Richard Heck, Ei-ichi Negishi and Akira Suzuk take home the prize for chemistry

Again, this one is a bit surprising that it happened so late.  These three researchers revolutionized organic chemistry by developing palladium-catalyzed cross coupling.  This technique has allowed the development of scores of pharmacologic drugs as well as been used to build modern consumer electronics.

And the Nobel Prize in Physics goes too...

Andre Geim and Konstantin Novoselov of the University of Manchester in England.  The prize was awarded to them for there isolation of single carbon thick polymers known as graphene.  While graphene has not yet made its ways into manufactured use, it is incredibly light and as strong as steel.  This discovery has the potential to revolutionalize material science just as polymers did decades ago.

Nobel Prize in Medicine goes to the pioneer of IVF

This year the Nobel Prize in medicine was awarded to Robert Edwards, the man that pioneered in vitro fertilization, or IVF.  This is probably long overdue as millions of children have now been born thanks to Dr. Edwards life work.  Congrats to you Dr. Edwards.

Nobel Prize Week is here

Hooray for the geeks in all of us.  This week the Nobel awards are announced, starting Monday with the award for Medicine. 

Herpes Simplex Virus type 2 Vaccine fails in stage three trials

The search for a vaccine to prevent Herpes Simplex type 2 infection (genital herpes) has been sought after for decades.  The need for an HSV-2 vaccine has recently been highlighted by the observation that people that have genital herpes have a greater increase of risk of getting HIV.  Unfortunately, making an HSV vaccine has proven quite elusive.  Some glimmer of hope, however, had emerged from a subunit vaccine produced by GlaskoSmithKlein (GSK).  In two independent stage II trials, the vaccine prevented HSV transmission in 70% of HSV-1 seronegative women (aka, women that had not been exposed to the closely related virus most often associated with cold sores), encouraging GSK to move to a larger stage three trial.  After 8 years of study, the results of that trail were released on Friday and, sad to say, the 70%  reduction in transmission observed in the stage II trial did not hold up.  In fact, the vaccine only reduced HSV-2 transmission by 20% which was not statistically different than the control group.  It is unclear what steps GSK will take from here but if they do continue with an HSV vaccine program, it probably will be starting from scratch.

FDA decision on Avandia

So this is a follow up to the post a couple months ago on the fate of Avandia.  In short, the manufacturer of the drug hid data about its safety.  It turns out the drug increases your risk for heart attack.  In light of the danger and the obfuscation by the drug company, the FDA put Avandia back under review. Last week the FDA finally released their decision, which was to change the status of Avandia to only be prescribed for diabetics who do not respond to safer drugs on the market.  Now, while I admit I would have liked the FDA to have removed the drug completely from the market, the fact that the drug does help some diabetics does make it worthwhile to keep around.  I do wish, however, the FDA would have taking a much harder stance on the drug company itself.  Sadly, the current state of the FDA, both its dependence on corporate money, and its lack of true regulatory power, would have made that option highly unlikely.

A Cancer Vaccine Shows Promise

I'm sure most everyone reading this blog has dealt with personally, or has had a close family member or friend that has been diagnosed with cancer.  While detection and treatment of cancer has greatly improved over the past two decades, it still is one of the most devastating diagnoses a doctor might have to give.  This is even more so the case with malignant forms of brain cancers as surgery and/or drug treatment typically only delays progression of the disease for a short time, in part, due to difficulty in operating on the brain, but also the fact that our bodies do a very good job of preventing many proteins and chemicals from reaching the brain (aka the blood-brain barrier) including many potentially helpful drugs.

Now, one of the holy grails of fighting cancer has been to make a vaccine to fight it.  The concept of making such a vaccine has been around for as long as I can remember.  In fact, my uncle, who died of kidney cancer, was asked by his doctors at the VA if he wanted to participate in a trial to make a vaccine for his cancer over a decade ago (he opted to not take part).  Unfortunately, the idea of a cancer vaccine has proven difficult to turn into reality.  There are a few reasons for this, but I want to highlight just a couple.  First, vaccines for infectious diseases (what we normally associate vaccines with) rely on the fact that the virus and/or bacteria looks very different than the cells in your body.  The immune system uses these differences to kill the bad stuff and leave our bodies in tact.  Cancer, however, doesn't look all that different from the rest of the body to the immune system, making it difficult to elicit a robust immune response.  Second, almost every cancer from every patient is slightly different, so making a single vaccine for more than one person is not really feasible.  For that reason, most attempts to make a cancer vaccine has required removing part of the cancerous material, growing it up in the lab, grinding it up with some adjuvants (think Red Bull for your immune system) and injecting it back into the patient.  Sadly, for most cases it hasn't really worked....well with the exception of a new study centered on glioblastomas (very deadly forms of brain cancer).

The new study, led by Dr. Parsa at UCSF, has used individual vaccines to treat glioblastomas in 8 patients.  While the usual prognosis of glioblastoma is measured in months, all 8 of the patients in the study are alive and well, all a full year after receiving the vaccine.  Is this a cure for glioblastoma?  No, probably not, but it is a huge step forward.  It will be very interesting to see how these patients fair as time marches on but we can hope that the continued use of this vaccine will extend the lives of many more cancer patients in the future.

More information on Human CMV

I managed to run across a very good website for women who are or who are thinking about getting pregnant.  It has many statistics about CMV transmission during pregnancy as well as stories of women who have endured through it.  I highly recommend checking it out it out.


http://www.stopcmv.org/

Writing hell is temporarily over

Hello again.  Long time no see.  My apologies again for my absence but I have a good excuse.  I have been working on a paper to submit for publication the past month and it has drained much of my mental capital.  I'm happy to report that the paper was sent to the Journal of Virology on Thursday and will be out of my hands for at least a month as it is reviewed.  I also see this is a great time to briefly explain what I do in the lab.

As mentioned in my last blog entry, I am working on new vaccine approaches to prevent transmission of the Human Cytomegalovirus, or HCMV.  Now, HCMV is something that 90% of the US population is exposed to by the time they hit their mid life crises.  Fortunately, it is very rare for HCMV to cause disease in healthy individuals, which is most of us.  It only really becomes a problem if you were to become immune compromised, or, if you were to happen to get infected while pregnant.  Even then, the virus would do very little to you, but could have devastating affects on the fetus.  In fact, infection of pregnant women is the leading cause of deafness due to infectious disease in the US and the developmental defects due to uteran infection of a fetus costs billions of dollars a year to treat.  Due to the morbidity and cost associated with HCMV infection, the Institutes of Medicine has given developing an HCMV vaccine "priority one" status, its top rating, and many labs over the past 30 years have been working towards a vaccine.  Sadly, none have really worked.

One of the reasons making an HCMV vaccine has been problematic is that the virus only infects humans, making an animal model to study vaccine efficacy unavailable.  No animal model means no pre-testing of vaccine candidates before going into actual humans and getting approval to inject humans with anything with out some sort of safety and efficacy testing in animals is very very difficult.  In lieu of this, I am working with a closely related virus, Rhesus CMV, in the hopes that our studies with it will translate into similar results with HCMV.  While not great, Rhesus monkeys are the closest thing we have to an acceptable animal model.  Fortunately for the monkeys and my own conscious, Rhesus CMV is endemic in the monkey population and, like HCMV, does not result in morbidity in healthy animals.  We are developing a vaccine that makes use of viruses that are unable to grow outside of the lab.  Ideally, this will generate a very strong immune response in the monkeys and prevent them getting the real virus when challenged.  If all goes well, we will then adapt the system for a human vaccine...granted that could be decades away.

Salt Lake City descended upon by Herpes...

OK, so maybe it was an army of herpes virologists, but scary for the residents of SLC nonethless. 

I must apologize for my absense from the blogosphere the past 10 days as I was attending a conference in SLC all about the Herps.  Now don't get too many crazy ideas, it was a professional meeting and as some of you know, I am studying vaccines to prevent infection of a specific Herpes virus and my return from the meeting has got Herpes on my mind.  Given that, I thought I'd take the opportunity to talk a little bit about the life that is herpes.

So, most everyone by the age of 15 knows about Herpes, well, atleast the type advertised on TV (just be glad they don't show any pictures of lesions).  What most people don't know is there is actually 8 human herpes viruses and its most likely you have atleast five of them in your body already (numbers 1, 3, 4, 5, and 6).  Chickenpox, Mono, cold sores, and rosacea are all caused by primary infection with my favorite little bugs and are what most people are familiar with.  It just so happens though, that Herpes viruses can also be much more devastating, leading to encephalitis, shingles, liver failure, lymphoma, blindess and even death.  Of course not all 8 cause all these ailments, but between them all, you got everything covered.  Fortunately many of the herpes viruses can be controlled by very good drugs (yes, valtrex is one of the best) but they are not the only solution.  We also have a vaccine for Varicella Zoster Virus (VZV or HHV3 or chickenpox/shingels) that is used in children and elderly adults.  There is also a vaccine for genital herpes, but unfortunately, that only works for women who have never seen HSV-1 or HSV-2 (a very small number indeed). 

Given the limited number of effective vaccines to the herpes viruses, there is a continued effort to make new ones, and that focus was present at the meeting.  I work on a vaccine for Cytomegalovirus (human herpes virus five), which costs our health care systems billions of dollars a year to treat infants that were unfortunate to be exposed early during gestation.  Sadly, we are a long way off from a vaccine for this little bugger or any of the other herpes viruses.  Forunately the money from the NIH seems to be flowing non stop in an effort to curtail the disease associated with these viruses.

Red tape and scientific discourse: a match not made in heaven...

So Science magazine had an article 2 weeks ago describing an interesting conflict in government science.  To give a brief history, last year a group of European researcher's published a paper that a murine (aka mouse) retrovirus was found in about 70% of people diagnosed with chronic fatigue syndrome.  This was a major publication as the cause of chronic fatigue has been quite elusive and, if true, discovery of the agent could lead to potential preventative measures and/or treatments down the road.  Since that publication, several labs have tried to reproduce the studies findings with mixed results.  Two notable groups working on this are one at the CDC in atlanta and a collaboration between the NIH and FDA, all of which are government research labs.  Now, the CDC and the NIH/FDA labs both did their own experiments with their own cohort of patients and found exactly oposite results.  The labs tried to publish the results and both were accepted by peer review, one to PNAS and one to Retrovirology. Now normally, this is sorta where the story ends.  The data would be published and the scientific community would then hash out which data was correct.  It might take years, but this is really how a consensus can be built.  Unfortuantely, the umbrella overseer of both the NIH/FDA and the CDC, HHS, stepped in and blocked publication of the two manuscripts.  Their rationale being that 2 government labs should report the same findings.  Sadly, that is not how science has worked in our country.  In fact, it actually implies that our government is not transparent in its treatment of scientific data.  Hopefully this is a one time incident and the offices of HHS will learn that only through analysis of all data in front of us can the scientific community truly understand the principles governing our lives.

The fate of Avandia

So the FDA has a great opportunity in front of it.  As some of you might have read, the safety of the drug Avandia has been brought into question.  It is now well established that, while the drug does provide some benefits to diabetics, it comes with cardiovascular risks.  Recent studies highlight these findings and also show that the drug is no more effective than its competitors.  While this alone should be sufficient to pull the drug from the shelf, the controversy goes much deeper.  Glasko Smith Klein, the maker of Avandia, had evidence as early at 1999 that there was significant cardiovascular risks for patients on the drug, but decided to hide that evidence from the public and the FDA.  They continued to hide increasing amounts of internal data for years in order to keep the money coming in (an internal memo from the company estimated that releasing the negative data could result in hundreds of millions of dollars lost), before the courts finally forced their hand. 

To me, and maybe to many of you, it seems logical that the drug be pulled from the shelf and huge penalties be thrown at GSK, however, I'm not to confident that will happen.  When a member of the review committee for Avandia suggested the drug not go to market over concerns about cardiovascular risks she was kindly asked to leave.  Hopefully the increased public awareness and mounting evidence will sway the upper echelon of the FDA towards the correct, ethical decision.

On the patenting of genes...

First off, my apologies to those who read this blog regularly for my delay in posting.  I'm actually doing some writing at work at the moment and I find my neurons can't write at home and at work without severe consequences involving bruised knees and lots of drool.  In any case, I had hoped to post today's topic immediately following the review of "The immortal life of Henrietta Lacks," but I found it quite difficult to maintain a neutral stance on the issue of patenting genes (which was the original goal, but to hell with that).

I'd like to start by simplying a very long story that I think many of us can relate to in some way.  For hundreds of years, one of the leading killers of moms and grandmas has been breast cancer.  I'd be surprised if I could find anyone that has not known some one that has dealt with this terrible disease.  For years, researchers wed themselves to the bench trying to find genes that might predict women who were at high risk for the disease, and thus more aggressive preventative care could be administered.  Finding these genes proved challenging and it wasn't until about a decade ago that a university lab made a very important observation that the risk of developing breast cancer was linked to a region of a specific chromosome, but they did not identify the exact gene.  Nonetheless, this discovery was a huge step forward and caught the eye of quite a few people, including a start up biotech company.  This company and the acedemic lab would compete to find the gene.  It was a grueling race for everyone involved, but, in the end, the resources of privatized research overwhelmed the acedmic lab and they found the gene first:  BRCA, four letters that have become part of many women's everyday lexicon.  Before publishing they had found the gene, the company applied, and was approved, for a patent on all things related to BRCA and not too long later, tests for mutations in BRCA became available.  Note: the patent issued was for all things related to BRCA and not just the test for the mutations found in many breast cancer patients.

While the identification of BRCA was a HUGE step forward for detection of women at risk for breast cancer, and the company that developed the test praised for their work, problems started to arrise....many of which are directly related to the patent.  First, the test administered by the company is very expensive (in price, but estimates on the actual cost of the test suggest a very nice profit margin) and not all insurance plans will cover the cost.  Second, the test doesn't screen for all the mutations that are known to be markers for increased risk of breast cancer, meaning you could get the test, be told you were not at risk, and choose to not to undergo more frequent screening for breast cancer, all the  while, you actually are at high risk.  So the result is we have women who can't get tested for economic reasons or were tested but markers that should be screened for weren't because the only test available doesn't screen for them.  Why doesn't some one else make a test for the new mutations?  well they can't, at least, not without permission from the patent holder whom seems more interested in the bottom line and less in good medicine.  As of writing this, there is one BRCA test available.

So how did the law get this way?  Patent law has always held that patentable items must be inventions and not something found in nature.  For example, if you found a new element in your backyard you would likely be heralded in all the scientific journals but you would not be able to patent it.  Why not? because you didn't make it.  So why can some one patent a gene?  did they invent it? ummm, no, millions and millions of years of natural selection did.  Then how did this gene get patented?  The answer can be traced  back to the last major oil disaster that struck the US (Exon Valdeez).  At that time, a quite inventive biotech company constructed a strain of bacteria in the lab that liked to eat oil.  In order to not lose all the money from their invention, they patented it and that patent was upheld all the way to the Supreme Court.  The basic idea being that the company had made a new tool that was not found in nature and thus could be patented.  This decision, however, has been used to support the patenting of genes.  Is it the same thing? In my opinion, not in a million years...making a tool in the lab is not the same as identifying a gene.  Nonetheless, tens of thousands of genes have now been patented.  Its rather insane and has huge consequences on scientific research (patents can be used to decide what other scientists can and can not work on), market competition and most importantly, providing good medicine. 

Now, as you can tell, I loath the patenting of genes and would like to see an end put to the practice.  Will that happen? possibly as there are a myriad of cases making their way up the courtroom ladder, including challenges to the BRCA patent.  The hope is that some of these cases will make it to the Supreme Court and they will clarify what can and can not constitute a biological patent.  Here's hoping.

Whooping cough epidemic strikes California

I have to say that it angers me to be writing an update about this topic, but I think it is important and deserves considerable attention.  As some of you may have heard, there is an outbreak of whooping cough in California that has led to the death of at least five infants and left over 900-infected.  While these numbers may not seem like a lot on short inspection, they are quite shocking when you consider that we have an effective vaccine to pertussis, the causative agent of whooping cough. 

So lets take a step back.  What is whooping cough?  Well, generally speaking its a cold like illness that is not terribly problematic in infected adults as it is a bacterial disease and can be controlled with a good round of antibiotics.  The problem arises when very young children become infected with the bacteria.  As young children's immune system and lungs are not fully developed, they are not equipped to handle pertussis, and the disease is much more severe and can be life threatening.  The name "whooping cough" actually derives from the  noise made from young children as they inhale after a long coughing fit.  The noise is quite unsettling and for those of stout constitution, here is a link to the noise that is made.

Now, pertussis has not really been a major health concern the past 50 years due to the vaccine that is given to children starting around 1.5 years old.  While not the best vaccine by far, the number of cases of pertussis related mortality in the US dropped from 10,000 a year, to less than 50 (I'd call that a nice decrease).  So why are all these new cases of pertussis showing up?  Sadly, as mentioned above, parents are not taking their kids to get vaccinated.  A similar phenomenon was observed last year with measles, another disease that we thought was off the radar.  So if you are a parent and reading this, I hope you have had your child vaccinated for pertussis.  If not, I'd encourage to talk to your pediatrician about the vaccine, both its risks and benefits.  Even if your kids are now a bit older, it is worth having a conversation about the vaccine as pertussis is also highly contagious and by vaccinated all your children you can help prevent spread.

Here are some useful links if you would like some more information:

CDC page dedicated to pertussis
Wikipedia article on pertussis and the vaccine

Could there be life in our solar system on the Moons of Saturn?

If you would have asked that questions a few years ago you might have been laughed at, but now, scientists are slowing starting to warm up to the possibility.  As some of you might remember, Titan, one of the moon's of Saturn, has been in the news alot the past few years due to it having an ocean.  Now, that ocean might be made up mostly of methane, but its still a liquid medium and where there is carbon, energy and liquid, we have the possibility of life.  Of course possibility and reality are not one in the same and determining if life exists on Titan is a long way away.  Nonetheless, scientists are working to determine if this is real and have set some basic criteria that would have to be met before we actually find a way to land on the sucker.  Well, as more data is collected by Cassinni, more of the criteria are being met.  These observations, and the fact that biologists here on earth continue to find microorganisms in the most extreme environments, really teases at the possibility of novel life on a sub-planetary body here in our own little neck of the galaxy.  Overall I'd say its an exciting time for the exobiologists.  If you want to read more on the criteria and the Cassinni missions, here is a link to a much more in depth time article.

Book Review: “The Immortal Life of Henrietta Lacks” by Rebecca Skloot

I first heard about “the Immortal Life of Henrietta Lacks” from a colleage at work. Every few days she’d tell me some interesting story or fact about Henrietta or HeLa cells at lunch and eventually I broke down and bought a copy for myself…and I’m very glad I did. Given the author, Rebecca Skloot‘s, background in biology, I expected a book describing the origins of and discoveries made from HeLa cells. While that was definitely a major discussion point of the book, Rebecca Skloot delved much further and truly brought to life the human side of this story, something very few have ever heard.


The book begins where most biographies begin, the birth and childhood of the protaganist, Henrietta. Given the lack of written documentation and the passage of time since Henrietta’s death, it isn‘t far into the book that we find ourselves at John Hopkin’s, nearing the “birth“ of HeLa, where documentation was more readily available. Now I have to be honest, when the book turned its attention to the isolation of HeLa, I expected the remainder of the book to focus on the science of HeLa cells, how they were maintained, what discoveries were made using them, the role of Human Papilloma Virus in their transformation etc. etc. And while these things were discussed to a limited extent, Rebecca Skloot took the story another direction, specifically, looking at the ethical issues regarding the use of Henrietta’s cells and the effect the isolation of the cells had on Henrietta’s family, particularly her children. In fact, the majority of the book chronicles the efforts of Henrietta’s youngest daughter to come to terms with the legacy of her mother’s cells.

Overall I found the book to be quite compelling and difficult to put down. While part of me wishes there was more detail given to HeLa cells themselves, I think Rebecca Skloot was correct in avoided those details, as it might have turned off a more general audience and taken away from the true questions she wanted the readers to ask themselves. Instead of turning into a technical history of HeLa cells, the reader is left with a myriad of ethical questions about medicine, namely, who should own tissue collected from medical procedures? Who should profit from the use of those materials? How much consent is needed from patients to save tissues collected from routine medical procedures? Etc. etc. While a lot of the issues revolving around Henrietta and her family would unlikely happen today as there are new rules in place (Thank you four hour HIPA training), the themes resonate to similar issues that are ongoing today. Is it ok to patent genes? What types of permissions from patients are needed to submit samples for the national bio bank? Who has rights to access those samples? Just to name a few.

All and all I highly recommend “The Immortal Life of Henrietta Lacks” for anyone interested in the history of science or medical ethics, and would still recommend the book for fun casual reading. Now, as stated in my bio, I am a research scientist and have used HeLa cells extensively over the course of my research life time. Before reading this book I never really thought about the story of the cells, they were merely a tool, but I now have a much greater appreciation of where they come from and the significance to those who knew Henrietta. While my data was not ground breaking, or even ground scratching, it did help me grow as a scientist and for that I am grateful to the contribution of Henrietta Lacks.

Lead poisoning kills over 100 people.

With all the news focus on the gulf spill, I think some other major medical news around the world is being push to the side.  There is one story in particular that I find most troubling, and this is a massive case of lead poisoning in Nigeria.  It seems that miners went a bit to far in shafts they knew were contaminated with high levels of lead.  The result is over 160 dead (and hundreds more suffering) due to lead poisoning in the water wells.  Here is a link to the yahoo story covering it.

Nostradamus predicted Farmtown will usher in the next great plague.

OK, so maybe those were not his exact words, I believe the strict translation says that “Fram Owtn” will usher in the next “black death“. Scholars for years have been trying to decipher what Nostradamus was referring to when he spelled out “Fram Owtn,“ but since the massive explosion of Facebook, the answer has become abundantly clear. By just slightly shifting the letters we can see that Farm Town will be the doom of us all….I mean, how can we deny the for sight of the man who predicted Hisler and the raise of a new nation to the West. Sadly, my favorite 16th century seer failed to give any more details into how the plague would come to be, but, after playing Farm Town, I think I have deciphered how.

For those of you that do not know, Farm Town is a virtual farming community that one can play while logged into Facebook. It teaches the WiFi generation the basics of farm management and agriculture, making its players tend to crops, raise livestock, build barns and decorate their farms in their own personal style so the neighbors will stop by and be jealous. While on the surface, this game sounds great, like the classic of my generation, the Oregon Trail, where thousands of children learned how to repair wagons and fend off typhoid by simply pressing the return key, the writers of the program left out a key basic farming tenant that might lead to the death of us all. Now, I‘m not sure if the omission of this detail was an oversight, or a vicious plot, but nonetheless, our youth are learning a farming technique that will wipe the human race from the earth.

What part of the game could possible lead to the greatest catastrophe since the extinction of the dinosaurs, you ask? Well the answer is simple, the raising of large numbers of pigs and chickens on the same farm. Sound silly? Think I’m nuts? Asking yourself how on earth raising two farm animals could be the end of days? Well its simple, its called reassortment, and its something that has happened before, and can be prevented from happening again.

Now I know some of you might be thinking, “what on earth is reassortment and what does it have to do with the next great pandemic?” Well, with out getting too technical, reassortment is a process that some viruses can use to swap out parts of their genomes with that of closely related viruses. Its sort of like a game of virus pick up sticks. Two closely related viruses infect the same cell, replicate their segmented genomes and, when it comes time to pack up new viruses, they grab a few pieces from their genome but also grab a few pieces from their roommate‘s. The end product is a Frankensteinian virus with genome segments from both the parents. Most the time, the consequences of this happening in the natural world are not readily apparent, and if I had to guess, often results in viruses that are unable to replicate on their own. However, sometimes reassortment can generate a hybrid virus that gains growth advantages compared to either of its parents (and isn’t that every parents goal, for their children to go beyond what they ever achieved). It is when this happens that scientists start to get worried, because some believe that this has happened before, resulting in very dire consequences.

Flash back to 1917. The Great War is in full swing and hundreds of thousands of young men are packed into small quarters…bunkers, trenches, barracks, etc. While these young men were ready to give their lives to fight for their country, little did they know that the biggest killer in WWI would not be the battlefield, but rather, would be the Flu. The 1918 Flu would take the lives of 50 million people before it had run its course. The source of this new strain of Flu has been the subject of much debate, but one theory is that the virus was a new strain generated by reassortment of three different flu viruses; one from swine, one from chickens and one from man. Remember, during WWI there were no such things as refrigerators and freezers and so fresh food required the transport of livestock along with the troops. It is believed that the density of pigs, chickens and people on army bases was at a critical mass, allowing for the different influenza strains to intermingle, giving birth to a new strain that no one had ever seen and resulting in the deaths of millions of people.

This concern over farming birds and pigs in the same area is still alive today. Remember the massive panic over “Avian” flu a few years ago? Again, the fear for scientists is the close association of birds with swine. Now, the lesson is simple, don’t cultivate the two together, which, is done in most of the industrialized nations. Its much more difficult to convince farmers in developing nations to do the same and is why, most efforts to monitor Flu reassortment focuses on regions of the world that is just beginning mass production of farm animals. As for Farm Town (or Farmville, or FarmStory), for those of you who play, or have kids that play, I’d encourage you to not raise chickens and pigs on your farm I’m thinking of starting a petition to get the writers of Farm Town to introduce a new calamity into the game allowing for a new pandemic flu if people put the pigs in the same pen as the chickens….for some reason I don’t think they will go for it.

WHO update on Swine Flu

Given that we are not hearing much about the swine flu these days, it may not come as much surprise that the number of swine flu cases around the world is pretty low.  While the virus is still sporadically popping up in certain parts of the world, the incidents are very few and far between.  Here is a link for the update by the WHO.

How big really is 0.5 mM?

So I find myself asking that question today.  In relative terms it is such a tiny length that it is hardly noticeable.  In fact, I'd be hard pressed to be able to distinguish two every day items if the only difference between them was 0.5 mM in length, however, when it comes to precision, 0.5 mM can be the determinant between amazing success or catastrophic failure.  Could you imagine what would happen if the support beams for the space shuttle were that uneven..and at the same time, physicists are able to accurately collide subatomic particles where 0.5 mM might as well be the atlantic ocean.  Why this sudden curiosity over 0.5 mM today, well, apparently, 0.5 mM is the difference in acrylamide gel thickness that I can successfully work with with out tearing it into pieces.  Better luck next time.

Physics is Phun!

Alright, so this isn't exactly medical news, nor is it a subject matter that I can say that I am well versed in (note: I am not currently, nor have ever been a theoretical physicist) but I have always had a soft spot for the origins of all that is that we know.  In fact, I was an astronomy major for my first 3 semesters of college until I realized that the subject matter was to far removed from everyday life.  None the less, whenever I see big astronomy or physics news, I get a little excited. 

Having made all those disclaimers, I'd like to mention something that happened in high energy physics that has many scientists excited.  Last week, the Fermi labs were able to show that collisions of matter and anti matter at very high energy would produce more muons than anti-muons.  What are muons and anti-muons?  To be honest, I'm not terribly sure other than they are components of the primary atomic particles like protons.  How does this benefit Joe public?  Well, at the moment probably not at all, but it does provide experimental evidence towards one of the biggest conundrums in astronomy and physics.  When the universe was formed in the giant ball of fire commonly referred to as the Big Bang, tons of matter and anti-matter was produced.  Now conventional wisdom, and all experiments before this advance, suggested that matter and anti-matter were always produced in equal amounts, and thus, should cancel one another out.  Under that model, there would be no matter (or anti-matter) in the universe, however, the fact that I'm typing this post that hopefully some one is reading it suggests that there is a flaw in the model.  Step in Fermi lab....products of a matter/anti-matter collision resulted in a slight imbalance toward regular muons and not anti-muons (about a 1% difference).  I realize that 1% may not seem like a lot, but when you consider the enormity of energy at the time of the big bang, well, it may have been enough to result in all the matter we see in the universe.  I find that option to be much more exciting than the theory where giant pockets of antimatter are floating around and we have just been lucky enough to avoid them...I mean, who likes to play dodge ball when the result of getting hit is total annihilation. 

So where does this leave us?  Well first, the result will need to be repeated, likely at the new collider in Switzerland, where higher levels of energy can be obtained.

Should future cartoons depicting God replace the bearded old man with a portrait of Craig Venter?

Probably not yet, though there definitely seems to be a lot of people who think he's messing with things he shouldn't be and there was a blogasm over the weekend regarding his most recent publication in science.

So, lets take a step back for those that are unaware what the big deal is.  Dr. Craig Venter was the pioneer of sequencing the Human genome and, since that task is complete, has moved on to the creation of artificial life.  Last week, Dr. Venter published his most recent advances toward this goal, which was to replace the genome of a bacterium with one that his company made artificially in the lab.  In effect, he "rebooted" a bacteria with a new operating system from another organism, opening the door to potentially design organisms for specific purposes.

Now, I'm sure most people can see the ethical dilemna of this advance.  It raises many of the same questions that have been around for decades regarding the use of standard molecular biology techniques...namely, should we (we being humans) be manipulating the basic building blocks of life (aka DNA)...or as many oponents of molecular biology call it...playing god.  I don't want to rehash this debate as its going on all over the internet at the moment and it would not be hard to find such a conversation if you are interested.  I would rather discuss the scientific implications of this advance under the pretense that there is no ethical debate (and for full disclosure, I do not have many hang ups over the ethical nature of this advance).

That being said, what does this advance do for every day Joe public.  At the moment, not really anything...just as the discovery of the LASER didn't see real world applications for years after its invention.  What it does do, is show proof of principle that genomic information can be engineered in the lab and introduced into bacteria.  This is a fairly large step forward from where the technology currently stands, where we can introduce peices of DNA into bacteria, but all of which are dependent on the bacterial DNA as well.  To me this is the major point, Dr. Venter has found a way to replace the entire bacterial genome with that of one made in the lab. 

So how long will it be before we see bacteria engineered for a specific purpose (such as turning carbon dioxide into some form of usuable fuel, for example)?  not clear, but I'm guessing we are several years  away(atleast a decade) at best.  How far are we from taking this one step further and replacing a human cell's DNA with DNA made in a lab....a really really really long way away.  While it may be possible at some point in the future, the size of the human genome is thousands-fold larger than that the average bacteria (its like going from the diameter of shooting marble to the length of a football field).  That doesn't mean that people won't start trying, but that is another can of worms for another time.

Gluten and Casien free diets do not affect autism behavior

There is a very interesting article today on Dr. Gupta's blog about the link between autism and diets rich in Gluten and Casien.  As some of my friends know, my family has a bit of history with Celiac's disease and my mom has been living on a gluten and casien free diet for some time.  While difficult, it is doable and both her and my dad are probably more healthy for it.  Sadly, the gluten/casien free diet seems to have no effect on autism as reported by a recent study.  For a more thorough discussion, check out Dr. Gupta's blog.

Bret Michaels admits to herpes...type one that is

Now I'm a big fan of the apprentice and while that absolutely has nothing to do with the focus of this blog, I think Bret Michaels just talked about the cold sores on his lips on national tv.  Did anyone else catch that cause I'm not sure my DVR is recording this week. 

If enough people believe it, does it make it true?

Evolution, yet another third rail in American Politics, has been getting a lot of coverage lately in the press.  Sadly, its not the coverage I would like to see...like the recent discovery that neanderthals and homosapiens may have intermingled (in the biblical sense).  Instead, the media (including me, not that I have elevated myself to the level of "the media") is covering the incredible backlash against evolution by conservative groups. The climate in politics has gotten so bad that republicans are attacking other republicans for even suggesting they believe that evolution may be real and that the bible should not always be taken literally. A prime example that came out this week...the primary races in Alabama.  Take a look at this attack ad...

This is of course coming on the heels of several states completely removing evolution or elevating intelligent design to equal status in science text books.  It scares me to think that one day in the near future, I could be teaching an intro biology class at a small university and actually have to explain the basic tenants of the theory of evolution.  Hopefully this anti-evolution fad is simply that, a fad, and will burn itself out. 

TV host takes on Small Pox?

I did a double take the other evening. I saw a commercial for an episode of Dr. Oz that was to focus on the next major bio-terrorism threat...smallpox. Just to be sure that I wasn't in some sort of scientific heaven, I checked the TV listings and, low and behold, there it was. Now, being a card carrying virologist, and having studied a BL-4 agent, I was quite curious as to what a daytime TV show doctor was going to do with such a sensitive topic...and thanks to my new best friend, my dvr, I was able to watch the segment.

As predicted, Dr. Oz pulled out all the stops...from misting the audience to simulate the spread of smallpox...to crazy lighting and seat arrangements...and of course, the obligate slide show of victims that died to small pox in the first half of the 20th century. It was a bit over the top, but all and all, I think he kept the fear of a smallpox outbreak in check with the facts. As many might remember, small pox was officially eliminated from the world back in the 1970's except for samples to be kept at two locations, one in the US and the other in Russia. There is concern amongst many scientists and security experts that smallpox may exist in other freezers throughout the world, but for now, all we have is speculation on that front. None the less, even if terrorists or rogue nations were to get hold of the virus (or make it), we have a very good vaccine that can be used up to four days post exposure to the actual virus. And, unlike the H1N1 vaccine, we have over 300 million doses of the virus already set to be distributed if needed.

The one major problem that I had with the show was that Dr. Oz and his experts failed to discuss one of the major problems with the vaccine. I realize that he might not want to detract from people taking the vaccine by scaring them with the potential side effects, but, I for one believe everyone has the right to know all the facts about what is going into their body. So here we go...The smallpox vaccine is a live virus vaccine. Its actually derived from another pox virus that was initially isolated from cows (aka cowpox). It was discovered a long time ago by Edward Jenner that milk maids were always spared during outbreaks of small pox. He realized that the milk maids were getting exposed to cowpox and that this exposure resulted in protection against the human version. This was the first, and to this day one of the most effective, vaccines to be made. Now, like many live virus vaccines, there are problems that can occur, most notably, death. While most people giving the vaccine will develop a small sore at the sight of inoculation, rarely the infection will become systemic, can leave to permanent neurological problems and cause complications during pregnancy. In addition, those vaccinated are infectious, and, if the virus is spread to some one with certain skin disorders, including eczema, severe complications can develop.

So, all that said, if smallpox breaks out in the US will I be standing in line for the vaccine? You betcha. Would I recommend everyone else get the vaccine? I'd say yes for almost everyone, though if you have a compromised immune system or a history of eczema or other skin disorders I would consult a physician first.

Image courtesy of the CDC.

What was that old saying about history...

Once again I'd like to take the time to discuss H1N1 since we are still around the one year anniversary of its dramatic entrance into our lives. I realize that covering the same topic twice in a week's time might go against all tenants of modern media but hey, I guess I'm just old fashioned that way. This time though, I'd like to focus on how we handled the news of this coming plague as is compares to how such things were handled in the past.

Picture this, suburbia 1952 (and yes, I am watching Golden Girls in the background), rows of new homes with pristine green lawns and American cars parked in the driveway stretch as far as the eye can see. Well, most of the houses at least. One stands out amongst the others as its taped off with giant signs warning neighbors to stay away. What reason would anyone quarantine off a house, and the family inside, you ask? Well, 1952 was the worse year in recorded history for the plaque of the time, Poliomyelitis. Of course, you history buffs know that 1952 wasn't the first year Polio virus reared its evil head, in fact, Polio is at least as old as the Pharaohs. So what was different about it in the early to mid 1900s? Mainly, society had changed and we had become more sanitary. While most of us think sanitation is a good thing (my olfactory senses definitely agree), there are some drawbacks, one of them being that very young children were not exposed to the Polio virus like they had been for millenia. Unlike most viruses, it turns out that Polio actually causes far worse problems for older children and adults than for infants and our new found sanitation did just that. What was once a virus that rarely caused any complications had become quite the monster, killing over 3000 people and paralyzing 20,000 others in 1952 alone.

As to be expected, the years of Polio related disease had struck fear into the heart of the nation. Extreme measures were often taken in the event of a new Polio diagnosis. Families were quarantined, schools and public places closed, children separated from parents, entire households worth of possessions incinerated, all to prevent the spread of the virus. We shouldn't blame people for their reactions during that time, there were no treatments nor a vaccine. Many of those paralyzed ended up in Iron lungs, some of whom never had the chance to leave. But even in all that despair there was also a common bond, through which something incredible happened. Instead of feeling helpless at the hands of Polio, a vision of a polio free world was born, a vision that managed to unite Americans in one of the greatest fundraising drives in our history...the March of Dimes. It was simple concept really, the March of Dimes asked everyone in the United States to give a Dime if they could spare, and even in times as tough as the Great Depression, they did. It allowed everyone to participate in defeating a true evil in the world, it provided a single focus. The March of Dimes raised millions of dollars in an incredibly short amount of time. Money that went directly to funding research on Polio virus. It would take years for the research to finally pay off, but in 1954, Dr. Salk would announce he was ready to test the first Polio vaccine. Millions of people volunteered their children to see if the vaccine worked...and work it did. In 1955 the vaccine was licensed and the March of Dimes organized campaigns to get the vaccine to anyone and everyone. And vaccinations they got, by the score. People lined up for hours on end to get their children the vaccine and, by 1961, less than 200 cases of Poliomyelitis were reported in the United States.

Now, lets flash forward to 2009. Polio is gone, in fact, it might actually only live in the lab after extensive vaccination programs around the world. We have a new enemy though, H1N1, a strain of influenza that threatens to turn the world on its head. Much like polio outbreaks of yesteryear, there is a lot of fear across the nation. The slightest hint of an outbreak closes schools in several metropolitan areas. People are afraid to fly and everywhere you go, everywhere you look, on every TV channel, all you see is H1N1. For months you couldn't get away from it, all very reminiscent of our old friend Polio. Unlike Polio though, the unifying drive to fight this disease seemed absent, at least to me. Maybe it was the fact that there are anti-flu drugs, or maybe it was the fact that a vaccine would likely be available before the end of the year, but the nation did not rally to fight H1N1. There was no March of Dimes, or a celebrity clad telethon for H1N1. In fact, there seemed to be a mistrust surrounding it. I might expect people to not get vaccinated out of laziness or forgetfulness, but, never in my life would I expect people to out right protest vaccination, but people did, lots of them. In fact, when it was announced that H1N1 would be included in the 2010 seasonal flu vaccine, blogs were overwhelmed with posts screaming that they would never take a vaccine that included H1N1, even though the seasonal Flu vaccine has been around for decades. The real question is why? why such the difference in reaction to H1N1? is it a lack of trust of Doctors? the government? the empty, unfounded, fabricated claims that vaccines cause autism? leprechauns that lost their gold? To be honest I'm not sure but I think its a little bit of all the above (well, of course the leprechauns). I'd love to know other opinions as to why this was/is as its very foreign to me.

If you are interested in learning more about Polio I'd recommend the wikipedia pages. They are quite thorough and seem to go on forever. There is also a very good episode of "This American Life" dedicated to what American was like during the polio years..highly recommended. Pictures above are courtesy of the CDC.

A year in the life of H1N1`

A year to the day, I was getting ready to board a flight from Boston to Washington DC to begin my search for an apartment. The night before my flight, news broke that the new Influenza strain, H1N1, had been isolated from a group of school children in Reading, not far from the Logan airport, and I honestly was a bit nervous about getting on a plane. Admittedly, I am a hypochondriac, but at that point in time, Swine flu was causing an international panic. Schools were closing at the slightest hint of the virus, Vice Presidents were warning people not to fly, dogs and cats were living in harmony...you get the idea. We really didn't know much about the virus except that it was a new strain of Influenza derived from pigs and that no one living had seen this virus before (we found out a little bit later that a similar virus had spread around in the 1950s and that the virus was more likely avian in origin, but I digress). It didn't help that the virus was particularly devastating to children and young adults . As for me, budgetary concerns (aka paying to delay my flight) soundly defeated my fear of H1N1 and I got on the plane.

When I arrived in DC, I eagerly began my apartment search, only to find that H1N1 had been isolated at the IMF and World Bank, just a few blocks from where I wanted to live. The management company for the first apartment I viewed made me wash my hands and wipe all the surfaces I touched with wet naps to make sure that the apartments were not contaminated. Every where I went, everyone was talking about Swine flu, it was completely unavoidable. It was if the whole world was about to come under siege and no one knew what to do about it.

That was a year ago, and a lot has happened since. Flu tracker estimates that there has been over 1.5 million cases of H1N1 around the world and the World Health Organization has isolated H1N1 in 214 nations and confirmed 17919 deaths were due to the virus. When I think of these numbers in isolation, they are shocking to me. It would be as if the entire population of DC were sick and the entire suburb of Fairfax city dropped off the face of the earth. I realize that isn't the fairest comparison (DC only has 600,000 people) but its a scary thought none the less. Oddly enough, those numbers pail in comparison to what I thought might happen when H1N1 first surfaced. At the beginning, no one really knew what the percent mortality would be or if the entire nation, or world, would be completely overwhelmed. Fortunately, we got off pretty light this time. A vaccine was made (albeit, not as quickly as many would have liked) and the virus was not as deadly as predicted. While there are still pockets of outbreaks across the globe, for the most part H1N1 has run its course for this season and all has returned to normal.

As for me, I did manage to make it back to Boston after my apartment search without picking up the virus. A month later, I moved to DC, started my job and spent the next 5 months telling friends and family to not overreact. Several friends came down with the flu, but were ok after a week or so. And then, on the second Monday in November, I came down with H1N1. I'm not sure where I got it from...I think the most likely candidate is the DC Metro (aka giant microbe incubators...sorta like preschools) but I have no evidence to prove that. It started rapidly. I was sitting at my desk in the lab and my back just started aching, and I mean really aching. I could barely straighten my back all the way. I told my boss of the symptoms and he instructed me to leave. I wouldn't make it back to work until the next monday. It was a very unpleasant experience but I, like 99% of others who got infected, survived. This year, it seems unlikely that H1N1 will have quite the splash in the news. At least in the US, a large percent of the population has antibodies to H1N1 (either from being infected or the vaccine) and H1N1 is included in the 2010 seasonal flu vaccine. It seems we dodged a bullet (albeit potentially a very slow bullet show from a bb gun). In the next blog entry I hope to talk more about how we reacted to the appearance of H1N1 and compare it to public reaction to another pandemic (non influenza) from 50 years ago. I think you will be amazed at the difference, I know I was.

FDA Approves first vaccine to fight cancer

So, I originally planned to make my first blog entry be an extensive, long-winded diatribe on a subject that would awaken the mind and arouse the senses, however, this isn't a blog about coffee and a truly historic event in vaccine biology occurred today. I'm pretty sure I'd be stripped of my vaccinologist (yes its a word, look it up) card if I didn't mention it. What was this amazing discovery you ask? Well, the FDA approved the first vaccine for fighting a human cancer. Specifically, the vaccine licensed as Provenge by Dendreon, is approved for the treatment of advance prostate cancer. Now ladies don't get to jealous or run out and try and get yourself your own prostate, you still have the best preventative anti-cancer vaccine out there (go HPV vaccine)...and men, don't get to excited. While this is a huge step forward toward cancer treatment, Provenge is only modestly effective at treating prostate cancer, extending life expectancy by an average of 4 months for patients that failed to respond to more traditional treatments. Downer aside, this is a huge push forward in the idea of individualized vaccines for treatment of cancer and hopefully marks the beginning of a wave of new cancer treatments that utilize the host immune response to control this awful disease. For more information about the vaccine, CNN has a decent article up ...

http://www.cnn.com/2010/HEALTH/04/27/provenge.prostate.cancer.fda/index.html?hpt=T2