Archives For science

Article and photo by Colin

 

Lies can make complex problems look simple; anti-vaxers want to keep your eyes on their distortions, rather than looking up to take in the real world.

Lies can make complex problems look simple; anti-vaxers want to keep your eyes on their distortions, rather than looking up to take in the real world.

 

Thanks to Jenny McCarthy and Megan of Living Whole for proving the point: anti-vaxers are lying to parents. Jenny McCarthy is in the news lately with an op-ed that starts with a whopper: “I am not ‘anti-vaccine.’” This is absolutely not true; McCarthy has worked hard for years to scare parents away from vaccinations. The root of her campaign is her insistence that vaccines cause autism, despite the conclusion of the community of experts that there is no evidence of such a link.

It’s absurd for her to claim now that she only wants “safe” vaccinations, since the dangers she complains about are primarily in her head. Vaccines, like any medicine, can’t ever be 100% safe, but they’re “among the most safe and effective public health interventions to prevent serious disease and death.” Science can’t make a vaccine “safer” if the problems she wants fixed don’t exist. It’s as if she was telling parents not to fly until Boeing finds a way to keep gremlins off their planes. They can’t do it because gremlins, like a vaccine-autism connection, don’t exist. Nevertheless McCarthy uses those false fears to drive a wedge between parents and their doctors, depressing vaccination rates while still shamelessly claiming she’s not “anti-vaccine.”

McCarthy has been lying for years about the dangers of vaccines. If the effect of those lies is to stop parents from vaccinating, then yes, she is an anti-vaxer. But she’s not stupid; she knows that people give more credibility to voices that claim to be “in the middle” or “just asking questions.” So she lies. She claims that she’s not an anti-vaxer, even though her goal and effect is to reduce childhood vaccinations, because she’s a more credible and effective anti-vaxer if she can persuade parents she’s just asking questions about the safety of the vaccination schedule. Since those questions have long since been answered, the only reason she’s still asking them is to spread fear, uncertainty and doubt about some of the safest medical products available, her pretense at a balanced stance is false and misleading.

It’s common for anti-vaxers to lie to enhance their credibility. It’s one of the only ways the movement can make progress, since the community of experts disagrees with their conclusions so fervently. One way is to claim false equivalence, as McCarthy does. But we recently saw a good example of an even bolder lie, courtesy of Megan at Living Whole.

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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).

 

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.

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

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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:

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

Continuing the “How to be a good scientist” series of posts that I have been doing here lately, I wanted to call your attention to this excellent piece written by Indira Raman (of my former institution, Northwestern University): “How to Be a Graduate Advisee”. I recommend all scientists read it, regardless of what stage they’re at in their career, because much of its advice applies to doing science in general.

Here are my reactions to a few points that I particularly appreciated:

“The science you are doing is the real thing. Although many students do not immediately realize it, graduate study is not a lab course, not a summer experience, not an exercise for personal enrichment.You are a real, practicing scientist, albeit a trainee, from day one”.

It is important for a young scientist to feel part of a larger community. At my graduate institution, a small but meaningful way that the program emphasized this was to explicitly request that members of the department at all ranks address each other by first names only. On day 1 of our graduate orientation, we were told “You are our colleagues now, so don’t use titles with us.” Small things like that make a very big difference to young graduate students. As a graduate student, take pride in your work and understand its context with respect to the rest of your discipline.

“Do not let yourself get accustomed to failure…..every day you should be able to account for what you did: practice articulating for yourself what worked, and what you will do differently tomorrow. The worst thing that can happen to you scientifically is to get used to going into the lab, doing a procedure in a fixed way, getting no useful result, and going home, with the sense that that is all that science is. You must see movement on your research, not necessarily as daily data, but as a sense that what you did today gets you closer to an outcome”.

I think this is the best piece of advice a graduate student could read. Mistaking motion for action is an easy trap to fall into, and I’m constantly struggling with this. I don’t have any great insights into how to “cure” this problem, besides offering what I do: when I recognize that I’m in a rut, I step back, reevaluate, talk to my PI or colleagues, and try a new approach. Sometimes even something as simple as taking a day off to go hiking and just brainstorm is enough to get myself back on the right track. While I’m in this mode, I try to ask myself at the end of the day what I specifically did to move myself closer to a larger goal. What do I need to do differently tomorrow? A tool that I often use for breaking things down into the critical “taking action” tasks vs. the optional ones is the “Today and Not Today” smartphone app. Don’t get hung up on the specifics, though–just find something (a tool, a protocol, a confidant) that works for you and use it!

“Cultivate the ability to get inspired. When you see other people excel scientifically—your peers or seniors—you can have several reactions. One is to dismiss those people as extraordinary, perhaps contrasting them with yourself so that you feel dejected or inadequate. A second response is to put those people down by criticizing an unappealing attribute that they have. A third, and perhaps the most constructive, reaction is to look at those people’s abilities as something to aspire to. What can you learn from them?”

Several years ago when I lived in Utah, I was invited to train at Gym Jones. Being surrounded by athletes of the highest caliber fundamentally changed my outlook–not only physically, but also professionally. It might seem odd that a gym could help me become a better scientist, but physical training was only a means to an end. Exactly what I learned there is a subject that could fill an entire post. But reading the point above reminded me of one particular core philosophy of the gym, articulated here by Mark Twight:


“You become what you do. How and what you become depends on environmental influence so you become who you hang around. Raise the standard your peers must meet and you’ll raise your expectations of yourself. If your environment is not making you better, change it.”

To become a better graduate student, you need to surround yourself with scientists who are better than you, and whose work inspires you to become better yourself. If you can’t find them in your own department, at the very least you should be following the work of the leaders in your field. Twitter is a good place for this, as are blogs and books. For example, here is a book that inspired me last year.

At the same time, recognize the dangers of imposter syndrome and know what is reasonably expected of you at each level. Comparing a graduate student’s scientific accomplishments to those of a tenured professor is inappropriate. Try to learn something from every experience, and from every person you encounter.

Raman goes on to talk about a number of other excellent points, from how to work with one’s advisor, to how to maintain one’s scientific ideals. I strongly recommend you take a look!

Thanks to @mwilsonsayres (http://mathbionerd.blogspot.com/) for the link!

by Colin McRoberts

A while back a friend asked me to help with a difficult conversation. Someone she cared about was expecting her first child, and had decided not to vaccinate her baby. My friend desperately wanted to change the mother’s mind to protect that child. But she wasn’t sure how to proceed. She had the facts on vaccines, and knew that refusing immunizations was a dangerous and irresponsible decision. But she wasn’t sure how to convince her friend of that without jeopardizing their relationship. There are some excellent resources for health care providers having this conversation with patients. But there wasn’t much that applied to her particular situation. So she asked me whether my experience as a negotiator gave me any insights that might help her plan for what was sure to be a difficult conversation.

As it happens, I had been thinking about the same thing. I’m particularly interested in how laypeople should approach a conversation like this, since laypeople can be much more persuasive than the family physician. In the real world, our family and trusted friends very often carry more weight than experts. The giant but useless homeopathy industry would collapse otherwise. So when you hear that one of your friends or relatives doesn’t plan to vaccinate, you have the opportunity for a conversation that could potentially change their mind and save that child from terrible harm.

Unfortunately, too many people approach that conversation timidly, without a solid strategy for persuading their friend. That makes it hard to respond when things take an unexpected twist, such as your friend spouting off antivaxer talking points you hadn’t considered. Other people are too aggressive, treating the conversation like the comments section of a blog post. That kind of combative and confrontational dialog can feel good, but it doesn’t accomplish much in the real world.

So what does a strategy for an effective, persuasive conversation look like? There is a world of advice we could give about that conversation. We’ve distilled it into four basic points: be sincere, ask questions, be sympathetic, and provide information.

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After the fold, we’ll go into some specific thoughts about each one. We want to stress, though, that this is just a framework. The conversation itself will be different every time. We want to know more about your conversations. If you’ve tried to talk someone into getting a child (or themself) immunized, please share your story in the comments section.
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Peer review is at the heart of the scientific method. Its philosophy is based on the idea that one’s research must survive the scrutiny of experts before it is presented to the larger scientific community as worthy of serious consideration. Reviewers (also known as referees) are experts in a particular topic or field. They have the requisite experience and knowledge to evaluate whether a study’s methods are appropriate, results are accurate, and the authors’ interpretations of the results are reasonable. Referees are expected to alert the journal editor to any problems they identify, and make recommendations as to whether a paper should be accepted, returned to the authors for revisions, or rejected. Referees are not expected to replicate results or (necessarily) to be able to identify deliberate fraud. While it’s by no means a perfect system (see, for example, the rising rates of paper retractions), it is still the best system of scientific quality control that we have. In fact, it’s such a central part of the scientific process that one can often identify questionable scientific findings by their authors’ objections to the rigor of review (and attempts to circumvent it by a variety of methods, including self-publication).

Yet the quality of this system is ultimately dependent on the quality of the reviewers themselves. Many graduate programs don’t explicitly teach courses on how to review papers. Instead, a young scientist may learn how to review a paper under the guidance of his or her mentor, through journal clubs, or simply through trial and error. I’ve been thinking about this topic a lot, and decided to put together a set of guidelines for young scientists. In doing so, I also hope to help non-scientists understand a bit more about the process.

I intend for this to be an evolving post, so I ask for my colleagues’ help in improving it. At the end the post, I’m assembling a list of resources for further reading. If you have any suggestions or resources, please send them to me and I’ll add them. Continue Reading…

This afternoon Ms. Couric’s show “Katie” featured the “HPV Vaccine Controversy” as part of its “Big Conversation”. The segment focused mainly on the vaccine Gardasil, which is administered to girls and boys around the age of 11, in an effort to immunize them against HPV before they become sexually active and likely to contract the virus.

Although Couric herself claims that she is personally “not anti-vaccine”, her show was extremely biased against the scientific consensus. She kept referring to the vaccine as “controversial” when there are no legitimate scientific studies showing it to be dangerous. I’m used to getting upset at journalists who give false equivalency between the scientific consensus on an issue on the one hand and a fringe belief on the other. But this was beyond the pale; Couric’s program didn’t even aspire to that “balance”.

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I had a “driveway moment” last night listening to Alex Jones rant about science topics on his radio program. He was obsessed with the hypothesis that humans are the descendents of a primate-pig hybridization. I had heard of it as it first made the rounds back in July, but I assumed that no one would take it seriously and ignored it. But the Daily Mail recently has not only reported it uncritically, it also called Dr. Eugene McCarthy’s evidence for this hypothesis “compelling”. I guess I shouldn’t find that surprising, because the Daily Mail routinely presents quackery as mainstream scientific findings.

What really drew my interest in the subject was the way Alex Jones discussed the news article.

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