Dear scientists: "It's good to blog"

Friday, February 27, 2009 at 1:39 AM Bookmark and Share
The well known science journal Nature came out with a nice editorial piece last week that affirms my decision to create this blog. The title of the piece says it all: It's good to blog.

Vaccination is to Autism as
Tobacco is to Lung Cancer... Ummm, What?!

Thursday, February 26, 2009 at 7:39 PM Bookmark and Share
Continuing this thread on vaccination against childhood diseases, a friend of mine pointed out the article Vaccine Court: Autism Debate Continues from the Huffington Post, authored by Robert F. Kennedy Jr. and David Kirby. You might take a few minutes and give it a good read.

There are two big issues at play in this article - particularly within the context of vaccination legislation - that should really be presented more distinctly. These are (1) the extent to which vaccines contribute to the incidence of autism or autism spectrum disorders (ASD), and (2) the consequences of whether or not we vaccinate our population against these types of infections. What I realized in reading this article is that talking ad nauseum about the first issue without also addressing the second is, quite frankly irresponsible and dangerous.

Before I explain why, lets mention some important background information. First, I will distinguish here between the infection (i.e. simply hosting a viruses, say HIV) and the disease (i.e. the symptoms caused by that virus, which for HIV would be AIDS). This is important because not all infections lead to disease (i.e. injury or death).

We also need to understand the role of herd immunity as it relates to infections that transmit from person to person. In short, a certain percent of the population needs to be vaccinated (or otherwise resistant) to infection in order to prevent a few infections from becoming a big epidemic. If to few are vaccinated, epidemics can take off and spread through the unvaccinated portion of the population, which is bad.

Think of vaccinated and unvaccinated individuals and fire-proof and flammable wooden sticks, respectively. A population then would be analogous to a pile of such sticks. With enough fire-proof (vaccinated) sticks in the pile, a single match won't start much of a fire. On the other hand, too few fire-proof sticks (too few vaccinated individuals), and whoosh! The pile goes up in flames. In the case of infectious diseases, the proportion vaccinated needs to be relatively high in order to prevent outbreaks, usually upwards of 80-90% in a given community.

Back to our two main questions. Speaking as someone with a strong quantitative background (i.e. an applied mathematics graduate student) the first thing I want to know regarding issue (1) is what evidence exists that children receiving vaccines show a significantly higher rate of ASD relative to unvaccinated children (all else being equal), and how much higher is it?

This next bit is what they leave out of the article, and is of fundamental importance to the vaccine-autism/ASD controversy: how we evaluate the answers we receive to the first question depends enormously on what we learn from issue (2). In short, if we have to pick our poison we had better know which option is worse! If we compare a sufficiently vaccinated population and one with low or no vaccination (all else being equal), how do they compare on both childhood disease and autism?

The evidence I have seen and that the experts have summarized for the rest of us suggests that there is at worst a relatively small number of cases where vaccines caused significant harm to the people that they were intended to protect. This is true of most drugs, medical treatments, safety mechanisms in automobiles, and countless other things we make and provide one another - simply put, nothing is perfect though we can usually do a little bit better and a whole lot worse.

So lets revisit the common (and very flawed) argument against vaccines that goes something like this: "vaccines cause injury and death, therefore they are bad and we should stop pushing them on the public." Sounds reasonable, right? Well, it isn't. A more relevant statement to make would go something like "if vaccines cause injury and death, we should categorize them as bad if they caused more injury and death than the diseases which they prevent."

While this comparison seems like a no-brainer, it hardly ever gets as much thought as it deserves! This is in part because of the concern (and in many cases fear) many parents have over the perceived risk of vaccines, and also because there is more anecdotal evidence on the vaccine-ASD issue floating around out there than on the vaccinated-unvaccinated issue despite the often unnoticed historical figures. We also have more control over our own individual choices about vaccination compared to our contracting diphtheria, for example, which focuses attention there instead of on the larger issue of society doing the greatest for its people.

This my friends, is why so many public health professionals and concerned citizens push so strongly to fight all the anti-vaccination rhetoric and fear that pervades that ether of public information and knowledge. Vaccines may cause great harm to a very small few - each and every case meaning the world to someone, and each deserving the appropriate level of recognition and in some cases redress.

But without vaccines, and without enough vaccine coverage to ensure we stand above the herd immunity threshold, the cost in human lives and human suffering would be much greater. And that folks, just isn't an acceptable alternative.

I'll leave you to look back to the tobacco analogy drawn in the article above, and how irresponsible it is to compare the tobacco industry with the medical industry. Tobacco products don't do much good for society (as far as I know) - and they certainly don't protect little boys and girls from the wrath of so many truly horrible diseases that once plagued our population.

Nice article on "Why We Vaccinate"

 at 12:38 AM Bookmark and Share
I was just browsing the blog Sandwalk and saw a like to a nice article entitled Why We Vaccinate by James D. Macdonald. Give it a read!

This article was inspired by this news story which reports on the death of one of five children in Minnesota recently infected with Haemophilus influenzae B (Hib).

Obama calls upon the nation to hit the books!

Tuesday, February 24, 2009 at 10:22 PM Bookmark and Share
Tonight in President Obama's address to Congress, he asked fellow citizens to further their education - and he backed up his request with a promise of support. Why? To summarize using his own words, the reason education is a big economic issue is that "the countries that out-teach us today will out-compete us tomorrow."

The following is an excerpt from his address (full transcripts at CBS news). Video of the address is also likely to be readily available. For more details, visit www.whitehouse.gov and see the president's agenda on education.

The President:
In a global economy where the most valuable skill you can sell is your knowledge, a good education is no longer just a pathway to opportunity - it is a pre-requisite.

Right now, three-quarters of the fastest-growing occupations require more than a high school diploma. And yet, just over half of our citizens have that level of education. We have one of the highest high school dropout rates of any industrialized nation. And half of the students who begin college never finish.

This is a prescription for economic decline, because we know the countries that out-teach us today will out-compete us tomorrow. That is why it will be the goal of this administration to ensure that every child has access to a complete and competitive education - from the day they are born to the day they begin a career.

Already, we have made an historic investment in education through the economic recovery plan. We have dramatically expanded early childhood education and will continue to improve its quality, because we know that the most formative learning comes in those first years of life. We have made college affordable for nearly seven million more students. And we have provided the resources necessary to prevent painful cuts and teacher layoffs that would set back our children's progress.

But we know that our schools don’t just need more resources. They need more reform. That is why this budget creates new incentives for teacher performance; pathways for advancement, and rewards for success. We’ll invest in innovative programs that are already helping schools meet high standards and close achievement gaps. And we will expand our commitment to charter schools.

It is our responsibility as lawmakers and educators to make this system work. But it is the responsibility of every citizen to participate in it. And so tonight, I ask every American to commit to at least one year or more of higher education or career training. This can be community college or a four-year school; vocational training or an apprenticeship. But whatever the training may be, every American will need to get more than a high school diploma. And dropping out of high school is no longer an option. It’s not just quitting on yourself, it’s quitting on your country - and this country needs and values the talents of every American. That is why we will provide the support necessary for you to complete college and meet a new goal: by 2020, America will once again have the highest proportion of college graduates in the world.


While I could nitpick at some of the issues he brought up (the notion of reform as a guaranteed means of improvement, is the first that comes to mind) I'll keep this post short and leave it at that, for now.

Other links of possible interest:

To vaccinate, or not to vaccinate... is that the question?

Monday, February 23, 2009 at 10:22 AM Bookmark and Share
A friend of mine posted a link to this video today, which I thought deserved some critical commentary. Before I get into it, click below to watch the clip. Even better click here to watch it in another window - I'm sure you'll want to go back and forth and review some of the video segments as you read on.


Lets start with Katie Couric's opening line in the piece, the rest of which is done by CBS's Sharyl Attkisson (whose strengths are more in matters of money and not medicine):
For years now parents have wondered if vaccines are linked to conditions like autism and ADD. Government officials and some scientists say there is no connection, and they are often backed by independent experts. But just how independent are they?
The first sentence implies those rightfully concerned parents haven't found any good answers, which is hardly the case. Plenty of answers can be found through one's local medical community, on the web at places like the National Network for Immunization Information, the U.S. Centers for Disease Control and Prevention, and so on. The claim that vaccinations cause autism and ADD have been investigated repeatedly by the scientific community and all the evidence suggests that vaccination won't give someone autism, ADD or the like - which is good news!

Taking those findings more skeptically, they suggest that even if vaccines were capable of causing autism or ADD, the odds of it happening to any particular individual are vanishingly small. That is, you are much more likely to be killed in some kind of accident in the months after getting the shots - and much less likely to develop autism or ADD.

The second part of this opening line is the real reason this clip caught my attention. The rather harmless sounding sentence calls into question the validity of all the work that has been done to understand the safety and risks associated with vaccines - by literally thousands of skilled people trained in using state of the art tools and methods to answer these kinds of questions - all cast into doubt by whether or not some organizations and individuals truly making independent claims from what the drug companies might say.

To give you a more clearly dubious yet analogous statement, this is like saying that if you walked into a car dealership - having done your homework and concluded that a Honda Civic was the perfect car for you - you should suddenly become overwhelmed with doubt about your decision upon hearing the clearly biased salesmen tell you to go with the Civic. Whether or not some (in this case, 3) individuals and organizations have a bias in favor of an otherwise good idea does not invalidate all of the other evidence supporting the notion that it really is a good idea!

The clip then goes on to point out financial ties between drug companies and three entities that one would expect to be "independent" from the likes of Merck and Wyeth: The American Academy of Pediatrics, Every Child by Two, and outspoken pediatrician Dr. Paul Offit, M.D.

I must mention that Dr. Offit would otherwise be someone concerned parents would absolutely adore, were they made aware of his dedication to preventing childhood diseases, his work in doing just that, and his books to help inform the public on these matters. Instead, Sharyl Attkisson further vilifies him with remarks like "he has gone so far to say that babies can theoretically tolerate '... 10,000 vaccines at once.' " (This statement is a testament to the amazing capacity of the human immune system to fend of pathogens, by the way - not some expressed desire make pincushins of infants!)

So what of their examples? Questionable or not, the consequences of any bias are blown way out of proportion here - although clearly some of these associations are to be frowned upon. AAP received $342K from Wyeth ("for a community grant program"), $433K from Merck (the same year their HPV vaccine was introduced), and unnamed funds from "another top donor, sanofi aventis." Each Child by 2 admits taking money, claiming no conflict of interest. However, their former treasurers - and the word "former" was absent from the script, but shows up in the visuals - included an official from Wyeth and one "paid advisor to big pharmaceutical clients" (which might sound bad, but without knowing the nature of the advising its hard to pass a quick judgment).

We could go on and on, for example the statement that
Today's immunization schedule calls for kids to get 55 doses of vaccines by age 6. Ideally it makes for a healthier society.
"Ideally?" How about "clearly" or maybe "demonstrably"? Immunizations as part of overall improved health care do make for a healthier society than without them. If you need some evidence of this fact, consider the last time someone in your neighborhood died from or became paralyzed by polio. Even better evidence is readily available if you look for it, such as in this article, for example.

Overall, I hope you can see how a little bit of critical thought on this piece turns up a lot of other issues that are probably more worthwhile to think about than how much money Merck gave the APP for a community grant program. Before you go, watch the piece again and let me know what you think!

Finally, I'll end with a teaser for an upcoming post where I'll come back to this thread and discuss a few other question from this clip. These come from the way that Dr. Paul Offit was dubbed a "vaccine industry insider" (the implication here is of course, not positive) because his Merck-funded position at Children's Hospital, and the nature of his work in trying to prevent childhood diseases.

It begs the question: What role should industrial/commercial/any scientists play in promoting products or information that by all measures will benefit society (in this case, that save lives)? When does "independent" trump "expert"?

The mice of Gough Island: Opportunity knocking!

Thursday, February 19, 2009 at 1:59 AM Bookmark and Share
These large, carnivorous, non-native cousins of the ubiquitous house mouse (Mus musculus) are about to get scrubbed off of Gough Island in the south Atlantic as part of measures to protect the seabirds that breed there. But before they go, we get the opportunity to study the evolution and ecology of one of the most well studied vertebrates in the lab, only this time - mother nature has done the experiment for us!

If you try and read up on the mice of Gough Island (e.g. google “Gough” and “mouse”), you’ll hear about the damage they are doing to the island’s nesting sea birds – some of which are of great concern as they are not known to nest anywhere other than this one island.

The mice of Gough Island have a different story. They were accidentally introduced by ships in the 19th century, and have since become larger in size than the typical house mouse, weighing in at a whopping 35g (normal mice are nearly half that size)! If you’re curious as to how they have reached this size, consider their life on Gough Island. There are no large predators, and their diet includes a hearty (though seasonal) food source: seabird chicks! And we aren’t just talking about hapless, naked, sparrow-sized birds here - some of them (such as albatross) are as large as a turkey!

Interestingly, this is a classic example of what some call the "island rule" for the evolution of body size: small animals seem to evolve to be larger than their mainland counterparts, and large animals tend to be smaller. This from the sizable body of knowledge arising from studies of the evolution of body size (which, for example, might occur in response to resource limitation, sexual selection via competition for mating opportunities, predation, and even predation by humans).

Super-sized or not, in order to protect the island's breeding seabirds from this jumbo sized pest, the UK has awarded The Royal Society for the Protection of Birds (a conservation organization) funding to eradicate them from the island, and most of the world seems to be quite pleased about it.

"But wait!"

In our effort to save the seabird colonies (which I fully support, I’ll have you know) we may be destroying a fantastic opportunity to learn something from what scientists call a natural experiment - a situation that arises in nature but can reveal to us the kind of information we might hope to get from specifically designed scientific experiment. In this case, the evolution of a wild population that has been adapting to a new environment over the better part of a century or more.

So why is this particular population so noteworthy? I’m glad you asked! First, there been very significant phenotypic changes in this population (suggesting there are likely to be interesting genetic or other evolutionary changes in the population that are worth studying) - fortunately, people are already hard at work studying these hefty little rodents. Second, we know about some of the major aspects of the ecology and natural history of this population - an important first step to understanding the role their environment has played in shaping the evolutionary trajectory of the population.

If that doesn't seem promising enough, the house mouse is probably the most well studied vertebrate on earth! Taking the tools and insights gleaned from studying from studying mice in the laboratory and combining them with studies of wild populations seems like a promising approach to advance our understanding of evolution in wild populations.

So, as we embark on ridding this island of its pesky rodent problem, I do feel a little bummed to see a monkey wrench thrown into the system. What would those mice look like in another century? As much as I would love to know, however, the price of loosing even one of the sea bird species that nest there would be far to great a cost!

If the links above have left you wanting more, check out the Payseur Laboratory website for some of the work on understanding more about the mice of Gough Island, and the Global Invasive Species Database which includes video of mice attacking an Albatross chick.

Happy Darwin Day!
PS: Most Americans don't believe in evolution...

Friday, February 13, 2009 at 2:03 AM Bookmark and Share
At least this seems to be the case, according to findings from a recent Gallup poll entitled On Darwin’s Birthday, Only 4 in 10 Believe in Evolution.

In Gallup's usual good form, the poll also included questions to uncover what major factors contributed to whether or not participants believe in the theory of evolution. The results? Well, they weren't all that surprising in retrospect: religious beliefs and level of education correlated well with whether or not participants believed in evolution, and whether or not they could associate the theory of evolution with Darwin. Interestingly, there is a short video from Gallup News from June 2007 giving the results of a similar poll showing Americans were split closer to 50-50 a couple of years ago.

For more details, check out the article - it includes informative data summaries and a more detailed discussion of the poll results. You can also find other related polls on the site, including One-Third of Americans Believe the Bible is Literally True, May 25, 2007, and Evolution, Creationism, Intelligent Design.

HIV: Modeling the experiment & the problem of evolution

Wednesday, February 11, 2009 at 8:22 PM Bookmark and Share
I just noticed a small article in the ScienceNOW Daily News on using microbicide gels to decrease the risk of contracting HIV. Give it a read!

So why did this article (and this more detailed information from the NIH) catch my attention?

Right now, as I type this, over 9,400 women in Africa are participating in a second, even larger clinical trial - the subject of some other interesting research I'll get into below. The results of that study will in large part determine whether or not this product makes it to market. Being my usual critical self, I immediately have two questions come to mind: "Will it be effective?" and "Is it safe?"

This first question will get a strong answer via this study - after all, 'effective' is relatively straight forward thing to describe and measure. But what do we mean by "safe"?? This brings me to the other big reason this article grabbed my attention: Dr. Sally Blower.

This past fall I had the pleasure of meeting Dr. Sally Blower, a mathematical biologist at UCLA, while I was visiting Ohio State's Mathematical Biosciences Institute during a workshop. She presented some of her research taking a critical look at the second study mentioned in the ScienceNOW article. Her technical paper on the matter can be found on her website.

To briefly summarize the work she presented, she and her colleagues were interested in addressing the possible risk of drug resistant strains arising from the use of these microbicide gels. HIV has a relatively high mutation rate (leading to lots of genetic variation in a viral population) and anyone already infected with HIV who is exposed to anti-retroviral drugs (ARVs) could unknowingly be facilitating natural selection on the virus, leading to drug resistant strains of HIV. Unfortunately, this is a very real problem in the fight against HIV/AIDS, and to let a high-risk product pass clinical testing could come at a price in the long run.

So to understand how well the experiment could assess this risk, as well as the efficiency of the microbicide gels as a means of protection against HIV infection, she and her colleagues created a computer model of the experiment. They began by simulating a population of women and men in which HIV was being transmitted.

As the omniscient creators of this virtual world, they were able to include and manipulate many key factors in the transmission process, including other means of protection (e.g. condoms), the efficacy of the gels, and so on. They were able to "parameterize [the] transmission model using epidemiological, clinical, and behavioral data to predict the consequences of widescale usage of high-risk microbicides" in the population. They then collected data from a number of simulations, following the same type of protocol as the real study, which they could then compare to the actual transmission process in the simulated population.

This clever use of mechanistic models and real world data accomplished two things. First, the computer model allowed them to assess the limitations of the real world experimental protocol, which helps researchers in their interpretation of the real-world experimental results. Second, because they were free to vary the model parameters and run the simulated experiment repeatedly, they could explore the simulated transmission process under different scenarios and describe how the factors included in the model contribute to the eventual outcome.

So did we learn anything from all of this? Among their results, they found that the "planned trial designs could mask resistance risks and therefore enable high-risk microbicides to pass clinical testing" - unfortunate news. On the other hand, their findings suggest that "even if ARV-based microbicides are high-risk and only moderately efficacious, they could reduce HIV incidence."

I can't say what the future holds for these microbicide gels, although I certainly hope they prove to be another means to battle against HIV worldwide. If you'd like more information on HIV/AIDS, check out the 2008 report on the global AIDS epidemic (I'd recommend browsing the "Media kit") from the United Nations Programme on HIV/AIDS.

Darwin Days @ Cornell: Dr. Massimo Pigliucci

Tuesday, February 10, 2009 at 9:40 PM Bookmark and Share
This week, many people across the globe are celebrating Charles Darwin's 200th birthday (this Thursday the 12th), and the 150th anniversary of the publication of the Origin of Species. Cornell University and the Museum of the Earth have put together a fantastic lineup of lectures and events and a website with all the details which can be found here.

This evening, and yesterday afternoon during the Ecology and Evolutionary Biology weekly seminar, I had the great pleasure of listening to Dr. Massimo Pigliucci. I won't go into great detail, but the bulk of his second talk "What's science got to do with it? When scientists talk nonsense about religion" was a gem to listen to, and touched on a many interesting issues central to the conflict between religion and science.

I would strongly encourage you to check out his website and blog, where you can find some of his writing, publications, lecture slides, and mention of some of his books on science, evolution, and philosophy.

Here is a short list of points that caught my attention during his talk, here written in my words and not his. These mostly related to evolution and creationism/intelligent design, but touch on aspects of general science as well:
  • When talking with someone (in his case, usually students) who is conflicted between their religious beliefs and learning about evolution, he gives these following words of advice: I won't ask you to believe it, I simply ask that you understand it.
  • Quoting Richard Feynman (the physicist) from The Meaning Of It All: Thoughts Of A Citizen-scientist, he reiterated that the root of much conflict between religion and science comes from the notion that (to use another Feynman quote) "Religion is a culture of faith; science is a culture of doubt. "
  • The conflict between evolutionary theory and creationism/intelligent design is not a scientific conflict, but a sociological and philosophical one. Science can only prove or disprove assertions about the natural world and is limited (if not unable) to prove or disprove assertions of a supernatural nature.
  • That said, when religions make claims about the natural world (e.g. the earth 10,000 years old) a scientific approach can be used to evaluate them.
  • Scientists would do well to learn about and apply the philosophy of science in their pursuits! Understanding the strengths and limitations of science can (of course) make for better science. I particularly enjoyed his commentary on statistics, which can be found on his website.
  • Waiting until high school or college to teach basic science and critical reasoning is a no-no! This should be taught from early on, just like we teach reading, writing and mathematics.
My time is up for now, but I hope you get a chance to check out some of Massimo's work as well as any of the "Darwin Day" events that might be going on in your neck of the woods. That's all for now! :)