Archives For genetics

This is the second post in a series discussing the recent publication of a 12,500 year old genome from Montana. You can find the first post here.

In the weeks following the publication of the complete genome from a Clovis child, there’s been a lot of press coverage of this study and its possible implications. I want to discuss a bit of the media coverage on this subject, since it raises issues that I think science journalists need to consider more carefully.

First of all, to recap the major findings of the original study (discussed in more detail at the link above):
1. Anzick-1, the 12,500 year old Clovis child whose genome Rasmussen and colleagues sequenced, is very closely related to living and ancient Native Americans.
2. Anzick-1 is more closely related to Siberians than other Eurasian groups.
3. Anzick-1 is more closely related to Central and South American Native American groups than to some North American groups.
4. The results from Anzick-1′s genome fit with the scientific consensus about the peopling of the Americas. This consensus encompasses the results of decades of archaeological, genetic, and paleoclimate research.

Unfortunately, several press reports chose to find controversy in a decidedly non-controversial story by giving undue weight to problematic “alternative” explanations of Native American origins, including the Solutrean hypothesis, and other “European contributions” to Native American ancestry.

140214_NEWSCI_NativeAmeGenome.jpg.CROP.promovar-medium2

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

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Last Wednesday, Dr. Morton Rasmussen of the Natural History Museum of Denmark and his colleagues announced that they had completely sequenced the genome of an infant boy, buried ~12,600 years ago in Montana. A few weeks earlier, I’d been approached by an editor at Nature, who asked me if I and my mentor Deborah Bolnick would be interested in writing a companion paper that would analyze and contextualize their results. We agreed, and the paper was published in last week’s issue, alongside Rasmussen et al.’s work. Because it’s (unfortunately) behind a paywall, I’d like to summarize what we said in that paper for non-scientists. There are a lot of things to talk about with regard to this study, including a consideration of ethical issues and the media’s response, so I’m likely going to do several posts on it. This first post is mainly a discussion of how we interpret the results.

For a TL;DR version of this post, here’s a link to a short interview I did on the subject last week with the BBC World Service.
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Nature publication

Jennifer Raff —  February 12, 2014 — Leave a comment

I haven’t been writing as much here recently, because I’ve been working on a “News and Views” article for Nature….and now I can finally talk about it! Here’s a link to my article: http://www.nature.com/nature/journal/v506/n7487/full/506162a.html, and to the paper that it’s discussing: http://www.nature.com/nature/journal/v506/n7487/full/nature13025.html. In the next few days I’ll post something here to discuss the main points of the article (for those of you who can’t access it), and also my reaction to the media coverage that the study is getting.

“You’re going against 40,000 years of evolution”

“This innate toughness that men have is crucial to our survival.”

These points, and many others along the same lines, were made by Mr. Gavin McInnes, author of “How To Be a Man” in a recent discussion of masculinity on the Huffington Post. His argument is based on a suite of assumptions common in our culture. It often forms the basis of misogynist arguments against feminism. Basically:

1. Evolution has made men naturally more “aggressive and tough”, and women naturally more “compassionate and domestic”.

2. Therefore in the modern world, as in past societies, men are the natural breadwinners, and women the natural caretakers of the home/children.

3. Going against these gender norms, as feminism has done in the last few decades, is going against nature, and disrespectful of the importance of childcare!

According to Mr. McInnes, women who work outside the home are “forced to pretend to be men. They’re feigning this toughness. They’re miserable.” You’ll hear a lot of people agreeing with this line of reasoning. But is it scientifically based? Continue Reading…

Cutting edge science

Jennifer Raff —  July 9, 2013 — 1 Comment

I’m attending my first Society for Molecular Biology and Evolution conference this week, and learning about some terrific research that my colleagues are doing. I just thought I’d share a few of the really neat things I’ve learned today.
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Today the United States Supreme Court issued a unanimous ruling on a case very important to genetics research and medicine.*

In ASSOCIATION FOR MOLECULAR PATHOLOGY V. MYRIAD GENETICS, INC., the Supreme Court addressed the question of whether genes could be patented. The defendant, Myriad Genetics, had identified and patented two very important genes implicated in breast and ovarian cancer: BRCA1 and BRCA2. Their patents meant that they had exclusive rights to sell genetic tests to identify the cancer-causing mutations in these genes, and controlled any research on them.

The Supreme Court ruled against Myriad Genetics. In their opinion, written by Justice Thomas, they stated that:

“a naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated, but that cDNA is patent eligible because it is not naturally occurring.”

cDNA has an identical sequence to the original gene, but has been synthesized from a messenger RNA copy of the gene with the non-coding portions (introns) removed. Here is a little tutorial that explains more about cDNA. (Perhaps Justice Scalia should watch it.**) Having a direct ‘read-out’ of the coding bits of a gene is necessary for many molecular biology applications, and this ruling is important to biotech companies (who have been patenting cDNA all this time).

This ruling is excellent news. It recognizes that the human genome isn’t ‘property’, which would have had a seriously detrimental effect on future genetics research and personalized medicine. It also means that all companies offering screens for cancer-causing variants can finally include BRCA1 and BRCA2 along with other genes tested. That will hopefully improve access to genetic information for many women with concerns about familial histories of breast and ovarian cancer, and allow them to make informed decisions about their health in advance of cancer appearing.

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*There’s a lot of discussion going on among geneticists about how badly the Supreme Court bungled the science. And it’s true that they made a lot of errors. However, I’d point out that most of us geneticists in turn probably don’t understand a lot about patent law.

**Justice Scalia issued a very odd opinion in which he agreed with the other justices about the outcome but as to the details of molecular biology:

” I am unable to affirm those details on my own knowledge or even my own belief.”

Belief? It’s perfectly reasonable to admit you don’t understand the science, but it seems strange to state that you may not believe it. This isn’t exactly controversial stuff. I’m very curious why he chose that word.

Further reading:
SCOTUS blog on the ruling: http://www.scotusblog.com/2013/06/opinion-recap-no-patent-on-natural-gene-work/

A nice discussion of the issues: http://www.pbs.org/wgbh/nova/next/body/gene-patents-and-personalized-medicine/

Do you want access to all government-funded genetic research results? You can download whatever you want (for free) here: http://www.ncbi.nlm.nih.gov/genbank/