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One of the biggest issues I’ve seen again and again in the comments sections of every vaccination article is a fundamental lack of understanding of how the immune system works. Many people talk vaguely of “toxins”, “pathogens” and “immunity”, but it’s clear that they have no idea exactly how this works. So I thought that I’d invite a regular commenter, Dr. Scott Nelson, to write an explanation. I think that Dr. Nelson, who teaches this subject in university courses, has done an excellent job of making a complex topic accessible to people who are not scientists or physicians.  (Note that we have provided hyperlinked definitions of many of these terms from Wikipedia for convenience. Dr. Nelson and I have both reviewed them and agree that they’re accurate. If you would like additional information beyond what is provided here, we recommend consulting any basic major textbook).

If you are “doing your own research” on vaccines, I urge you to read all the way through the end, and then watch the video, which shows an animation of the processes that Dr. Nelson describes.  Finally, because I think it’s important to illustrate the vast differences between the scientific explanation of how the immune system works, and the “alternative medical” explanation, I’ve included the homeopathic version at the end of the post. I encourage you to share your thoughts on which you find most compelling, and why. My comments following Dr. Nelson’s are in bold


A common thread through many anti-vaccine posts is fear about “all the stuff that you are jabbing into a kid”. I would like all the people who think this to perform a simple experiment. Take a piece of meat-any meat-make sure it’s fresh and smells good. Put it on the counter in a nice warm place-about body temperature-cover with a screen if you like. Let it be for three days and then look at it carefully, note all the different shapes and colors. If you know somebody with a microscope, scrape a bit of stuff off and look at it under a microscope. How many different things do you see now? Each spot, each color, each bug you see under a microscope represents something that the immune system is dealing with every second of everyday. After all-wasn’t it exposed to the exact same air that you’re breathing right now? Your body is that piece of meat-your immune system is what keeps it from rotting. Right now, our best estimates are that there are 10 microorganisms for every cell in your body. Your immune system “knows” them all and has responded in various ways, which science is currently exploring. Continue Reading…

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My most recent post (“Dear parents, you are being lied to”) has sparked a very lively discussion. I encourage you to continue to share your thoughts on it, but I also want to follow up by asking for your reactions to one comment that I found particularly interesting. (I’ve edited it a bit for brevity)

As a pediatrician who’s spent extensive time working in the US and overseas and has seen children die from EVERY disease (except small pox) for which there is a vaccine I am appalled at the lack of education by the general public on the vaccine issue. This is my rant: I had two unvaccinated children in the US die from whooping cough, one from tetanus, and 2 from meningitis in the past few years. Perhaps this reflects our country’s generally poor understanding of math and science in general. A recent large study in the US showed that no matter how scientists try to educate US parents about disease and disease prevention, whether it is vaccines or hand washing, parents simply cannot follow the logic.

It’s devastating to see children die from preventable disease and despicable that it is happening here. I would like to know why those whose children end up in the PICU with tetanus or whooping cough now trust us to save the life of their child? Why do you run to a doctor when you are terrified your child has tetanus after refusing to vaccinate? Why am I now competent to save your child’s life when they have meningitis or epiglottis, but I wasn’t competent enough to keep them from getting sick? If there was no medical help for your unvaccinated child if they acquired a vaccine preventable illness would you think about vaccinating? If you’re not willing to run to your anti-vaccine friend, treat your child with advice from non-scientific sites on the internet, go to your chiropractor, or your holistic healer with your dying child perhaps you shouldn’t be taking their advice about vaccines. –Anonymous

To those of you who simply don’t trust the medical community’s use of vaccines, I am curious what you make of this physician’s point. Given your reservations about vaccines, do you trust an MD to treat yourself or your children for any medical issues at all? If so, why do you trust his/her education and experience on some points but not others?

I invite anyone, pro- or anti-vax, to share your thoughts on this. Please respect each other by following the commenting policies (and feel free to alert me if I miss a comment in violation of them).


Standard of care.

In light of recent outbreaks of measles and other vaccine preventable illnesses, and the refusal of anti-vaccination advocates to acknowledge the problem, I thought it was past time for this post.

Dear parents,

You are being lied to. The people who claim to be acting in the best interests of your children are putting their health and even lives at risk.

Continue Reading…

This is the second post in a series discussing the recent publication of a 12,500 year old genome from Montana. You can find the first post here.

In the weeks following the publication of the complete genome from a Clovis child, there’s been a lot of press coverage of this study and its possible implications. I want to discuss a bit of the media coverage on this subject, since it raises issues that I think science journalists need to consider more carefully.

First of all, to recap the major findings of the original study (discussed in more detail at the link above):
1. Anzick-1, the 12,500 year old Clovis child whose genome Rasmussen and colleagues sequenced, is very closely related to living and ancient Native Americans.
2. Anzick-1 is more closely related to Siberians than other Eurasian groups.
3. Anzick-1 is more closely related to Central and South American Native American groups than to some North American groups.
4. The results from Anzick-1′s genome fit with the scientific consensus about the peopling of the Americas. This consensus encompasses the results of decades of archaeological, genetic, and paleoclimate research.

Unfortunately, several press reports chose to find controversy in a decidedly non-controversial story by giving undue weight to problematic “alternative” explanations of Native American origins, including the Solutrean hypothesis, and other “European contributions” to Native American ancestry.


Clovis tools from the Anzick site. From Rasmussen et al. 2014.

Continue Reading…

This post comes courtesy of Jeff Westfall, someone I’ve known and respected as a leader in the martial arts community since I moved to Indiana in 1992. I’m absolutely delighted that he agreed to share his insights into pseudoscience in the martial arts with us. You can read details of his background on his school’s website here. –Jenny

I’m Jeff Westfall for the Martial Brain

Recently on Facebook I saw a video of a Finnish martial artist named Jukka Lampila who called what he did Empty Force or EFO, and claimed that with it he could control an attacker without touching him. His Facebook page proclaims him the founder of EFO. The video begins with clips of Lampila fending off ‘attacks’ from his students. He waves his arms; sometimes he twitches, and in each case the ‘attacker’ seems to be magically thrown to the mat without ever being touched by Lampila. He also shows an example of ‘controlling’ someone on the ground. He kneels calmly beside a supine student with the back of his hand gently resting on the man’s chest. “I don’t need to use any energy” he asserts as the student appears to try with all his might to regain his feet to no avail. It is a sad display of martial arts charlatanism.

Continue Reading…

Last Wednesday, Dr. Morton Rasmussen of the Natural History Museum of Denmark and his colleagues announced that they had completely sequenced the genome of an infant boy, buried ~12,600 years ago in Montana. A few weeks earlier, I’d been approached by an editor at Nature, who asked me if I and my mentor Deborah Bolnick would be interested in writing a companion paper that would analyze and contextualize their results. We agreed, and the paper was published in last week’s issue, alongside Rasmussen et al.’s work. Because it’s (unfortunately) behind a paywall, I’d like to summarize what we said in that paper for non-scientists. There are a lot of things to talk about with regard to this study, including a consideration of ethical issues and the media’s response, so I’m likely going to do several posts on it. This first post is mainly a discussion of how we interpret the results.

For a TL;DR version of this post, here’s a link to a short interview I did on the subject last week with the BBC World Service.
Continue Reading…

Nature publication

Jennifer Raff —  February 12, 2014 — Leave a comment

I haven’t been writing as much here recently, because I’ve been working on a “News and Views” article for Nature….and now I can finally talk about it! Here’s a link to my article:, and to the paper that it’s discussing: In the next few days I’ll post something here to discuss the main points of the article (for those of you who can’t access it), and also my reaction to the media coverage that the study is getting.

It seems that every week there are exciting new findings from ancient DNA research.  This is wonderful news, because we’re learning incredible things about the relationship between humans and Neandertals, the prehistory of ancient populations, and even previously unknown hominins.  But on the flip side, we’re also seeing news reports of extremely questionable results, and I’ve gotten more than one inquiry recently from people excited or confused by them. I though it would be a good idea to write a bit about how regular people can figure out whether a study is legitimate or not.

The first step in distinguishing good ancient DNA studies from bad ones is the same as distinguishing pseudoscience from legitimate science in general: ask where the results are published. Are they in a peer-reviewed journal? Or does the author present it as “science by press release,” stating something like:

“Peer review will of course be considered, but this information belongs to THE WORLD; not a few academics…”

The next steps require you to know a bit about ancient DNA itself, and how research is conducted. What most casual readers may not understand is how difficult recovering DNA from ancient remains is….and how easily it can become contaminated.

The TL;DR version is that for an ancient DNA study to be considered authentic, at minimum it:

  • Must be conducted in the proper facilities
  • Must be conducted by personnel practicing sterile techniques
  • Must utilize negative controls
  • Must have a subset of results reproduced by an outside laboratory
  • Must yield phylogenetically reasonable results (or produce extraordinary evidence to support unusual results), that match the characteristics of ancient DNA.
  • Must conform to any additional standards necessary, depending on the sample and experimental design

Here’s why:

Continue Reading…

“Scientists should tithe ten percent of their time on public education…” –Carl Sagan

Nye and Ham

Many of us in the scientific community have a longstanding policy not to debate with creationists, in part because doing so gives an unwarranted credibility to their disingenuous arguments. So when Bill Nye chose to debate Ken Ham in the Creation Museum on whether creationism was a viable explanation for life, there was a lot of wincing and predictions that Nye would unintentionally do damage to public perception of evolution. I was also skeptical that this debate would do any good. But I think that most of us scientists had overlooked the fact that Nye is an experienced entertainer as well as science educator–a combination of traits that most of us don’t possess, and one perfect for this venue. Nye did an astounding job at calmly explaining the overwhelming evidence for why creationism (with special attention to Noah’s ark and the flood) simply couldn’t explain the origins and diversity of life on earth. Ham, on the other hand, seemed really flustered and didn’t even make an attempt (beyond trotting out token creation scientists in an attempt to give creationism some legitimacy) to address the questions at hand with evidence. He was completely out of his league, and it showed.

Ken Ham's explanation of evolution

Screenshot of one of Ken Ham’s slides explaining what a non-Young Earth Creationist Christian must believe about God’s plan.

One of the most telling parts of the debate was the question that was asked of both men: “What, if anything, would convince you to change your mind?”

Ham’s answer: “Nothing.”
Nye’s answer: “Evidence.”

I really encourage you to watch the entire debate here, but if you’re not up for three hours of viewing (and I don’t blame you), you can see shorter excerpts and an interview with Nye here.

And here are some other reactions to the debate:

Nye was right to do this debate. Not only did he win with excellent presentation and overwhelming evidence, he managed to convey to viewers the beauty and humility of the scientific process. Nye didn’t have any problem saying to some questions: “I don’t know–but I can’t wait to find out!!!”: the motivation that drives every single scientist when he or she goes to work in the morning. If nothing else but this gets conveyed to the people who watched the debate, I’d still be pretty happy. I don’t know if the people in the Creation auditorium had ever heard the evidence he presented before. (They seem to be proud of their lack of understanding of evolution). I doubt he changed any of their minds, but I can’t help but wonder if some of the people watching the stream went to bed last night with a slightly better understanding of the scientific process. I hope they did.