Familial [mis]identification rates and experiments in video

Happy to say that a paper I wrote along with Erin Murphy, Yun Song, and Monty Slatkin is out today over at PLoS ONE (and on the arXiv).  In the paper, we implement the familial searching method of Myers et al. and estimate power, false positive rate, and rates of distant relatives misidentified as near relatives.  Short story: we find very high power and low false positive rate, however we also see high rates of relative misidentification.

These results are relevant to people inside and outside of the scientific community involved in decisions about the implementation of familial searching methods.  With that motivation [and generally], I’m experimenting with explaining my research through different media apart from technical manuscripts.

Adhamh Hoeltzel, Alex Safron, Mosaic Project youth leadership, and I collaborated to make a charismatic and informative general audience video explaining the idea and impact of familial misidentification in social context.  I’m hoping to see this video used in high school classroom or other educational contexts to introduce ideas and stimulate questions about forensic genetics.

For a quick technical overview, I made a short video abstract which outlines the basic questions and results for a scientific audience (video abstract idea thanks to Eline Lorenzen, more information coming soon).

Finally, I wrote a guest post for Haldane’s Sieve to motivate and explain the work to population geneticists without background in forensic science.

I’m curious to learn how these different formats are received and see other scientists’ alternate-media projects.  Most importantly, I’m excited to see more engaged discussion of forensic identification methods and their implementation.

Clarence Thomas got it right!

I know – that’s a first.  The supreme court made a wise and unanimous decision on the Association for Molecular Pathology v. Myriad Genetics case.  You can no longer patent a gene. However, the supreme court upheld Myriad Genetics’ rights to patent cDNA from BRCA1 and BRCA2 – which might explain why Myriad Genetics’ stock jumped after the ruling.  Apparently, the investors had feared worse.  Exactly what a patent on cDNA entails may be up to future litigation, but it should not preclude many common genotyping platforms as a diagnostic tool for BRCA1 and BRCA2 mutations.

What are the long term consequences of the ruling?  We can probably expect private companies to invest less in basic research on the molecular genetics of disease.  It might be harder to make a profit on discovering disease related mutations.  On the other hand, it will be easier to develop new diagnostic tools based one existing knowledge.  We might expect a shift in focus in private companies from basic research towards development of diagnostics. That is not necessarily a bad thing.  But somebody else has to pick up the slack on basic research.

The mantra for funding of genomics research at the National Institute of Health (NIH) – the major funding body of genomic and medical research – has been ‘translational’.  Apparently, the phase in genomic research in which we focus on basic discoveries is over.  Now we need to focus on translating these discoveries into medical applications – diagnostics and treatments.  That is all good – but with the expected fallout of the supreme court ruling,  somebody has to continue the drive for basic research.  It is time for NIH to once again step up on funding for basic research in the genomic sciences.


Addendum:  Hilariously, while Scalia voted in favor of the ruling – he dissented on the basic principles of molecular biology. Apparently, it is not only global warming and evolution that is being challenged.  I expect soon to see a dissent on the shape of the earth or the placement of the earth in the solar system.


BAPG meeting in Berkeley Oct. 5th

The next Bay Area Population Genetics meeting will be hosted by our group at UC Berkeley on October 5th.  You are hereby invited.  Please
register and sign up for talks/posters at http://tinyurl.com/lglzosw.

For more information about previous meetings, see here.



Do it: 2013 Workshop for Young Researchers in Mathematical Biology

You know you want to go…
2013 Workshop for Young Researchers in Mathematical Biology (WYRMB)
August 26 – 29, 2013
Application deadline: May 1, 2013
The workshop is intended to broaden the scientific perspective of young researchers
(primarily junior faculty, postdocs, and senior graduate students) in mathematical biology and to encourage interactions with other
activities include plenary talks and poster sessions, as well as group
discussions on issues relevant to mathematical biologists. Several
abstracts will be chosen
for short talks as well as poster presentations.
Limited funding is available on a competitive basis.
cordially invite young mathematical biologists to participate. For full
consideration, please apply by May 1, 2013. To apply, click this link

Plenary Speakers

Lisa Fauci, Tulane University

Kresimir Josic, University of Houston

Claudia Neuhauser, University of Minnesota

Sebastian Schreiber, UC Davis

Arthur Sherman, Laboratory of Biological Modeling, NIDDK, NIH

John Tyson, Virginia Tech

Lani Wu, Southwestern University

SMBE 2012 in Dublin

Many Nielsen lab members are Symposium organizers, selected speakers, or presenting posters SMBE 2012 in Dublin. The meeting is off to a great start! You can follow it on twitter with the hashtag #smbe12.

Introduction to Unix & Perl

Seems like we’re on a roll with computational learning tools this month.

Here is a freely-available Primer for Unix & Perl, designed for biologists designed by our neighbors at the University of California – Davis: http://korflab.ucdavis.edu/Unix_and_Perl/

Top rated graduate programs at UC Berkeley

Sure, rankings aren’t everything, but I don’t think it hurts to be proud of the accomplishments of our graduate advisors, graduate students, and the ground-breaking research they’re conducting.

Today U.S. News Rankings and Reviews released new annual rankings for Business, Law, Engineering, Medical and Education graduate schools, so I was curious about the rankings of Science programs. Curiously, they only “periodically” rank programs in the sciences, social sciences and humanities, and the health arena. So, although the results are from 2010, we can appreciate them anyway. US News ranks the following UC Berkeley graduate programs in the top five in the country:
– Biology
– Chemistry
– Computer Science
– Earth Sciences
– Math
– Physics
– Statistics

Let’s keep up the good work!

The lab in photos: Bay Area Pop Gen

The lab at the BAPGV

Part of the radicalized youth and other members of the lab “occupy” the Bay Area Population Genomics V conference. In this occasion, the meeting took place at Stanford and was pleasantly organized by Dmitri Petrov.


In general terms the meeting was very nice: with attendants from UC Berkeley, UC Davis, UCSF, SFSU, and Stanford, with interesting talks, good breakfast, nice lunch… but (and this is a very important but), the room temperature was very chilly -a good strategy if you want to keep the audience awake-

Poster session

There was also a space dedicated to poster presentations. In the photo you can see Joshua Schraiber asking random questions to Benjamin Peter (the guy with the backpack and main author of the poster)

Taking notes

Being a prospective graduate student in the lab, it’s not a bad idea to have good transcription skills, especially if you plan on taking notes and write down some ideas for your future PhD project.


Dienekes’ Outrage

Some of the radicalized youth in my group made a post on this blog on their experiences with the Occupy movement in Oakland and in Berkeley – something I had encouraged them to do as I felt other academics might be interested in hearing about it.  You don’t very often see career scientists dedicate a significant amount of their time for social justice causes.  So I figured that there might be some interest in this, as an inspiration for some – or perhaps as a curiosity for others.  As expected the post has been read a lot.  In fact, Dienekes featured a post on his own anthropology blog commenting on my group’s original blog post.

The original post showed pictures of students and postdocs in my group holding a sign arguing that capitalism reduces fitness.  The post then proceeded to argue in favor of this point using the fact that the life expectancy of an African American in West Oakland is 15 years shorter than that of a person growing up in East Oakland.  Dienekes was shocked by this travesty and decided to make a blog post about it.   To my surprise his outrage was not about the social conditions in West Oakland but rather about the loose use of fitness employed in the blog.  He took the statement by my students and postdocs literally  and pointed out that if you include all the different components of fitness, and not just viability, there is in fact no good scientific evidence that the absolute fitness of individuals growing up in capitalist societies is reduced.  You might now rightly wonder about a number of scientific issues relating to this debate.  For example, what is the standard we compare to here?  A feudal society?  Or Vietnam or Cuba perhaps? I am not sure.  But the real question to me is of a more psychological nature: how many years do you have to be locked up in a university to believe that using the word fitness, without including all of its components, is more outrageous than the social conditions in West Oakland?

Most of the students and postdocs in my group are from Europe, and many have not been here for long.  They have perhaps not quite gotten use to American political discourse and may not express themselves in a way that most Americans find convincing.  But at least they haven’t quite lost their sense of empathy and care for other people.  I figure that if I keep them here, in an American academic environment, for a couple of years more they will get cured of that problem and will be able to concentrate fully on their research careers without getting distracted by the economic and social problems they encounter in the neighborhoods around campus on their commute from and to work.  If I push them hard, they may even eventually end up getting real jobs and move up in the East Oakland hills. They will then never have to worry about the problems in West Oakland again, and can spend all their time making sure they include all components of fitness when making blog posts.


Up and running…

We are up and running with the new web site and Blog for the Nielsen group.  We will use this space to spread our opinions about the state of affairs in evolutionary genomics.  If you disagree with us – leave a comment.