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.]

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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

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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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.

 

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

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.

Sexual harassment in physical anthropology

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