DeCode Genetics: Genomics Studies In Iceland Precipitate Legal and Ethical Problems

The company deCode Genetics announced a number of discoveries this spring after analyzing thousands of human genomes, or complete DNA sequences, from the people of Iceland.  The company, bought in January 2015 by the Chinese company, WuXi Pharma Tech, is helping to usher in the Age of Genomics (click on the underlined word to view the link ), where precision medicine  attuned to patient genetic makeup will be practiced.  In other words, if your DNA is sequenced and you have a G here and a T over there, then your doctor can diagnose and hopefully treat you early for a given disease with a genetic component. Furthermore, if your DNA sequence and genetic risks are known, it’s easy to identify your relatives who may also be at risk for the same disease.  This is especially important where early diagnosis can affect quality of life or even survival, as in the case of hereditary breast cancer.  Other diseases reported on by deCode Genetics include dyslexia, schizophrenia, Alzheimer’s disease, and cardiovascular disease, among others (look here for publications). 
 

What is the DeCode Genetics study, what are the issues, and how do these issues concern you?  Read on to find out!

Figure 1. Drawing of DNA. Source: https://www.genome.gov/about-genomics

The Power of Ice(land)

The overall goals of deCode Genetics are to use population genomics to find common disease genes and then to use this information to help develop drugs for treatment of the diseases. To that end, DeCode sequenced the entire genomes of 2,636 Icelanders and also performed SNP analysis of 101,584 more.

In layman's terms, DNA sequencing of the entire genome,  down to almost the last A, T, G and C, is like watching a movie forwards and backwards in order to understand every frame.  Scientists at Decode “watched” the “movies” 20 times to make sure there were no errors in the DNA sequences they deciphered.  For all you DNA aficionados out there, both strands of all 46 chromosomes were sequenced.

SNP analysis, or single nucleotide polymorphism analysis, is like taking a snapshot of a movie at specified times in order to get a general idea of the “movie” or DNA sequence.  Scientists can even target analysis to specific “scenes” or genes.   

The people of Iceland were studied because the population is small, with about 270,000 people in 1997 at the beginning of the study (look here for population data).  Also, the people of Iceland have  a genealogy that is well studied with some family trees drawn back to about 900 A.D., when the country was founded.  Finally, the people of Iceland have national health care and medical records are readily available. All this data on so high a percentage of the population makes it easy to correlate mutations , or changes in the DNA sequence, with specific diseases. Moreover, if you have the family tree data, you can start with the data you know and you can infer what the genes and the disease risks of relatives are without actually having to sequence their DNA, in a process called imputation. 

Lawsuit Freezes the National Health Sector Database

The company DeCode was founded in 1996 and in 1998, the Icelandic Parliament passed the Health Sector Database Act, which allowed for the construction of three Icelandic databases for research. These included a genetic database, a genealogical one and one based on medical records.  By 2000, DeCode Genetics was licensed to construct the Health Sector Database (HSD) from the national health records. “Presumed consent “ was given for the genetic and genealogical databases, which meant it was assumed that everyone in Iceland would give consent.  However, there was an opt-out provision for people who did not want their medical records to enter the third database, the HSD. Many people had high hopes for the study bringing pharmaceutical money into Iceland. Eventually, though, 7% of the Icelanders opted out of the HSD due to privacy concerns. 

photo of worker with medical records, http://en.wikipedia.org/wiki/Medical_record

Subsequent laws eroded the HSD opt-out provision and in a 2001 lawsuit filed on behalf of Ragnhildur Guomundsdottir, a minor, by her mother asked the lower courts to uphold the girl’s right to opt-out of turning over the health records of her dead father to the HSD.  The case went through the courts until finally the Icelandic Supreme Court ruled in 2002 that the rights of the girl to opt-out of giving her dead father’s medical records to the HSD were protected. The ruling stated that genetic testing may affect people other than the one being tested and thus the girl’s right to privacy must be protected by protecting the privacy of her dead father’s medical records. You can read an analysis of the case here. This lawsuit effectively stopped construction of the HSD .

DeCode Genetics Frozen Out of Contacting Potential Cancer Patients

Fast forward to 2015.  If scientists at DeCode Genetics know either by direct evidence or by imputation that a person carries or has a high risk of carrying a mutation that can cause a preventable death, do they have an obligation to inform the person? Many would say yes, but the initial DeCode Genetics studies were begun with the promise that participants’ identity would never be revealed and the participants would never be contacted. This creates a dilemma where the company must chose between acting with moral conscience and contacting affected people or following medical ethics and not contacting them.

For example, scientists at DeCode have said that it would be possible to identify up to about 2,000 individuals who have inherited BRCA2, which greatly increases risk of cancer to the women and men who inherit it.  Early warning would allow affected women the opportunity to chose between careful monitoring for development of cancers and prophylactic removal of their breasts and/or ovaries in order to decrease the chance of getting and dying from cancer.  You can read more here to learn about DeCode's dilemma and here to learn about choices for women and men if they have inherited either BRCA1 or 2.  You can also read here about Angelina Jolie’s recent decision to undergo prophylactic  double mastectomy due to having inherited BRCA1, which is another inherited breast cancer mutation. The Icelandic Ministry of Welfare has convened a special committee to determine what to do in the case of deCode having important medical information that they cannot ethically reveal.  

What do you think deCode should do? Should they contact those people with genetic diseases for which there is a treatment or cure even though it is against medical ethics? Or, should they wait until the law is changed and then contact the affected people?  Or, should they allow residents of Iceland to opt-in if they wish to learn of diseases which may affect them?  

A Family Tree from http://ghr.nlm.nih.gov/handbook/inheritance/runsinfamily

President Obama Rolls Out Precision Medicine Initiative

If you’re wondering if genomics research and precision medicine will ever come to the United States, the answer is yes.  In fact, it’s already here and patients with cancer often undergo genetic tests to determine which treatments will best improve their chances of survival with minimal side effects.  

In January of 2015, President Obama in his State of the Union address requested $215 million dollars for the Precision Medicine Initiative to collect genomic data from 1,000,000 Americans with the hope of nudging the field of personalized medicine along.  The budget includes $130 million to the National Institutes of Health to collect the data, $70 million to the National Cancer Institute to advance cancer genomic studies, $10 million to the Food and Drug administration to work on the databases, and $5 million to the Office of National Coordinator to work on privacy issues.  You can read more here and here. 

Population genomics and precision medicine are the future of medicine and you’ll be reading a lot more about them in the future.  Careful consideration of the ethical and legal issues must be made in the U.S. and elsewhere in order to avoid some of the common pitfalls.

Green St. Paddy’s Day Dinner and Workout: Good for You, Good for the Planet

Green St. Paddy’s Day Dinner and Workout:

Good for You, Good for the Planet

It’s St. Patrick’s Day today and the color of the day is green! If you’re like me, you probably want to eat a delicious dinner and work in a good workout while still managing to be "green" (click on the link to find out more.)  Check out my St. Patrick Day plans below to make a "green" dinner that's locally-sourced and to visit a "green"gym that's LEED certified.  Although almost everything's green today, I'll definitely be skipping the green beer!

Veg Out This St. Paddy’s Day

Tired of corned beef, cabbage and potatoes for St. Paddy’s Day? In this tasty version of a Reuben sandwich, the corned beef is replaced by tempeh (click on the link to find out more) and the bread is replaced by potatoes, making this dish both vegetarian and gluten-free.   Because most of the ingredients for this dish are local to Ann Arbor, Michigan, this is a very “green” dish for locavores  near my neck of the woods to prepare! 

Ingredients for the Broiled Tempeh Reuben Casserole

Broiled Tempeh Reuben Casserole 

The recipe is adapted from Eat Clean Live Well, by Terry Walters. The ingredients or ones similar to what's pictured are available at the People's Food Co-op, Busch's, and Whole Foods  in Ann Arbor or a farmer's market or food store near you. 

Russian Dressing

4 T mayo

2 T ketchup

3 T finely chopped sweet gherkins (or sweet pickle relish)

Casserole

2 cups fingerling or baby potatoes

4 T olive oil or more, divided

½ cup onion

1/2 teaspoon caraway seeds

12 ounces tempeh cut into ¼ inch strips

1½ cups sauerkraut, drained

4 ounces shredded regular or vegan Swiss cheese (I use Dairy Fresh from WI with no animal rennet)

salt to taste

1) Broiling is a dry heat method of cooking where the heat is applied by an element at the top of your oven or toaster oven.  The broiler might even be in it’s own oven drawer located below the regular oven.  You will need to use an 8-inch  x 8-inch all-metal pan (like a cast-iron skillet or broiler pan) or a ceramic dish designed for high heat. Don't use Pyrex. For more on broiling try Wikihow or Better Homes and Gardens.

2) Scrub the potatoes in running water and then steam them, covered, in a half inch of water until soft when pricked half way through with a fork.  Cut the potatoes into pieces about 1 inch by 0.5 inch, so halving or quartering the fingerlings should be about right.   Place the potatoes in a broiling dish or pan.  Add a little salt to taste.

3) Peel and thinly slice the onion. Add 1 T of olive oil to a frying pan and sauté on medium high until it turns a brown, about 5 minutes.  Add the caraway seeds until they become fragrant, about a minute.  Spread them over the cooked potatoes.

4) Slice the tempeh evenly into ¼ inch slices.  Add 3 T of olive oil to a frying pan, turn the heat to high and when the oil is fragrant, add the sliced tempeh, browning on both sides. My family likes tempeh best when it is thin and well browned.  Lay the slices in a single layer on top of the potatoes and onions. 

5) Mix together the mayo, ketchup and chopped pickles and spread the dressing on the tempeh.

A serving of Broiled Tempeh Reuben Casserole

6) Drain the sauerkraut and add it to the frying pan on medium heat to warm it though.  Distribute it on top of the tempeh and dressing.

7) Grate the cheese.  Sprinkle it on top of the sauerkraut and broil on high until golden brown.  This serves four, but everyone in your family will want the leftovers for lunch, so make extra!  

Be a LEED-er When You Exercise

Today I visited the Health and Fitness Center at Washtenaw Community College, which is located in a LEED  Gold–certified building.  The acronym "LEED" stands for "Leadership in Energy and Environmental Design" and certification consists of a rating system for the design, construction, maintenance and operation of buildings.  The amazingly friendly staff was wearing green because EVERYONE is Irish on St. Paddy’s Day! 

Staff on St. Patrick's Day at the Health and Fitness Center at WCC

Green is also the color for sustainability and the game at the gym today was to find out in what ways the building is "green."  Members can play by reading the shamrock- bedecked flyers with information that are posted around the gym and winners can earn a discount at the Primo Fitness Café.

 LEED Gold plaque at WCC Fitness Center

Here’s what I found out in the gym (quoted from the flyers),

“The building is at least 20% more efficient than buildings with conventional mechanical systems,” high-efficiency long-life LED lights turn on only when there’s insufficient daylight, “natural light from windows and skylights reduces electricity costs, temperature control is maintained with room monitoring sensors for automatic adjustments, interior wood products including benches an counters are made from recycled materials, and at least 75% of construction waste was diverted from landfills.”

 
In the women’s dressing room I learned, “Dual-flush toilets help reduce water consumption, low-flow faucets conserve water while providing acceptable water pressure, formaldehyde-free carpeting and drywall were used, there is a green cleaning program using green products, and ozone system for laundry sharply reduces demand for hot water and toxic chemicals.”

Near the outside doors, I discovered, “Water retention ponds catch water runoff, permeable parking lot allows rainwater to be absorbed into the ground, sidewalks are made of pervious pavement to allow water drainage, and low maintenance landscaping requires little or no irrigation.”

How cool is that?  The WCC gym is "green" in so many ways!  Driving there, however, is not and you can minimize driving by going with a friend or by combining going to the gym with other errands. Fewer driving trips means lower impact on the environment.

If you don't belong to a gym, or if you want to be super-green, you can always lace up your shoes and go for a walk or a run, right out your own front door!  Or if it's bad weather, you can stay indoors and do the Seven Minute Workout (try the YouTube site for a video or the New York Times blog for an explanation).  Because you have no driving trips at all if you exercise at home, this is the exercise option with the very lowest impact on the environment.

Do make your friends green with envy and enjoy your sustainable St. Paddy’s Day dinner and workout.  It’s good for you and good for the planet!

Notes:
1) The sauerkraut and classic tempeh came from The Brinery (MI).
2) The fingerling potatoes came from Tantre Farms (MI).
3) The Swiss cheese that is free of animal rennet came from Dairy Fresh (WI).
4) Here's another article on the LEED Gold certification of the WCC Fitness Center.
5) Washtenaw Community College offers CON 180, Introduction to Green Building, which includes the topic of LEED certification. Click here for the WCC academic schedule.

Mark Your Maps: Aldo Leopold Weekend in Wisconsin

Mark Your Maps: Aldo Leopold Weekend in Wisconsin

Mark Your Maps …

“To those devoid of imagination a blank place on the map is a useless waste; to others, the most valuable part.”

For all you avid map-readers out there, this quote appears in Aldo Leopold's book, A Sand County Almanac (ASCA, p. 294), first published in 1949. The quote explains Leopold’s view that the wilderness in "the blank place on the map" has immense value even if humans have no roads into it, no ways to extract products or recreational pleasure from it and no lines in the ledger signifying its economic value.  If Leopold were asked, “When a tree falls in the wilderness and there is no one to hear it, will there be a sound?,” he would give a resounding, “YES!”  And he would probably point to a blank place on a Wisconsin map to show you where the tree fell.

Courtesy of the Aldo Leopold Foundation,
www.aldoleopold.org

Aldo Leopold was a wildlife manager, forester, professor and author of the book, A Sand County Almanac.  In it, he conveys the idea of a land ethic in which we humans need to act as responsible members of our biotic communities and manage our ecosystems for the long haul and not just for short-term gain.  Over two million copies of this book have been sold and it's considered one of the finest environmental books ever written.

To honor Leopold’s life and work, each year the state of Wisconsin celebrates (by decree) the Aldo Leopold Weekend during the first full weekend in March.  This year, there will be low-key celebrations at the Aldo Leopold Center in Baraboo, Wisconsin and elsewhere (for events, click here) March 7-8 2015. Activities may include readings from A Sand County Almanac, screenings of the film “Green Fire,” Dutch oven cooking workshops and Aldo Leopold Bench Building workshops (for potential activities click here).  

…But Would You Please Stay On The Path?

If you don’t mind a quick look down this side path with me, Aldo Leopold was concerned about the impact of people, including our roads and recreational activities, on wilderness areas.  He wrote, "Recreational development is a job not of building roads into lovely country, but of building receptivity into the … human mind.” (ASCA p. 295.)  He recommended saving examples of different types of wilderness areas for a variety of purposes, including for low-impact recreation, for scientific study, and for use by wildlife.

Photo of A Sand County Almanac and Wisconsin Recreation Atlas

A recent article in the New York Times takes this idea further, describing the subtle and not-so-subtle harm that people do to animals simply by engaging in recreational activities in wild areas. Wolverines near ski resorts waste precious energy in winter avoiding skiers; birds avoid 100 meters on each side (!) of hiking and cycling paths and rear fewer young as a result; and opening an area in Connecticut to hiking caused a wood turtle species to vanish within 10 years. The article states that the solution may be to restrict human activity to certain times of the day or to certain parts of a natural area in order to best allow animals to live and rear their young.

While wildlife managers are working out their recommendations for making minimal impacts on wildlife, it makes sense when you’re out in nature to control your pets (maybe leashing Lassie?), to pack out what you pack in and to stay on the trail so the wild animals and plants can thrive instead of merely survive.  For ideas on how to help make your outdoor activities low-impact, check the online L.L. Beans guide or the helpful  Wisconsin DNR site.

All Cooped Up in Here

Here’s a little more about naturalist and conservationist Aldo Leopold, who was born in Burlington, Iowa in 1887.  Leopold was an outdoors enthusiast and during his lifetime enjoyed hunting, fishing, journaling, sketching and bird watching.  He graduated from the Yale School of Forestry in 1909 and was hired as one of the first foresters in the U.S. Forest Service, working in Arizona and New Mexico.  He was instrumental in getting the first wilderness area, the Gila Wilderness Area in NM, designated as such in 1924.  In 1933, he published the first book on game management ever written and he became the first chair in game management in the U.S. at the University of Wisconsin in Madison.

In his personal life, Leopold married Estella Bergere and they had five children, Starker, Luna, Nina, Carl and Estella. In 1935, the Leopolds bought, as a vacation property, an abandoned farm with a burned-down house and worn-out soil in Baraboo, Wisconsin.  They turned the old chicken coop into their living quarters, which they called the Shack and, over the years, planted tens of thousands of trees and worked to restore the prairies. Aldo Leopold carefully recorded the resulting changes to the land and wildlife over the years in his many notebooks. What looked like a crazy investment in a run-down farm became a long-term ecological restoration project that shaped many of Leopold's ideas about land conservation.  Below, you can see a photo of the Shack and a copy of the Leopold-style bench, which you might be lucky enough to build at an Aldo Leopold Weekend event.

Courtesy of the Aldo Leopold Foundation,
www.aldoleopold.org 

Leopold was a prolific writer and in the 1940’s, he wrote A Sand County Almanac to get his message about land conservation out to the public.  Although it was rejected by a number of publishers, it was finally accepted for publication by Oxford University Press in late February of 1948.  In March of that year, Leopold died of a heart attack while helping a neighbor fight a fire near the Shack property.  In case you’re wondering about Leopold’s five children, they all grew up to follow in their father’s footsteps, working in the natural sciences and conservation. (For more information click here.)

In 2007, the Aldo Leopold Foundation opened a center to help it fulfill its mission to “foster the land ethic through the legacy of Aldo Leopold.” The center is  platinum LEED-certified  building and was built on the Leopolds' Baraboo property using trees planted years earlier by the family. Today, we would say this was built in a sustainable manner, although Leopold might have said it was built with a land ethic in mind.   

Land Conservation: the Ultimate MMP Collaborative Game

Leopold described the land ethic like this, “The land ethic simply enlarges the boundaries of the community to include soils, waters, plants and animals, or collectively: the land. (ASCA , p. 239)  He went on to say that because we humans are part of a larger ecological community, we have an obligation to use and maintain the land wisely.  “A land ethic, then, reflects the existence of an ecological conscience, and this in turn reflects a conviction of individual responsibility for the health of the land. Health is the capacity of the land for self-renewal. Conservation is our effort to understand and preserve this capacity.” (ASCA, p. 258) 

Courtesy of the Aldo Leopold Foundation,
www.aldoleopold.org

A land ethic includes avoiding use of resources as stakes in a zero sum game where the winner takes all at the expense of the environment. Regarding environmental resources, business as usual is like playing Monopoly, where there is only one winner left at the end of the game and he or she owns most of the resources.  Business using the land ethic is more like playing Pandemic, where the players all win if they can work collaboratively to find a solution to the problem at hand.  We could even say that natural resource management is the ultimate, massively multi-player (MMP), collaborative game where we all win if we can just work it out.

The solution to ecological problems, according to Leopold, is for individuals and governments to use their ecological conscience to make correct decisions about conservation.  Because it's so difficult to assign an economic value to species of songbirds or wildflowers, for example, such decisions should not be based on solely on their economic worth.  Each species is part of a biotic community and the community as a whole may not survive if separated from its parts of supposedly low economic value. Decisions made using an ecological conscience and keeping the land ethic in mind are better because, "A thing is right when it tends to preserve the integrity, stability and beauty of the biotic community.  It is wrong when it tends otherwise." (ASCA p. 262)

Happy Trails to You!

I hope you find a way to celebrate the Aldo Leopold Weekend coming up March 7-8, 2015. Borrowing  A Sand County Almanac from your local library and reading it would be one way to participate.  Putting up a bird feeder and watching the birds or taking a long walk in a natural setting near you would be another.  Happy Trails to you!  

Notes and Resources

1)  The abbreviation “ASCA” refers to the book, A Sand County Almanac by Aldo Leopold and the page numbers to the paperback edition published by Ballantine Books in New York in September of 1970.
2) The Wisconsin Recreation Atlas is published by National Geographic and was last updated in 2012.
3)  Environmental problems are quite complex and can’t be easily modeled with a simple board game like Monopoly or Pandemic.  However, the cooperative environment management game Okolopoly does a pretty good job of modeling this complexity.  It was produced in the 1980's in Germany as a board game and also in an online version. 
4) Note I've stopped just short of calling ecological resource management an MMPRPG because no roles are taken.