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.