Another open thread on vaccines

Jennifer Raff40 Comments

IFLS has reposted my “Dear Parents” article this morning, with a very kind note (thank you!). This means that we have a lot more traffic on the site than is usual, and I want to extend my welcome to all the new followers, commenters, and curious onlookers.

https://www.facebook.com/plugins/post.php?href=https%3A%2F%2Fwww.facebook.com%2FIFeakingLoveScience%2Fposts%2F1372572689430405&width=500

A couple of things:

  1. I know that there are several broken links in the article. Since I wrote it about two years ago, I’ve occasionally gone back and tried to update them. But I haven’t done it recently, and today I’m pretty swamped with work and meetings. I will try to get to it throughout the day, but it may take a little while. I’m very sorry about that!
    Edit: Broken links should now all be updated, thanks for your patience.
  2. The comments section of the Dear Parents article and the Open thread (both linked to in the IFLS repost) are getting extremely full, and it can be difficult to read very threaded comments. If you would like to start new comment threads here, please feel free. I only ask that you abide by the commenting policies of my site, and have patience if your comment doesn’t show up immediately–it is being held in moderation until I can get to it. I try to approve comments as fast as they come in, but there will be occasional delays.
  3. If you write to me asking for a copy of my guide to reading scientific papers, I apologize if it takes me a few days to get it to you. Moderating comments is taking a lot of my free time today, but I will try to respond as quickly as possible.

I’ve been working on a response to some of the recent events about the Vaxxed documentary, and I believe that Colin has a piece he’s working on as well, so please check back for more throughout the week. Alternatively, you can subscribe to the blog to get email updates, like our Facebook page (see the right hand side of this post for links), or follow me or Colin on Twitter if you want notifications of new posts. As always, thank you so much for reading!

No, We Don’t Actually Know That Modern Humans Killed Off The Hobbits

Jennifer Raff4 Comments

This article is cross-posted from the Social evolution forum where I occasionally write about issues in human evolution.

A new paper out last week in Nature by Sutikna et al. has generated a great deal of excitement, by reporting a revised date range for the diminutive hominin, H. floresiensis, nicknamed the “hobbit” because of its stature (just 3.5 feet for adults). The previous accepted date range for H. floresiensis (95,000-12,000 YBP) implied that humans and hobbits co-existed on Flores for some considerable period of time, prompting fun analogies to the setting of J.R.R Tolkien’s legendarium, Middle-earth, in which humans, hobbits, dwarves, and other races co-existed and interacted. (I actually love this comparison, because it really resonates with my students and makes teaching human evolution easier.)

The original dates for H. floresiensis were based on the (then reasonable) assumption that the depositional sequence in one part of the cave was representative of other parts of the cave. But caves are very active geological systems, and it often turns out—as in this case—that stratigraphy isn’t uniform. When researchers excavated elsewhere in the Liang Bua cave, they found new stratigraphic details (erosion of older deposits followed by filling in of younger deposits) that prompted them to redate the sequence. These new data gave a range of 100-60,000 YBP for the skeletal remains of H. floresiensis and 190,000-50,000 for floresiensis-associated artifacts. The end of this date range—50,000 YBP—happens to be close to the estimated appearance time of modern H. sapiens on the island, which raises some intriguing questions.  For those of you interested in a detailed analysis of the errors of the original dates, and a discussion of some still-unresolved issues with the paper, I highly recommend John Hawks’ post What the revised Liang Bua chronology leaves unanswered.

The cave at Liang Bua. By Rosino - [1], CC BY-SA 2.0, https://commons.wikimedia.org/w/index.php?curid=4567792

Unfortunately, some in the media have gone beyond discussion of those questions and breathlessly reported that these new dates likely mean that our species wiped out the hobbits. While that hypothesis certainly remains a formal–and fascinating– possibility, it’s only one of several. It’s based simply on the observation that under the current chronology, approximately the same time modern humans got to Flores, we stop seeing hobbit tools in the deposits at Liang Bua.

But I want to point out that we have no direct evidence (as yet) showing any interaction between H. sapiens and H. floresiensis, as the authors noted in the closing sentence of their manuscript:

“Parts of southeast Asia may have been inhabited by Denisovans or other hominins during this period, and modern humans had reached Australia by 50 kyr ago. But whether H. floresiensis survived after this time, or encountered modern humans, Denisovans or other hominin species on Flores or elsewhere, remain open questions that future discoveries may help to answer.”

So as of right now, we actually don’t know that humans killed off (either directly or indirectly) hobbits. But this is probably the interpretation that the interested public has walked away with after this week. Call me conservative, but I’m a bit uncomfortable that our speculation might have given people the impression of greater certainty than we actually have.

There are two other aspects of this new finding that interest me. The first is the implication that these older dates have for the debate over whether H. floresiensis was a pathological modern H. sapiens or a separate species with distinctive morphology, likely caused by insular dwarfism. The older date range for these fossils suggests that H. floresiensis was indeed a separate species. Furthermore, as Kristina Kilgrove discusses, these new dates also undermine cryptozoological interpretations of the Indonesian legend of Ebu Gogo as deriving from sustained interactions between humans and H. floresiensis as recently as 12,000 years ago.

The second aspect of these new dates that I find interesting is that although they mean that the hobbits were older than we initially thought, they still fall within the range of time in which it’s possible to obtain ancient DNA from skeletal remains. I have no idea whether there will be further attempts to extract aDNA from the hobbits (previous attempts were unsuccessful), but I continue to be hopeful that someday we will have hobbit DNA. If H. floresiensis is, as some suspect, a descendant of H. erectus, then their genomes could give us a glimpse of that species’ genetic diversity and help us better understand the evolutionary history of ourselves, Neanderthals, and Denisovans.

 

Vaxxed: From Coverup to Catastrophe to Cancellation to Insignificance

Colin17 Comments

Vaxxed, the anti-vaccine documentary made by a team of anti-vaccine activists (but curiously, no vaccine experts) has come and gone and come again. Other people have written extensively about what happened, some with lots of facts and some with raging, paranoid fantasies. As the movie is likely to disappear into relative obscurity soon, let’s take this chance to explore some lessons learned from the last couple of weeks—some for vaccine opponents, and some for mainstream science and health advocates.

Update: The filmmakers have added Q&A sessions at the 5:45 p.m. shows on April 1 and 2, and the 3:30 p.m. show on April 3. So I can reinstate my recommendation! Go see it. Ask critical, but not disruptive, questions. What data was actually deleted? If the movie omits Thompson’s strong support for vaccination, why? (Remember that Thompson, the guy whose phone calls underlie the whole movie, made a point to declare publicly, “I want to be absolutely clear that I believe vaccines have saved and continue to save countless lives. I would never suggest that any parent avoid vaccinating children of any race. Vaccines prevent serious diseases, and the risks associated with their administration are vastly outweighed by their individual and societal benefits.“) Why rely on a computer scientist instead of an epidemiologist for the science in the movie? Why was Hooker’s study retracted by the journal in which he originally published it, and why did that journal declare that it has “serious concerns about the validity of [Hooker’s] conclusions“? 

The people behind Vaxxed made a movie because their claims wither and die when they’re exposed to actual critical discussion. They want to create the appearance of a discussion, without any of the messy facts. Show up. Provide context for their propaganda. Even one person can make a difference, either by asking questions at the discussion panel or by reporting back on what those questions and answers were.

So if you can attend, please also record the discussion panel afterwards. (Not the movie itself, you’ll get kicked out.) The outside world would love to hear how conspiracy theorists feast on a film like this. The first press conference, before the film even aired, already devolved into “GMOs, chemtrails, and fluoride.” We can’t be there, so we’d love to hear your observations and thoughts!

Continue reading →

Surviving my first year as a new professor: Tools of the trade

Jennifer Raff2 Comments

Regular readers of this blog may have noticed that I’ve been writing a lot less frequently since last August. Between teaching, setting up my lab, training students, applying for grants, and getting some papers finished for publication, I’ve had very little time to write more than about 1 post a month. (I’m hoping to publish a bit more frequently in the near future, as I have some exciting things to write about. Fortunately, Colin has had a bunch of interesting experiences with the ConspiraSea cruise recently, and a lot more free time than I do, so I hope that’s helped to fill in the gaps a bit. Thank you, Colin!).

I’ve been reading a lot of other blogs about new faculty experiences (The New PI Sets Up A Lab is one of my favorites) and I’ve found them to be tremendously helpful in both advice and in assuring me that I’m not alone in feeling pretty constantly overwhelmed. And while this blog’s focus is not going to change to be a “new professor blog”–our scope is broader than that–I do want to write an occasional post about my current experiences that I hope might be useful (?) someday to any aspiring new PI. This will be one of those posts, and its emphasis will be on some of the tools I rely on consistently for managing my life.*

(If you’re here mostly for the vaccine talk or general science stuff, there are some new posts on these subjects in the queue for VM in the next two weeks).

  1. Staying organized

One of the biggest challenges of my new job is having so many different obligations throughout the day. It’s not just that I have a lot of things to do–it’s that I have many, many different types of things to do. I’m constantly having to switch roles: lecturer (and entertainer) one hour, collaborator on a grant in progress the next, writer the next, advisor to a student the following hour, reviewer of a manuscript immediately after. Having to switch my brain rapidly from task to task, keeping just enough focus for each so I can get them done quickly and move on to the next without wasting time is really difficult for me. My time is valuable in a way that it’s never been before, a fact which is really sobering and a tiny bit scary.

On top of that, I’m incredibly distractable, so trying to figure out how to manage that while still being productive has been a challenge. I talked to my dear friend Lyn Christian, who’s a business/productivity coach, and she told me to quit beating myself up for letting myself get distracted and accept that it’s part of being human. Instead, she urged me to work around the inevitability of interruptions by quitting multitasking, scheduling out larger blocks of time for each task than I think I’ll need, schedule in “play time” on the internet, and ruthlessly prioritizing tasks. (Maybe these are things that people already know, but in my case her advice really helped). I started using her productivity app (Today and Not Today) and it has seriously made a difference. These days I use it together with my google calendar; I figure out what’s absolutely critical in a given day, schedule a block of time for it on my calendar, and then let my apple watch remind me when it’s time to switch tasks. Technology!

2. Staying positive

I’ve often finished the day feeling like I haven’t gotten anything meaningful done, even when I know that I’ve worked a solid 9 hours. I read some piece of advice somewhere that one should track one’s tasks throughout the day, both because it makes faculty evaluations a little easier, but also because it gives a solid metric for how the day was spent. So I’ve been doing that this year, and it does indeed help me appreciate just how many different things I do in a day (see #1 above). I’ve been using “Day One” as a journal, and I have it set to remind myself to start an entry in the mid-afternoon. I’m *mostly* good about doing this on weekdays.

3. Outsourcing everything

My partner travels A LOT for work, and so most weeks I’m juggling work and household without any extra help. I really just can’t do it all by myself, so I’ve accepted that I have to outsource as much of the non-essential stuff as possible, even if it seems a little extravagant. I’m still figuring out how much of this is reasonable, but for now I’m using a cleaning service every couple of weeks (I think I need this more often, to be honest), and delivery services for as much as I possibly can. I really like cooking and I find it relaxing, but I hate taking the time to plan meals and shop for ingredients, so I use Blue Apron every week. Although it’s probably interchangeable with any other similar service, I really love it. I also use Stitchfix for clothes, although that one can be REALLY hit or miss.  And for regular household stuff, I’m using Amazon delivery services a lot more than I probably should. But they’re incredibly convenient, and that makes a huge difference to my sanity. I would totally use Task Rabbit as well, if it was available in my area.

 

So I’m curious what tools other folks use. If you have a recommendation for either a tool or a good new professor/new PI blog, please drop a link in the comments!

 

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*I want to note that although I get offers for sponsored posts all the time, I uniformly reject them all–I don’t want this to become that kind of blog. I haven’t been paid to mention anything on here, and the only thing that I received for free was the Today/Not Today app.

An Interview with Andrew Wakefield

Colin150 Comments

Andrew Wakefield and I were both on the ConspiraSea Cruise in January 2016. By the last full day of the cruise, we’d had a few encounters ranging from standing in the same line for coffee to a fairly tense exchange during one of his lectures. I asked Wakefield after that lecture if he would answer a few questions regarding the so-called “CDC Whistleblower.” He consented, and this is the interview that resulted. Wakefield was aware that I was recording and that I am a critic of his position on vaccines and autism; he did not refuse to answer any of my questions.

2016-01-29 15.13.13
Wakefield lecturing on the cruise

This transcript is my own work, and I welcome any corrections. I’ve edited it slightly to make it more readable and remove irrelevant dialog. I have also added parenthetical comments to note where a statement is inaudible on the recording, which is not of high quality, and provide my best guess at what was said in a few places. I have not changed the substance of any question or answer.

Wakefield answered several questions before I turned the recording on. According to my memory and my notes, I asked him questions about the Thompson documents such as what specific deviations there were from the approved study plan (as he had alleged such deviations in two lectures). He referred me generally to his letter of October 2014, written with Brian Hooker and attorney James Moody, and directed to the federal Office of Research Integrity. He indicated both that he had documents from Thompson at the time he wrote that letter, and that Congressman Posey subsequently received additional documents from Thompson. At that point I began the recording.

I am not an expert in the documents Wakefield discussed. So in order to provide context for these answers, we have asked Matt Carey of Left Brain Right Brain to provide commentary. Carey is a published scientist, a parent of an autistic child, and extremely familiar with the Thompson documents. He has written an in-depth analysis of the Thompson documents and was able to provide an important counterpoint to Wakefield’s claims. Please read that excellent analysis prior to this interview if you are not familiar with the affair. The questions and answers will make little sense without context.

My questions are in black, Wakefield’s answers are in red, and Carey’s comments are in green. We welcome your own comments as well.

Continue reading →

ConspiraSea Day 7: I failed.

Colin32 Comments

This is Day Seven, the last in my seven-day series of updates from or about the ConspiraSea Cruise. You can read Day 1 here, Day 2 here , Day 3 here, Day 4 here, Day 5 Part 1 here, Day 5 Part 2 here, Day 6 here, and an explanation for what I was doing here. We’ll have an index page up soon collecting these and future pieces. This is the last of the seven-day series, but not my last post about conspiracy theories. We’ll be posting an exclusive interview with Andrew Wakefield soon, and then I have a number of analytical pieces planned for future updates.

This is the most difficult of the ConspiraSea articles I’ve written. I have to confess a very personal and frustrating failure. I made just one serious attempt to persuade someone on the cruise to reject some very bad and dangerous advice. This was contrary to my “do not interfere” policy, but I couldn’t just stand by and watch someone’s future ruined by charlatans. And unlike many attendees, whose minds were made up before they ever boarded the boat, this person claimed to be persuadable and actively sought out my advice. I don’t know for certain whether I could have changed their mind, only that I didn’t. I hope this piece and the news in it reach that person, and I hope it’s not too late.

I can’t give you any details about the person I’m writing this for. I promised them anonymity, and I seriously considered not writing this at all. But if I don’t, then I have no way to reach them and give them an important update. And it’s important to show how dangerous some conspiracy theories can be; I have some responsibility to the people like this person who might be persuaded to make safer, better decisions. I’ll call that person Q, to protect their privacy while still telling a coherent story. Because this piece isn’t just for Q, but anyone in the same situation or who’s just curious about whether pseudolaw is as dangerous as pseudoscience or pseudomedicine.

As far as everyone but the two of us are concerned, this is what Q looks like:

Pessoa_Neutra.svg
Q

Q’s age, race, gender, nationality, profession, education, marital status, shoe size, politics, military service—all of that is irrelevant. All you need to know is that Q is a human being. And Q’s future is in real danger because of the advice two pseudolegal gurus were selling on the ConspiraSea Cruise. Specifically, Q took advice from a dangerously incompetent and ignorant “attorney in law,” Sean David Morton. A man whom Q trusted. A man who never told Q that not long before the cruise began, he’d been indicted on serious criminal charges. Q probably has no idea that he was arrested by the IRS Criminal Investigation Division as soon as he got off the boat, or that he’s now facing over six hundred years of jail time for doing the same sort of things he advised his audiences to try for themselves.

Indictment
You don’t ever want to see your name on a header like this. I’ve concealed the name of his co-defendant; it’s a matter of public record, but it’s also irrelevant to this message.

 

I don’t know Q’s full name and I don’t have any way to make contact. And I’m sure there are other people from the cruise who are in the same situation, about to implement some of the horrible ideas they got from Morton. So I’ve asked the ConspiraSea Cruise organizers to notify attendees of these developments. I think they need to know that one of the lecturers who gave them legal advice is facing enormous criminal liability for taking his own medicine. I suggested they simply send out a request for prayers and good thoughts on Morton’s behalf in light of his recent legal issues. I thought that would be a decent compromise because people like Q would be put on alert, and cruise organizers wouldn’t have to explicitly criticize one of their guests. They’ve refused. The person I wrote to, whom I believe to be a personal friend of the guru in question, responded only, “I have no comment to make about Sean David Morton.”

I do. I hope it reaches you, Q.

Continue reading →

Sexual harassment in physical anthropology

Jennifer Raff11 Comments

Astronomy.

Astronomy again.

Molecular biology.

Story after story about sexual harassment of students and trainees by professors has been coming out recently. Today Michael Balter has just published an important news piece about the same thing happening much closer to home–in my discipline, physical anthropology. Specifically, in the subfield of paleoanthropology.

The story is very complex, but the gist is that a young research assistant has come forward with allegations that she was sexually assaulted by her supervisor, Brian Richmond, in his hotel room at a European conference.

Outsiders may never know for sure what happened in that Florence hotel room. But the incident ultimately triggered a cascade of other allegations against Richmond and a resolve by some senior paleoanthropologists to do battle against sexual misconduct, hoping to change the climate of their field. The charges and the community’s response also roiled two leading institutions, which struggled with shifting cultural expectations, inadequate reporting and disciplinary tools, and the challenge of treating all parties fairly.

Please read the entire story, carefully reported by Balter here. Continue reading →

ConspiraSea Day Six: You know who exposes real conspiracies? The media.

Colin20 Comments

This is Day Six in my seven-day series of updates from or about the ConspiraSea Cruise. You can read Day 1 here, Day 2 here , Day 3 here, Day 4 here, Day 5 Part 1 here, Day 5 Part 2 here, and an explanation for what I was doing here. We’ll have an index page up soon collecting these and future pieces.

Day Six was tough for me personally. The main reason is something I’ll write about for Day Seven, but it didn’t help that the seas were particularly high. I’d become seasick on a small-boat excursion the day before (thanks to Michael Badnarik who offered good advice for dealing with it) and even though the cruise ship was mostly very stable, my memories of the Saturday lectures feel like they’re covered with a thin, greasy film.

It also didn’t help that the first session of the day was listening to Winston Shrout give well-meaning people really terrible advice about how to handle their mortgages. That definitely added to my queasiness. I don’t know much about real estate, but I’m pretty sure that the Vatican hasn’t just released the necessary money to pay off everyone’s mortgages. And I’m pretty sure that Winston Shrout wasn’t involved in a multi-trillion dollar transaction that would have done the same thing if HSBC hadn’t sabotaged him. And I’m pretty sure that referring people to NESARA is, at best, a waste of their time. But more about pseudo-law on Day 7. Continue reading →

ConspiraSea Cruise Day 5 Part 2: I Took The Bait

Colin24 Comments

Colin here, taking over the job Jennifer’s graciously been doing by editing and posting my own writing. I’m no longer on the ConspiraSea Cruise doing research for a book on irrational beliefs. Now I’m home (briefly) and writing up my experiences. This is a fuller explanation of what happened on the fifth day. You can read Day 1 here, Day 2 here , Day 3 here, Day 4 here, Day 5 Part 1 here, and an explanation for what I was doing here. 

I have just one more full day to go, then a very personal post about the very last morning of the cruise. I want to move forward quickly because we aren’t done after that. In the future I’ll write in more detail about individual presentations and my thoughts about what the conference has to teach us about irrational ideologies and the debates around those beliefs.

In the last post, I explained how I wound up as the primary audience of a long, angry lecture by Andy Wakefield. Here’s a much more detailed explanation of what happened, and some thoughts on why it happened and why it matters.

2016-01-29 15.13.13

And I apologize in advance for the fishing puns. Honestly, I tried to stop.

Continue reading →

A skeptic on the ConspiraSea cruise, day 5: I Just Can’t Do Another Nautical Pun

Jennifer Raff29 Comments

Colin is currently on the ConspiraSea Cruise doing research for a book on irrational beliefs. He is emailing summaries of each day’s experiences to me for posting here on Violent Metaphors. This is the fifth day’s report. You can read Day 1 here, Day 2 here , Day 3 here, Day 4 here, day 5 (part 2) here , and an explanation for what he is doing here.  If you would like to give him questions or advice, please comment on this post–I’ll make sure he sees it. –Jennifer

So that was the state of affairs going into Friday. I was generally aware of what happened, as were a lot of people on the boat; the reporters made it pretty clear that Thursday’s events were bizarre and alarming. As I’ve said, I haven’t ever felt unsafe on this ship. But I also haven’t been ambushed in any sessions, had anyone pop up by surprise, or been singled out and yelled at. (With one exception, which we’ll come to—and even that wasn’t in a threatening context.) I know the journalists have asked organizers whether they’ll be safe, and there’s been some discussion of having security available if it happens again. I would be surprised if it were necessary—but not quite as surprised as I would have been on Wednesday. Continue reading →