Thursday, August 14, 2008

The DNA Network

The DNA Network

Vaccines, part I [Discovering Biology in a Digital World]

Posted: 14 Aug 2008 02:18 PM CDT

A long time ago, I saw a movie called "The Other Side of the Mountain." The movie told the story of Jill Kinmont, a ski racer who contracted polio and lost the use of her legs. I was sad for days for afterward, but also relieved to know that Jill Kinmont's fate wasn't going to be mine. I wasn't going to wake up in an iron lung after a ski race, and neither were my friends, because most of the children in my generation had been vaccinated against the Polio virus.


PHIL_2612_lores.jpg
This image shows a polio survivor learning to walk. The image comes from the CDC Public Health Image Library

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How to Kill Education: Replace Degrees with Technical Certificates [adaptivecomplexity's column]

Posted: 14 Aug 2008 02:03 PM CDT

In yesterday's Wall Street Journal, we read an argument for getting rid of the college degree. You've heard this argument before: under our current system, a college degree doesn't mean anything, because most of the time you don't come out with any directly applicable job skills:

The solution is not better degrees, but no degrees. Young people entering the job market should have a known, trusted measure of their qualifications they can carry into job interviews. That measure should express what they know, not where they learned it or how long it took them. They need a certification, not a degree.

In fact, this could even extend to grad schools:

Why not present graduate schools with certifications in microbiology or economics -- and who cares if the applicants passed the exam after studying in the local public library?

This is a surefire way of destroying education in this country. You don't go to college primarily for specific job skills, you go for an education. Sure, this system may help some employers:

Certification tests would provide all employers with valuable, trustworthy information about job applicants.

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DNA Testing by DDC Sets Longtime Inmate Free [The DNA Testing Blog]

Posted: 14 Aug 2008 01:52 PM CDT

DDC’s forensics division has worked with The Ohio Innocence Project and the Franklin County Prosecutor’s office to provide DNA testing that resulted in the release of longtime prison inmate Robert McClendon. After 18 years of imprisonment, a Franklin County, Ohio, judge ordered McClendon's release after DNA analysis found no match between McClendon’s DNA sample and [...]

The impact of online publishing [The Seven Stones]

Posted: 14 Aug 2008 12:18 PM CDT

"I haven't browsed a table of content in ages; I find all my papers by Pubmed searches anyway". We have probably all heard this remark, which reflects a general trend as how online publishing has changed the way we retrieve scientific publications. In a study published today in Science, Evans ("Electronic Publication and the Narrowing of Science and Scholarship", Evans, 2008) presents data on citations patterns showing that the appearance of electronic publications has been accompanied by a decrease in the number of citations and a progressive restriction of citations to recent papers:

Collectively, the models presented illustrate that as journal archives came online, either through commercial vendors or freely, citation patterns shifted. As deeper backfiles became available, more recent articles were referenced; as more articles became available, fewer were cited and citations became more concentrated within fewer articles.

The interpretation offered is that online availability has driven citations to become more focused while less relevant articles are more easily filtered out. In addition, Evans argues that facile navigation through the network of hyperlinked citations may amplify the tendency to be influenced by other's choice when citing "reference" studies and thus accentuates the dominance of a restricted number of articles:

By enabling scientists to quickly reach and converge with prevailing opinion, electronic journals hasten scientific consensus. But haste may cost more than the subscription to an online archive: Findings and ideas that do not become consensus quickly will be forgotten quickly.

It is probably difficult to be sure that all sources of bias and confounding factors can be eliminated in this type of analysis. For example, on the Friendfeed discussion thread, LJ Jensen asks whether the sheer amount of published research could explain why scientist restrict their citation to the most recent literature. See also some additional discussion in the associated News & Views (Couzin, 2008)

In any case, the study highlights two complementary strategies in information retrieval: finding relevant papers by targeted searches versus staying informed on a broad range of topics by systematic browsing. In our Google-driven era, we may have the tendency to forget the importance of good old-fashioned 'table-of-content-skimming' to stimulate cross-disciplinary thinking, widen our horizon and cultivate scientific curiosity.

Perhaps it is a specificity of printed media to provide "poor indexing" and therefore enforce broad exposure to unrelated areas of research. On the other hand, some web technologies already help to browse through vast amounts of online publications (for example an RSS aggregator helps me to generate a daily literature survey; this can be further combined, for example here at Frienfeed, with other community-centered feeds; other aggregators highlight information by automatic clustering: Postgenomic and Scintilla). However, these tools remain imperfect and, in our reflection on the future of scientific publishing, we will need to find the right balance between the two strategies above and think of how the increasing efficiency of search engines can be complemented by means providing a continuous exposure to diversity.

By Secretary or By Professional Report [The Gene Sherpa: Personalized Medicine and You]

Posted: 14 Aug 2008 10:31 AM CDT

A recent study caught my eye. Done by multiple centers..... from the Division of Laboratory Systems,* Centers for Disease Control and Prevention, Atlanta, Georgia; the Wadsworth Center, New York...

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VADLO - Google for Scientists? [The Daily Transcript]

Posted: 14 Aug 2008 09:23 AM CDT

More thoughts on animal research: Pets and wild animals benefit, too [Discovering Biology in a Digital World]

Posted: 14 Aug 2008 09:00 AM CDT

Every year people adopt pet dogs, cats, birds, and other creatures and take them to their local veterinarians for all the usual vaccinations and exams. The usual vaccinations protect your pets from diseases like rabies, distemper, Feline Immunodeficiency Virus, and Feline Leukemia. But it's not just pets that get protected by vaccines. Agricultural creatures: fish, chickens, sheep, cows, pigs, and horses receive vaccines and increasingly, wild animals are getting vaccinated, too.

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Daily Lol: Matrix in Medical School [ScienceRoll]

Posted: 14 Aug 2008 07:15 AM CDT


I found this hilarious video at Clinical Cases and Images:

Sexy Worms, an E-Tongue, and Kita Running [Sciencebase Science Blog]

Posted: 14 Aug 2008 07:00 AM CDT

Spectroscopynow.comHere is a sneak preview of the various science news items I have scheduled to appear on August 15 over on SpectroscopyNOW.com

Stay young and beautiful - NMR spectroscopy has been used uncovered the secret of eternal youth and the ability to attract sexual partners almost at whim. The results suggest it all hinges on a novel group of pheromones. Unfortunately, before you head for the local pharmacy to stock up, these are pheromones of the lab-technician’s favourite worm, the nematode Caenorhabditis elegans, so they are likely to have no effect whatsoever on human behaviour or longevity.

Electronic wine tasting - The wine buff’s palate is a complicated multisensory organ as anyone who knows their Bordeaux from their Beaujolais knows. Now, researchers have taken a step towards an artificial nose based on a system amenable to multivariate analysis. The system integrates a multisensor to test wine and grape juice samples for adulteration or vintage fraud.

The Kita runners - Protein folding is one of the great conundrums of the twenty-first century. How exactly does a linear string of amino acids “know” into what three-dimensional cross-linked structure to fold itself? Moreover, how might molecular biologists predict this folding from first principles and how might the misfolding seen in prionic diseases, Alzheimer’s and other disorders be prevented or even reversed? A new clue about the folding of proteins comes from studies with a novel technique known as kinetic terahertz absorption spectroscopy (KITA).

Green and peasant landscape - There’s also a bonus item on science in art. Post-impressionist artist was rich beyond his wildest dreams but only posthumously. He may have chopped off part of one ear, but he had double vision. At least that’s the idea that emerges from new X-ray studies of one his more mundane paintings - Patch of Grass - which reveals a portrait of a peasant woman beneath.

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Sexy Worms, an E-Tongue, and Kita Running

CureTogether: Patients and Researchers [ScienceRoll]

Posted: 14 Aug 2008 05:36 AM CDT


CureTogether, a new web 2.0 startup, plans to bring together patients and scientists to create an open-source health research system.

An excerpt from the Kurzweil.net article:

The first conditions being studied are migraine, endometriosis, and vulvodynia; each affect more than five million Americans. Patients will also be able to share ideas and provide their anonymous medical data to an aggregate database available “open source” to any researcher in the world to study.

“We chose these conditions because they are underfunded, involve daily pain, and have personal meaning for us,” said co-founder Alexandra Carmichael. “We saw the suffering of our close family and friends with these chronic conditions, and we wanted to do something to help.” So they partnered with the Chandran Family Foundation for Healthcare Research and Education and researchers at the University of Alabama at Birmingham. “We may expand to other conditions if enough patients come together to request it,” she added.

It seems to be something similar to what 23andMe is doing. Looks promising.

Animal Rights’ Firebombings [Bitesize Bio]

Posted: 14 Aug 2008 05:17 AM CDT

It would seem that animal rights’ terrorists are at it again, this time with a spate of firebombings in Southern California.

One might be sympathetic to the child-like adoration of animals, without a doubt. You might even naively think that researchers using animal test subjects are some kind of torturers. Then you find out that there are protections for the ethical treatment of animals for research, like the Animal Welfare Act. And then you find out that this research saves lives in the long run.

knockoutmiceAs I’ve mentioned before, these extremists harbor no interest whatsoever in participating as civil members of a civil society. I’m sure that there are plenty of people who outwardly look like decent people, who have signed up as supporters of such activist groups. But looks can be deceiving. Supporting such animal rights extremist groups is the mark of someone who is uninformed and condones violence.

I don’t say this for the sake of ranting, just to get your attention a little. The solution, as always, is educating people.

As Drug Monkey points out, a good start is to get potential new animal rights extremism supporters to read the Animal Welfare Act. That, afterall, is the law we should be talking about. (laws matter, right?) As the original act states (click the AWA link for its expansions and clarifications):

Enacted August 24, 1966, Public Law 89-544 is what commonly is referred to as The Animal Welfare Act although that title is not mentioned within the law. It authorizes the Secretary of Agriculture to regulate transport, sale, and handling of dogs, cats, nonhuman primates, guinea pigs, hamsters, and rabbits intended to be used in research or “for other purposes.” It requires licensing and inspection of dog and cat dealers and humane handling at auction sales.

Another area to educate people on is the guidelines that major scientific organizations put implace to police themselves. Such as the Institute for Laboratory Animal Research run by the National Academies of Science. Not only do ILAR and other groups establish internal guidelines and help scientists to follow them, they publish reports and books constantly re-evaluating and validating current standards to ensure humane treatment of animals. Take this book, for instance, which establishes the factual basis for the causes of animal distress and how to alleviate it:

The first in a two-part update of ILAR’s 1992 report, Recognition and Alleviation of Distress in Laboratory Animals, focuses on the distress experienced by animals used in laboratory research. This book aims to educate laboratory animal veterinarians, students, and researchers, animal care staff, and animal welfare officers on the current scientific and ethical issues associated with stress and distress in laboratory animals. The report evaluates pertinent scientific literature and generates practical and pragmatic guidelines for the recognition, alleviation, and minimization of distress for animals in the laboratory setting.

And you can read a lot more also at Speaking of Research. For instance, SoR explains the animal model, as neatly explained in "The Animal Research War", by Michael Conn and James Parker:

If you are going to study a human disease you can't, for ethical reasons, perform the initial work in humans; you have to develop a model. Some models may be in vitro - literally, in glass tubes – but as you learn more and more, you must eventually test ideas in vivo- in living animals. That means you have to have a way of producing the disease that allows you to study it.

Let's consider AIDS, one of Podell's interests. You could take its causative agent, the Human Immunodeficiency Virus (HIV), grow it in a test tube, and kill it by pouring bleach on it. Do you now have a way to kill HIV? Yes, you do. Do you have a treatment that can be used in humans? Absolutely not: bleach is toxic. Killing HIV in a test tube and killing it in a living animal are two very different accomplishments.

To complicate things further, viruses grow differently in test tubes than in humans. Humans have an immune system: test tubes do not. A virus growing in a test tube is not a good model for the human disease, but drugs that don't kill the test tube virus probably won't work in humans either – and these might be eliminated from further consideration.

Animal models allow closer approximation to a human response. They are not perfect, of course; animals host different diseases and different responses. While the fundamentals of life are the same – there is a 67 percent similarity between the DNA of humans and earthworms – there are differences in species and even in individual animals. Some animals are good human-like models for one thing and some for another; some have a cardiovascular system that is similar to humans while others have similar skin.(3)

And lots of people are talking about this (hardly an exhaustive list, I’m sure):

Drug Monkey
Discovering Biology in a Digital World
Terra Sigillata
Adventures in Ethics and Science
Evolving Thoughts
Respectful Insolence
A Blog Around the Clock
The Frontal Cortex
Built on Facts
Dr. Joan Bushwell’s Chimpanzee Refuge
Greg Laden’s Blog

Let’s fight extremism and support civility, decency, and the proper grasp of the facts, shall we?

Disaster Map [ScienceRoll]

Posted: 14 Aug 2008 05:10 AM CDT


There is an interesting, interactive map of disasters and emergencies worldwide. You can also see and read more about recent epidemic hot points. It was created by the National Association of Radio-Distress Signalling and Infocommunications; Emergency and Disaster Information Services (EDIS); Budapest Hungary.

You can order free AlertMail or event report.

The Confucius Genealogy Compilation Committee Rejects DNA Testing [The Genetic Genealogist]

Posted: 14 Aug 2008 02:00 AM CDT

iStock_000002679865XSmallSee the new article at Seed Magazine “Inheriting Confucius,” which discusses efforts to generate a family tree containing the 2 million+ descendants of Confucius.

Kong De-Yong, a 77th(!) generation descendant of Confucius, has been compiling the tree for the last 10 years.  Although the Committee is accepting submissions from women and other previously excluded groups, it is not accepting DNA contributions.  According to the article, this “hints at the limits of Chinese engagement with the age of genomics, and demonstrates how high cultural stakes can constrain science.”  Unfortunately, as the author of the article suggests, many people might be afraid of the results of such DNA testing: “Given the potential implications of genetic knowledge for long-presumed members of the [Confucius] family, they think it better not to know.”

However, there is of course no need for the Committee’s participation in order to learn more about Confucius’ DNA or Confucuis’ descendants (although it would be nice, of course).  A Confucius DNA Project has already been initiated by the Beijing Institute of Genomics, and Confucius descendants can submit a sample for analysis for the price of $125.

1 comment:

Alexandra Carmichael said...

Thanks for mentioning CureTogether! We're excited to be included as part of The DNA Network.
Have a wonderful day!
Alexandra Carmichael
CureTogether.com