Eisen Lab Blog

Pipet or Pipette?! And some updates on our project :)

First of all, how do you spell the thing?? I’ve seen it both ways.. pipet and pipette. I’m thinking it’s pipette because it doesn’t have the red squiggly spelling error sign under it. Just wondering!

 

Now for the good stuff! We’ve been rocking and rolling in the lab. (Except for the week I came down with the flu) We have so many samples and it would be a bummer to do EVERYTHING (DNA extractions, PCR, Gel confirmation, etc) for every single sample and have disappointing results. While we are optimistic about our results, we are currently preparing samples from the first coral ponds at different time points for sequencing just so we can see how our results look in terms of succession of the microbial community in the pond. If we get cool results (crossing our fingers) we’ll go back to the pipettes and prepare the rest of the samples!

 

We’ve got a lot of work to do but we are making progress. We are presenting to the lab next Friday about our project. I am really excited to get feedback from experts who know a lot more than me!

NCEAS 3-week intensive workshop in ecological analysis and synthesis

Forwarding this email

Hello NCEAS friends,

The National Center for Ecological Analysis and Synthesis (NCEAS) is
pleased to invite applications from early-career researchers for a 3-week
intensive workshop in ecological analysis and synthesis, to take place at
NCEAS in Santa Barbara CA June 19-July 10, 2013.

All travel and living expenses of participants will be covered during the
workshop, thanks to generous support from the Packard Foundation.

Applications are due March 1. For more information and application
instructions, go to:
http://www.nceas.ucsb.edu/news/nceas-summer-institute-2013

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Advice on asking for letters of recommendation (updated May 2013)

This is based off an e-mail I sent recently to a student and someone suggested I post it here:

Asking for letters of recommendation

In general I, and others are happy to write letters of recommendation for people… it’s part of our jobs after all.  However, there are some tips I would offer anyone soliciting letters at any stage of their career.

1)  Don’t ask me for a letter only a few days before it’s due.  This seems like such a simple concept but one that is violated so often.

2)  If you ask me for a letter, you need to send a copy of your CV.  No matter how long I’ve worked with you, there’s probably still information in there I didn’t know and this helps me write a letter that doesn’t sound like a form letter.

3) Send me a description of the program you’re applying for and why.  Again, this helps me write a better letter and doesn’t force me to have to trawl the internet for information

4) Make it as easy as possible for me to write the letter!  This is especially critical with professors.  If the letter needs to be mailed, you should hand me a stamped, already addressed envelope so all I have to do is drop in a letter and throw it in the outgoing mail.  If it’s an electronic form provide me with detailed instructions and links.

5) Don’t attempt to bribe me.  I’m not kidding… for example once I got a handwritten request for a letter of recommendation along with $50.  This is not a good idea!

(Updated with two more in May 2013)

6) Before asking a post-doc or a project scientist for a letter of recommendation make sure that you don’t actually need one from the professor.

7) Don’t list me as a reference for anything without at least asking first.

The gurus of evolution predict the future #PLOSBiology

Nice commentary / viewpoint piece in PLOS Biology last months: PLOS Biology: Evolutionary Biology for the 21st Century

Citation.Jonathan Losos, Stevan J. Arnold, Gill Bejerano, E. D. Brodie III, David Hibbett, Hopi E. Hoekstra, David P. Mindell, Antónia Monteiro, Craig Moritz, H. Allen Orr, Dmitri A. Petrov, Susanne S. Renner, Robert E. Ricklefs, Pamela S. Soltis, Thomas L. Turner (2013) Evolutionary Biology for the 21st Century. PLoS Biol 11(1): e1001466. doi:10.1371/journal.pbio.1001466

They discuss issues like Biodiversity Informatics (see Figure to the left) and evolutionary applications like evolutionary medicine, food production, sustaining biodiversity, computational algorithms, and justice.  They also discuss issues like the oncoming onslaught of specimens and the need to link up with museums who have expertise in dealing with such issues.  Anyway – it is worth a look.  Not the most visionary of pieces ever but it has some concrete suggestions and predictions that will be of use.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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Labmeeting Feb, 19th 2013

This week’s lab meeting will be led by Phillip Seitzer from the Facciotti lab. The title for the talk is: “JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison”.
We will be meeting from 1:30 to 3:00pm in room 4202 at the Genome Center.

Worth a look (from arXiv): Robust estimation of microbial diversity in theory and in practice

I confess I do not have the time right now to delve into this in detail but this seems of interest: Robust estimation of microbial diversity in theory and in practice. From Bart Haegeman, Jerome Hamelin, John Moriarty, Peter Neal, Jonathan Dushoff and Joshua S. Weitz (full disclosure -I am friends and co-author with some of the authors here).

Abstract: Quantifying diversity is of central importance for the study of struc- ture, function and evolution of microbial communities. The estima- tion of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably es- timate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in compar- ing species richness estimates by applying Chao’s estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (“Hill diversities”), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao’s estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.

It is in press in ISME and freely available at arXiv.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Psyched: have rescued old MobileMe and other websites after Apple annoyingly cancelled them by posting to Dropbox

A few years ago I used to post many things for the Web through Apple’s Mobile Me service.  Annoyingly, Apple ended up treating this like they treat connectors and plugs for their phones and Macs.  They just decided to move their online system to iCloud and deleted all the old websites through Mobile Me.  Which left me in a lurch.  And then I forgot about it.  But I have been rediscovering how annoying this is since I had a lot of information out there on old papers and projects and now it is gone from the interwebs.  So I have ben trying to re-share all of this stuff.

One way has ben to post data from old papers to Figshare.  See for example:

But I also had all sorts of website related material that is annoyingly gone.  And yesterday I discovered at least a simple solution to this.  I can put all my old websites in my Dropbox public folder and share the link to those files with others and they work pretty well.

See for example my re-releasing of some of my April 1 and other joke websites:

 Also – I have reposted some of the my old websites

I have always been into sharing scientific information on the web since, well, the web came out.  And I am going to dig around for other old websites to post them via Dropbox.  If anyone knows an easy way to upload / convert an old website into WordPress, I suppose I could load in all the old pages into my current wordpress site, but this was a much easier temporary solution.  Still annoyed with Apple but glad Dropbox allows a simple solution.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

Soliciting opinions on paper "A congruent phylogenomic signal places eukaryotes within the Archaea"

Been reading this paper which I posted about to Twitter recently: A congruent phylogenomic signal places eukaryotes within the Archaea.  It is very interesting.  Not sure what to make of it though.  So – in contrast to my normal ways of putting my ideas out there first and asking for / hoping for comment I thought – let’s mix things up.  So – I am soliciting comments from people BEFORE I write down my comments.  Any ideas / thoughts / comments would be welcome.

Full citation:

Proc Biol Sci. 2012 Dec 22;279(1749):4870-9. doi: 10.1098/rspb.2012.1795. Epub 2012 Oct 24.
A congruent phylogenomic signal places eukaryotes within the Archaea.
Williams TA, Foster PG, Nye TM, Cox CJ, Embley TM.

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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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My new microbial art for my office: salt evaporation ponds and goethermal spring stamps

Thanks to Russell Neches in my lab I found out about the Earthscapes series stamps from the US Postal Service.  Two of the stamps feature microbial ecosystems and I ordered framed, enlarged versions of the photos for my office.

They are available at the links below:

Go microbes.
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This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

PLoSOne paper: Parallel polymorphisms for pepper population phylogenetics, from #UCDavis, not #Pepperspray

Interesting new paper from colleagues at UC Davis: PLOS ONE: Characterization of Capsicum annuum Genetic Diversity and Population Structure Based on Parallel Polymorphism Discovery with a 30K Unigene Pepper GeneChip.

Press release is here: http://www.news.ucdavis.edu/search/news_detail.lasso?id=10497

Good to see something on peppers from UC Davis not about spraying.

——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

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