One of the most uninteresting parts of being a Scientist

Reformatting manuscripts for a new journal is, in my opinion, one of the most tedious parts of being a scientist. I won’t say that it is a total waste of time, but it comes close.

I do understand that each journal has a unique format, structure and feel. Each journal wants to make its format consistent for its readers. And, each journal has a slightly (or vastly) different audience that its format caters to.

But, sweet, mother of pearl, it can be frustrating for authors to update, change, add, and repackage information for a new journal. This one allows sub-headings, another does not. This one allows you to merge “Results” with “Discussion”, another does not. Some journals and articles have specific word limits, others let you include as much content as you like (although some charge by the page). There are varying limits on the number of tables and figures. Even different pricing for color within figures.

I am very lucky to live in the digital age, where technology exists to easily cut, paste, add, and subtract content. My dad tells me a story where, for his Master’s Thesis, he literally cut out, then taped in new content, because otherwise he would have had to retype the entire tome.

And citations, whew! I am so glad for the software to assist with updating these. There are so many different formats for citing in the text (only the first author’s last name, or up to three authors’ last names, or numbered by the first time the citation is present, or some other variant). The bibliographies can be equally involved regarding the small, but important, differences between journals.

Given all of the changes, and the amount of time, that go into choosing to submit to a journal with a different format (which means that, unfortunately, the manuscript has already been rejected from one journal), there are some good things. A new format does require the author to consider their analysis and results from a new structural perspective, considering how to tell the story in a new way. Hopefully the process will also give authors the chance to catch any minor writing errors, and think of new, clearer ways to explain observations.

I am not entirely convinced that the benefits outweigh the time spent trying to wrangle a manuscript into the appropriate format.

Pitching yourself

Several people in the lab are applying for jobs right now, so the recent article by Roberta Kwok about elevator talks in Nature seems particularly relevant:

http://www.nature.com/naturejobs/science/articles/10.1038/nj7435-137a?WT.mc_id=TWT_NatureJobs

Nancy Baron is quoted in the article, where she “suggests thinking about four key topics”:
1. the problem
2. why it matters
3. potential solutions
4. the benefits of fixing it.

I wanted to highlight how important I think these short interactions are, not just for explaining science to a lay audience, but for interacting with peers and collaborators. So much of the doctoral work is focused on precision, on figuring out the nitty gritty details, that when we finish, we sometimes forget how long it took to learn and become comfortable with all of the terminology and background. Another aspect of graduate school, and perhaps to a greater extent the postdoc, and applying for jobs, is to emphasize the areas we are experts in. As such, it is difficult to sometimes admit that we don’t know it all. Coupled together, these can result in two very intelligent people speaking to one another, but not fully understanding each other.

While it may seem like an oversimplification (instead of just a simplification), and go against our very nature to provide details, the ability to concisely give an accessible overview of our science can only improve our interactions. Anyone who wants to know more can easily ask.

SMBE Sattelite meeting on Eukaryotic-Omics at UC Davis

UC Davis has received funding to host an SMBE Satellite Meeting on Eukaryotic -Omics this spring – meeting dates have been set as Monday April 29 – Thursday May 2nd, 2013, and further details can be found at the meeting website: http://www.smbe.org/eukaryotes

The SMBE Satellite Meeting on Eukaryotic -Omics will bring together an interdisciplinary pool of researchers to discuss current efforts, challenges, and future directions for high-throughput sequencing approaches focused on microbial eukaryotes (environmental studies of non-model organisms). The meeting program will encompass investigations of eukaryote biodiversity, ecology, and evolution, using approaches such as rRNA marker genes, shotgun metagenomics, metatranscriptomics, and computational biology tools and software pipelines.

Program announcements, registration details, and travel award information have been posted to the meeting website. The official conference hashtag will be #SMBEeuks on Twitter.

Our call for travel award applications includes a heavy focus on diversity-encouraging early-career applicants as well as those from underrepresented groups. Please pass on this meeting announcement to anyone who might be interested in attending. Deadline for abstract submission and travel grant applications is Feburary 22, 2013.

 

Recent publications:Gene survival and death on the human Y chromosome

The last manuscript from my thesis research was accepted for publication in December, but I’ve been too distracted to blog about it. It is available through Open Access (thanks, in part, to the Miller Institute for allowing me to use my research funds to pay for the OA fee).

Mol Biol Evol. 2012 Dec 17. [Epub ahead of print]

Gene Survival and Death on the Human Y Chromosome.

Source

Statistics Department and Integrative Biology Department, University of California-Berkeley.

Abstract

Y chromosomes have long been dismissed as “graveyards of genes,” but there is still much to be learned from the genetic relics of genes that were once functional on the human Y. We identified human X-linked genes whose gametologs have been pseudogenized or completely lost from the Y chromosome and inferred which evolutionary forces may be acting to retain genes on the Y. Although gene loss appears to be largely correlated with the suppression of recombination, we observe that X-linked genes with functional Y homologs evolve under stronger purifying selection and are expressed at higher levels than X-linked genes with nonfunctional Y homologs. Additionally, we support and expand upon the hypothesis that X inactivation is primarily driven by gene loss on the Y. Using linear discriminant analysis, we show that X-inactivation status can successfully classify 90% of X-linked genes into those with functional or nonfunctional Y homologs.

 

Recent publications: Selective sweeps – distinguishing effects of standing variation from de novo mutation

PLoS Genet. 2012 Oct;8(10):e1003011. doi: 10.1371/journal.pgen.1003011. Epub 2012 Oct 11.
Peter BM, Huerta-Sanchez E, Nielsen R.
Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America.
Abstract
An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection.

Non-academic careers

In case you’re interested in non-academic jobs, below is an announcement forwarded to the lab that might help you find a position.

Insight Data Science Fellows Program

Applications now open for 2013
http://insightdatascience.com

Silicon Valley technology companies are hiring data scientists to help them glean insights from the terabytes of data that they collect everyday. The Insight Data Science Fellows Program is a postdoctoral training fellowship designed to bridge the gap between academia and a career in data science.

Insight highlights:

– 6 week fellowship in Palo Alto, CA includes tuition scholarship and a $5,000 living expense reimbursement.

– 100% placement rate for Insight Fellows who completed job search in 2012.

– Insight Fellows are now data scientists at LinkedIn, Facebook, Google,Twitter, Square, Microsoft, and other top tech companies.

For more information and to apply for the January, June and August 2013 sessions, please visit: http://insightdatascience.com

ASHG 2012

This was my year attending the annual meeting of the American Society of Human Genetics (ASHG). Wow! The meeting was enormous, but well-organized. The process for uploading presentations, as well as the technology personnel themselves were fantastic, from a speaker/moderator view. Even though the broad focus is human genetics, I found that, similar to the annual meetings of Evolution or SMBE, the topics vary significantly, and often sessions of similar interest (to me at least) were scheduled concurrently. The venue and schedule were very amenable to switching between sessions, and for facilitating interactions during the breaks. I especially liked that there was space to allow posters to stay up multiple days, and to stagger presenters from each poster topic.

I tweeted less than usual, but I blame this on a conference being too close to home (such that I could attend the conference, but still had all the responsibilities of being “home”).

Here’s a synopsis of ASHG2012. In particular, I’d like to point out that the Nielsen lab got a bullet point, as did my talk!

– The Nielsen Group is still working on high altitude adaptations. They don’t see hard sweeps. Of course I didn’t get confirmation of whether these were old variants, but it looks as if a lot of preliminary stuff did not have the power to detect anything in the first group. As usual they are up to something.

– Speaking of the Nielsen Group, Melissa Wilson Sayres’s work on purifying selection on Y chromosomal lineages was persuasive to me. Basically, effective population differences (e.g, polygyny) just can not explain the lower diversity of the Y lineages (they ran simulations). Luckily for the phylogeographers this won’t impact the utility of Y trees (positive selection would, but that’s not what she’s talking about). I’m a little confused whether it was Sayres’ talk or not, but these results may explain the discordance in coalescence between mtDNA and Y lineages (the former has a deeper coalescence).”

I didn’t mention it specifically, but yes, I do think that purifying selection may be able to explain the differing estimates of the TMRCA (time to most recent common ancestor) obtained from mtDNA and chromosome Y studies, by reducing the time to coalescence for the Y lineage.

I’d love to hear what you all took away from the conference.

ASHG2012

Many from the Nielsen lab are presenting posters and talks at the 2012 meeting of the American Society of Human Genetics.

If you are here, please come talk to us.

If you aren’t, you can follow the meeting on twitter with the hashtag: #ASHG2012. I’ll be tweeting (@mwilsonsayres).

Vote!

There are many in the Nielsen lab with strong opinions about social, economic, and environmental policies. We don’t always agree, but we have many civil discussions.

While the presidential race is getting most of the attention, here in California, we have several other things to vote on as well:
11 propositions (there are very strong, and conflicting, opinions for a few of these)
US Congress members
– State senate and assembly members
– Local ballot measures

You can check out ballotpedia.org to learn more about propositions in your area.
You can find your polling place by simply googling “polling place” and entering your address.

If you are able to vote, and haven’t yet done so, please make some time today to contribute your opinion to the political process.

I voted by mail last week.

Recent publications: Michael DeGiorgio investigates the effects of geographic sampling

Mol Biol Evol. 2012 Oct 10. [Epub ahead of print]

Geographic sampling scheme as a determinant of the major axis of genetic variation in principal components analysis.

Degiorgio M, Rosenberg NA.
*Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

Abstract
Principal component (PC) maps, which plot the values of a given PC estimated on the basis of allele frequency variation at the geographic sampling locations of a set of populations, are often used to investigate the properties of past range expansions. Some studies have argued that in a range expansion, the axis of greatest variation (i.e., the first PC) is parallel to the axis of expansion. In contrast, others have identified a pattern in which the axis of greatest variation is perpendicular to the axis of expansion. Here, we seek to understand this difference in outcomes by investigating the effect of the geographic sampling scheme on the direction of the axis of greatest variation under a two-dimensional range expansion model. From datasets simulated using each of two different schemes for the geographic sampling of populations under the model, we create PC maps for the first PC. We find that depending on the geographic sampling scheme, the axis of greatest variation can be either parallel or perpendicular to the axis of expansion. We provide an explanation for this result in terms of intra- and inter-population coalescence times.