Archaeological Fantasies and the genetic history of the Americas

The excellent podcast Archaeological Fantasies recently had me on as a guest for a wide ranging discussion on genetics. We covered everything from the genetic prehistory of the Americas to issues surrounding ancestry testing companies. Here’s a link to the episode (apologies for the fact that I kept cutting in and out–apparently our university wireless connection isn’t very good).

Since so much of our discussion focused on haplogroup X2a and models for ancient American prehistory, I decided to break from the normal tradition here at VM and actually re-publish a post to make it easier for people to get answers to any questions they might have. And if you have specific questions about content from the podcast, please feel free to leave them in the comments on this post.

This post was originally published last year to address some questions that Deborah Bolnick and I were getting about our paper “Does Mitochondrial Haplogroup X Indicate Ancient Trans-Atlantic Migration to the Americas? A Critical Re-Evaluation.”  I’ve edited it slightly to reflect the fact that the paper itself is now open access, and you should be able to download it here or at my academia.edu page. (I’m actually really shocked at the number of downloads it’s gotten…apparently this is a topic that a lot of people find interesting!).

As soon as my syllabi for the upcoming semester are finished, I will try to write up another post that summarizes recent findings in North American anthropological genetics, and what they mean for our understanding of the initial peopling of the Americas. In the meantime, if you’re interested in ancient DNA I highly recommend you get up to speed on some of the methods by reading this post.

 

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Guest post by Rosi Sexton: Why ‘why’ matters

A few days ago, I published this post about the pseudoscience I see frequently in MMA communities. For a different perspective, I invited former professional fighter, osteopath, and all around brilliant person Rosi Sexton to share her thoughts with us. While her position is a bit ‘softer’ than mine, I think it’s important to get a diversity of perspectives, particularly from people who are actually treating patients. Enjoy! –Jennifer

Cupping seems to be the new therapy buzzword around these Olympics. I’ve had a few discussions with people asking me what I think about all these athletes sporting cupping marks on their backs and shoulders. My answer? “Well, that depends”.

Let’s get a few things straight before I go any further. In common with most of the skeptics who have already commented on this latest trend, I think it’s very unlikely that cupping has much of a direct physiological effect. There’s no evidence to suggest that it affects the underlying tissues very much at all, never mind in a way that’s likely to be performance enhancing.

So case closed? Cupping is nonsense, as with so many other ‘trendy’ interventions.

Not so fast. In the absence of claims made for specific physical outcomes, cupping is just a physical activity. It makes no more sense to say that “cupping is nonsense”, any more than it makes sense to say that Morris dancing is nonsense: both activities seem a little odd to me, but if there are people who enjoy them for their own sake, then I’m not about to argue with their experience. Although I’ve never had a cupping treatment, several friends tell me they find it nice and relaxing.

“But where’s the evidence for that?” the skeptics ask; and here’s where I think the problem lies. Sometimes we fail to distinguish adequately between objective claims about fact (“this treatment will make your muscles stronger”) and subjective claims about personal experience (“I had this treatment, and it made me feel really good”). When we start to imply that people’s individual experience is invalid, or wrong, because they don’t have scientific evidence to support it – that’s when sportspeople start to complain that the scientists are arrogant, out of touch curmudgeonly killjoys.

Imagine that someone has conducted a large survey about leisure activities. Suppose the results come back, and it turns out that on average people find quiet country walks and loud, alcohol fuelled parties equally enjoyable. Does this mean that you that your introverted great aunt Agatha will be persuaded to forgo her gentle Sunday afternoon stroll in favour of accompanying you to a nightclub? Unlikely. Telling her there’s evidence that the two activities are equally enjoyable probably wouldn’t be persuasive – because enjoyment is subjective, and Aunt Agatha knows what she likes. The fact that things like pain, discomfort, pleasure and happiness are all subjective and difficult to measure isn’t a reason not to research them – but it does raise difficulties that should be taken into account. I have misgivings about measuring something as complicated as pain on a 1-10 scale, for example; but we have to start somewhere. It also means that we should be very clear about what the research does, and doesn’t, say when we apply it to individuals.

It’s not quite that simple, of course. Perhaps that athlete finds the treatment pleasant and relaxing because he’s been told it’ll have beneficial effects on his performance, when in fact this is highly questionable. The ethics of using placebo effects in top level sport – where winning and losing can be measured in milliseconds – is a subject that needs a whole separate post, but that’s not what I’m advocating here. I think it’s possible to be clear and honest about what’s known about a treatment, and to allow for a person’s individual subjective experience at the same time.

Talking openly with the athlete about why they are using a particular treatment, and being very clear about what they expect it to achieve is an important part of that process. If an athlete I’m treating tells me that she wants to use a treatment like cupping, then my first question is to ask why she’s doing it. I want her to think about what she’s likely to get out of it, and to ensure that it’s not being used instead of evidence based treatment to address any underlying problems. If it’s only giving some temporary relief, could the time and money might be better spent elsewhere? What are the risks of adverse effects, and are the benefits worth it?

As a clinician, I find that framing the conversation in this way to be a more effective way of communicating with my athletes. By taking a hard line against misleading claims but not against the practice itself (except where it’s likely to be actually harmful), it encourages the athlete to apply their own critical thinking. We talk about how athletes can monitor their own experience more methodically, to see whether particular changes to their plan have a consistent (subjective) effect or not.

Learning how to sensibly navigate the large gaps between our small islands of knowledge is something that those in high level sport constantly struggle with. No athlete can afford to use only methods that have been proven rigorously by science – despite the best efforts of sports science there is simply too little evidence out there. At the same time, it’s easy to get suckered in by the latest trendy therapy or product; when winning and losing come down to tiny margins, many athletes feel that they can’t afford to take the risk of not using something just in case it does make a difference. Applying a sceptical thought process while at the same time allowing for personal experience and individual circumstances gives a framework for evaluating these unknowns, whether it’s a “wacky” therapy like cupping, a new training method or a cortisone injection.

Two questions you should never be afraid to ask:

“What, exactly, is this supposed to achieve?”

“What reason do I have to think it can do that?”

I’ve never experienced cupping, but I did have a hot stone massage once. It was lovely. It didn’t cure my neck pain, of course (nor was I expecting it to) – but it was a very pleasant distraction from it for an hour or so. Your mileage may vary.

Pseudoscience is common among elite athletes outside of the Olympics too…and it makes me furious.

Skyline

The many stories yesterday featuring Olympians appearing with cupping marks on their skin have brought renewed attention to pseudoscience in sports. Cupping, which involves putting a hot jar onto the skin, forming a suction that “draws out” toxins or unblocks energy meridians or something like that, might seem like a relatively benign form of pseudoscience, but it can be quite harmful.  Orac has a great post (complete with a gruesome photo) describing the harms of this particular practice:

Cupping is nothing more than an ancient medical practice based on a prescientific understanding of the body and disease, much like bloodletting and treatments based on the four humors. As the case of Lin Lin shows, it’s all risk for no benefit. It has no place in modern medicine, or at least shouldn’t.

I’m completely unsurprised to find that pseudoscience is common among the elite athletes competing in the Olympics. I’ve seen similar things rampant in the combat sports world as well.

Over the course of my martial arts career, I’ve had the opportunity to train with many extraordinary MMA fighters. What I observed in these elite professional fighters–most of them either competing in the UFC, or well on their way to it–was a razor-sharp focus on doing whatever it took to improve. This meant grueling eight hour training days, and equally grueling recovery practices to allow them to sustain that level of activity. The recovery practices included ice baths, contrast showers, yoga, expensive massages and bodywork, and a whole host of alternative medical treatments including acupuncture, energy work, and dubious supplements. And behind nearly every fighter, there’s usually at least one chiropractor lurking around in background.

[My interactions with these MMA chiropractors are so similar that they almost follow a script.  He (and it’s always a he) invariably introduces himself as “Dr. First Name”, even in casual social situations, and tries to impress his listeners by boasting about how many important clients he has.]

Screen Shot 2016-08-09 at 9.43.06 AM

This story gets at the psychological aspects of why elite athletes pursue useless–and sometimes even harmful–alternative practices. What I’ve observed among fighters is this exact mentality.   Magical thinking has long been endemic to martial arts, and there are few voices in the community who challenge these ideas, particularly when they’re promoted by influential teachers and coaches. Competitive martial artists, like MMA fighters, are so determined to do anything it takes to give themselves the extra edge that they are especially likely to listen to anyone who promises them a benefit to training, to recovery, to mental conditioning.  Another important motivation is the money that fighters can make through sponserships from alt med practitioners and supplement manufacturers. These athletes make so little money from fight contracts that they can’t afford to turn down any source of additional revenue.  This makes them vulnerable to all kinds of practices that are ‘desperately implausible’ , as the formidable enemy of pseudoscience David Colquhoun characterizes them.

If I sound angry here, it’s because I am. I see these quacks taking large fees from vulnerable fighters who can’t afford them…. but are convinced that they can’t afford not to pursue any possible advantage.  I’ve seen creepy alt med sponsors lurking around events and attaching themselves to athletes as if they were coaches. I’ve seen more than one person in the MMA world injured by pseudoscientific ‘treatments’, and more than one athletic career ruined by supplements.  This exploitation makes me furious.

I hope that as more attention is focused on pseudoscience in the Olympics, more attention will also be paid to these issues in MMA, and the work of people who are trying to push back against the BS in the community, like  Rosi Sexton, and Jeff Westfall.

#Vaxxed, reviewed: What happened outside of the movie.

This is part II of our series on the movie “Vaxxed”, which Colin, my sister Julie, and I saw in Kansas City on June 11. In part I, Colin focused on some of the factual inaccuracies of the movie. He talked about how a person attending the movie would have walked away with an extremely distorted understanding of the CDC, a distortion deliberately encouraged by Mr. Wakefield and the makers of the documentary.

Here, I’m going to focus not so much on the documentary itself as on what happened after the documentary: what the “Vaxxed” team said during the Q&A session, how the audience responded, conversations that I had with protestors after the movie, and a conversation that Colin and I had with Mr. Wakefield. Continue reading

#Vaxxed, reviewed: What happened inside the movie

Jennifer and I saw Vaxxed in Kansas City on June 11, along with her sister Julie. We have a lot of observations and thoughts about the movie, so we’ll probably be doing several articles discussing the film itself, the audience’s reaction to it, the protestors, our responses, and a lot more. Jenny’s post is here, and covers some of what happened after and as we left the movie.

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Not exactly a full house; theater staff said about 1,100 tickets were sold for the entire week. The number may go up, but that’s consistent with the movie’s low numbers.

My first, strong reaction was that very few people leaving the movie would have any idea what happened with the “CDC Whistleblower.” The audience left knowing next to nothing about the events it’s supposedly about; I confirmed that by talking to people afterwards, and they had very little grasp on the facts.

That’s no surprise. The movie is propaganda—it’s not educational, it’s manipulative and inflammatory. We can’t fact-check every statement or point out every strategic omission in the movie, so here are some simple and obvious illustrations of how it deceives audiences.

To fans of the movie who have seen it: I don’t expect this will change your mind. I don’t think much of anything would, really; I asked people on the ConspiraSea Cruise what evidence would change their minds, and not a single person could describe evidence that would persuaded them they were wrong. (Even Wakefield gave me a roundabout, evasive response.) Doesn’t that sound like ideology to you? Even if this doesn’t change your mind, I hope it makes you think. Do you know what William Thompson really thinks about vaccines? Or about Wakefield or Hooker? Do you know what data the CDC supposedly destroyed, or whether anyone has ever found any actual problems with the study it performed? Do you know what other independent organizations have found the same thing the CDC did—a total lack of any causal connection between vaccines and autism? Most fans of the movie don’t know anything about these subjects. If it leaves you scared and angry but misinformed, doesn’t that make it propaganda? And if you think it did leave you informed, well, see how many of these facts you actually knew.

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How to flunk out of the University of Google

As I’m putting the (hopefully) final touches on a short textbook that I’m writing entitled “Handbook on Science Literacy”, I’ve been thinking a lot about how to recommend a person go about systematically investigating a scientific issue without having any background in it. Sure, you can learn how to read and understand a scientific article, but let’s be honest—far too many people choose instead to do a quick web search and let that settle the question. This practice works okay in some instances, but in others it produces misleading or wrong answers.

I want to share with you my strategies for flunking out of the University of Google.

This is one instance where flunking is a good thing. A graduate of the University of Google chooses to accept only information that supports his or her position, and ignores or dismisses information in conflict with it. A graduate of the University of Google will not be able to answer the question “What kind of evidence would change your mind on this subject?” It’s insidious, because once their opinions are formed in this way, they tend to identify with other people who share those opinions, and any new information that comes their way will either be accepted or rejected on the basis of which position they’ve already taken (the cultural cognition effect)

None of us want to be that kind of person.

Flunking out requires a decent amount of work, and the willingness to accept that you might be wrong about a subject from time to time. You’ll need to become more aware of your own cognitive biases, and have some strategies for overcoming them.

So as a preliminary step down the road to science literacy, I’ve put my thoughts on this together into a guide to learning about a subject in which you have no background. It’s an exercise; please don’t shortcut the process and go to Wikipedia, or you’ll miss the whole point.

Flunking out
How to flunk out of the University of Google.

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A Skeptic on the ConspiraSea Cruise

This is an index to our posts relating to my experiences on the ConspiraSea Cruise. Eventually we’ll convert this to a permanent page and keep it updated with new pieces and media coverage. Look forward to more indices as well, covering major Violent Metaphors topics.

In January 2016, I attended the seminar-at-sea for conspiracy theorists as background research for my book, tentatively titled “The Good Fight.” Supporters generously helped offset the costs of my attendance by contributing to my crowdfunding campaign, which explains a bit of my methodology–in short, I went to listen, not to argue or disrupt.

Itinerary and Cunning Hat
This photo went out in our first update; at least one person on the cruise recognized the hat.

The ConspiraSea Posts

I wrote a series of posts covering the details of the cruise, one per day:

Day One: A Skeptic on the ConspiraSea Cruise
An explanation of the project and an introduction to each of the conspiracy theorists presenting on the cruise.

Day Two: Reverse the Constitutional Polarity of the Baryonic Trustee Matrix: Legal Gibberish on the ConspiraSea Cruise
Pseudolaw, the pinstriped cousin of pseudoscience. And a quick end to my plan to withhold all criticism until after the cruise, as I see some exceptionally objectionable nonsense foisted off on an unsuspecting crowd by two speakers under indictment for serious federal crimes.

Day three: Nothing to Fear
How cruisegoers reacted to me, and how I reacted to them.

Day Four: Troubled Waters
A showcase of angry paranoia, as some of the conspiracy theorists misbehave.

Day Five Part One: I Just Can’t Do Another Nautical Pun
Continuing the story of an alarming and bizarre confrontation, and beginning the story of Andrew Wakefield’s angry lecture to me.

Day 5 Part Two: I Took the Bait
Andrew Wakefield, having failed to draw in the actual journalists, springs his trap on me and reveals a core of anger under his work to suppress vaccination rates.

Day 6: You Know Who Exposes Real Conspiracies? The Media.
Profiling Andrew Wakefield, Jeffrey Smith, Leonard Horowitz, Sherri Kane, and their attempts to protect their various conspiracy theories from public scrutiny.

Day 7: I Failed
A personal plea to one particular conference attendee, who very nearly fell afoul of the pseudolegal nonsense being preached by Sean David Morton–a self-proclaimed legal warrior who knows how to beat the system, but got arrested by federal agents immediately upon leaving the cruise and is currently awaiting trial on serious fraud charges.

Bonus: An Interview with Andrew Wakefield
In which Andrew Wakefield grants a personal interview, and we fact-check his claims. They do not do well. 

As I write additional pieces relevant to the ConspiraSea Cruise, we’ll link them here as well.

Media Coverage

The ConspiraSea Cruise itself got plenty of media coverage, as did my book project and the series of blog posts above. We’ve collected some links here and again we’ll update them when we have something to add.

Print

Anna Merlan of Jezebel wrote a brilliant piece that captured the who/what/where/when/why as well as the overall feel of the cruise. (Check out the art, too–every section heading is a dainty masterpiece.) We’re eagerly awaiting Bronwyn Dickey‘s piece in Popular Mechanics, which should be out soon with photography from the supremely talented Dina Litovsky.

Aeon Magazine asked me to write a piece about pseudolaw, which is not as widely understood as pseudoscience. It lead to an interesting discussion in the comments about which is more dangerous, a question I’m not sure can be answered.

Wired Magazine interviewed me for a great piece that again resulted in energetic comments, a few of which demonstrated the kind of feverish paranoia that drives conspiracy theories.

Factor, a Spanish-language blog, interviewed me for a couple of pieces about the ConspiraSea Cruise. Writing about me, they saidColin es un amor: un pacifista del escepticismo. It’s a lovely summary of my philosophy, and I try to live up to it every day.

Audio

Kylie Sturgess and I talked for an episode of the Token Skeptic podcast; it was a conversation between her home base in Australia and my hotel room in Copenhagen about a cruise from Los Angeles to Mexico. International intrigue!

The consistently excellent Prism Podcast ran two episodes about the ConspiraSea Cruise and my thoughts on Andrew Wakefield. It was a real treat to chat with Dr. Clay Jones and Dr. Grant Ritchie.

Video

Nothing yet, and it’s hardly my focus. We have had a serious inquiry about the film/TV rights, though. They’re still available. Personally I suggest casting Vincent D’Onofrio as the noble, humble, brave, heroic writer. Or maybe Peter Weller.

A writerA KingpinA Crusader

 And the Far Out

If you write about conspiracy theorists, sooner or later someone’s going to call for your “indictment for genocide by prosecutors at the International Criminal Court.” And sure enough, a couple of the people we profiled pounded out not one but several feverish attacks on my “criminal psychopathology and moral turpitude” and “obese darkness.” We appreciate the publicity, even if it’s completely inaccurate and completely goofy.

Behind the scenes at NASA: The HERA project

HERA1
Side view of the HERA project facility. The hygiene module, where bathrooms and showers are housed, is in the foreground.

 

What happens if you put a group of adults together in a confined space and leave them isolated for weeks? Can they get along? Can they work together to productively carry out complex tasks, stay in shape, and conduct scientific research?

This sounds like the premise for a reality show (minus the scientific research part, which sadly doesn’t play well on television). And in a way it is: these adults are filmed every second of the day. But instead of entertainment, this project has one very serious goal: develop strategies for keeping humans healthy, sane, productive, and safe for long duration voyages into space.

The Human Exploration Research Analog (HERA) project is a critical component of NASA’s Flight Analogs Project, which carries out research on different aspects of human long-duration spaceflight. I recently visited NASA to give a talk on genetics to ISS scientists, and was able to tour the HERA facility and talk about the project with its former director, Joe Neigut. Because this isn’t the sort of thing that one gets to access on the regular Johnson Space Center tour, I asked the NASA officials if it would be all right for me to write a blog about my experiences to share with readers, and they kindly agreed, stipulating only a few restrictions on what I was allowed to share in the interests of research integrity.  So here’s what I saw and what I learned.  Continue reading

Another open thread on vaccines

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

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.