextBio life science search engine has been made available to the general public. Using NextBio, any researcher or clinician can search the world’s public life sciences data and literature - over 10,000 [...]

What does DNA mean to you? #3 [Eye on DNA]

Posted: 30 Apr 2008 03:28 AM CDT

dna dundeeThis week, I asked Bertalan Mesko of Scienceroll:

What does DNA mean to you?

Even if the structure of DNA was discovered more than 50 years ago, DNA means the future for me. As personalized genetics is getting closer to people, DNA will be one of the most used words and not just in the scientific community. Plenty of the therapies used in our time will be revolutionized soon and our DNA will play the main role in the future of medicine regardless the dangers it can lead to.

Re-cycling Electroporation Cuvettes [Bitesize Bio]

Posted: 30 Apr 2008 03:24 AM CDT

If you have ever worked out the price of an electroporation cuvette you will realise that, at several dollars each, they are worth recycling.

Accounts on how amenable electroporation cuvettes are to recycling vary, but I find that as long as you treat them well it is possible to use single cuvette many times.

It’s the metal parts of the cuvette you need to worry about the most - you need to get them clean of DNA and cells and dry again quickly to prevent corrosion.

So the key is to wash and dry as soon as possible after transformation.

My protocol is to wash with water first to clear away most of the residual cells/DNA, then treat briefly with HCl to destroy any remaining DNA - which you obviously don’t want hanging around the next time you do a transformation - then wash with 70% ethanol. The ethanol rinses away the HCl and sterilises the cuvette but because it is volatile it makes it easy to dry the cuvette in air.

So the protocol in detail is:

1. Rinse the cuvette five times with purified water. Ensure, especially with 1-2mm gap cuvettes that the chamber is fully washed out in all washing steps.

2. Fill the cuvette with 0.2M HCl and allow to stand for 10 minutes (but no longer as this will promote corrosion).

3. Rinse the cuvette five times with 70% ethanol, again ensuring the chambers are fully washed.

4. Under a sterile hood if possible, decant the ethanol and use a pipette (or syringe and hypodermic needle for small gaps) to remove as much residual ethanol as possible.

5. Air dry for 60 minutes, then replace the cap.

…and now your cuvettes are ready to go again.

Metagenomics just keeps getting bigger ... [The Tree of Life]

Posted: 30 Apr 2008 02:36 AM CDT

Yet another tip of the hat form the scientific community to the growing field of metagenomics. Today Ed Delong, one of the pioneers of using metagenomic methods to study microbes, was elected to the National Academy of Sciences. Congrats to Ed for this well deserved recognition (now I note, he has done many things in ocean microbiology that are not metagenomics ... but we will pretend here that this was all about his metagenomics work).

Other people elected of particular relevance to this blog -- David Hillis, a great evolutionary biologist, and Rosemary Grant, of Darwin's finches fame.

Francisco J. Ayala - Evolution - Scientists Who Believe in God - - New York Times [The Tree of Life]

Posted: 30 Apr 2008 02:26 AM CDT

Good to see someone other than Francis Collins getting some press about bridging the gap between evolution and religion. Today it is Francisco Ayala, an evolutionary biologist at UC Irvine. There is an interesting story about him in the New York Times today (Francisco J. Ayala - Evolution - Scientists Who Believe in God ).

Now, I thought I knew a good deal about Ayala but I did learn a bit in the article about his life and background (e.g., he was a Dominican priest, which I did not know). I personally think the "religion" vs. "evolution" debate is pretty silly much of the time and succumbs to the modern obsession with controversy. Ayala's new book "Darwin's Gift to Science and Religion" apparently addresses this issue and I hope it does a better job than Collins' book, which I found to be wanting in many areas. Of course, I guess I am a bit biased since I have had a soft spot for Ayala for many years and since he just wrote a very positive review of my new Evolution textbook. Now, if Collins wrote a positive review, I do not think I would like his book any more, but who knows ...

Lessons Learned From a Genetic Genealogy Quiz [The Genetic Genealogist]

Posted: 30 Apr 2008 02:00 AM CDT

On April 9th, 2008, I posted a quiz about genetic genealogy here on the blog. (If you haven’t taken the quiz yet, it is available here; it only requires a few minutes and might make the following analysis more clear and personally relevant). I created and posted this quiz because I thought it was a fun way to interact with my readers, and because I thought it was educational material to share with others.

As readers began to take the quiz, I realized that there was valuable information contained with the results. The following is an analysis of those results with a few preliminary conclusions. As I proceed, don’t feel bad about missing any of these questions, since this isn’t meant to be a critique of any single individual (especially since individual responses were not recorded). I merely hope to share the results as a whole in an effort to help inform and educate. The quiz was, and still is, meant to be fun.

Additionally, this analysis is also not meant to be a negative critique of genetic genealogy. There are MANY benefits to genetic genealogy testing, when it is used correctly. It can break (and has, many times, broken) through brick walls, validate traditional genealogical research, and confirm or deny a genetic relationship between two individuals in a relevant genealogical timeframe. As one of the correct answers in the quiz stated, genetic genealogy “is the forefront of science, and I get to play along.”

As of today, the quiz has been completed a total of 375 times. Most of the questions were easily answered, ranging from 80% correctly answered (”We all came from Africa, so why bother with a genetic genealogy test?” - Correct answer: Many things have happened in the last 100,000 years) to 97% correctly answered (”Genetic genealogy is a scam, created by big business to capitalize on consumer ignorance” - Correct answer: False). For some of these, the incorrect answers were probably a result of the ‘fun’ element I added to the quiz, such as creative (but less-correct) answers. Each question, however, had an answer that I considered to be the “best” answer.

Prior Research Required?
Only two of the questions had correct answer rates below 80%, and perhaps not surprisingly the questions were directly related. The most problematic question in the quiz, with a correct answer rate of just 46%, was the following: “I can sign up for a genetic genealogy test without doing any prior research.” The answers were:

  • A1. True - heck, I’ve been doing genealogy for years.
  • A2. True - after all, I saw it on TV.
  • A3. False - no way! (correct)
  • A4. Why would I have to research genetic genealogy?

Although the service I used did not track which answers were selected, I have a feeling that many individuals chose “A1″ rather than the correct answer of “A3″, under the assumption that experience with genealogy prepares an individual for genetic genealogy. However, the fact that a genealogist has been doing research for years does not mean that they should undergo genetic testing without prior research. The other incorrect answers, “A2″ and “A4″ are also problematic in that they suggest that either (1) TV reporting/coverage provides enough background information to fully inform an individual about genetic testing, or (2) that no research is needed for genetic genealogy.

Health Information Revealed?
The need for research before genetic testing is evident from the second-most frequently missed question, with 26% answering incorrectly, which states: “The results of a genetic genealogy test might reveal health information about me.” The answers were:

  • A1. True! (correct)
  • A2. False!
  • A3. My DNA knows exactly how much I weigh.
  • A4. Genetics has nothing to do with my health information.

Again, I am uncertain which incorrect answers were chosen, but “A2″ and “A4″ are essentially the same answer and suggest that there is no connection between a genetic genealogy test and genetic disease or health. “A3″ is one of the ‘other’ elements I mentioned in the introduction (and my sorry attempt at humor!).

A total of 1 out of 4 individuals was unaware that a genetic genealogy test can reveal medical information. I have previously highlighted this problem here at TGG, and I included it in both my eBooks (see the sidebar). Many people are unaware, for example, that a Y-DNA test, provided by some of the major genetic genealogy testing firms, can reveal male sterility. Additionally, a full mtDNA sequence can reveal any one of a number of metabolic or other genetic disorders. Although the percentage of these results is extremely low and I don’t think this should discourage people from genetic genealogy, I do believe that people MUST be aware of the possibilities BEFORE swabbing their cheeks.

Today I received the following comment: “This quiz fails to distinguish between facts - you can get a test done without doing any research - and values - you should do some research first. Poor.” I have to admit that receiving this comment stung a little, but then I realized that the author of this comment served to perfectly reinforce the results of the quiz. A genetic genealogy test is a genetic test. Although it is not meant to detect genetic disease or reveal other secrets contained within the genome (such as adoption and illegitimacy), it is fully capable of doing so. As with ANY type of genetic testing, the tested individual must be aware of the possible outcomes before consenting to the test. Educating individuals about the possible outcomes of genetic genealogy is just one of the goals of the Genetic Genealogist. I have a feeling that my regular readers were among those that answered these difficult questions correctly.

Thank you to everyone who took the quiz or wrote about it on their blog or newsletter. I hope you enjoyed taking it, and I hope you’ll consider taking future quizzes. To stay up-to-date on the latest in news and information about genetic genealogy and personal genomics, subscribe to my feed.

CSIRO unveils a new class of fatty acids [Think Gene]

Posted: 30 Apr 2008 01:37 AM CDT

CSIRO Entomology business manager, Cameron Begley, said researchers believed the discovery opened up an entirely new class of chemistry. "Some of these alpha-hydroxy polyacetylenic fatty acids act as indicators for a range of different conditions, such as mechanical stress or heat, and display self-assembling properties. Others display anti-microbial properties," he said. Australian scientists working within the Crop [...]

Scientists at Yale provide explanation for how cancer spreads [Think Gene]

Posted: 30 Apr 2008 01:35 AM CDT

Metastasis, the spread of cancer throughout the body, can be explained by the fusion of a cancer cell with a white blood cell in the original tumor, according to Yale School of Medicine researchers, who say that this single event can set the stage for cancer's migration to other parts of the body. Their work was [...]

Hyperviscous fluids: Better treatment for severe blood loss [Think Gene]

Posted: 30 Apr 2008 01:19 AM CDT

Intravenous administration of isotonic fluids is the standard emergency treatment in the U.S. for patients with severe blood loss, but UC San Diego bioengineering researchers have reported improved resuscitation with a radically different approach. Building on earlier studies in humans that have shown benefits of intravenous fluids that are eight times saltier than normal saline, [...]

Biomarkers identified for idiopathic pulmonary fibrosis [Think Gene]

Posted: 30 Apr 2008 01:18 AM CDT

The first evidence of a distinctive protein signature that could help to transform the diagnosis and improve the monitoring of the devastating lung disease idiopathic pulmonary fibrosis (IPF) is being reported by University of Pittsburgh School of Medicine researchers in this month's edition of PLoS Medicine, an open-access journal of the Public Library of Science. In [...]

Brookhaven scientists explore brain’s reaction to potent hallucinogen, salvia divinorum [Think Gene]

Posted: 30 Apr 2008 01:17 AM CDT

Brain-imaging studies performed in animals at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory provide researchers with clues about why an increasingly popular recreational drug that causes hallucinations and motor-function impairment in humans is abused. Using trace amounts of Salvia divinorum – also known as "salvia," a Mexican mint plant that can be smoked [...]

A missed creative science opportunity? [Omics! Omics!]

Posted: 29 Apr 2008 10:42 PM CDT

Either Science or Nature (I can't find the item now) had a blurb noting that a Chilean observatory will play a prominent role in an upcoming James Bond movie -- the hideout of the villain (original press release here). A bit later in the item it is mentioned that the observatory will basically be simply compensated for its costs.

Given the state of public science funding, it's too bad they didn't extort something more. This isn't somebody's production-costs-charged-to-my-personal-Visa indie film, but 007 himself. Budget never seems to matter much in those films, so why not extract a bit of cash?

The movie is at least titled 'Quantum of Solace', so maybe that's some science there. If the observatory could have held out a bit longer, perhaps they could have gotten something better. Imagine, for instance, the effect on interesting young males in science if Bond's love interest was an astronomer, with a requisite seduction scene taking place around a telescope! Imagine the classic Bondian double entendre opportunities!

Ah well, perhaps it's just jealousy. Nobody builds funky buildings for biologists in stunningly scenic locations (the Salk Institute perhaps excepted). Q's gadgets haven't yet involved synthetic biology (I suppose it doesn't film well) -- alas, no devices made from codons.

Is this a blog or a column? Yes! [T Ryan Gregory's column]

Posted: 29 Apr 2008 09:57 PM CDT

Well, the move to the new site has gone ok, though it seems some old readers are a bit unhappy. All I can say is that the site is a work in progress and that some exciting changes are in the works.