Category Archives: Medicine

Guest Blog on Scientific American – Bacteria, the anti-cancer soldier

James Byrne of the Disease of the Week! blog (also on Twitter) is the latest guest blogger on the Scientific American Guest Blog. Check out his post – Bacteria, the anti-cancer soldier.

Superbug in the Triangle!

Well, hopefully not the real MRSA in your home! But the book Superbug will be introduced to the audiences around here. Author Maryn McKenna (Twitter) will be in the Triangle this week.

First, on Wednesday October 6th at 7:30 pm, Maryn will be reading at my most favourite bookstore in the world – Quail Ridge Books in Raleigh. I’ll be there.

Then, next day, on Thursday October 7th at 7:00 pm, she will be going over to Durham to read/sign at The Regulator Bookshop. I may try to come to that again.

Join us if you are in town for one or the other or both events!

Wellness and Writing Connections Conference

Wellness and Writing Connections Conference:

The annual Wellness and Writing Connections Conference will be held October 22-23, 2010 at the Georgia Tech Global Learning Center in Atlanta, GA.

This two-day conference brings together a number of powerhouse leaders in the field of writing for health and healing. Breakout sessions include writing and healing in wartime, writing and compassion fatigue, and writing in integrative medicine, in addition to topics in journaling, memoir, psychological journaling, student writings, and more.

Now, more than ever, creative expression, writing, and the arts are being used in medical settings to process experiences of illness and trauma. Research led by Dr. James Pennebaker has shown that the use of writing has physiological benefits to health and can aid in healing from both physical and emotional trauma.

The Friday evening keynote address will feature Roy Fox, Professor of English Education and Director of the Missouri Writing Project at the University of Missouri. The keynote address on Saturday evening will feature Brenda Stockdale, Director of Mind-Body Medicine for the Radiology Clinics of Georgia. Additional speakers include Lucille Allegretti-Freeman, Tim Blue, Susan Borkin, Angela and Dennis Buttiner, Claudia-Hill Duffee, Carolyn Graham, Claudia Hough, Elaine Handley, Leatha Kendrick, Laura Miller, Diana Rash, Jean Rowe, and Barbara Stahura.

To find out more information and to register, contact Director John Evans at or visit and the Facebook page.

[click on the image to see large]

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Grand Rounds Vol. 6 No. 49 – a conference in a tropical island resort

The summer is almost over, but we can try to remain in the summery mood just a little bit longer. Perhaps we can go to a medical conference held at a luscious tropical island resort, listen to presentations, chat in the hallways, and then have great fun at the bar in the evenings. And call it Grand Rounds. No coats and ties allowed – this meeting is supposed to be fun!

Day 1 – Morning session: Biomedical Science

Let’s start with controversy! Laika’s MedLibLog digs into the XMRV controversy with another comprehensive treatment prompted by the newest paper in the field – Does the NHI/FDA Paper Confirm XMRV in CFS? Well, Ditch the MR and Scratch the X… and… you’ve got MLV. And Abbie at ERV covers the same paper without mincing her words – ouch! – in XMRV and chronic fatigue syndrome: Scientific Blue Balls.

Diane Meier at The John A. Hartford Foundation blog wrote a review and summary of a blockbuster study on palliative care and quality (and length!) of life: Palliative Care: We Still Have a Lot to Learn.

Day 1 – afternoon session: The Brain and The Mind

SharpBrains contributors have two entries this week. The first one is by Jo Ellen Roseman and Mary Koppel at AAAS: The Brain in Science Education: What Should Everyone Learn? The second one is Why working memory matters in the knowledge age: study by Dr. Tracy Alloway.

How to Cope with Pain reviews exciting, new, non-invasive and non-medication treatments for pain, in Brain Re-training To Decrease Pain.

Will Meek, PhD is working through human psychology, one post at a time. The latest installment is Romantic vs Committed Love.

Dinah at Shrink Rap, differentiating normal moods from those associated with mental illness: Emotion versus Mental Illness.

Day 1 – hallway conversations: Practice, Patients, Nursing and Cases

Katrina Racial Violence is a poignant recollection of treating a Katrina survivor, who had been threatened with violence, by Toni Brayer, MD at EverythingHealth.

‘Nancy Nurse, RN, MD’ on the Muse, RN is a post motivated by the phrase “If she’s so smart, why isn’t she a doctor?”. Its a little dicey…but Nurses need some dice every once in a while.

Medical Resident, from A Medical Resident’s Journey responds to a recent blog post in the New York Times by Pauline Chen on medical errors: On Medical Mistakes…. And another post on the same topic, at Supporting Safer HealthcareI Care For You; I Am Your Doctor – focuses on the fact that, unfortunately, communication can break down at this most crucial time.

Physician Quality Report Cards, Part II on Kent Bottles Private Views is a post about a physician’s resistance to administrative review and patient feedback. Doctor report cards, NFL football, teachers, controversy, and nasty comments. What more could you want in a blog post?

Fizzy, last week’s host of Grand Rounds over on Mothers in Medicine, starts with a cartoon and writes about looking too young to be a doctor: Get confident, stupid!

Waterworks at Other things amanzi is a great story by Bongi about a joke he played on a not-so-hard-working urologist.

From Kimberly Manning, FACP at ACP Hospitalist, Life at Grady: Black and white, a story about a patient questioning his doctor’s race.

When do medical students start learning to practice medicine defensively? It didn’t take long for this one to encounter the opening lesson: Defensive Medicine 101… it starts now, at The Notwithstanding Blog.

And a little comparative medicine from Dog Zombie: Comparative medicine: what is a wallaby?

Greg Friese at Everyday EMS Tips: Paramedic that Knows Everything Declines Additional Learning

Day 2 – morning session: Medicine and Technology

Livetweeting surgery is becoming all the rage these days. Ramona of Suture for a Living writes about the latest case: Double Hand Transplant on Twitter.

Physicians are a group that greatly adopted the use of smartphones in theor work. Ryan DuBosar at ACP Internist comments in QD: News Every Day–What smartphone are you using?

In Doctors Not Using Email Like It’s 2010 It’s 2010, Elaine Schattner, MD at Medical Lessons considers physicians’ selective use of email, a no-longer-new technology that might, if embraced, facilitate communication between doctors and patients.

Michelle R. Wood of Occam Practice Management looks at some Famous Last Words in regard to technology, and how those words turned out…including the worries about the “paperless” Health Information Technology.

Day 2 – afternoon session: History of Medicine

Delia O’Hara at Birth Story introduces us to a historical figure of Alexis Carrel, who pioneered vascular surgery and transplant surgery.

At From the Hands of Quacks, Jaipreet Virdi gives us a glimpse of quirky medicine from the past, in How to Avoid Deafness and for those who want to know more, there is a Reading List.

Day 2 – hallway conversations: Healthcare policy

Louise at Colorado Health Insurance Insider discusses Amendment 63 On The Ballot In Colorado which will determine who can purchase health insurance.

Day 2 – evening at the bar: The Fun Stuff

The Happy Hospitalist tried something new – to draw a cartoon: Parkinson’s Cruise Cartoon (The Happy Hospitalist Original)

The Poetry Contest at The Examining Room of Dr.Charles ends tonight. Many great health/medical poems were submitted and some of them were posted there. Here is Thirteen Ways of Seeing, a poem (in 13 parts) by Aidel Moodnick.

And with this, the tropical island resort conference ends. Have a great trip home! We’ll see you all again next week at the Grand Rounds hosted by Musings of a Dinosaur.

Call for submissions for Grand Rounds, medical blog carnival

The next edition (Vol. 6 No. 49) of Grand Rounds, the medical blog carnival, will be hosted by me, right here at A Blog Around the Clock. I have hosted it a couple of times early on, but have not done so in a few years. Time to get back to it!

So send me all your posts that have something to do with medicine: fun and quirky stuff, personal stuff, biomedical science, healthcare policy, nursing, patients and cases and medical practice and Medicine2.0 and everything you can think of that is related to medicine and health.

The deadline for submission is August 30th by midnight Eastern time. The carnival will be posted some time in the morning of August 31st.

Send you entries to: nick AT blogborygmi DOT com (though it would be nice if you could also CC it to me at Coturnix AT gmail DOT com if you can remember).

Health and Medicine Poetry Contest

From Dr.Charles (sorry for copying and pasting the whole thing, but I thought all of the information is necessary):

Announcing the first annual 2010 Charles Prize for Poetry. Bold and pretentious name aside, the award will be given to the writer who submits for consideration the most outstanding poem within the context of health and medicine.

Open to everyone (patients, doctors, nurses, students, etc.). Limit 1 or 2 entries per person.

Poems should be related to experiencing, practicing, or reflecting upon a medical, scientific, or health-related matter.

The winner will be selected by a panel of three judges, including me. These other judges may or may not be Nobel Laureates, you never know, but all appreciate poetry. I may ask for your permission to post a copy of your poem on this blog as we go, with or without attribution as you wish.

Is such an eponymous contest grandiose? Yes. Does the limited poetry I’ve written carry the gravitas needed to make me an authority on the subject? No way.

But should your poem be selected as the winner, you shall receive a plaque, an award of $500, and a tasty cherry tomato from my garden. Seriously. At least one person has written that winning the cherry tomato is more important to her than all the gold in the world. I’m sorry that my budget is not higher, but I thought I could swing $500 without enlisting sponsorship. Who needs an iPhone anyway?

So have fun, find inspiration, and send your entry to:

drcharles.examining *at*

Contest closes August 31st.

The Vaccine Song (video)

Books: ‘The Poisoner’s Handbook’ by Deborah Blum

Poisoner's Handbook cover.jpgIf you picked up The Poisoner’s Handbook ( looking for a fool-proof recipe, I hope you have read the book through and realized at the end that such a thing does not exist: you’ll get busted. If they could figure it all out back in 1930s, can you imagine how much easier they can figure out a case of poisoning today, with modern sensitive techniques? And if you have read the book through, I hope you found it as fascinating as I did. Perhaps you should use your fascination with poisons to do good instead, perhaps become a forensic toxicologist?
My SciBling Deborah Blum (blog, Twitter) has done it again – written a fast-paced page-turner, full of action and intrigue, and with TONS of science in it. It reads like a detective novel. Oh, wait, it is a detective novel. Who said that an author has to invent a fictional detective, an Arsene Lupin or Hercule Poirot or Sherlock Holmes or the Three Investigators? There existed in history real people just like them, including Charles Norris and Alexander Gettler, the heroes of The Poisoner’s Handbook.
Charles Norris was the first Chief Medical Examiner of the City of New York, or at least the first one who was actually qualified for that position which, before him, was a political appointment not requiring any expertise. Norris served in this role from 1918. to 1935. and revolutionized both the position and the science of forensic medicine. Alexander Gettler was one of his first appointees, who served as New York City’s chief toxicologist until 1959.
The two of them used their prominent position to set the new high standards for the profession of a public medical examiner, and also set the new high standards for the scientific research in forensic pathology, including forensic toxicology – the study of the way poisons kill and how to detect it. They affected rules and legislation with their work, they sent clever murderers to the electric chair, and exonerated the innocents who were headed that way due to mistakes of the non-science-based courtroom battles. And in order to do that, they needed to do a lot of their own research during many years of long days and nights in the lab performing meticulous and often gruesome studies of the effects of various substances on animals, people, living and dead tissues and coming up with ever more sensitive and clever methods for detecting as small quantities of the poison as was technically possible at the time.
In the author’s note at the end of the book, Deborah Blum notes that there were many other forensic scientists before, during and after the Norris-Gettner era, and many of them got mentioned in the book or are cited in the EndNotes (which I discovered only once I finished the book – I hate the way publishers do this these days!). But it is also true that Norris and Gettner were the leaders – they used their prominent position and political clout, and their meticulous research defined the high standards for the nascent discipline. In a way, the central importance and prominence of these two men worked well for the book – here we have two interesting characters to like and follow instead of a whole plethora of unfleshed names. And as each chapter focuses on one poisonous substance and one or two notorious cases of its use, it is just like following Holmes and Watson through a series of Sir Arthur Conan Doyle’s stories – the two characters are the connecting thread, and they evolve throughout their lives and throughout the book, case by case.
Apart from being a history of forensic toxicology, the book has several other themes that keep recurring in each chapter, as they chronologically unfold. The book is also a history of 1920/30s New York City, and a history of technology and engineering. Carbon monoxide poisoning? That was the beginning of the car craze. Gas? Everyone cooked and heated with it at the time. Some other poisons were easily found in many over-the-counter products in stores and pharmacies.
Having just read On The Grid, I was also attuned to the discussions of infrastructure of NYC in the early 20th century. How did people transport themselves? Air pollution? Gas? Clean water? Wastewater? All sources of potentially toxic chemicals. How efficient was garbage collection? Not much….thus there were many rats. And rats needed to be controlled. And for that, there was plenty of rat poison to be bought. And rat poison can kill a human as well – inadvertently, as a method for suicide, or as a murder weapon. It is kinda fun to see some of the same infrastructure issues, like garbage disposal and pest extermination in N.Y.City, addressed from different angles in different books – this one, On The Grid, as well as Rats, another fascinating science book that covers New York City engineering, infrastructure and politics of the time. All the threads tie in together….
Another topic addressed in each chapter was Prohibition. One can certainly die of a huge overdose of ethyl alcohol normally found in drinks, but at the time when producing and selling drinks was illegal, people still drank, perhaps even more. And what did they drink? Whatever they could find on the black market – home-made concoctions brewed by unsavory types more interested in profit than the safety of their product. Instead of ethyl, those drinks were mostly made of methyl (wood) alcohol which is much more dangerous in much smaller doses. Prohibition saw a large increase in drinking-related deaths, a fact often loudly pronounced by Norris, leading to the eventual end of Prohibition. Can we apply that thinking to the War On Drugs now?
And the story of Prohibition has another element to it – the importance of regulation. An unregulated substance is potentially dangerous. By solving a number of poisoning cases, and by doing their research on the toxicity of then easily available substances, Norris and Gettner have managed to initiate regulation of a number of toxins, or even their removal from the market altogether. Some substances that were found in everything, even touted as health potions (even radioactive substances!!!) were discovered by forensic toxicologists to be deadly, and were subsequently banned or rigorously controlled. Today we have entire federal agencies dealing with regulation of dangerous chemicals, but in the early 20th century, it was the time of laissez-faire murder, suicide, suffering and death.
Finally, after I finished this fascinating book, I realized it gave me something more: an anchor, or a scaffolding, or a context, for every story about poisons I see now. Now every blog post on Deborah’s blog makes more sense – I can fit it into a body of knowledge and understanding I would not have if I have not read the book. This really goes hand in hand with the recent discussions of #futureofcontext in journalism – see The Future Of Context for starters. The idea is that news stories do not provide enough context for readers who tune into a new topic for the first time. A story that is an update on an ongoing story is not comprehensible without some context, which the news story cannot provide. So now various media organizations are experimenting with ways to provide context for people who are just tuning in. The perfect source of context for a topic is a book, especially now that every book appears to have its own website with links and news and a blog and a Twitter feed and a Facebook page. The book provides context, and all these other things provide updates.
For example, reading Bonobo Handshake may not provide much more context for me about animal behavior and cognition since I already have that context, but it certainly now makes it easier for me to understand the news stories regarding conservation of great apes. And without that book I would never have sufficient background in the recent history of Congo to understand and appreciate this comment thread. ‘On The Grid’ gives me context for all news regarding infrastructure. Explaining Research is a great recent example of a book that is a great start on the topic, but which constantly reminds the reader that this field is in flux and that the book’s website contains frequent updates and additional resources. The Immortal Life of Henrietta Lacks provides fantastic context for the discussions of medical ethics and its evolution in the USA in the past several decades, which I riffed off a little bit in my latest interview.
What reading The Poisoner’s Handbook did for me is to give me enough knowledge and understanding on the topic that I can really appreciate it. I now get excited about news stories regarding poisons because I feel I understand them better. While reading Deborah Blum’s blog was interesting before, now it is more than interesting – it is exciting and I can’t wait for a new post to show up. I did not know how much I did not know. Now that I do, I want to know more. I am hungry for more knowledge, and more news, and more stories about toxins and poisons and how various strange and not so strange substances affect our bodies – where they come from, how they get in, how they hijack or disrupt our normal biochemical processes, how they kill us, and how do we figure that all out in the laboratory or in the basement of the mortuary. I hope you will feel the same once you finish reading this book. You will do that now, OK?

The Benefits and Burdens of Genetic Testing

New podcast and forums at World Science: The Benefits and Burdens of Genetic Testing:

Listen to a story by reporter Marina Giovannelli, followed by our interview with Mayana Zatz.
Download MP3
Our guest in the Science Forum is geneticist and genetic counselor Mayana Zatz. She directs the Human Genome Research Center at the University of Sao Paolo.
Zatz has been working with patients with inherited disorders for nearly two decades. When it comes to genetic testing, Zatz advocates caution. Tests for some inherited disorders have helped people decide whether or not to have children. But in most cases, Zatz says genetic testing raises complex psychological and ethical issues:
* Should children be tested for late-onset disorders like Huntington’s disease and cerebellar ataxia? Doing so could lead to a life of dread, as they wait for a disease for which there is no cure.
* Interpreting the results from a genetic test can be difficult, especially for complex diseases like cancer or Alzheimer’s which are triggered by multiple factors, not just genetics.
Come join the conversation with Mayana Zatz. She’s taking your comments and questions through July 13th.
* Have you had your genes read? How did the results change your life?
* Should companies offering such tests be regulated?
* What kinds of medical benefits can we expect from genomics research in the coming years?

Real Guys Immunize

guyzimmunize logo.jpgLast week I went to Philadelphia to a very interesting meeting – a Social Media Summit on Immunization. Sponsored by Immunization Action Coalition, this was a second annual meeting for health-care non-profits, organized (amazingly well, with great attention to detail) by Lisa Randall (and, I am sure, a small army of helpers).
Over a day and a half of the meeting there were two simultaneous sessions at each time slot, but I did not have much opportunity to ponder my choices as I was at the front of the room at three sessions, and participated actively in several others. The style was very ‘unconference-y’, with barely any PowerPoint – we talked and showed stuff on the Web as needed.
We discussed pros and cons of using various online platforms for spreading the message about vaccinations (which also means pushing back against anti-vaccination propaganda), making sure that all of the representatives of the non-profits understand they don’t have to use all (or any) of them unless this can be useful for the work they want to do and the goal they want to achieve. But if they do feel it is necessary, we were there to explain and demonstrate how to do it: static pages, blogs, Facebook, Twitter, YouTube, etc., the best practices and strategies for using each of these platforms, the metrics for measuring the spread of their message, etc. This was a LOT of stuff, and we covered a lot of ground, but I hope we were useful.
On the second day, we had a very interesting discussion following the presentation by Anna Kata, anthropologist from McMaster University, whose recent paper, A postmodern Pandora’s box: anti-vaccination misinformation on the Internet, analyzed the arguments by the anti-vaccination groups use in their online discussions. What is most interesting is that every single one of these arguments is nothing new – each has been used from the very beginning of vaccination, in 1796, from personal attacks on Edward Jenner, to arguments about “playing God”, to fear of putting animal material into bodies, to suspecting a conspiracy by government, industry and medical profession, to arguments for personal freedom, to proposing alternative theories of health (and disease and treatments). It never really stopped, it just has some very prominent spokesemen right now, visible in the media.
What is important is that people who reject vaccination are not the uneducated and the poor. The poor tend to trust the authority of physicians and will gladly vaccinate – if they can afford it. It is the upper-middle-class, at least nominally well educated, that refuses to vaccinate their kids. Trying to change their minds by presenting them the information does not work – they do not treat that information as valid. They live in a post-modern world in which everyone is entitled to their own facts. Their notions of body, health, and disease are very holistic, very New-Agey, so medical information does not mean anything to them. But they (not the activists, but parents seeking information) can be swayed by peer pressure. And nothing works better than for them to hear, from their friends, family, neighbors, colleagues and physicians, over and over again “I vaccinated my kids, trust me, I know what I’m doing, you should vaccinate yours, too.” If people they trust vaccinate, they will start wavering in their beliefs and may end up vaccinating themselves in the end. It is that social pressure, and need to socially conform, that is much more powerful than all the medical information in the world.
As a demonstration of the way, and ease of the way, for putting together a social media strategy, a group of ‘Social Media Ninjas’, about 5-6 of them who have never met or worked together before, took over one of the rooms and all of its computers during the meeting. They had 24 hours from start to finish. They started by crowdsourcing ideas, then picking one and running with it. The one they picked was focused on explaining ‘herd immunity’ and the target audience was men.
Almost all of the activity in persuading people to vaccinate their kids targets women, as it is supposed that mothers are the only ones making decisions about their children. This leaves out half of the population. And that half of the population can really help. In some families, still in the 21st century I know, the father has the last word. In other families, mother may resist vaccines out of fear and insecurity and her husband’s support can make all the difference – they can study the issue together, discuss it and make the decision together.
So the Social Media Ninja team, in that 24-hour period, came up with the name – “Real Guys Immunize” – drew a logo, and built a static web page, which explains what this is all about, provides brief FAQs and links to external resources. It also provides an easy way for readers to post personal stories.
They started a Twitter account (and the #guysimmunize hashtag), a YouTube channel and a Facebook page. They designed an e-card for Father’s Day. They had a couple of participants write blog posts (see here and here). And they put together a cool slideshow:

They decided against making a video (24 hours was too short, and nobody in the room was a real video-maven) though this can be done later, and made other changes to the original plan as the 24 hours passed. At the very end, they presented all of that to the gathering, including the first metrics of their reach (whatever one can measure after such a short time):

The site (and everything else associated with it on social media) is not really owned by anyone – it was just an experiment done to show how such a thing is made. So, if anyone is interesting in taking over this initiative and moving it forward into the future, there is a contact e-mail there, just click.

Going Mad The American Way

New podcast and forum at PRI World Science:

Listen to a story by reporter Laura Starecheski, followed by our interview with Ethan Watters.
Our guest in the Science Forum is journalist Ethan Watters.
His latest book is Crazy Like Us: The Globalization of the American Psyche.
“America is homogenizing the way the world goes mad,” Watters writes. He contends that Americans are exporting their view of mental illness to the rest of the world.
Watters says culture influences not only how people deal with mental disorders but how mental disorders manifest themselves. Yet those cultural differences are disappearing as Western notions of mental health become popular worldwide.
Some examples Watters cites in his book:
• Anorexia nervosa, the eating disorder, is now common in countries with no history of the disease.
• Modern biomedical notions of schizophrenia are replacing the idea of spirit possession in places like Zanzibar.
• By selling pills for depression, pharmaceutical companies have caused a rise in the diagnosis of depression in Japan.
Bring your thoughts and questions about culture and mental illness to Watters. The discussion is just to the right.
* Is America’s view of mental health reflective of the nation’s individualistic culture?
* Have you or a family member been diagnosed with mental illness? Has your ethnic or religious background influenced your response?
* Would Americans benefit from importing ideas of mental health from other countries?

Related reading: The Americanization of Mental Illness.

Public vs. Publicized: Future of the Web at WWW2010

2010-logo-small1.jpgIt is somewhat hard to grok how much a Big Deal the WWW2010 conference is when it’s happening in one’s own backyard. After all, all I had to do was drop the kids at school a little earlier each morning and drive down to Raleigh, through the familiar downtown streets, park in a familiar parking lot, and enter a familiar convention center, just to immediately bump into familiar people – the ‘home team’ of people I have been seeing at blogger meetups, tweetups and other events for years, like Paul Jones, Ruby Sinreich, Fred Stutzman, Ryan Boyles, Wayne Sutton, Kim Ashley, Henry Copeland and others.
But it is a Big Deal. It is the ‘official’ conference of the World Wide Web. Yup, Tim Berners-Lee, the guy who invented the Web, was there. I saw him, though I did not talk to him. I mean, what excuse could I come up with to approach him? Ask him to autograph my web browser?

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A new medical research blog

Introducing Beaker, inspired by our panel at AAAS a couple of months ago. Go take a look.

Evolutionary Medicine: Does reindeer have a circadian stop-watch instead of a clock?

ResearchBlogging.orgWhenever I read a paper from Karl-Arne Stokkan’s lab, and I have read every one of them, no matter how dense the scientese language I always start imagining them running around the cold, dark Arctic, wielding enormous butterfly nets, looking for and catching reindeer (or ptarmigans, whichever animal the paper is about) to do their research.


If I was not so averse to cold, I’d think this would be the best career in science ever!
It is no surprise that their latest paper – A Circadian Clock Is Not Required in an Arctic Mammal (press release) – was widely covered by the media, both traditional and blogs, See, for example, The Scientist, BBC, Scientific American podcast and Wired Science.
Relevant, or just cool?
It is hard to find a science story that is more obviously in the “that’s cool” category, as opposed to the “that’s relevant” category. For the background on this debate, please read Ed Yong, David Dobbs, DeLene Beeland, Colin Schultz, and the series of Colin’s interviews with Carl Zimmer, Nicola Jones, David Dobbs, Jay Ingram, Ferris Jabr, Ed Yong and Ed Yong again.
I agree, it is a cool story. It is an attention-grabbing, nifty story about charismatic megafauna living in a strange wilderness. I first saw the work from the lab in a poster session at a conference many years ago, and of all the posters I saw that day, it is the reindeer one that I still remember after all these years.
Yet, the coolness of the story should not hide the fact that this research is also very relevant – both to the understanding of evolution and to human medicine. Let me try to explain what they did and why that is much more important than what a quick glance at the headlines may suggest. I did it only part-way a few years ago when I blogged about one of their earlier papers. But let me start with that earlier paper as background, for context.
Rhythms of Behavior
In their 2005 Nature paper (which was really just a tiny subset of a much longer, detailed paper they published elsewhere a couple of years later), Stokkan and colleagues used radiotelemetry to continuously monitor activity of reindeer – when they sleep and when they roam around foraging.
You should remember that up in the Arctic the summer is essentially one single day that lasts several months, while the winter is a continuous night that lasts several months. During these long periods of constant illumination, reindeer did not show rhythms in activity – they moved around and rested in bouts and bursts, at almost unpredictable times of “day”. Their circadian rhythms of behavior were gone.
But, during brief periods of spring and fall, during which there are 24-hour light-dark cycles of day and night, the reindeer (on the northern end of the mainland Norway, but not the population living even further north on Svaldbard which remained arrhythmic throughout), showed daily rhythms of activity, suggesting that this species may possess a circadian clock.
Rhythms of Physiology
In a couple of studies, including the latest one, the lab also looked into a physiological rhythm – that of melatonin synthesis and secretion by the pineal gland. Just as in activity rhythms, melatonin concentrations in the blood showed a daily (24-hour) rhythm only during the brief periods of spring and fall. Furthermore, in the latest paper, they kept three reindeer indoors for a couple of days, in light-tight stalls, and exposed them to 2.5-hour-long periods of darkness during the normal light phase of the day. Each such ‘dark pulse’ resulted in a sharp rise of blood melatonin, followed by just as abrupt elimination of melatonin as soon as the lights went back on.
reindeer melatonin.jpg
Rhythms of gene expression
Finally, in this latest paper, they also looked at the expression of two of the core clock genes in fibroblasts kept in vitro (in a dish). Fibroblasts are connective tissue cells found all around the body, probably taken out of reindeer by biopsy. In other mammals, e.g., in rodents, clock genes continue to cycle with a circadian period for a very long time in a dish. Yet, the reindeer fibroblasts, after a couple of very weak oscillations that were roughly in the circadian range, decayed into complete arrhytmicity – the cells were healthy, but their clocks were not ticking any more.
reindeer fibroblasts.jpg
What do these results suggest?
There is something fishy about the reindeer clock. It is not working the same way it does in other mammals studied to date. For example, seals and humans living in the Arctic have normal circadian rhythms of melatonin. Some other animals show daily rhythms in behavior. But in reindeer, rhythms in behavior and melatonin can be seen only if the environment is rhythmic as well. In constant light conditions, it appears that the clock is not working. But, is it? How do we know?
During the long winter night and the long summer day, the behavior of reindeer is not completely random. It is in bouts which show some regularity – these are ultradian rhythms with the period much shorter than 24 hours. If the clock is not working in reindeer, i.e., if there is no clock in this species, then the ultradian rhythms would persist during spring and fall as well. Yet we see circadian rhythms during these seasons – there is an underlying clock there which can be entrained to a 24-hour light-dark cycle.
This argues for the notion that the deer’s circadian clock, unless forced into synchrony by a 24 external cycle, undergoes something called frequency demultiplication. The idea is that the underlying cellular clock runs with a 24-hour period but that is sends signals downstream of the clock, triggering phenotypic (observable) events, several times during each cycle. The events happen always at the same phases of the cycle, and are usually happening every 12 or 8 or 6 or 4 or 3 or 2 or 1 hours – the divisors of 24. Likewise, the clock can trigger the event only every other cycle, resulting in a 48-hour period of the observable behavior.
If we forget for a moment the metaphor of the clock and think instead of a Player Piano, it is like the contraption plays the note G several times per cycle, always at the same moments during each cycle, but there is no need to limit each note to appear only once per cycle.
On the other hand, both the activity and melatonin rhythms appear to be driven directly by light and dark – like a stop-watch. In circadian parlance this is called an “hourglass clock” – an environmental trigger is needed to turn it over so it can start measuring time all over again. Dawn and dusk appear to directly stop and start the behavioral activity, and onset of dark stimulates while onset of light inhibits secretion of melatonin. An “hourglass clock” is an extreme example of a circadian clock with a very low amplitude.
While we mostly pay attention to period and phase, we should not forget that amplitude is important. Yes, amplitude is important. It determines how easy it is for the environmental cue to reset the clock to a new phase – lower the amplitude of the clock, easier it is to shift. In a very low-amplitude oscillator, onset of light (or dark) can instantly reset the clock to Phase Zero and start timing all over again – an “hourglass” behavior.
The molecular study of the reindeer fibroblasts also suggests a low-amplitude clock – there are a couple of weak oscillations to be seen before the rhythm goes away completely.
There may be other explanations for the observed data, e.g., masking (direct effect of light on behavior bypassing the clock) or relative coordination (weak and transient entrainment) but let’s not get too bogged down in arcane circadiana right now. For now, let’s say that the reindeer clock exists, that it is a very low-amplitude clock which entrains readily and immediately to light-dark cycles, while it fragments or demultiplies in long periods of constant conditions.
Why is this important to the reindeer?
During long night of the winter and the long day of the summer it does not make sense for the reindeer to behave in 24-hour cycles. Their internal drive to do so, driven by the clock, should be overpowered by the need to be flexible – in such a harsh environment, behavior needs to be opportunistic – if there’s a predator in sight: move away. If there is food in sight – go get it. If you are full and there is no danger, this is a good time to take a nap. One way to accomplish this is to de-couple the behavior from the clock. The other strategy is to have a clock that is very permissive to such opportunistic behavior – a very low-amplitude clock.
But why have clock at all?
Stokkan and colleagues stress that the day-night cycles in spring help reindeer time seasonal events, most importantly breeding. The calves/fawns should be born when the weather is the nicest and the food most plentiful. The reindeer use those few weeks of spring (and fall) to measure daylength (photoperiod) and thus time their seasonality – or in other words, to reset their internal calendar: the circannual clock.
But, what does it all mean?
All of the above deals only with one of the two hypotheses for the adaptive function (and thus evolution) of the circadian clock. This is the External Synchronization hypothesis. This means that it is adaptive for an organism to be synchronized (in its biochemistry, physiology and behavior) with the external environment – to sleep when it is safe to do so, to eat at times when it will be undisturbed, etc. In the case of reindeer, since there are no daily cycles in the environment for the most of the year, there is no adaptive value in keeping a 24-hour rhythm in behavior, so none is observed. But since Arctic is highly seasonal, and since the circadian clock, through daylength measurement (photoperiodism) times seasonal events, the clock is retained as an adaptive structure.
This is not so new – such things have been observed in cave animals, as well as in social insects.
What the paper does not address is the other hypothesis – the Internal Synchronization hypothesis for the existence of the circadian clock – to synchronize internal events. So a target cell does not need to keep producing (and wasting energy) to produce a hormone receptor except at the time when the endocrine gland is secreting the hormone. It is a way for the body to temporally divide potentially conflicting physiological functions so those that need to coincide do so, and those that conflict with each other are separated in time – do not occur simultaneously. In this hypothesis, the clock is the Coordination Center of all the physiological processes. Even if there is no cycle in the environment to adapt to, the clock is a necessity and will be retained no matter what for this internal function, though the period now need not be close to 24 hours any more.
What can be done next?
Unfortunately, reindeer are not fruitflies or mice or rats. They are not endangered (as far as I know), but they are not easy to keep in the laboratory in large numbers in ideal, controlled conditions, for long periods of time.
Out in the field, one is limited as to what one can do. The only output of the clock that can be monitored long-term in the field is gross locomotor activity. Yet, while easiest to do, this is probably the least reliable indicator of the workings of the clock. Behavior is too flexible and malleable, too susceptible to “masking” by direct effects of the environment (e.g., weather, predators, etc,). And measurement of just gross locomotor activity does not tell us which specific behaviors the animals are engaged in.
It would be so nice if a bunch of reindeer could be brought into a lab and placed under controlled lighting conditions for a year at a time. One could, first, monitor several different specific behaviors. For example, if feeding, drinking and defecation are rhythmic, that would suggest that the entire digestive system is under circadian control: the stomach, liver, pancreas, intestine and all of their enzymes. Likewise with drinking and urination – they can be indirect indicators of the rhytmicity of the kidneys and the rest of the excretory system.
In a lab, one could also continuously monitor some physiological parameters with simple, non-invasive techniques. One could, for example monitor body temperature, blood pressure and heart-rate, much more reliable markers of circadian output. One could also take more frequent blood samples (these are large animals, they can take it) and measure a whole plethora of hormones along with melatonin, e.g., cortisol, thyroid hormones, progesterone, estrogen, testosterone, etc (also useful for measuring seasonal responses). One could measure metabolites in urine and feces and also gain some insight into rhythms of the internal biochemistry and physiology. All of that with no surgery and no discomfort to the animals.
Then one can place reindeer in constant darkness and see if all these rhythms persist or decay over time. Then one can make a PhaseResponse Curve and thus test the amplitude of the underlying oscillator (or do that with entrainment to T-cycles, if you have been clicking on links all along, you’ll know what I’m talking about). One can test their reproductive response to photoperiod this way as well.
Finally, fibroblasts are peripheral cells. One cannot expect the group to dissect suprachiasmatic nuclei out of reindeer to check the state of the master pacemaker itself. And in a case of such a damped circadian system, testing a peripheral clock may not be very informative. Better fibroblasts than nothing, but there are big caveats about using them.
Remember that the circadian system is distributed all around the body, with each cell containing a molecular clock, but only the pacemaker cells in the suprachiasmatic nucleus are acting as a network. In a circadian system like the one in reindeer, where the system is low-amplitude to begin with, it is almost expected that peripheral clocks taken out of the body and isolated in a dish will not be able to sustain rhythms for very long. Yet those same cells, while inside of the body, may be perfectly rhythmic as a part of the ensemble of all the body cells, each sending entraining signals to the others every day, thus the entire system as a whole working quite well as a body-wide circadian clock. This can be monitored in real-time in transgenic mice, but the technology to do that in reindeer is still some years away.
Finally, one could test a hypothesis that the reindeer clock undergoes seasonal changes in its organization at the molecular level by comparing the performance of fibroblasts (and perhaps some other peripheral cells) taken out of animals at different times of year.
What’s up with this being medically relevant?
But why is all this important? Why is work on mice not sufficient and one needs to pay attention to a strange laboratory animal model like reindeer?
First, unlike rodents, reindeer is a large, mostly diurnal animal. Just like us.
a1 reindeer.jpg
Second, reindeer normally live in conditions that make people sick, yet they remain just fine, thank you. How do they do that?
Even humans who don’t live above the Arctic Circle (or in the Antarctica), tend to live in a 24-hour society with both light and social cues messing up with our internal rhythms.
We have complex circadian systems that are easy to get out of whack. We work night-shifts and rotating shifts and fly around the globe getting jet-lagged. Jet-lag is not desynchronization between the clock and the environment, it is internal desynchronization between all the cellular clocks in our bodies.
In the state of almost permanent jet-lag that many of us live in, a lot of things go wrong. We get sleeping disorders, eating disorders, obesity, compromised immunity leading to cancer, problems with reproduction, increase in psychiatric problems, the Seasonal Affective Disorder, prevalence of stomach ulcers and breast cancer in night-shift nurses, etc.
Why do we get all that and reindeer don’t? What is the trick they evolved to stay healthy in conditions that drive us insane and sick? Can we learn their trick, adopt it for our own medical practice, and use it? Those are kinds of things that a mouse and a rat cannot provide answers to, but reindeer can. I can’t think of another animal species that can do that for us. Which is why I am glad that Stokkan and friends are chasing reindeer with enormous butterfly nets across Arctic wasteland in the darkness of winter 😉
Lu, W., Meng, Q., Tyler, N., Stokkan, K., & Loudon, A. (2010). A Circadian Clock Is Not Required in an Arctic Mammal Current Biology, 20 (6), 533-537 DOI: 10.1016/j.cub.2010.01.042

Personalized Medicine: Too Much Information / Too Little Information

Next American Scientist Pizza Lunch:

It’s not often that we get to dive a little deeper into a topic encountered at a recent pizza lunch talk. But we will this month. In March, Geoff Ginsburg from Duke briefed us well on the current science regarding genomic (or personalized) medicine and its promising applications. At noon on Tuesday, April 20, Jim Evans from UNC-Chapel Hill will discuss the complexity of implementing this new medicine with a talk entitled: Personalized Medicine: Too Much Information / Too Little Information. Like Dr. Ginsburg, Dr. Evans is a doctor-scientist. He is also editor of the journal Genetics in Medicine and sits on an advisory committee to the U.S. Secretary of Health and Human Services on genetics, health and society.
American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for the slice count) to
This time, we’ll be back at our home base, Sigma Xi in Research Triangle Park. You’ll find directions here:

New public health blog

Long-time observers of the progressive blogopshere are likely aware of Barbara O’ Brien and her blogging at The Mahablog, Crooks and Liars, AlterNet, and elsewhere. She was a panelist at the Yearly Kos Convention and a featured guest blogger at the Take Back America Conference in Washington, DC.
Now, Barbara has a new project – Mesothelioma Blog – where she is dissecting the Health Care Bill, the public concern of health care, and related issues in health care in the United States. The topics include health reform, public health, and asbestos contamination.. Check out Mesothelioma Blog today, post comments, subscribe and bookmark and spread the word.

American Scientist pizza lunch – genomic and personalized medicine

From the American Scientist:

Our American Scientist pizza lunch talk falls later than usual this month to accommodate our magazine’s May-June issue deadline. Keep open the noon hour on March 30 and come hear Geoff Ginsburg, director of the Center for Genomic Medicine at Duke University, discuss genomic and personalized medicine.
To keep you on your toes, we’ll convene at a different spot: the easy-to-get-to headquarters of the NC Biotechnology Center here in RTP. Actually, as many of you know, there would be no pizza lunch this year without the support of the Biotech Center. In addition to their financial help, center staff kindly offered to host one of our gatherings this year.
American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for the slice count) to
Directions to the NC Biotechnology Center are here:

Science Cafe Raleigh – Our bodies: the Final Frontier

From the NC Museum of Natural Sciences:

OUR BODIES: The Final Frontier
Tuesday, March 23, 2010 – 6:30-8:30 pm with discussion beginning
at 7:00 followed by Q&A
Location: Tir Na Nog 218 South Blount Street, Raleigh, 833-7795
We have come to think of the world as known. It isn’t. Even basic parts of our own bodies remain totally unexplored. For example, have you ever stopped to wonder why you are naked? Aside from naked mole rats, we are among the only land mammals to be essentially devoid of hair. Why? Join us for a discussion about the human body and its adaptations to a world filled with predators, pathogens and parasites. Bring your appendix, if you still have one, and learn about its special purpose.
About the Speaker:
Rob Dunn is an ecologist in the Department of Biology at North Carolina State University where he studies the global distribution of life and how it is changing as we change the world. He also studies ants. Dunn’s award-winning book “Every Living Thing” (Harper Collins, 2009) explores the strange limits of the living world and the stranger scientists that study them. His next book, “Clean Living is Bad for You … and Other Modern Consequences of Having Evolved in the Wild,” will be out in 2010. Dunn also writes articles for magazines including National Geographic, Natural History, Seed, Scientific American and National Wildlife. To read more of Rob’s writing, sign up for his email list at:
RSVP to For more information, contact Katey Ahmann at 919-733-7450, ext. 531.

Cambodian Attitudes and Mental Health on the Eve of the Khmer Rouge Trials

At Pizza Lunch talks, we hear a lot about efforts to decipher the physical world. But what about psychological realms? How do you measure them, especially on a large scale among people scarred by trauma? At noon on Thursday, Feb. 18, come hear Dr. Jeffrey Sonis discuss “Cambodian Attitudes and Mental Health on the Eve of the Khmer Rouge Trials.” The UNC-Chapel Hill physician and public health researcher is studying how Cambodians are responding to the genocide trials.
American Scientist Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to anyone who might want to attend. RSVPs are required (for an accurate slice count) to
Directions to Sigma Xi:

Should it be legal to buy and sell organs?

The current forum discussion on PRI/BBC The World is Tackling the Global Organ Shortage. This week’s guest is Dr. Mustafa Al-Mousawi, past president of the Middle East Society for Organ Transplantation. Listen to the podcast and ask Dr. Al-Mousawi questions in the forum. He’ll be checking in and responding throughout the week:

Worldwide, there is a dire shortage of organs for transplantation.
In the United States alone, more than 100,000 people are waiting for new hearts, lungs and kidneys. Many of these patients will die waiting.
Frustrated, some patients turn to a global black market in organs.
To tackle the organ shortage, countries are experimenting with various strategies.
Israel just enacted a new law to boost the number of donors. The law favors donors over non-donors when it comes to receiving an organ. And some Americans are pushing a controversial solution – legalizing the buying and selling of organs.
Iran is already doing that. The Iranian government gives every kidney donor $1200 and one year of free health care. This system has increased the availability of organs, but at what price?
We spoke about the Iranian law with transplant surgeon Dr. Mustafa Al-Mousawi, past president of the Middle East Society for Organ Transplantation.
He argues that the Iranian system may have reduced the organ shortage, but it is unfair to the donors, who are often poor and underprivileged.

Forum: Preventing Future Bhopals

It was 25 years ago yesterday that thousands dies in the Bhopal disaster.
Yesterday, Rhitu Chatterjee did the story about it (listen or read the transcript) on PRI The World.
Also yesterday, Rhittu and Elsa Youngsteadt interviewed Henrik Selin of Boston University about the topic (download the MP3 of the podcast here) and you can ask questions and join the discussion in the forums. Dr. Selin will be checking in and responding from now until next Thursday, December 10th.

AIDS Day (and Techie Tuesday) in RTP in an hour

You can follow the event virtually in Second Life – just click here and teleport.

World AIDS Day and Techie Tuesday in RTP

“Celebration of Life”
Research Triangle Global Health Excellence & World AIDS Day
Date: December 1, 2009
Time: 4:30 pm to 7:30 pm
Location: RTP Headquarters – 12 Davis Drive
Catering By: Nantucket Café & Neomonde
Did you know the Triangle region is a center of excellence in global health?
Help celebrate World AIDS Day and find out how RTP companies and stakeholders are making an impact on HIV/AIDS and other important global health concerns.
Global health organizations in the Park are helping people live longer, more productive lives by working to address HIV/AIDS and other life-threatening conditions. Please join The Research Triangle Park and partner organizations for a special Techie Tuesday to celebrate those that are addressing modern global health challenges, including HIV/AIDS, through research and support services in the RTP and global communities.
Throughout the evening, experts in the field of global health will share insights from their work in one of the main conference rooms of the RTP Headquarters.
Dr. Myron S. Cohen
Director, UNC Center for Infectious Diseases
Chief, Division of Infections Diseases
J. Herbert Bate Distinguished Professor of Medicine & Microbiology, Immunology & Public Health
Dr. Nicole Fouche
Executive Director, Triangle Global Health Consortium
As part of the event, RTP will host a food drive to donate canned goods and non-perishable items to the Alliance for Aids Services Carolina food pantry. Please consider bringing a canned item to the event to help the cause (click here for a list of canned items to donate).
Also, if you are interested in organizing a collection within your company to donate goods at the Techie Tuesday event, please contact Alice Lockhart at for more information.

More information

The podcast of the radio show is now online

You can listen to the Friday episode of Skeptically Speaking here. I am at the beginning, first 10 minutes or so, explaining what ScienceOnline2010 is all about. But the rest of the show with Paul Ingraham is very interesting as well.

Genomics of Emerging Infectious Disease PLoS Collection

If you follow me on Twitter or peruse the links in my daily Tweetlinks summaries, you may have noticed I posted several links to a new Collection at PLoS. This one is not a PLoS ONE Collection, but a PLoS-wide one, spanning six of the seven journals in the house.
The Collection Genomics of Emerging Infectious Disease, was compiled by Jonathan A. Eisen (who you probably know from his excellent blog), the Academic Editor-in-Chief at PLoS Biology.
Jonathan, together with PLoS Biology Senior Editor Catriona J. MacCallum, wrote the introductory editorial explaining what the Collection is about and I particularly like the comparison to the world of birding:

When an American robin (Turdus migratorius) showed up in London a few years ago, birders were rapidly all atwitter and many came flocking to town [22]. Why had this one bird created such a stir? For one main reason–it was out of place. This species is normally found in North America and only very rarely shows up on the other side of the “pond.” Amazingly, this rapid, collective response is not that unusual in the world of birding. When a bird is out of place, people notice quickly.
This story of the errant robin gets to the heart of the subject of this collection because being out of place in a metaphorical way is what defines an emerging infectious disease. Sometimes we have never seen anything quite like the organism or the disease before (e.g., SARS, Legionella). Or perhaps, as with many opportunistic pathogens, we have seen the organism before but it was not previously known to cause disease. In other cases, such as with as pandemic H1N1 2009 or E. coli O157:H7, we have seen the organism cause disease before but a new form is causing far more trouble. And of course organisms can be literally out of place, by showing up in a location not expected (e.g., consider the anthrax letters [2]).
Historically, despite the metaphorical similarities with the robin case, the response to emerging infectious disease is almost always much slower. Clearly, there are many reasons for these differences, which we believe are instructive to consider. At least four factors are required for birders’ rapid responses to the arrival of a vagrant bird: (1) knowledge of the natural “fauna” in a particular place, (2) recognition that a specific bird may be out of place, (3) positive identification of the possibly out-of-place bird, and (4) examination of the “normal” place for relatives of the identified bird.
How are these requirements achieved? Mostly through the existence of high-quality field guides that allow one to place an organism such as a bird into the context of what is known about its relatives. This placement in turn is possible because of two key components of field guides. First, such guides contain information about the biological diversity of a group of organisms. This usually includes features such as a taxonomically organized list of species with details for each species on biogeography (distribution patterns across space and time, niche preferences, relative abundance), biological properties (e.g., behavior, size, shape, etc.), and genetic variation within the species (e.g., presence of subspecies). Second, a good field guide provides information on how to identify particular types (e.g., species) of those organisms. With such information, and with a network of interested observers, an out-of-place bird can be detected with relative ease.
In much the same way, a field guide to microbes would be valuable in the study of emerging infectious diseases. The articles in this collection describe what can be considered the beginnings of species-specific field guides for the microbial agents of emerging diseases. If we want to truly gain the benefits that can come from good field guides it will be necessary to expand current efforts to include more organisms, more systematic biogeographical sampling, and more epidemiological and clinical data. But the current efforts are a great start.

On the PLoS blog, Catriona J. MacCallum explains:

The collection is a collaborative effort that combines financial support from with the editorial independence and rigor of PLoS and the expert opinion of leading researchers from several different disciplines. You can read more about’s involvement in a blog post from Frank Rijsberman. In one of the articles (from PLoS Biology), Gupta et al. discuss’s vision as a funding agency for how the international community might unite to best take advantage of the new technology for combating infectious disease. The challenges are large and each article ends with a section summarizing what these are and how they might be overcome.

You can also download and listen to the podcast about the Collection, in which Dr.Kirsten Sanford interviews Jonathan Eisen and two of the authors of Collection artices Siv Andersson, and Raj Gupta (both Dr.Eisen and Dr.Sanford will also attend ScienceOnline2010, for those of you interested in the event).
The press release (also here) also contains all the relevant links:

Emerging infectious diseases are caused by a wide range of organisms, but they are perhaps best typified by zoonotic viral diseases, which cross from animal to human hosts and can have a devastating impact on human health. These zoonotic diseases include monkeypox, Hendra virus, Nipah virus, and severe acute respiratory syndrome coronavirus (SARS-CoV), in addition to influenza A and the lentiviruses (HIV) that cause AIDS. As Albert Osterhaus and colleagues from the Erasmus Medical Center, Rotterdam, The Netherlands, point out in their article in the collection, the apparent increased transmission of pathogens from animals to humans over recent decades can be attributed to the unintended consequences of globalization as well as environmental factors and changes in agricultural practices.
Articles in the collection also shine a spotlight on specific pathogens, some familiar and widespread, such as the influenza A virus, some “reemerging,” such as the Mycobacterium tuberculosis complex that causes tuberculosis, and some identified only relatively recently, such as the bacterium Helicobacter pylori, which is associated with peptic ulcers and gastric cancer. Others discuss the broader implications of genomics research in this area, such as what it means for researchers in developing countries or for our biosecurity. As Jacques Ravel and colleagues from the US University of Maryland School of Medicine note, genomics can and should be used proactively to build our preparedness for and responsiveness to biological threats.

On the official Google blog Frank Rijsberman writes:

The first outbreak of the new “swine flu” strain, now known as H1N1, earlier this year in Mexico caught the world by surprise. Public health officials around the world tried to stop the virus at the borders but were largely helpless. Shortly after, on the other side of the world from Mexico, I saw the health check posts in Cambodia at the airport and at a borderpost with Vietnam, right when the country found its first H1N1 cases which were flown in by US exchange students. The weapons used by the health officials to combat the spread of the virus were primarily paper survey forms and thermometers; the virus won, very quickly. Genomics is rapidly changing both the way diseases are diagnosed and the way medications and vaccines are developed – but will it give us the tools to prevent the next pandemic?

So take a look at the Genomics of Emerging Infectious Disease Collection today and read all the exciting articles in it.

PLoS Medicine’s 5th anniversary competition

On Speaking of Medicine:

PLoS Medicine turns 5 years old on October 19th, 2009. To highlight the crucial importance of open access in medical publishing we’re holding a competition to find the best medical paper published under an open-access license anywhere (not just in PLoS) since our launch.
Vote for your choice from the 6 competing papers, detailed below — nominated and then shortlisted by our editorial board. Winners will be announced during Open-Access week (19-23rd October 2009). If you’re interested in how we came up with this shortlist of top-quality open-access medicine papers, please read on below the poll.

Go vote!

Influenza — What’s more contagious, the virus or the hype?

sconc flu.JPG

Democracy w/o Newspapers panel at Netroots Nation (video)

Well worth your time to watch:

Introducing PLoS Currents: Influenza

Yesterday PLoS and Google unveiled PLoS Currents: Influenza, a Google Knol hosted collection of rapid communications about the swine flu.
In his blog post A new website for the rapid sharing of influenza research (also posted on the official Google blog), Dr.Harold Varmus explains:

The key goal of PLoS Currents is to accelerate scientific discovery by allowing researchers to share their latest findings and ideas immediately with the world’s scientific and medical communities. Google Knol’s features for community interaction, comment and discussion will enable commentary and conversations to develop around these findings. Given that the contributions to PLoS Currents are not peer-reviewed in detail, however, the results and conclusions must be regarded as preliminary. In time, it is therefore likely that PLoS Currents contributors will submit their work for publication in a formal journal, and the PLoS Journals will welcome these submissions.

The response from the community has been overwhelmingly positive so far. For example, Frederic Lardinois writes, on ReadWriteWeb – Finally a Good Use for Google Knol: Sharing Information About Flu Research:

Overall, we think this is a great project. Knol is a good, easy-to-use platform for these kinds of publications, and given that the articles are also archived on other servers, this project also doesn’t rely on Google to keep Knol’s servers running indefinitely.
PLoS, being a non-profit, is also the right organization to give this project a try. Commercial publishers are still wary of the Internet, and while the open access movement has been gathering some support over the last few years, a lot of research in most scientific fields will still be hidden behind paywalls for a long time.

On Tech Babble: PLOS Currents : Influenza:

PLOS Currents : Influenza is built utilizing Google Knol and a new service from the National Center for Biotechnology Information (NCBI) called Rapid Research Notes. This service allows the user an easy way to follow current research and search for relevant scientific information.
As we approach influenza season, expect greater levels of concern and interest in H1N1.

Steven Salzberg, one of the moderators of PLoS Currents: Influenza, wrote on his blog – Opening up influenza research with a new kind of journal:

What’s the difference between this and a regular journal? Well, first of all, submissions won’t be thoroughly reviewed, which means they don’t “count” as journal papers, but it also means you can publish them later in a peer-reviewed journal. The Public Library of Science has already bought into this model – they’re sponsoring PLoS Currents, after all – and we expect other journals to do so also. So why publish, you might ask? That’s easy: in a highly competitive field such as influenza research, different scientists are often racing to answer the same question. By publishing super-rapidly in PLoS Currents, you will get a citable, time-stamped reference that establishes your discovery, and most importantly, establishes when you made it.
The big win here, we hope, is that scientists will be empowered to announce their results to the world without worrying about being “scooped” – a common fear that leads to many results being kept secret for months while papers are prepared and revised. This in turn will speed up scientific progress overall, which is the real goal behind PLoS Currents.

Eddie Holmes, Chief Moderator of PLoS Currents: Influenza, wrote in a guest-post on the PLoS Blog – Welcome to PLoS Currents: Influenza:

The central idea of PLoS Currents: Influenza is to rapidly disseminate data and ideas in the realm of influenza research, stimulated by the ongoing epidemic of swine-origin influenza virus (H1N1pdm). Given this backdrop, it is no surprise that some of first contributions consider important aspects of the H1N1pdm epidemic.
Although PLoS Currents: Influenza was inspired by H1N1pdm, it will cover all types of research on all types of influenza virus. Indeed, the emergence of H1N1pdm brings into focus the need for basic research into many fundamental aspects of influenza biology.
These initial contributions have given PLoS Currents: Influenza an excellent start. The next few months should prove to be very exciting. I therefore encourage all of you working in the area of influenza to send a contribution to PLoS Currents: Influenza, however preliminary, so that your data and ideas are rapidly distributed to a wide audience.

Iddo Friedberg, on ByteSizeBio: PLoS Currents: Influenza. Because knowledge should travel faster than epidemics:

So here we have all chief elements of scientific communication: credibility (by the moderators), timeliness (immediate online publishing) and attribution (by public archiving). PC:I is heavily skewed towards timeliness. The rationale being that in Influenza research and monitoring, time is of essence. After all, a report going through the usual peer review mill can take months: which is exactly the time required for a full-blown pandemic.
Not that other scientific fields are not in need of timeliness. Physicists and mathematicians have known that for almost two decades now. Nature Precedings are also providing an outlet for rapid communication in life sciences. But the combination of speed, accessibility and credibility offered by PC:I is indeed something new and welcome.

Vincent Racaniello on Watching The Watchers: Rapid Sharing of Influenza Research:

Contributions that will be welcome at PLoS Currents: Influenza include research into influenza virology, genetics, immunity, structural biology, genomics, epidemiology, modeling, evolution, policy and control. The manuscripts will not be subject to peer-review, but unsuitable submissions will be screened out by a board of expert moderators. This policy will enable rapid publication of research.
The path to publishing original scientific research is often long and tortuous. A manuscript describing the findings is prepared and submitted to a scientific journal (such as Nature, Cell, Journal of Virology). The manuscript is assigned to two or three expert reviewers, generally scientists involved in the same area of research. If their reviews are favorable, the paper is published. Usually additional experiments are called for, which may require additional time to complete. Many months to a year may pass before the paper is published, although some manuscripts (e.g. those on 2009 pandemic influenza) may be expedited. The point is that PLoS Currents: Influenza will allow everyone – including non-scientists – to read about research soon after the authors have prepared the paper.
PLoS Currents: Influenza is a terrific idea, and I welcome this venture with great enthusiasm. I hope that PLoS Currents will grow to include other areas of science.

David Bruggeman on Pasco Phronesis blog – PLoS Currents – An ArXiv for the Rest of Us?:

Presently in beta, Currents is accepting “new scientific data, analyses, and ideas” and encouraging the discussion and analysis of this information. The material is not peer reviewed as it would be for a regular PLoS publication, but is screened by moderators who are experts in the field at issue. The idea is that the work posted and discussed in Currents would lead to papers in peer reviewed journals at a later date.
So policy research could find its way into a science journal – excellent.
While the material is hosted by Google, as the PLoS explains on its blog, it is also archived at the National Center for Biotechnology Information. Hopefully the Currents topics will not be simply reactive, but consider a number of different topics that aren’t breathing down our collective neck.
As the ScienceInsider article suggests, this is not the first time a preprint collection has been suggested for biomedical topics. Apparently when PLoS co-founder (and current PCAST co-chair) Harold Varmus tried this when he was leading the National Institutes of Health, some scientific societies raised a ruckus and the effort was discontinued. Hopefully history won’t repeat itself.

Glyn Moody, on his blog ‘Open….’, writes – PLoS Reinvents Publishing and Saves the World:

As someone who has been writing about open access for some years, I find myself returning again and again to the Public Library of Science. That’s because, not content with pioneering open access, PLoS has time and again re-invented the broader world of scientific publishing. Now, it’s done it again.
The current system of publishing papers is simply too slow to deal with pandemics, where speed is of the essence if we’re to have a chance of nipping them in the bud. It’s good to see PLoS stepping in to help address this major problem.
This is really exciting from many viewpoints. It’s pushing the ideas behind open access even further; it’s reshaping publishing; and it may even save humanity.

So, what do you think?

Weight Loss – what works, really?

You may remember Dr.Charles whose blog was here on for a while two years ago. He took a hiatus from blogging, but is now back at it with a vengeance at his new site which I warmly recommend you visit.
Today’s post is interesting – and not just because it is partially about a PLoS ONE paper – Why Exercise is Not the Best Prescription for Weight Loss which fits perfectly within the ongoing discussion about weight-loss and dieting going on a couple of my SciBlings’ blogs right now.
PalMD is going on a diet and monitoring his progress publicly, on his blog.
Dr.Isis tells him he is doing it wrong.
And don’t forget that a couple of years ago Chad went on a successful – and also highly public – diet: see his updates (each with some additional thoughts about dieting) here, here, here, here, here and here.
So, who’s right? What are your experiences? And what can I do with my 6’1″ and 126lbs – weight I’ve had since I was a teenager? Nothing seems to work to help me gain – I eat a lot, actually….

The World Science podcast/forum: May Berenbaum – DDT vs. Malaria: The Lesser of Two Evils?

The World is a radio show co-produced by WGBH Boston, Public Radio International and BBC. You can probably hear it on your local NPR station – if not, you can find all the shows recorded on the website.
You may remember that I went to Boston a few months ago, as a part of a team of people helping the show do something special: use the NSF grant they recently received to expand their science coverage and, in collaboration with Sigma Xi and NOVA, tie their radio science coverage to their online offerings.
The result is The World: Science website, a series of weekly science podcasts with Elsa Youngsteadt and David Kohn (subscribe to the RSS feed) and, starting this week, something new.
First, the radio show will have a brief segment on a science topic that includes an interview with a science-related person. A longer version of that story/interview will be on the website as a podcast, with additional links to outside sources. And, most exciting, the person who was interviewed for the show will come by the online forum for a week after the show and answer readers/listeners’ questions. Like an online version of a Science Cafe.
Today, the guest will be entomologist May Berenbaum. In the podcast and in the forum she will address the DDT debate: Is it really as bad as the critics say? (Even Rachel Carson thought it had value.) Is it really as good as the proponents say? (Sure, it may help with malaria control for a while, but eventually the mosquitoes will develop resistance.) Here’s an op/ed May had in the Washington Post a few years ago: If Malaria’s the Problem, DDT’s Not the Only Answer.
So, listen to the podcast and join the conversation which has already started and will be ongoing until next Friday. We hope that, with all of you checking in and spreading the word, the discussion will grow.
You should also follow the news about this endeavor on Twitter, in the FriendFeed room and a Facebook page. Join, friend, follow, subscribe. And come back next week and next and next. And don’t feel shy to give feedback as this is just in the early stages of development and we are open to suggestions.

Open Access, Achievements and Looking Forward (video)

Ginny Barbour, Part 5: Open Access, Achievements and Looking Forward from PLoS on Vimeo.

PLoS Medicine’s Fifth Anniversary and Future Plans (video)

Ginny Barbour, Part 4: PLoS Medicine’s Fifth Anniversary and Future Plans from PLoS on Vimeo.

Jay Rosen: ‘The Web is People’ (video)

Open Access to Health Information (video)

Ginny Barbour, Part 3: PLoS Medicine Open Access to Health Information from PLoS on Vimeo.

Speaking of Medicine

If you read this blog even superficially, you are probably aware of everyONE, the community blog of PLoS ONE. The blog has been so successful, that our colleagues at PLoS Medicine have decided to follow our example and start their own community blog.
And, today they are ready to reveal – Speaking of Medicine. Go check it out – click on all the tabs on top for all the additional information. Bookmark and subscribed. Spread the word about it. And come back often and use it – and post comments.

Why the anti-vaccine movement even exists? And how it got started?

An article that is likely to make the rounds of the science/medical blogosphere (and get the anti-vaccer trolls out of the woodwork):

Researchers long ago rejected the theory that vaccines cause autism, yet many parents don’t believe them. Can scientists bridge the gap between evidence and doubt?

Writes Liza Gross in the latest Feature article in PLoS Biology: A Broken Trust: Lessons from the Vaccine-Autism Wars:

Until the summer of 2005, Sharon Kaufman had never paid much attention to the shifting theories blaming vaccines for a surge in reported cases of autism. Kaufman, a medical anthropologist at the University of California, San Francisco, knew that the leading health institutions in the United States had reviewed the body of evidence, and that they found no reason to think vaccines had anything to do with autism. But when she read that scientists and public officials who commented on the studies routinely endured malevolent emails, abusive phone calls, and even death threats, she took notice.
“Hecklers were issuing death threats to spokespeople,” Kaufman exclaims, “people who simply related the scientists’ findings.” To a researcher with a keen eye for detecting major cultural shifts, these unsettling events signaled a deeper trend. “What happens when the facts of bioscience are relayed to the public and there is disbelief, lack of trust?” Kaufman wondered. “Where does that lead us?”
Struck by how the idea of a vaccine-autism link continued to gain cultural currency even as science dismissed it, Kaufman took a 26-month hiatus from her life’s work on aging and longevity to investigate the forces fueling this growing divide between scientists and citizens (see Figure 1). She wanted to understand how parents thought about risk and experts, how these attitudes shaped parents’ decisions about vaccination, and what the vaccine wars might teach us about the long-term erosion of public trust in science….

Read the whole thing

Afraid of flu? Bill Nye has a simple solution

Teaching physiology – Cardiac Arrhythmias: the best video ever!

Harold Varmus is everywhere!

VarmusBookCover.jpgLook what came in the mail yesterday! The Art and Politics of Science by Harold Varmus and, since he is in some way my boss, with a very nice personal inscription inside the cover. I am excited and already started reading it.
And speaking o Varmus, he seems to be everywhere. See this article in TimesOnline:

A major investment in fighting tropical infections and chronic conditions like heart disease and diabetes in poor countries would transform international perceptions of the US, according to Harold Varmus, who co-chairs the President’s Council of Advisers on Science and Technology.
In an exclusive interview with The Times, Dr Varmus said that American diplomacy had undervalued the role of medicine and science in fostering friendly relations with developing nations.
He is asking President Obama to endorse a plan from the US Institute of Medicine that would almost double annual US support for global health to $15 billion by 2012. ….

The World Pneumonia Day

Nicholas Kristof from the New York Times has written a blog entry about pneumonia being under recognized on the global health agenda, in the media and by people in industrialized countries. Many people don’t know that pneumonia kills more children than malaria, measles and AIDS combined:

It’s been remarkable to watch how malaria has become, over the last five years, a “cool” disease. After decades in which it received little funding or attention (that’s partly our fault in the media), malaria is now a major cause, with funding pouring into everything from bednets to vaccines to research into genetic tinkering with mosquitoes so that they can’t infect people with malaria. The upshot is going to be huge numbers of lives saved.
One of those active in the malaria campaign is Lance Laifer, and he’s now plotting a new effort to take on pneumonia. Respiratory tract infections are a huge problem in the developing world and kill vast numbers of kids, and so some attention could make a huge difference. More power to him and others trying to focus on pneumonia…

Go and post comments.
The World Pneumonia Day is on November 2. You can join the Facebook group to stay in the loop and receive information until then.
Hat-tip: Rose Reis.

Medbloggers at BlogWorld/New Media Expo ’09

Kim is excited:

It’s official!
The Medbloggers are now a part of BlogWorld/New Media Expo 09!
Thanks to sponsorship from Johnson & Johnson and MedPage Today, the “Medlblogger Meet-Up” is now a reality.
But it is so much more than “just” a meet-up.
A full day of topics, voted on by the medical bloggers themselves, will be presented, with plenty of time to mix and mingle with our blogging colleagues.
Blog World/New Media Expo 09 will take place at the Las Vegas Convention Center the weekend of October 15-17.
New blogger, established blogger, podcaster or internet broadcaster, there is a place for you in Las Vegas!
Interested in just the Medblogger topics?
You’ll want to join us on October 15th, when the Medbloggers will take their place in the premier blogging conference by holding a full day of sessions and meetings devoted specifically to medblogging.
Want to get deep into the heart of blogging as a lifestyle? Ready to take your blog to the next level?
Then you’ll want to attend the entire BlogWorld/New Media Expo conference where you will learn from the very best of the blogosphere. If you’ve heard of them, they will be at the BlogWorld/New Media Expo 09.
The option is yours.
The pleasure is ours.
Please join us!
Registration opens at soon!

Science Blogging plus/vs Science Journalism

Tomorrow’s Nature has a nice, long article about the plight of science journalism and the potential role of science blogs in filling the void as science journalists are laid off and the news-media are going bankrupt and shutting down.
No commentary for me about it yet today – I hope others will start first.
The introductory editorial is here: Filling the void: As science journalism declines, scientists must rise up and reach out.
The main article is here: Science journalism: Supplanting the old media? (allows comments)
The PDF is really pretty (and has additional images and boxes in the margins with quotes, numbers, etc.).
As a part of doing research for this article, Geoff Brumfiel did a survey of a number of science journalists, and you can download the Excel spreadsheet with the responses here.
People interviewed for the article and quoted within include John Timmer, Larry Moran, Carl Zimmer, PZ Myers, Michael Lemonick, Derek Lowe and myself, among others.
Let me know what you think.
Update: Good (or, some of them, at least interesting, to be nice) responses by (including commenters) Jessica Palmer, Michael Tobis, Pharynguloids, Larry Moran, Janet Raloff, LouScientist and John Timmer.

Something for the Pain: One Doctor’s Account of Life and Death in the ER


Wednesday, March 25
7 p.m.
“Something for the Pain: One Doctor’s Account of Life and Death in the ER,” a book reading and discussion by author Paul Austin, MD hosted by the American Medical Writers Association, Carolinas Chapter. Austin, a former firefighter who is now an emergency room physician at Durham Regional Hospital, has written “a relentlessly honest look at modern emergency medicine,” in the words of Publisher’s Weekly. At the Friday Center, UNC-Chapel Hill. Please RSVP by March 18 to Ellen Stoltzfus (

World’s Biggest Scientific Fraud?

Wow! This is massive!
From Anesthesiology News:

Scott S. Reuben, MD, of Baystate Medical Center in Springfield, Mass., a pioneer in the area of multimodal analgesia, is said to have fabricated his results in at least 21, and perhaps many more, articles dating back to 1996. The confirmed articles were published in Anesthesiology, Anesthesia and Analgesia, the Journal of Clinical Anesthesia and other titles, which have retracted the papers or will soon do so, according to people familiar with the scandal (see list). The journals stressed that Dr. Reuben’s co-authors on those papers have not been accused of wrongdoing.

There is more about it in New York Times and the Wall Street Journal.
My SciBlings Orac, Janet and Mike have more details, thoughts on ethics and implications.
This case is Big!

From cloning to stem cells: How can pigs help us solve problems in human medicine?

From Sigma Xi:

NCSU molecular biologist Jorge Piedrahita has cloned pigs and explored why they are not carbon copies despite sharing the same DNA. Now he is trying to crack puzzles that could result in transgenic animals useful in human and veterinary medicine. His studies in cloned pigs led him to an unusual family of genes called imprinted genes, involved in placental function and fetal development. Recently he found they are implicated in human diseases too and is developing stem cell technologies in swine to try to speed up clinical applications in people.
To learn more, come hear Piedrahita discuss “From cloning to stem cells: How can pigs help us solve problems in human medicine?” at the next Sigma Xi Pizza Lunch at noon on Wednesday, March 25.
Pizza Lunch is free and open to science journalists and science communicators of all stripes. Feel free to forward this message to others you think might be interested. RSVPs are required (for a reliable slice count) to
Directions to Sigma XI:
Hope to see you there,

Daylight Saving Time

Yup, it’s tonight.
If you were around here a few months ago, the day after the Fall Back day, you probably read this post.
Disregarding the debate over rhetoric of science, that is probably my best, most detailed explanation for what happens to our bodies on those too strange days of the year – Spring Forward and Fall Back day.
Spring Forward is much more dangerous, so be very careful in the mornings next week, especially on Monday. Take it easy, get up slowly, be a little late for work if you can afford it. Life and health are more important than a few minutes of work and being punctual on a day like that.
And that post also contains a bunch of links at the bottom to other posts on the topic.

Harold Varmus on Daily Show last night

Under the fold:

Continue reading

Now it’s our job to keep the Democrats’ toes to the fire

Senator Tom Harkin luvz him some alternative medicine. And he hates when the studies demonstrate those things don’t work, so he tries to push them into the Obama Administration’s health care plan by force. Read Orac, PalMD and PZ for details (and for info what you can do). This administration is supposed to be reality-based – let’s make sure the wackos don’t change that….

The Malaria Song

Jennifer, one of Miss Baker’s students, wrote a blog post about Malaria and, for that occasion, she also wrote and composed a song, then she filmed herself singing it and posted the video on YouTube:

Not your grandparents’ Biology class….