Experimental man blog moves to Technology Review!

April 22nd, 2009

Today the Experimental Man blog moves to the Technology Review website. Here is the inaugural blog on the new site:

 

Welcome to the Experimental Man Blog!

A blog about how leading-edge bio-science and technology is impacting individuals and society.

This blog is an outgrowth of my new book, Experimental Man: What one man’s body reveals about his future, your health, and our toxic world. In the book I report taking over 250 tests in the realms of genes, environment, brain and body and explore what these tests can tell us about one person’s health, past, present, and future.

I have delved into my inner secrets about everything from my proclivities for diseases to the levels of pesticides, metals, and dioxins inside me. I’ve had my brain scanned for belief in God, greed, altruism, fear, love, risk-taking, and more. Check out the Experimental Man Index for a list of tests and some of my results. (Example: over 7 million genetic markers sequenced; 22 hours in an MRI; and almost 2 liters of blood given up — despite my squeamishness about needles).

Are these tests useful? What do they tell us? And do we want to know?

I embarked on this journey as a science journalist attempting to understand and better explain a blizzard of abstract and complicated new discoveries in peronalized medicine by humanizing the story. The book arose out of two articles that used this journalist-as-guineapig method: for Wired on DNA and for National Geographic on environmental toxins.

A companion to the book is The Experimental Man Project website, which contains the detailed results of my tests (genetic sequencing, levels of environmental toxins in my blood, brain scans, and more) and links with dozens of informational sites about personalized medicine and all of the labs and companies that tested me. The site is interactive with the book by chapter and page number. There are also tests you can take, such as this brain age test. The Experimental Man Project is a joint effort with the Center for Life Science Policy at UC Berkeley.

This blog began on the Experimental Man site and already has several months of offerings — check out previous blogshere on everything from Zombie genes to the rise of envirogenomics, the ibrain sleep test, and discount DNA.

I will continue to blog here on the emerging era of personalized medicine. This will include postings on tests and discoveries, and also on their implications for society.

One aim is to cover how science and technology–and common sense–could reshape American healthcare as the Obama Administration and the U.S. Congress debate health reform. We are living in one of those critical moments in history when crisis could shape great improvements for society–or not.

Read and enjoy!

Obama’s budget director has the caffeine fast-metabolizer gene

March 29th, 2009

 

Peter R. Orszag, the 40 year-old budget director for President Barrack Obama, had his DNA tested, and has my favorite genetic marker

This from the from the front page of The New York Times yesterday: 

“His epic caffeine intake concerned him until he solved the problem with typical Orszagian efficiency: he underwent genetic testing, and confirmed he could safely metabolized large amounts and happily moved on to the next worry.”  

This is a subtle signal that genetic testing is starting to hit the mainstream when it is casually mentioned in the second paragraph of a profile of a public figure along with other basic biographical information. 

This genetic marker in the CPY1A2 gene has been linked with a rapid metabolizing of caffeine — though this is a preliminary results. I also have the variation that allows me to suck down Joe all day and barely feel the caffeine. This is according to a study published in the Journal of the American Medical Society in 2006. 

 

Indeed, I have always ben able to drink lots of coffee, even before bed, and feel a minimal bump from the caffeine. My father also drinks copious amounts with little impact — and sure enough has the “decaf” genetic variation, too! 

So those of you with the AA version of the rs762551 marker in CPY1A2, grab a latte and drink up! 

Photo: Todd Heisler/The New York Times

 

 

Rolling Stone’s top 100 people changing America

March 20th, 2009

Scientists and environmental activists mix it up with Taylor Swift, Danger Mouse, and Barrack Obama

This from the Genome Web Daily Scan:

“Rolling Stone has come up with a list of people they say are “changing America.”Hidden in between teen pop/country singer Taylor Swift (number 100 — yes, we’re confused, too) and Barack Obama (number 1) are Craig Venter (number 71), Leroy Hood (63), Jay Keasling (number 40), and Steven Chu (number 24). RS says Hood is changing “the future of medicine” by [giving] physicians tools to diagnose and treat disease even before any symptoms appear” and that Keasling is changing America’s energy troubles “engineering bacteria to convert cornstalks and wheat chaff into synthetic hydrocarbon fuels that can power planes, trains and automobiles.”"

I would also add slow-food guru Michael Pollan (69), new Obama green advisor Van Jones (89), virus-hunter Nathan Wolfe, physicist Lisa Randall (43), Robert F. Kennedy, Jr. (34), and of course John Stuart and Stephen Colbert (5). 

“Envirogenomics”: Linking environmental toxins to genetics

March 19th, 2009

 

Photo by Kathrin Millier

A fish, DNA, and mercury story 

This is an excerpt from Discover Magazine (April). For the complete article, click here.

 

When the halibut on my hook breaks the surface, writhing in a splash of seawater off the coast of Bolinas, California, I am thinking less of this fish’s fate than of my own. Considering that I plan to kill and eat it, this might seem cruel. Yet inside the fat and muscle cells of this flat, odd-looking creature is a substance as poisonous to me as it is to him:methylmercury, the most common form of mercury that builds up inside people (and fish). At the right dose and duration of exposure, mercury can impair a person’s memory, ability to learn, and behavior; it can also damage the heart and immune system. Even in small quantities, this heavy metal can cause birth defects in fetuses exposed in the womb and in breast-fed newborns whose mothers’ milk is laced with it.

Scientists have assured me that one serving of halibut contains nowhere near a dosage that might cause harm. These are the same scientists, though, who admit that no one knows for sure what the threshold dose is that causes mercury to subtly poison cells in the brain and the liver, two organs where it tends to accumulate.

As frightening as that sounds, most of us were born with a defense against exposure to mercury, initiated by specific sequences of genetic code that cause most people to expel the metal in 30 to 40 days. Not everyone carries this natural resistance, however. A small minority of people carry a genetic mutation that apparently causes their cells to retain mercury for far longer—in rare cases up to 190 days—greatly increasing the chance for cellular damage.

Such genetic differences may explain why some people are more susceptible to mercury poisoning than others. This possibility is driving a nascent but growing effort among scientists to link the impact of mercury and other environmental factors (everything from pollutants and diet to the sun’s ultraviolet rays) to the individual genetic proclivities that each of us is born with. “Toxicologists say that ‘the dose makes the poison,’” says mercury expert Jane Hightower, who practices internal medicine in San Francisco, “but it’s clear that some people are more sensitive to even small exposures than others.”

For lack of a better term, I’ll call this new science human envirogenomics, the fusing of environmental toxicology and genetics, two fields that until recently didn’t interact much with each other. Yet researchers are finding that the interplay of the two makes us who we are and often determines whether we are healthy or sick. “Recent increases in chronic diseases like childhood asthma and autism cannot be due to major shifts in the human gene pool,” says physician and geneticist Francis Collins, former director of the National Human Genome Research Institute. While acknowledging that changes in diagnostic criteria and heightened awareness may play a role, Collins says that much of the increase “must be due to changes in the environment, which may produce disease in genetically predisposed persons.” One day, envirogenomics could provide clues to a person’s sensitivity to environmental toxins (such as mercury) and the potential for damage based on that person’s genes. Doctors might then better understand how to prevent such harm and how to treat patients exposed to deleterious chemicals.

Go here for the rest of the article.

 

Were humans and dinosaurs alive at the same time?

March 13th, 2009

New survey reveals that only 59% of Americans know that dinosaurs came before humans 

Take a science literacy test (see below)

Yikes! Reforms and additional funding and respect for science and education in the Obama Administration could not have come too soon. The California Academy of Sciences and Harris Interactive have conducted a survey that shows Americans do not do well on basic science literacy. This is despite a civilization that we live in that depends on science and technology. Take a peek at the article copied below from R&D magazine.

The Magazine Article:

Are Americans bad at science? If so, are they worse than anywhere else? We know the answer to one of those questions. A new national survey commissioned by the California Academy of Sciences and conducted by Harris Interactive says that the U.S. public is unable to pass even a basic scientific literacy test.
The good news: U.S. adults do believe that scientific research and education are important. About 4 in 5 adults think science education is “absolutely essential” or “very important” to the U.S. healthcare system (86%), the U.S. global reputation (79%), and the U.S. economy (77%).

People are starting to realize that innovation and industry—not making cheap mortgages a government mandated right—are what propels successful economies. That means people have to understand science.

To test your already existing scientific literacy, take this Richard Carrier literacy test.

If you’re already confident in your knowledge, here’s what other people do not know:

  • Only 53% of adults know how long it takes for the Earth to revolve around the Sun.
  • Only 59% of adults know that the earliest humans and dinosaurs did not live at the same time.
  • Only 47% of adults can roughly approximate the percent of the Earth’s surface that is covered with water.*
  • Only 21% of adults answered all three questions correctly.

Knowledge about some key scientific issues is also low. Despite the fact that access to fresh water is likely to be one of the most pressing environmental issues over the coming years, less than 1% of U.S. adults know what percent of the planet’s water is fresh (the correct answer is 3%). Nearly half didn’t even hazard a guess. Additionally, 40% of U.S. adults say they are “not at all knowledgeable” about sustainability.

“There has never been a greater need for investment in scientific research and education,” said Academy Executive Director Dr. Gregory Farrington. “Many of the most pressing issues of our time—from global climate change to resource management and disease—can only be addressed with the help of science.”

This survey was conducted by telephone within the United States by Harris Interactive on behalf of the California Academy of Sciences between December 17 and December 21, 2008 among 1,002 adults ages 18+.

The approximately correct answer range for this question was defined as anything between 65% and 75%. Only 15% of respondents answered this question with the exactly correct answer of 70%.

 

GENES: The zombie gene (living-dead DNA?)

March 7th, 2009

Researchers at the University of Washington in Seattle have discovered a gene that is dormant in most of our recently-evolved monkey brothers. In humans and great apes. however, the gene was reactivated about 25 million years ago — reborn by the invasion of a retrovirus that attached itself to the gene and turned it back on. 

The formerly dead gene is one we could probably do without. It’s is involved in Chron’s disease, an inflammation of the gastrointestinal tract. But it is the first time that scientists have found evidence of a gene being resurrected by a virus. 

“This is probably the first example of a gene coming back from the dead after being gone for 25 million years,” Evan Eichler, a genome researcher at the University of Washington in Seattle who led the study, told The Scientist in a story posted yesterday.

This discovery is significant in at least two major ways: first, because our genome is packed with dormant genes that might some day be activated by a wayward virus; and second because it offers further proof that a virus can be used as a vehicle by scientists to intentionally deliver new genetic instructions to genes to treat disease.

I’m reminded of a favorite story of mine from paleontologist Jack Horner of the Museum of the Rockiesin Bozeman, Montana — he is the model for the main character in Jurassic Park — who likes to talk about how chickens could become dinosaurs with a bit of DNA tweaking. Apparently, the mighty and ferocious T-Rex has evolved into various birds, including the chicken. Dormant dino genes still exist in a chicken that could be activated to grow teeth, little hands, and a tail. “I’m not sure why anyone would want to do this,” says Horner, with a grin, “but this is the real way to have a Jurassic Park.”

Check out my book, Experimental Man, the chapter “My Dinosaur DNA”, pages 87-91 for the complete story of the chickenosaurus.

 

 

 

 

 

 

 

11:45 am Monday

March 6th, 2009

President Obama is set to announce a reversal of President Bush’s restriction of federal funding for embryonic stem cell research — at 11:45 am on Monday, March 9. 

This not only activates funding for this promising and exciting research, it also provides a symbolic closure to the Bush years when science too often was superseded by politics and ideology.

Read more in the New York Times.

A Birthday Gift for Darwin

February 24th, 2009

Will President Obama recognize Charles Darwin’s 200th birthday by lifting federal funding restrictions for embryonic stem cell research? 

Column originally appeared on Portfolio.com.

The symbolism couldn’t be riper: a newly installed, pro-science president signs a promised executive order overturning his predecessor’s anti-stem cell policy on this day and in this year, which also celebrates the 150th anniversary of Darwin’s seminal work, On the Origin of the Species.

Already, the half of Americans that profess to deny Darwin’s central theory of evolution are cringing at this birthday being celebrated by the other half who do believe. Many of the nonbelievers also oppose embryonic stem cell research, although this number has been dropping, particularly as treatments and cures using these special cells inch ever closer.

Just a few days ago, the Food and Drug Administration approved the first-ever human tests using embryonic stem cells, those cells formed in an embryo soon after conception that can grow into any tissue in the body. Geron Corporation of Menlo Park, California will implant stem cells in up to eight paraplegics in effort to repair their spinal chord injuries. 

If all goes well, the stem cells will help repair a material around nerve cells known as myelin, which should restore the ability of nerve cells to carry signals and to function. Some cells may also be spurred to regenerate. 

Other companies are poised to begin testing embryonic stem cell treatments for a market that analysts say could equal over $8 billion by 2016 – including therapies derived from “adult” stem cells, those taken from fully-formed humans to regenerate specific cells in the heart, pancreas, and elsewhere.

It seems eons ago that President George W. Bush signed an executive order in 2001 limiting federal funding for embryonic stem cell research, a move applauded by the religious right who consider human life to begin at conception. Critics have long complained that this move crippled crucial research, delayed therapies, and caused unneeded suffering and death.

In 1859, Charles Darwin had no idea that stem cells existed, and that they are the crucial building blocks developed by complex organisms over the course of billions of years to launch the process of creating a person – or a toad, falcon, spider, and guppy. 

He also might be astonished that his theory is denied by millions of people – by 54 percent of Americans, and more than half of his own countrymen in Britain, according to a recent poll.

Perhaps this is understandable at one level, since Darwin challenges our fundamental view of the place of humans in the universe. If God created us, then we are special. If we are descended from bacteria, pufferfish and chimpanzees, we are merely another organism.

This sort of thinking misses the point about Darwin’s enduring theory: that understanding the progression of life for some 3.5 billion years on Earth is fascinating in its complexity and diversity. It also provides us the tools to understand the wonders of stem cells, which finally, after years of being starved of federal funding, are poised to be unleashed.

 

 

Reading my mind: A start-up wants to attach its iBrain to your head while you sleep to detect abnormalities and disease—and perchance to detect your dreams

January 26th, 2009

 

Below is an article from my column “Natural Selections” on Portfolio.com:

I‘m in a bathrobe clutching a stuffed otter trailing wires while seven strangers watch me climb into bed.

Trailing from the fuzzy animal’s rear end are two wires. One leads out of my hotel bedroom and into an anteroom where the people now saying good night have set up monitors and laptops. The other is attached to an electrode affixed to my forehead.

I’m at the Estancia resort in La Jolla, California, where researchers at a San Diego start-up company called NeuroVigil are investigating what my brain is doing during the one-third of my life that I spend asleep.

The founder of NeuroVigil is Philip Low, a young neuroscientist who also holds a chair at the Salk Institute, which sprawls out just to the north of the Estancia, abutting the beach and the Pacific Ocean.

Low and his team are experimenting with a prototype of a new invention called the iBrain, which uses a single electrode attached to the forehead that measures brain activity during sleep.

Most sleep-measurement devices are multiple electrode caps that need to be run in a controlled setting, such as a hospital. The iBrain, when it is finished, will be used in a person’s home—or, in my case, in the bedroom of this rather posh suite.

The finished iBrain will be wireless, says Low, and will report data during the night to NeuroVigil’s data centers via one’s own laptop, via the internet, or perhaps via the device itself.

But will the commercial version be imbedded in a stuffed otter, as this one is? Low says probably not; the otter was added at the last minute to protect the ungainly iBrain prototype from being squashed if I roll over in my sleep. Presumably, the real product will be smaller and less fragile.

NeuroVigil, which plans to sell the iBrain to researchers, physicians, hospitals, businesses, and consumers, will analyze the brain waves it picks up using a patented algorithm also developed by Low. The program, he says, uses grids to detect structural changes that occur in a sleeping person’s brain and can reveal neurological disorders.

“We are using sleep as a microscope to study brain activity,” Low said.

With long, wavy-black hair, a penchant for European-cut suits, and a charismatic intensity, Low came to the Salk in 2001 at the invitation of Nobel laureate Francis Crick, the co-discoverer of the double helix structure of DNA. Low and Crick worked together on sleep until Crick’s death in 2004.

Still in his twenties, Low finished his Ph.D. in 2007, which he said was just one page in length, with a very long footnote titled, “A New Way to Look at Sleep: Separation & Convergence.” Low is a fellow at the Crick-Jacobs Center
for Theoretical and Computational Biology at Salk.

When I met him, Low was getting a lot of publicity for using his iBrain technology to test brain waves in songbirds. Using some of his new algorithms, Low analyzed E.E.G.’s of zebra finches and discovered a previously unknown similarity between birdbrains and mammalian brains—periods of rapid-eye-movement (R.E.M.) sleep, slow-wave sleep (S.W.S.), transition stages, and quick E.E.G. transitions. 

“No one thought that birds, which lack a neocortex, would show these patterns,” he said. His Chicago lab also was able to record patterns in the sleeping finch’s brains that were identical to when they were awake and singing, suggesting they might have been dreaming about singing. That finding may offer clues to how humans dream.

Low’s company also recently won $250,000 in seed funding from the annual West Coast 250K Venture Challenge offered by the Silicon Valley venture firm Draper, Fisher, Jurvetson. Low says he has turned down millions of dollars from venture capital firms and funded the company using credit cards. He has attracted several prominent scientists to its advisory board. 

The company hopes to begin selling the iBrain within a year, and have not yet priced the device or their service. “We want lots of people to use this, so it won’t be too expensive,” says Low.

Low tells me that the iBrain technology and his algorithms could be used to detect not only neuro-abnormalities that can cause shifts in how the brain performs in EEGs much in advance of cognitive symptoms.

He believes the device will be added to the growing pantheon of diagnostic tools that range from cholesterol levels to genetic profiles, and that one day scanning brain waves with his portable device will be routine for everyone from transportation workers to soldiers.

He even sees applications for detecting pandemics and bioterrorism threats, although he wouldn’t elaborate, he says coyly, for proprietary reasons.

This was the first time they had tested the device outside of a hospital or a clinic, so they brought in traditional sleep-monitoring devices to make sure they were getting a strong signal from my snoozing brain.

Low worried that I would have trouble falling asleep with an electrode stuck on my head and connected to the fluffy otter. But he didn’t know how easily I can snooze. I fell asleep soon after they turned out the light, while the team gathered around the equipment in the anteroom.

Several weeks later, I received my results. I was normal except for a funny alpha wave that sometimes suggests alcoholism or a debilitating muscle disorder. But Low says that the wave pattern was more likely caused by the placement of the electrode. Here is NeuroVigil’s report on my brain while sleeping:

“Patient had a good Sleep Efficiency (92.7 percent). Sleep Onset Time was normal. Distribution of sleep stages was typical. … The patient is not likely to suffer from depression or sleep apnea. … Total wake time for the bedtime period was short. In-depth analysis of sleep stages using SPEARS [Low's algorithm] revealed no sign of pathologic brain rhythm generation.”

Taking this test was fun, though I wonder if this product could face some of the issues that confront genetic testing if employers, the government, or insurers use it in the wrong way to screen for abnormalities and behavioral quirks.

Low acknowledges the potential for abuse. “Like any test of this sort, we would need to protect people from abusing this technology,” he says.

I thought of one more use for the iBrain—dating services such as Match.com that offer an iBrain vetting of prospective dates. If this happens, however, I suggest losing the otter. 

 

Genetic drift in Iceland… evidence from 1000 year-old skeletons

January 19th, 2009

The scientists at deCode Genetics have discovered what happens when a small group of people is isolated on, say, a smallish island that bestrides the Arctic Circle and continues to procreate for a millennium or so. The results may explain how human differences have emerged rather rapidly over the 150,000 years or so since our ancestors left Africa. 

According to a study out of deCode published on January 16 in PLoS Genetics, DNA from skeletons of Icelanders who lived 1000 years ago — soon after the island was settled by Vikings and other Euroepans — are more similar to modern Europeans than to modern-day Icelanders. The skeletons were unearthed from burial sites over the past several decades and preserved in the National Museum of Iceland.

One interesting issue this raises is how the genetic drift in Iceland might have impacted modern Icelanders being tested by deCode as a template for discovering human genetic markers for traits and diseases. DeCode’s groundbreaking studies in gene marker discovery for everything from heart attack to restless leg syndrome have been among the best in the world, and many have been validated by testing other populations in Europe and North America and elsewhere, though one wonders if the “drift” caused subtle genetic differences for certain traits that are more unique to Icelanders than perhaps previously suspected.  

Read the story in Genomeweb Daily News and the study in PLoS Genetics.