Monday, November 24, 2008

The DNA Network

The DNA Network

In rheumatoid arthritis, kicking the habit brings relief [The Navigator - Navigenics Blog]

Posted: 24 Nov 2008 08:28 PM CST

Michael Nierenberg, M.D.

imageGot rheumatoid arthritis? Get rid of your cigarettes. New research suggests that your aching joints will thank you for it.

For years, scientists have known that smoking increases a person’s risk for developing this inflammatory condition, which causes pain, swelling and stiffness in the joints.

Studies also indicated that tobacco smoke increases the severity of the disease in those who have it.

Now comes the first solid evidence that kicking the habit may actually help arthritis sufferers control their disease.

Rheumatoid arthritis patients who stop smoking "may see an improvement in the number of joints that hurt them every day and in how they feel overall," said Dr. Mark C. Fisher, leader of the new study in a written statement. The results were presented recently at the Rheumatology Annual Scientific Meeting in San Francisco.

Medicine Meets Virtual Reality 17: Interviews and a blog [ScienceRoll]

Posted: 24 Nov 2008 04:10 PM CST

I’m honored to be in the organizing committee for next year’s Medicine Meets Virtual Reality conference that will take place in Long Beach, CA between 19 and 22 of January, 2009.

Now I write a blog for the conference and publish a series of interviews with famous participants. The first interviewee is Dr. Albert “Skip” Rizzo and the topic is virtual reality therapy. Check it out!



What are your favorite iPhone apps? [Discovering Biology in a Digital World]

Posted: 24 Nov 2008 01:10 PM CST

Now that I've downloaded really important applications like a timer for cooking, a program for playing with molecular structures, and an app that lets me listen to NPR on my phone, I'm ready for more.

I'm seriously overwhelmed by the iTunes App store. I found a program for learning human anatomy, a laboratory calculator for making solutions, music programs, wow!

Who knew?

I know some schools are using iPhones for teaching, but I never realized how much was out there.

Deepak recommends something called TouchPhysics.

What are you using? What cool apps do you suggest?

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Finding the Off Switch in Leukemia Cells [adaptivecomplexity's blog]

Posted: 24 Nov 2008 12:09 PM CST

Cancer cells of all types have one thing in common: they have escaped the built-in controls of cell reproduction, and as a result, tumors grow as the out-of-control cells keep dividing.

This out-of-control cell division in cancer is very closely connected to a process called differentiation, the process by which a cell stops dividing and transforms itself from a stem cell into a specialized cell like a red blood cell. There is a trade-off: differentiated cells are specialized and tend to not divide; undifferentiated cells tend to divide but don't carry out specialized functions. The problem with cancer cells is that they are more like undifferentiated, dividing stem cells than the non-dividing, differentiated cells we want them to be.

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Slideshow: Health and Medical Eduation in Second Life [ScienceRoll]

Posted: 24 Nov 2008 10:59 AM CST

Tid Bits - Classics Edition [The Daily Transcript]

Posted: 24 Nov 2008 10:54 AM CST

I love the classics - be it Greek plays, Roman history, all of the great myths or all of the ancient philosophers that lie at the base of our western civilization. (Weren't those Atomists so prescient?) And yes, I also managed to marry a classics major. That's why I thank the FSM that I live in an age where you can obtain all this information for free and downloadable onto your iPod.

So what's out there?

Well a few months back I was in despair (along with hundreds of others) about the apparent downfall of the History of Rome Podcast. Well over the weekend Mike Duncan, just like Cincinnatus, came back from retirement and came out with a brand new episode on the great general Sulla (Pompey, Crassus and young Julius Caesar have even made an appearance). I strongly advise you to subscribe to this podcast, it's probably the best solo web production out there. I also advise you to start from the beginning where Mike summarizes the Aeneid and the Romulus and Remus myth. From there you'll need to listen to about 40 shows to be up to date (although we are on episode #34, some previous shows were split into sections "a", "b" and "c"). And the revival came just in time, as my wife and I have been plowing through HBO's miniseries Rome, a reenactment of the rise and fall of Caesar finishing with the crowning of Augustus.

Speaking of classics, I've also noticed that an audio version of Thucydides' The History of the Peloponnesian War and Herodotus' Histories Vol. 1 have recently been made available for free from (Other great works you can download from Librivox include The Iliad and The Odyssey.)

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$1500 MicroArray Challenge [ScienceRoll]

Posted: 24 Nov 2008 08:19 AM CST

I’ve come across the $1500 MicroArray Challenge on Medgadget.

This isn’t just any picture of a microarray — it’s a cryptogram with a $1,500 message.

Peter C. Johnson, M.D., president and CEO of Scintellix, created this painting called ‘MicroArray.’ He has embedded a cipher based on the dots in the pastel. Pit your skills against this cryptogram and decipher what’s turning on these ‘genes.’

The first to unravel the hidden message will win $1,500. The first 50 registrants will receive a MicroArray copy poster and a poster tube.

Every Monday, starting from November 17, a clue will be provided to put you on the right track. You can check this website for clues as they come in.

You have until December 31 to prove that you are a master code breaker. Feel free to give the Microarray Challenge a shot as many times as you like up to once a day. All entries will be considered.


I tried to use the colours as nucleotides and then place the codes of the possible amino acids in order, but no result…


Medicine 2.0 Blog Carnival: Edition 35 [ScienceRoll]

Posted: 24 Nov 2008 08:10 AM CST

It’s always a pleasure for me when my mentor, Ves Dimov at Clinical Cases and Images, is the host of the Medicine 2.0 blog carnival. He told me about the possible impacts of web 2.0 on medicine and healthcare back in 2006 and that’s why I started to focus on this field.

As usual, this edition at Clinical Cases and Images is unique (the carnival is a Google Docs Presentation and the submissions are posted on Twitter as well).

Medicine 2.0 is a blog carnival about the impact of web 2.0 on medicine and healthcare.


Checking out the new Ebola virus and playing some tricks with BLAST [Discovering Biology in a Digital World]

Posted: 24 Nov 2008 07:30 AM CST

Ebola virus has impressed me as creepy ever since I read "The Hot Zone: A Terrifying True Story some years back by Richard Preston. (I guess he has a new book, too, Panic in Level 4: Cannibals, Killer Viruses, and Other Journeys to the Edge of Science but I haven't been in airport for the past couple of weeks, so I haven't read it yet.)

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ResearchBlogging.orgInfectious agents that cause diseases with gruesome symptoms really excite those of us with an interest in microbiology. Tara has written about this paper, too, and summarized the details.

I thought I'd show you how to have fun re-analyzing the data, demonstrate a new and unexpected feature that I happened to find in NCBI BLAST, and see if we can reproduce the phylogenetic tree from the paper by using the tree algorithms at the NCBI. Making phylogenetic trees is often kind of painful in the classroom, for various reasons, and I wanted to see if we could find a more user-friendly method.

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But no one ever gets the truth from plastic man [A Free Man » Science]

Posted: 24 Nov 2008 05:41 AM CST

About midway through Yann Martell’s Man Booker Prize winning novel “The Life of Pi”, the protagonist finds himself washed up on an island populated solely by meerkats. After a time on the island he begins to suspect that all is not as it seems - the meerkats take to the trees every night and one day Pi takes a bite of a fruit growing from one of the island’s trees and finds human teeth inside. It begins to dawn on him that the island is carnivorous, each night digesting anything that has the misfortune to remain on the ground.

For some reason, Pi’s carnivorous island was the first thing that popped into my head when I heard a news story on the NewsHours with Jim Lehrer podcast recently about what was described as our rapidly growing eight continent. There are no meerkats and it is not strictly carnivorous and it’s not really an island, but the Great Pacific Garbage Dump is as disturbing and potentially dangerous as Martell’s fantasy island.

My initial reaction to the NewsHour report is that it was a typical case of what tends to be a melodramatic and lacking in understanding response of the mainstream news media to a juicy science story. Surely there isn’t a continent of garbage out in the Pacific Ocean. The good news is that the media has overreacted, “continent” is not the right word. The Great Pacific Garbage Dump is not visible from the air (because most of it lies slightly below the surface of the water) nor does it have a particular nautical position (due to the shifting wind directions and currents). The bad news is that there are two massive accumulations of plastic waste swirling around in the doldrums of the northern Pacific Ocean. Charles Moore, the founder of the Algalita Marine Research Foundation and the man who had the misfortune of discovering the dump, estimates that the plastic garbage in the Pacific covers approximately five million square miles (about 1.5 times the land mass of the United States) and contains over 3.5 million tons of largely consumer waste.

By most accounts the trash finds its way to its home in the North Pacific through a long and circuitous route. Trash is dumped into rivers, in both North and South America and Asia, that empty into the Pacific. Ocean currents carry the trash, picking up more debris as it travels, around the Pacific before depositing it in the doldrums of the North Pacific Gyre. 80% of the trash in the ocean originates on land and a majority of that is from consumer products. Thus, it is a hard truth that we - you and I - are the problem. Here is how it works: say that you inadvertantly drop some innocuous bit of plastic - a clear plastic wrapper from a box of candy. The next time it rains, that wrapper gets washed into a storm drain which will flow into your nearest watershed and ultimately into the ocean. That little wrapper floats its way around the Pacific currents until it comes to rest in the Gyre where it will join the rest of the trash. This plastic waste will be around longer than you and I, longer than our children, longer than our grandchildren, longer than our great-grandchildren. Nobody really knows how long it takes for plastic to biodegrade because it basically doesn’t. Conservative estimates are around 450 - 500 years. We are creating a problem that will outlive us by centuries.

It isn’t just an aesthetic problem. In short, it’s devastating to marine ecosystems. Forty percent of albatross chicks are killed each year by consuming plastic accidentally fed to them by their parents. More than a million birds and marine animals die each year from consuming or becoming caught in plastic and other debris. But there is a less obvious and more frightening consequence to our trashing of the oceans. Moore’s group does a lot of research into the ecological effects of plastic debris on marine ecosystems. Recently they have been looking at plastic particulate levels in and around the Garbage Patch. The small bits of plastic that are a byproduct of the slow degradation of the plastic debris have been found to accumulate a lot of nasty chemicals - polycyclic aromatic hydrocarbons, chlorinated and legacy pesticides and hormonally active additives. This latter class are particularly nasty beasties, some of which have been implicated in an increased risk of breast cancer. Moore and his colleagues found that the ratio of plastic particles to plankton in the Gyre was between 1.4:1 and 6.9:1. In other words, there is more plastic particulate matter in this part of the ocean than there is plankton. You don’t have to be a biologist or have an in depth knowledge of food chains to recognize what this means: small fish eat plankton (or plastic particles), big fish eat small fish, humans eat big fish. We are eating our own toxic garbage.

I don’t wish to sound melodramatic or preachy but this is a problem that is getting worse on a daily basis and one that we cannot repair. We can, however, do something to slow the accumulation of rubbish in the oceans. 80% of the trash out there comes from us directly, so it is up to us to do something to make it better.

Here are ten things we can do about it:

  1. Don’t use so much plastic. Make a concerted effort to reduce the amount of plastic that you purchase. It’s not easy. I’ve been making a concerted effort since I heard this story and it’s absolutely stunning how much excess plastic you get when you purchase anything. Note how much plastic crap you come home with on your next trip to the supermarket. Preferentially purchase items packaged in glass or paper. Virtually any material is better than plastic.
  2. I’m a beach bum. Roughly 10% of the crap out in the Pacific comes from trash left on beaches. So, don’t leave trash on beaches and maybe pick some of it up when you’re out there. Boy Z, Timmins and I are headed out to the beach shortly and I’m bringing a bag with me to pick up.
  3. Recycle. Plastic recycling is very low efficiency - only about 3.5% of plastic is recycled in any way. This is due in part to contamination of plastics with non-plastics, food waste and non-recyclable plastics. Clean up your plastic before recycling and make sure that you only include recyclable plastics. If your community does not recycle plastic then demand that they do.
  4. Along the same lines, buy recycled products or products containing recycled materials.
  5. This is kind of a no-brainer. But do not litter. Most of the Great Pacific Garbage Patch is thought to be a result of litter working its way into the river system.
  6. Consider volunteering or donating to the Algalita Marine Research Foundation or other environmental organizations.
  7. Think about the watershed when cleaning up around your hose. Sweep your sidewalks rather than hosing them. Wash your car on the grass so that the water sinks into the ground rather than storm drains.
  8. When you go shopping do not take a plastic bag. Use a cloth or other reusable bag.
  9. Buy in bulk. Most of the plastic that you bring home with you from the shop is packaging, the higher the product to packaging ratio, the less trash generated.
  10. For god’s sake, don’t use so much plastic.


Image credits:

Plastic trash

North Pacific Gyre Map

Food chain

I was leaning towards Radiohead’s “Fake Plastic Trees” for this post, as it seemed appropriately gloomy. But, The Kinks have been in my head lately, possibly because they are apparently reuniting.

This posting includes an audio/video/photo media file: Download Now

Breast is Best in Melamine Scandal [Sciencebase Science Blog]

Posted: 24 Nov 2008 04:00 AM CST

breastfeeding-babyThe melamine in milk scandal continues to draw interest. You recall, across Asia, in particularly in China, infant formula milk was discovered to be contaminated with a starting material for making plastics and fire retardant materials, melamine. Thousands of babies were hospitalised with possible renal failure, and several died.

But, could some good have come out of this scandal? Apparently, breast-feeding rates have bounced back across Asia, according to some reports and a roundtable, Secure nutritious diet: Save children’s lives, organised jointly by Save the Children UK and others is using the melamine scare to help promote the breast is best message. It has been demonstrated time and again that breastfeeding reduces infant mortality rates particularly in the developing world. One wit even suggested that the melamine contamination was done deliberately to promote breastfeeding, a nonsense, obviously.

Others are now reporting that the formula manufacturers are hoping to restrict this renewed enthusiasm for breastfeeding by heavy promotion of their products even if they are in breach of WHO guidelines on marketing of breast milk substitutes.

Others benefiting from the melamine scandal, although not in the same cynical way are chemical analysis companies, who, according to the Boston Globe are seeing improved business as food safety scares raise the profile of state-of-the-art testing equipments, including melamine test kits. The Gainesville Sun even reported on a woman who had developed her own testing kit for melamine.

As was mentioned in a comment on a previous melamine post, the US FDA has updated its import alert on melamine: “Detention without physical examination of all milk products, milk derived ingredients and finished food products containing milk from china due to the presence of melamine and/or melamine analogs.”

Breast is Best in Melamine Scandal

Manipulating molecules on my new iPhone [Discovering Biology in a Digital World]

Posted: 23 Nov 2008 09:26 PM CST

Some people, like Imelda Marcos and our new Dr. Isis, have a thing for fancy shoes.

I go crazy for gadgets.

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For my birthday this year, my family bought me a new iPhone! Yeah!

So, I've been killing several hours today filling it with cute little iPhone apps. Who knew one little phone could be so much fun?

One app, I enjoy, is called Molecules.

Molecules lets you download structure files from the Protein Data Bank (PDB) and play with the structures on your phone!

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What's that taste? [Discovering Biology in a Digital World]

Posted: 23 Nov 2008 09:30 AM CST

This wasn't in the lab, but it was an accident, and it was funny later on.

Normally, I wouldn't think twice about storing bacterial cultures in a refrigerator. After all, bacteria on a petri plate, inside of a plastic bag, are kind of stuck. They can't get out of the plates, and even if they did, they certainly can't crawl out of a plastic bag.

I thought soil bacteria, on agar plates, were mostly harmless.

Reposted from DigitalBio's greatest hits.
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What could be worse than snakes on a plane? [Discovering Biology in a Digital World]

Posted: 21 Nov 2008 07:37 PM CST

Using the MRSA database to teach students about data analysis and public health [Discovering Biology in a Digital World]

Posted: 21 Nov 2008 03:50 PM CST

There's no question that the ability to work with information is one that will be required and valued for a long time to come. I think it's imperative for teachers to have students practice this skill whenever an opportunity comes about. The problem for many teachers is finding the time to identify good data sets.

MRSA stands for Methicillin-resistant Staphylococcus aureus (MRSA), a serious problem for hospital patients. Six of out seven people who become infected with MRSA, get it from some kind of health-care facility. In 2007, the CDC issued a report claiming that 18,000 people die every year from invasive MRSA infections, a higher number than US deaths from AIDS.

Luckily, the Seattle Times has put together a nice database on MRSA infections that can be freely used by anyone and can serve as a nice teaching resource as well.

Having students work with information from the MRSA database would be useful for instructors who teach graphing skills, statistics, microbiology, nursing, epidemiology, or any area of public health.

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Here's how.

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