Infovores & Ignotarians

In the world of flesh, there are those who consume it and those who do not. The carnivores and the vegetarians.

What about the world of information? There are those who consume it and those who do not. The infovores and the ignotarians. The term “Infovore” describes a person who indulges in, even desires, information consumption (hat tip FutureLab). What is the opposite of an infovore? By definition, its one who limits the intake of information, like a vegetarian limits meat consumption. These people might be referred to as Ignotarians.

So who is winning out there in the world of the web (errr…probably some selection bias here)? The Infovores or the Ignotarians? Check out this GoogleFight to discover: Infovores vs. Ignotarians.

NPR on PGx Testing

Listen to this NPR piece on pharmacogenetics, which includes:

The piece closes with this thought:

"Other experts, including Russ Altman of Stanford University, say
pharmacogenetics is such a new science that most doctors didn’t learn about it
in medical school. Clinicians have to find a laboratory that offers the test and
learn how to read the results, he says."

Toward this end, DNA Direct (my employer) has put the physician-writer Dr. Alan Eshleman on the case with the launch of a new blog on pharmacogenetics.  He’ll be writing from the perspective of a physician that is not a pharmacogenetics expert, but is interested in learning about this new science and sharing his experiences with other physicians.

The blog is up and functional, but you’ll have to ignore the dust because we’re still working on layout/design.

Also, for information on drug metabolism, check out our website Genes & Drugs.

Nicholas Wade on $1K genome

Nicholas Wade has another piece on the $1000 genome.  Here are a couple snips, starting with an update on what a human genome costs, then and now:

"The first human genome decoding, completed by a public consortium of universities in 2003, cost more than $500 million. With the same technology, dependent on DNA sequencing machines made by Applied Biosystems, a human genome could probably now be decoded for $10 million to $15 million, experts say."

There seems to be a lot of fluctuation in the estimates of the price of the first human genome, typically ranging from $500M or $3B?  Can we nail this one down to within at least one order of magnitude?

David Bentley, Solexa’s chief scientist, takes an oddly conservative stance on personal genomics:

The demand for whole genome sequencing is a long way off, in Dr. Bentley’s view, but not so distant that it is too early to think about the consequences of generating such information. He advocates that two people should control access to a person’s genome sequence — the patient and the physician.

Why not the patient alone? Dr. Bentley said genomes would be so difficult to analyze correctly that interpretation should stay within the medical profession. Otherwise, freelance services will spring up, offering to predict whether a person will get heart disease or their age of death. This potential for misinformation “would have a huge adverse impact on the medical use of genetic information,” Dr. Bentley said.

What does it mean that genomic interpretation services should "stay within the medical profession"?  Does this mean that interpretation should be made by qualified genetics professionals?  In which case I agree.  If staying within the medical profession means making appointments, travel, waiting rooms, and all the rest, then forget it.  Why does the above paragraph pre-suppose that "freelance services" would be inferior?  Couldn’t these services be superior by employing trained genetic experts–of which there is real scarcity in the world, including in the medical profession?

Nicholas Wade. "The Quest for the $1,000 Human Genome" NYTimes, July 18, 2006.

The Incidentalome

A very important paper was published last week in JAMA.  The punch line is this: Once the new high throughput diagnostic testing technologies — like massive SNP panels — are widely deployed there will be a significant spike in both true-positive and false-positive results.  The implications of this fact are deep and wide.

If you’ve got access to JAMA, check it out.  Otherwise, I’ll summarize the important parts the paper later this week. 

Isaac Kohane, Daniel Masys, and Russ Altman. "The Incidentalome: A Threat to Genomic Medicine" JAMA 296(2): 212-215. July 12, 2006. (sorry subscribers only)

Private Little Revolutions

Best sentence I read today:

"The doctor-patient relationship hinges on informed consent, but the FDA says only a doctor may do some of the informing."

Peter Huber is referring specifically to the informing that is done via diagnostic testing such as pregnancy testing, HIV testing, genetic testing, and innumerable other blood/urine/tissue testing.  Diagnostic testing is a means of extracting and communicating information about personal biology.  Diagnostics are informational devices. 

Some believe there are forms of your personal biological information that you should NOT have access to, or at least access should be complicated to achieve.  AND if you do manage to get access, this information should only be dispensed in a professional setting (i.e. a clinic).  Huber’s thesis:

"Diagnostic technology is on a collision course with the FDA.  A dipstick (or something much like one) is coming to diagnose just about anything: infectious disease, disease caused by your own cells gone haywire or the threat of disease caused by imperfect genes…If the FDA will allow it…"

Some diagnostic tests, like the pregnancy test, have successfully passed through the regulatory gauntlet, and have become, in limited circumstances, common fixtures of drug store shelves, internet commerce, and even home use.

While difficult to imagine, pregnancy testing was once only allowed through a physician.  Today nearly one-third of all U.S. women have taken a home pregnancy test.  In the early part of the 20th century, there were technological barriers to home pregnancy testing — diagnosing pregnancy involved injecting rabbits with a woman’s urine, i.e. the Rabbit Test.  By the late 1970s, once the technology to diagnose pregnancy had been improved and simplified, a different kind of barrier arose: social barriers.  As historian Sarah Leavitt  has recently documented, Consumer Reports in 1978 was no fan of the home pregnancy test:

…the need for an early pregnancy test was seen as evidence of promiscuity. A state health official told the magazine: “there is no reason for a woman in Maryland to buy a kit such as the EPT unless she doesn’t want to be seen at the health department.”  The suggestion that only immoral women with something to hide would need a home test kit led the magazine to conclude that “even if it is used correctly, the EPT appears to be a needless purchase” for its readers.  The editors recommended that women visit their doctor or a clinic to get results instead—but women found ways around these strictures and increasingly demanded access to private, personal, informed, and nonjudgmental health care, of which the pregnancy test was a part.

Consumer Reports has since changed its tune of course.  Twenty years after its original article, inuendos of the immoral nature of home testing had been dropped (they had follow-up articles in 1996 and 2003).

Lynch_clearblueeasy

Caption: Did you know that David Lynch directed an
advertisement for the home preganancy test Clear Blue Easy?

Sarah Leavitt beautifully summarizes the impact of the home pregnancy test:

Women in this generation who take home pregnancy tests are able to know something about themselves and their futures in a time frame that was simply not possible for their grandmothers, or even their mothers.  The kit modified the network of actors involved in diagnosing pregnancy, taking the event from the doctor’s office to the home. It has also modified the time frame of pregnancy by reconfiguring the original discovery. Its revolutionary status, therefore, is small but personal, removing the moment of pregnancy diagnosis from the institutional gaze of the doctor to the private gaze of the pregnant (or not-pregnant) woman herself. It is an example of the way in which the women’s health movement worked to recapture women’s control over much information related to pregnancy.

If Peter Huber’s thesis is correct, there is a similar need for "private little revolutions" in other aspects of health care, a need to recapture control over other forms of personal biological information.

Peter Huber. The Patient’s Right to Know. Forbes.  07.24.06

Sarah A. Leavitt "A Private Little Revolution": The Home Pregnancy Test in American Culture. Bulletin of the History of Medicine 80.2 (2006) 317-345. (sorry subscribers only)

CHECK OUT Sarah Leavitt’s exhibit: "A Thin Blue Line: A History of the Pregnancy Test Kit"

For more on DAT, see Bruce Friedman’s post and the links within.

Access to Digital Research Literature

If you’re truly an information maven, you’ve probably assembled a toolbox of tactics to get access to journal articles containing the info you want to consume (without paying the often outrageous per article fees).  Kevin Kelley over at Cool Tools offers a description of another tool to add to your arsenal: the digital library card.

In most states, you can get a library card from a public library
outside of your county of residence — as long as you can prove state
residence (true for the San Francisco Public Library). Often you will
have to go the actual state library in person to pick up your card, but
once in hand, you can access the library from the web. Fanatical
researchers are known to have a wallet full of library cards from
numerous public library systems within their respective states. Some
states, Ohio and Michigan being two of the better known, have statewide
consortiums of private, corporate and public libraries, which allows
you access to the combined services and databases licensing power of
them all.

If your local library system does not provide free online access to
digital content databases, the cheapest way to get into these expensive
databases is to pay for a library card from the New York Public Library.

If you’ve never heard of Cool Tools, you should consider subscribing to the weekly digest — its a great and fun resource.

Getting access to scientific and medical literature can be a real pain
in the neck.  Luckily there are organizations like PLOS and folks like Peter
Suber over at Open Access News working to change this state of
affairs.

Genetics Carnival #2

Hsien-Hsien Lei is hosting the second genetics carnivals called Mendel’s Garden over at her Genetics and Health Blog.  Check it out.

Your microbiota is SOOOO agnotobiotic

Cheap personal microbiomics will make the
human microbiota gnotobiotic!  It just rolls off the tongue (an
decreasingly agnotobiotic human organ).  Does all this verbage leave a bad taste in your mouth

Microbiota: The collection of micro-organisms in a particular environment, such as the human body, e.g. the human gut microbiota.

Microbiome: The collection of genetic material (all the genomes) in a particular microbiota.

Gnotobiotic: Describes a microbiota with a known set of micro-organisms.

Agnotobiotic: Describes a microbiota of unknown or poorly defined composition.

Here are some stats to cleanse your palate:

We are born relatively germ-free.  Its unknown the extent to which we acquire our microbiomes from family members, but this may be another type of genetic heritability.  In this case, genetics is definitely not destiny.  We will increasingly be learning how to "reprogram" our microbiomes. 

Microbiota management, flora farming, bug doping. Oh My!

Additional reading and references below the jump.

Read more

University of Utah DNA Learning Center

The University of Utah deserves a huge amount of praise for a fantastic educational site about genetics.  Bright, lucid graphics.  Interactive features and multimedia (WOW!).   Well-written, lay-person friendly content.

The topics range from genetic basics, pharmacogenetics, to medical marijuana.  Check it out.

Atul Butte at PARC Forum

Among the many perks of life in the Bay Area are the frequent geek events which ensure all stripes of technophiliacs are kept occupied.  Long Now Seminars. Future Salons. Nerd Salons. The Hillside ClubDorkbotPARC Forums.  And on and on.  (not to mention the myriad Web 2.0 scene)

The famed PARC has hosted a seminar series for years — dating back to the late 70s.  I recently attended a talk delivered by Atul Butte of Stanford on genomics and medicine.  Talks like this one are more commonly being archived online, taking advantage of the long tail of the internet.

Atulbutte_parc2006

Atul Butte, Stanford University School of Medicine. "Exploring Genomic Medicine Using Integrative Biology" June 15, 2006 at PARC. audio and video


Also see the PARC Forum archives.

(Unfortunately, not everyone is putting their talks online…not even a transcript?)