Thursday, September 4, 2008

The DNA Network

The DNA Network

Science Faux Pas Example #1: 97% of internet users have internet access [The Tree of Life]

Posted: 04 Sep 2008 07:57 PM CDT

I am starting a new series here on Science Faux Pas.  Here is one of my favorites from Nature a while back.  They report in this promotion that 97% of Nature's readers have internet access.  How did they determine this? By an online readers survey.  The real question is - who are the 3% that completed the survey but said they did not have internet access?

I am going to try and make a collection of these over time so if you have any or can point to some out there please let me know.  It may not be as fun as Carl Zimmer's tattoo series, but there are some doozies out there.

Michael Shermer on Why Numbers and Gut Feelings Don't Mix [adaptivecomplexity's column]

Posted: 04 Sep 2008 04:12 PM CDT

Early Cancer Detection: Dogs with frickin' laser beams [Bayblab]

Posted: 04 Sep 2008 02:35 PM CDT

You may recall from several years ago, reports of dogs who could sniff out cancer. Based on odour, trained dogs could distinguish urine from bladder cancer patients from controls at a better-than-chance rate (mean success rate of 41% vs. 14% expected by chance alone in this study).

Since then, more canine cancer detection experiments have been done. In 2006, this double-blind study showed that ordinary household dogs could be trained to identify breast- and lung-cancer patients with incredible accuracy (88% and 99% respectively) and specificity (98% and 99% respectively) compared to conventional diagnosis and biopsy confirmation, based on breath scent. The dogs were able to 'diagnose' both early- and late-stage cancers.

Fast forward to 2008. While a Korean company is cloning cancer-sniffing dogs, a group at the University of Oklahoma - intrigued by the dogs, and having already published proof of concept to identify volatile compounds in breath - announced a project to develop a tool for laser-based detection of cancer biomarkers. The goal is to eventually develop an 'electronic nose' for rapid, accurate, non-invasive cancer diagnosis.
According to McCann, "Improved methods to detect molecules have been demonstrated, and more people need to be using these methods to detect molecules given off from cancer. We have developed laser-based methods to detect molecules. Mid-infrared lasers can measure suspected cancer biomarkers—ethane, formaldehyde and acetaldehyde." McCann will use nanotechnology to improve laser performance and shrink laser systems, which would allow battery-powered operation of a handheld sensor device.
Because of the importance of early detection, this device - if sensitive enough to detect early-stage cancers with a simple breath test - could have major implications for survival rates. Unfortunately right now it's just a press release and, as pointed out in the release, an actual product is 5-10 years away, but in the meantime more biomarkers can be investigated and more cancers can be screened as candidates for laser-based diagnosis. As McCann states, "the science supports it, and the dogs tell us there is something there."

Walk like an Egyptian…metabolize like an Asian? []

Posted: 04 Sep 2008 02:19 PM CDT

If you give Watson a drug for Caucasians and he metabolizes it like an Asian, you won’t help him, and you might hurt him. You also owe him the courtesy of seeing and treating him as an individual. The most important difference between him and you is technological and economic, not hereditary: His genome has been sequenced. Now for the rest of us.

Will Saletan on race, genes and the future of medicine.

Medicine 2.0 with the eye of a medical student blogger [ScienceRoll]

Posted: 04 Sep 2008 01:35 PM CDT

This is the slideshow I gave at the Medicine 2.0 Congress in the Medical Bloggers’ Panel.

Help save the world and get $100,000 seed grant to do it [The Tree of Life]

Posted: 04 Sep 2008 01:21 PM CDT

Just got this email and thought I would share since it does relate to some of the themes of my blog. I note that the Gates Foundation is VERY supportive of Open Access publishing as one of their previous grants helped support the journal "PLoS Neglected Tropical Diseases." I am hoping that at some point the Gatges Foundation will require OA publishing for all of the projects they fund.
The Bill & Melinda Gates Foundation is now accepting grant proposals for Round 2 of Grand Challenges Explorations, a US$100 million initiative to encourage unconventional global health solutions.

Based on your feedback, we have made changes for Round 2 of Grand Challenges Explorations. We modified the topics from Round 1 and added two additional topics. We will no longer require applicants to register for a topic in advance of submitting their proposals. We also updated the application form in response to feedback from the initial round.

Grant proposals are being accepted online at until November 2, 2008, on the following topics:

New! -- Create new vaccines for diarrhea, HIV, malaria, pneumonia, and tuberculosis
New! -- Create new tools to accelerate the eradication of malaria
-- Create new ways to protect against infectious diseases
-- Create drugs or delivery systems that limit the emergence of resistance
-- Create new ways to prevent or cure HIV infection
-- Explore the basis for latency in tuberculosis

Initial grants will be $100,000 each, and projects showing promise will have the opportunity to receive additional funding of $1 million or more. Full descriptions of the new topics and application instructions are available at

We are looking forward to receiving innovative ideas from scientists around the world and from all scientific disciplines. Anyone can apply, regardless of education or experience level. If you don't submit a proposal yourself, we hope you will forward this message to someone else who might be interested.

Thank you for your commitment to solving the world's greatest health challenges.

While we are waiting for costs of sequencing to drop [Next Generation Sequencing]

Posted: 04 Sep 2008 01:11 PM CDT

With the advent of NGS technologies it is now possible for any lab to re-sequence a human genome in a few weeks. Possible, yes, but still to expensive to do it routinely. For this reason array capture technologies have emerged which selectively capture pre-selected regions of the genome e.g. all known coding regions. Today the company Olink [...]

10 Things about GE crops to Scratch From Your Worry List [Tomorrow's Table]

Posted: 04 Sep 2008 01:07 PM CDT

As New York Times columnist John Tierney points out in a recent article, many consumers worry about things that are not actually a threat to human health or to the environment. This is especially true in the case of food, farming and genetic engineering. While there are plenty of issues to debate (how can we make the best seed available to farmers that need it; how can we conserve land, how can we have productive farms without harming the environment), there are some scientific facts that have not yet seeped into the public consciousness.

With September upon us, perhaps you're in the mood for a break, so I've rounded up a list of 10 things not to worry about this fall. You can make your own nominations on this blog.

1. GE crops require more pesticides

Two classes of pesticides are affected by GE crops: Herbicides that kill weeds and insecticides that kill insects.

There is now clear and ample evidence that BT crops have reduced the use of insecticides- here and abroad. In China, cotton farmers were able to eliminate 150 million pounds of insecticide in a single year by using GE varieties. For comparison, in California, we spray 190 million pounds each year. Although BT-cotton in China has been dramatically effective in reducing pesticide use, after 7 years some farmers started spraying again to control secondary insect pests that are not controlled by Bt. This points to the need to integrate GE crops into organic farming systems that also use crop rotation and beneficial insects to control secondary pests.

In India a huge proportion of the farming expenses are going to insecticides. Although GE seed are more expensive, the yields are 80% higher and the farmer saves on insecticide costs.

In the US, pesticide use on corn, soybeans, and cotton declined by about 2.5 million pounds in the United States since the introduction of GE crops in 1996 (Fernandez-Cornejo and Caswell 2006).

In the case of herbicides applications, usage per acre has declined since the advent of herbicide-resistant crops (Fernandez-Cornejo and Caswell 2006), and because glyphosate breaks down quickly in the environment, the overall net effect is a reduction in the toxicity of herbicides used. For example, conventional soybean growers used to apply the more toxic herbicide metolachlor to control weeds of soybeans despite the fact that metolachlor is a known groundwater contaminant and is included in a class of herbicides with suspected toxicological problems. Switching from metolachlor to glyphosate in soybean production has had huge environmental benefits not measured in pounds of active ingredient but in environmental impact (Fernandez-Cornejo and McBride 2002). Another agricultural benefit is that herbicide-resistant soybean has helped foster use of low-till and no-till agriculture, which leaves the fertile topsoil intact and protects it from being removed by wind or rain. Also, because tractor-tilling is minimized, less fuel is consumed and greenhouse gas emissions are reduced (Farrell et al. 2006).

2. Corporate control of GE seeds forces poor farmers to buy seed each year

Most conventional and organic farmers in California already buy their seed. Farmers choose to buy hybrid seed and other improved seed because they are higher yielding.

Although the US seed industry is dominated by large corporations, this was the case before GE came into play. In less developed countries, such as China and Bangladesh, national breeding programs distribute seed for free because farmers cannot afford to buy the seed. That means that improved seed (transgenic or otherwise) are given freely to farmers who can then self their own seed. For example a flood-tolerant gene cloned in my lab and used to develope new varieties in collaboration with colleagues has been distributed free to Bangladeshi farmers.

3. If we could just distribute the food available, impoverished people would not need GE seed.

Many rural poor in Africa and S. Asia cannot afford to buy food. They must grow their own. Rather than relying on shipments from abroad, they need help improving their own production practices. This includes access to improved seed, farming practices and sound government policies. Now that is something we do need to worry about.

In China, there are proven health benefits to families because of the reduction in pesticide use after the introduction of GE crops. A recent analysis predicts that the lives of thousands of children will be saved once golden rice is launched in 2011.

4. We don't need GE to improve seed, we can use marker-assisted breeding.

Marker assisted breeding is a hybrid of conventional breeding and GE that relies on modern genetic techniques to modify seed. Flood tolerant rice, developed through marker assisted breeding, has the potential assist 75 million farmers who live on less than a dollar a day in major flood zones in places like Myanmar, Bangladesh, and India.

There are other agricultural problems, however, that cannot be addressed using marker-assisted breeding. For example, in the 1990s, papaya orchards on the island of Hawaii were threatened by papaya ring spot virus. Dennis Gonsalves, a former plant virologist at Cornell who is now with the U.S. Department of Agriculture, developed a genetically engineered papaya variety that was completely resistant to the virus. The GE papaya yielded 20 times more than the conventional variety was was distributed freely to growers. It's a great example of genetic engineering benefiting local farmers. There was no other tool available to combat papaya ringspot virus, nor is there now.

5. GE crops harm human health.

There is virtually universal scientific consensus that GE crops currently on the market are safe to eat. After over 10 years of consumption there has not been a single validated report of negative health effects from any GE crop. In contrast every year there are thousands of reported pesticide poisonings (ca. 1200 each year in California alone).

Every new GE crop must be evaluated on a case-by-case basis. Lets direct our efforts to generating new crop varieties that will benefit the maximum number of people.

6. GE crops harm the environment

GE crops themselves have had no negative environmental effects after over 1 billion acres have been planted.

The rising problem of herbicide resistant weeds and its consequences, for example, are a significant environmental (and practical) problem. But this is a problem anytime an herbicide is used extensively and is not an environmental consequence of the GE crop itself. The same result would occur if the crop is GE or non-GE (and many such herbicide tolerant non-GE crops have been generated).

Like non-GE crops, GE crops produce pollen. Thus pollen flow from GE crops poses essentially the same risks as non-GE crops. There is no example of a domesticated crops escaping into the wild and wreaking environmental harm. This is because they are highly domesticated and need a farmers care to survive. As Freeman Dyson once said, "Have you seen any wild poodles lately?"

A positive spin off of the whole GE debate is that now there is more attention being placed on the ecological effects of pollen flow from domesticated crops to wild populations.

7. GE crops reduce biological diversity

Bt has had some real benefits in reducing chemical insecticide use and in enhancing insect biodiversity. The recent analysis by Cattaneo et al (2005) clearly shows that there is similar biodiversity (ants and beetles) in GE cotton fields vs non-GE cotton fields. In contrast, broad-spectrum insecticides (which are used on the vast majority of non-GE cotton fields throughout the world) significantly reduces ant and beetle species richness.

If we hadn't genetically modified our crops by conventional methods over the last 50 years, we would be using twice as much of the Earth's surface to grow the same amount of food. In the future, if we don't increase yields, we'll need to use double the amount of land to produce the same amount of food. Sparing land from becoming farmland, is the greatest benefit to biodiversity. For this reason, some ecologists see the application of GE as a way to spare even more land from destruction by enhancing yields (Qaim and Zilberman 2003; Snow et al. 2005).

8. The regulation of GE crops is lax.

GE crops are more stringently regulated than other crops. That is, other crops are not regulated at all. Hundreds of thousands of children are dying each year because of vitamin A deficiency, thousands more are poisoned with pesticides, more land is being put into production every year, which negatively affects global warming. In contrast there has not been a single case of harm from GE crops to human health or the environment, even after over 1 billion acres grown. Their is broad scientific consensus that the GE crops currently on the market are safe for human health and the environment.

9. Organic agriculture has solved all agricultural problems. We don't need GE.

Organic farming seeks to maximize the health of the environment, the farmer, and the consumer. Organic farming came about as a response to the environmental and health problems associated with overuse of chemicals on conventional farms. Genetic engineering has contributed to this goal by reducing pesticide use (see #1). There are certain environmental or disease problems with no organic or conventional solution. There's nothing to make plants resistant to certain viruses, for example. Flood, drought, frost and salt tolerance have also been developed through GE and are now being tested.

10. We have already seen what is scientifically possible and it is not impressive.

Every time a GE crop has been approved, farmers have embraced it and the GE acreage for each crop has quickly grown to 50 to 90 percent of the total acreage.
To date most of the GE production is soybeans, corn, and cotton carrying two traits (herbicide tolerance and insect resistance). With unprecedented discoveries in genetics, many more traits are in the pipeline.

Medicine 2.0 Congress: Backchannel [ScienceRoll]

Posted: 04 Sep 2008 12:50 PM CDT

We are attending the Medicine 2.0 Congress in Toronto and you can follow us through the backchannel.

1) Twitter

2) Blogs:

3) Flickr

It was much more stressful to moderate a panel than to give my own presentation. I had only 8 minutes to finish but it went ok. I will publish the slides here soon.

(I will update this post as soon as I can.)

A photo from Maarten

The blogger panel from right to the left: Keith Kaplan, Sam Solomon, Jen McCabe Gorman, Peter J Murray and myself.

A beetle is a beetle is a beetle, right? [Genome Blog]

Posted: 04 Sep 2008 11:00 AM CDT

A beetle is a beetle is a beetle right? Not to a population biologist. This current epidemic contains millions of mountain pine beetles (MPB) spread across both Alberta and BC. Once beetles take flight each year in search of new trees, where do they go? Who is moving where? Is there anything different about beetles in different areas? These questions may prove crucial to our understanding of this and future outbreaks. However, before we can ask in depth questions we need a basic understanding of current beetle populations. Since we can’t just ask beetles these questions, we’re lucky that genomics offers tools which can help.

Personalized Therapeutics at IU [PredictER Blog]

Posted: 04 Sep 2008 10:43 AM CDT

In August 2008, the Indiana University Department of Medicine's Division of Clinical Pharmacology began a new series of compelling seminars that may be of great interest to those involved in predictive health research ethics. The Personalized Therapeutics Seminar series commenced on August 5th with a presentation on the FDA's Sentinel System for Post-market Drug Safety Surveillance given by Barbara Evans, J.D., Ph.D. from the Health Law and Policy Institute at the University of Houston Law Center. Additional speakers this fall, all from the Indiana University School of Medicine, have included Dr. Noah Hahn presenting on the Indiana University Cancer Biomarker Study, Dr. David Haas addressing PREGMED and the search for individualized pharmacotherapy in pregnancy, Dr. Zeruesenay speaking about emerging in vivo phenotyping methods and Dr. Tatiana Foroud addressing the results of whole genome association studies and how they may change our approach to medicine. The next seminar, entitled Personalized Therapeutics in Breast Cancer: A Model for Translating Pharmacogenomics, will be presented Dr. David Flockhart, Chief of the Division of Clinical Pharmacology, on September 9th. All seminars in this series are held on Tuesdays from 12:00pm – 1:00pm, in room W7120 on the 7th floor of the Wishard Myers Building.

For a complete schedule, please see:

Amy Lewis Gilbert

Dark box? Black box? [Reportergene]

Posted: 04 Sep 2008 09:21 AM CDT

I have been gone through a 2007 interview to Mark Roskey (vice president of reagents and applied biology at Caliper Life Sciences) appeared in Nature Methods. According to Roskey:
It should be one box that researchers put sample in and get an answer out.
Mark, are you talking about PhD students?

The Ends Justify the DNA [FinchTalk]

Posted: 04 Sep 2008 07:59 AM CDT

In Next Gen experiments, libraries of DNA fragments are created in different ways, from different samples, and sequenced in a massively parallel format. The preparation of libraries is a key step in...

Medicine 2.0 Congress: Live [ScienceRoll]

Posted: 04 Sep 2008 05:28 AM CDT

I’m currently attending the Medicine 2.0 Congress in Toronto. I will give two presentations today and will try to moderate the Medical Bloggers’ Panel as well. Fingers crossed. The slideshows will be uploaded soon.

I will Twit and blog about the whole event so stay tuned for more!

Coping With a Quarter Life Crisis [Bitesize Bio]

Posted: 04 Sep 2008 04:22 AM CDT

7+ years’ training-a batchelor’s and a PhD-and for what? Starting at the bottom in a profession that offers repetitive work, poor pay, long hours and frustratingly hard-to-come-by successes. And to make it worse, you can’t afford a decent apartment, your standard of living is low and your relationship is suffering.

Sound familiar?

If so, then you may be suffering from a quarter-life-crisis, a phenomenon that is being increasingly recognized by psychologists.

Like it’s more established cousin, the mid-life-crisis, a quarter-life crisis is about adjusting to a major life transition.

But instead of being all about the feeling of youth slipping away, which we all know is easily cured by getting a tattoo and buying a fast car, the quarter life crisis is about dealing with the transition from being an aspiration-filled youth to a twenty-something experiencing the mundane reality of everyday working life.

Bioscientists, are particularly prone to the quarter-life-crisis because they normally spend a prolonged time in education. In this bubble, life is filled with a heady mix of pursuing a passion for science, camaraderie amongst peers and continuous positive feedback from educators. This, of course, contrasts starkly with the real working world so when the time comes to transition to a job, the bump to earth can be hard.

In a saturated job market, (post)-graduates are likely to find themselves unemployed, under-employed and/or poorly paid. Of course, this leads to disillusionment; the feeling that all of that hard work was for nothing. This can be compounded by the financial pressures that come with trying to maintain a decent standard of living and pay off college loans on a small salary.

And to top it all… having to come to the same place, to do the same job EVERY day? With no summer break?? That’s just like being a cog in a wheel!

When reality bites, it bites very hard indeed.

So if you are suffering from a quarter-life crisis - where do you turn? Well, there are several good books that can help you through. Try Quarterlife Crisis: The Unique Challenges of Life in Your Twenties and Managing the Quarterlife Crisis, for instance. You could also visit, which is packed with useful advice and information that could help, and probably more importantly, is a place where you can talk to fellow “sufferers”.

Of course, you may have identified with the opening paragraph of this article even though you have been out of college for many a year. In that case I would say that you are just suffering from “being a scientist”, for which there is no cure! :)

Interview with Forensic Genealogist Colleen Fitzpatrick, Ph.D. Part II [The Genetic Genealogist]

Posted: 04 Sep 2008 02:00 AM CDT


Yesterday I posted the first part of a two-part interview with Colleen Fitpatrick, a forensic genealogist.  In that interview, we discussed Colleen’s participation in a project to identify the remains located at a military crash site from 1948.

Today, we discuss her work on identifying the Titanic’s Unknown Child, among other projects.

The Genetic Genealogist:  On April 17, 1912, two days after the RMS Titanic sank in the North Atlantic, the salvage vessel Mackay Bennett discovered the body of a young boy. The sailors paid for a monument, and the boy was buried in Fairview Lawn Cemetery in Halifax, Nova Scotia. In 2008, after an initial false identification based on dental records, the boy was identified as Sidney Leslie Goodwin. You were part of the team that identified Sidney. Can you tell us about that experience?

Colleen Fitzpatrick: In my opinion, working with the Armed Forces DNA Identification Laboratory is the most compelling job that a genealogist can have. Our scientists and genealogists are dedicated to their research, willing to go the extra mile to get results.  It is thrilling to me to be in on the development of cutting edge technology that has the potential to solve the highest profile genealogical mysteries in the world.

image The case of the Unknown Child on the Titanic has found a niche in genealogical history. In 1912, the only clues for identifying the child were at best primitive observations (see the 1912 vintage information used to attempt an identification for the Unknown Child on the Titanic to the left) He was a male about two years old, wearing a grey coat with a brown serge frock and shoes. There was nothing out of the ordinary that might identify him as someone's relative or friend.

Almost a century later, however, our team used amazing new techniques that reached into the scraps of what was left of his body to read genetic information encoding his identity. We also had advanced knowledge about forensic dentistry at our disposal. With only three tiny teeth to work with that had survived the damp soil and acid rain of Nova Scotia for nearly a hundred years, we had all the tools we needed to restore the child's identity to him. Sidney Leslie Goodwin is again a person, who can now speak for the dozens of children who have never been able to tell us their own stories.

And the rest is history……

TGG:  Although you identified one of Sidney’s distant male relatives for Y-DNA testing, the article suggests that the test was halted because the mtDNA test identified the boy. Did the Y-DNA test ever proceed?

image CF:  When the mitochondrial DNA match was made between the remains and the Goodwin family, we no longer needed to make a Y-DNA comparison.  This was a good thing.  Y-DNA degrades rapidly, and there is only one Y-chromosome per cell.  So our chances of harvesting enough of the right kind of Y-DNA to make an identification were low.  But if we were not able to find a match using mtDNA, our only hope was to resort to using Y-DNA even if we had only a slim chance of success. Fortunately, a Y-comparison was not necessary.

My Y-DNA research was important, however, because it reunited long lost Goodwin family members from Australia and New Zealand with their English and American cousins. Each of the Goodwins had a piece of their family story to share that created a more complete picture of the family tragedy. To thank me for my efforts on their behalf, the family invited me as an honorary Goodwin to the memorial they held in Halifax on August 6 for Sidney and his family.

TGG:  You recently published a new book entitled “The Dead Horse Investigation” about a recent project to identify the date of a famous photograph. Can you tell us a little more about the book?

clip_image012CF:  “The Dead Horse Investigation: Forensic Photo Analysis for Everyone” is all about identifying old photos. (See The name is taken from a picture that was published in the Sheboygan Daily Press a couple of years ago. It depicts a man in top hat and tails sitting on a dead horse lying at the intersection of Griffith and Indiana Avenues in Sheboygan, WI. Using every trick in the book, we were able to pin down when the photo was taken to only a handful of days in the 1870s. The only things we could not figure out were the name of the man and name of the horse.

The book contains many new ideas on how to find the who, what, when, and why of a photo, along with cases studies on how many of these ideas have been applied. The only thing the book does not cover is how to extract DNA from a photograph. We haven't figured out how to do that yet.

TGG:  Colleen, thank you very much for providing this information and doing this interview!

Quick Post - Spore Sounds Cool [The Tree of Life]

Posted: 04 Sep 2008 01:50 AM CDT

Nothing conclusive here. I have not tried it yet. But Spore sure sounds like a cool evolution game to play. See Carl Zimmer's NY Times article and his blog for more.

Nano-fications [business|bytes|genes|molecules]

Posted: 04 Sep 2008 01:23 AM CDT

NanotubesImage by St Stev via Flickr Over the last 14 years, I have flirted with nanotechnology at three different times; during my Masters in India, during the initial part of my PhD, and a couple of years ago when I was trying to figure out software solutions for nanomedicine. Each time, I have walked away feeling strangely unsatisfied. I have always found nanotech fascinating, still do. It’s incredibly cool and geeky. I have seen some wonderful examples of the success of nanotech, and the promise, and have friends actively involved in the field, but reading an article in Tech Review on nanotubes for drug delivery brought back some of those old feelings of dissatisfaction.

Why? Well, when I saw the post, I thought I had found an old article from 2006. There just seems to be a lot of proofs of concept and research projects out there, but I just don’t see the progress, that one event (or series of events) that makes some of that promise become reality.

In electronics, in some areas of materials science, nanotech is going to play a big role in the future. I’d like to think that it will be critical in the next generation of analytical measurement in the life sciences, and very likely in drug delivery as well, although I don’t think it will be with carbon nanotubes. Thinking back, I believe there are two aspects that have contribution to my occasional frustration with the field. The first is to do with the broad swathe that people put on the field by calling it an industry and funding “nanotechnology”. There is no such thing as a nanotechnology industry. It is a field of science and engineering, with a number different applications. The second is a long standing irritation with people applying the “nano” label to things which don’t really fit that label, e.g. I’ve heard people call protein folding nanotechnology and you don’t want to be near me when someone says that, or be prepared for a stern talking to :)

So, here’s my question to you. Where do you stand on the promise of nanotech? Do you have the kind of high expectations I do? Do you share some of my frustrations?

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