Another day, another anti-vaccine paper retracted

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I haven’t written here about the CDC “whistleblower” issue, because I was in Shanghai when the story broke with both limited internet access and limited desire to take time away from adventures to write. Orac did an excellent job of staying on top of the story, and I refer the interested reader to his series of posts on the subject, as well as this excellent summary by Todd W. at Harpocrates Speaks, and this one by Retraction Watch.

However, as many people who read Violent Metaphors have a specific interest in vaccine/anti-vaccine issues, I thought it would be worth talking about the most recent development in the story; specifically, the retraction of Brian Hooker’s journal article purporting to show an increased risk of autism among African American boys who receive the MMR vaccine.

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The Discovery Institute challenged me. Here’s my response.

Casey Luskin, a blogger for the Discovery Institute, recently took issue with my proposal that when reading a scientific paper, one should check the institutional affiliation and credentials of its authors. I believe the part that he particularly objected to was my statement that one might not wish to use the Discovery Institute as a “scientific authority on evolutionary theory.”

Luskin wrote:

“In other words, study a paper carefully, but if the authors work with Discovery Institute, disregard everything they are saying from the outset. That’s the ground rule that comes before any other tips. It’s a great way to keep yourself carefully in the dark about things you know nothing about. And she calls us “agenda-driven”?

Imagine how journal editors would behave if they followed Raff’s advice. Or better yet, imagine what would happen if Raff herself were a journal editor. Someone affiliated with Discovery Institute (or any group friendly to ID) submits a paper, and you immediately toss it in the trash without even taking it seriously. More than a few such editors probably share her philosophy. That doesn’t exactly inspire confidence in the peer-review system, even though of course there are already plenty of reasons to lack such confidence.”

It’s a very telling reaction on his part. Continue reading

Cutting off our nose to spite our face: Scientific funding in the age of sequestration

My friend Alexander Nakhnikian has been thinking and writing a lot about American politics and science. He kindly agreed to share his thoughts here on the impact of the sequester on American research. –Jennifer

Science is important. Really, really important. Most Americans agree about this. Unfortunately, we don’t always act as though scientific progress is a high priority. That’s partly because of the American love/hate relationship with science as a way of viewing the world, which is most evident in the fights over creationism, climate change, and vaccination. But there’s another factor in play that often gets overlooked because it seems so mundane: Money. We need it. Lots of it. And these days, we don’t have it.

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Doing archaeology with DNA

Imagine you’re an archaeologist. (I know you wanted to be one when you were younger, so let’s pretend you never got sidetracked) You’re digging at a cool site somewhere and you find two completely different types of pottery*. The older type is black with a swirly design and was the only pottery used at this site during that time period. The younger type is red with no decoration. When the red pottery appears at the site, the old black pottery suddenly disappears and is never again made. How do you interpret this?

a) The people at the site suddenly decided that they hated black-colored pottery with a swirly design and only wanted plain, red-colored pottery. So they either invented it for themselves, or perhaps they learned how to make it from some other group.
b) The people at the site (who used black-colored pottery with a swirly design) were invaded by people who only used red-colored pottery. Soon, there was nobody left (or willing) to make the older type of pottery.
c) A few people living in another region who used red-colored pottery married people at this site, and brought their special pottery with them. Soon everyone adopted this kind and abandoned the old style of pottery.

I’m sure you can think of other possibilities as well. This is a simplified example, but in fact all three of these scenarios (with different technologies, of course) have actually happened in human prehistory.

How can we choose the correct interpretation between these possibilities? This is one of the biggest questions that anthropology grapples with: When we see cultural change in the archaeological record for a region, is it the result of new ideas/technologies/language being adopted by the inhabitants, or is it the result of people moving into a region and bringing the culture with them? Is it the movement of just ideas (diffusion) or a movement of people (migration)? Or something else?

There are many ways to try to figure this out, depending on what type of data you have available from a site. Maybe, in addition to the pottery, you have the skeletons of the people who lived there, and so you can compare skeletal traits of the people in the two time periods and see if they look very different from each other. Or you can do an analysis of the isotopes in their skeletons and see if they had very different diets (a suggestion that they came from different places). Or, maybe you can get DNA from their bones and see if they come from genetically distinct populations. This last approach is what I and other anthropological geneticists do, and in recent years it’s really revolutionized our understanding of human prehistory. We can directly test hypotheses of human migration by looking at patterns of genetic variation in both present-day populations, and their ancient ancestors. In many cases, DNA can reveal subtle details about the past that archaeological or osteological approaches alone can’t.**

So, we choose skeletons from both pottery-containing layers, and after getting the appropriate permissions, we isolate, amplify, and sequence mitochondrial DNA from them.

Why mitochondrial DNA? It’s a genome that exists separately from our nuclear genome (which is what’s in your chromosomes). Non-coding parts of the mitochondrial genome, called ‘hypervariable regions’, accumulate mutations faster than the rest of the genome, and studying them allows us to ‘see’ much more recent evolutionary events than would otherwise be possible. In addition, mitochondrial DNA is maternally inherited, so it provides a way to trace individual maternal lineages through time and space. Finally, mitochondria exist in many copies per cell (vs. 2 for nuclear DNA). So it’s therefore much more likely that we’ll be able to get mitochondrial DNA from ancient bones where preservation is poor.

DNA in ancient bones is degraded and prone to contamination from modern DNA. So it has to be extracted and handled in a special isolation laboratory, and only by researchers who a) know what they’re doing, b) are willing to dress ridiculously, and c) are willing to cope with a very high failure rate, since ancient DNA is extremely difficult to work with and often isn’t preserved at all.
Shadoboxing in the ancient DNA lab

Venting frustration in the ancient DNA lab when samples don’t work.

Let’s assume we were able to get DNA from a reasonable number of individuals buried in both layers. We sequence it, and figure out which maternal lineages are present in each temporal ‘population’. Using statistical tests, we determine that the two populations are genetically significantly different from each other. So, this is a population replacement, right?!

Maybe. Remember that because we’re looking at mitochondrial DNA, we are only assessing maternal lineage history. There are men at this site as well, and there’s a male history that we simply aren’t getting at with mitochondrial DNA. In order to provide the most complete answer to that question, we’d need to look at Y-chromosome DNA too, which is (of course) exclusively paternally inherited. But since Y-chromosome DNA is in the nuclear genome, it’s much less likely to be preserved in ancient human remains. So quite often the only information we can get about human prehistoric past is limited to female lineages.

Even bearing in mind these limitations, however, by finding significant genetic differences between the black-pottery-using individuals and the red-pottery-using individuals at this site, we’ve just been able to confirm a hypothesis that cultural changes were associated with the immigration of people into this region, and not simply the sharing of ideas. In my next post, I’ll go over a specific study that employs this approach to test similar hypotheses (on a larger scale) about the genetic prehistory of Europe.

*Sorry, you’re not Indiana Jones. You’re a good archaeologist, who excavates carefully and gets excited about scraps of pottery.

**But without these other types of data, drawing conclusions just from genetics alone can be very problematic. The best approach, in my opinion, is to integrate archaeological, osteological, linguistic, and cultural data, if possible. But since I’m an anthropological geneticist, I’m going to talk mostly about that perspective on the past.