iEVOBIO Coming soon (6/20-21): Metagenomics, Biodiversity, Barcoding, Data Integration, and more

Last year, iEVOBIO was a fun, interesting meeting for many reasons (not the least of which is that I was the keynote speaker).  If you want to learn more about last years meeting check out my blog post: Summary of #iEVOBIO Day 1 #evolution #phylogenetics #informatics #opensource

But I note, that meeting was so, well, last year.  This year, the meeting is focusing on metagenomics, barcoding and biodiversity as well as data integration (see the meeting website for more information: iEvoBio: Home).  From the website:

Wanted: Sample collections for the Earth Microbiome Project (EMP); help make an open Field Guide to the Microbes

The Earth Microbiome Project (EMP) is "a systematic attempt to characterize the global microbial taxonomic and functional diversity".  A little more detail is provided on the project website:

The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information.

This project is certainly incredibly ambitious.  But hey, why not aim high?  The project is being coordinated by Jack Gilbert, Folker Meyer, and Rick Stevens from Argonne National Lab and the University of Chicago as well as Janet Jansson from Lawrence Berkeley National Lab and Rob Knight from U. Colorado Boulder. 

I note I am not unbiased here as I am one of the members of the EMP Steering Committee (others on the Committee include Jed Fuhrman, Janet Jansson, and Rob Knight).  

If you want to learn a bit more about the origins of the project, read this paper which is a report from a meeting where the idea came together as well as a follow up paper. 

Anyway, the reason I am writing this post is that the EMP is looking for collaborators and participants.  In particular we are hoping to line up lots of large sample collections that could be included in future analyses.  Currently a pilot project is being done on ~10,000 samples.  These will be characterized in a variety of ways including collection of metadata and also generation of sequence information for DNA from the samples (including both rDNA and metagenomic sequencing).  But the EMP wants more - much more.  So the EMP is recruiting anyone who either currently has, or could possibly collect, large collections of samples for microbial characterization along with rich contextual data about the samples.  The contextual data would ideally include as much information about the physical, chemical and biological parameters found at the time of sampling as possible. These parameters include, but are not limited to, nutrient concentrations, temperature, salinity, porosity, moisture content, time of day, latitude and longitude, depth below surface, elevation, pH, etc.

Lawrence Lessig on Copyright "The architecture of access to scientific knowledge" #CERN

Not much to say other than that Lawrence Lessig is worth listening to.


The Architecture of Access to Scientific Knowledge from lessig on Vimeo.
Lecture at CERN, Geneva, Switzerland, 18 April 2011: A new talk about open access to academic or scientific information, with a bit of commentary about YouTube Copyright School.

Hat tip to Russell Neches for pointing this video out to me ...

The @nytimes missed a great chance to suggest what astronauts can do as NASA changes: go deep, into the ocean that is

I just got home from a day in the East Bay with family and read with great interest the above the fold story in the New York Times about NASA Astronauts looking for something else to do these days: With Flights Winding Down, NASA Astronauts Seek New Opportunities. While I for one wish we would keep sending people into space (well, that is, if they want to go), I think if space trips are cut back for some time there is something that the astronauts could do in the meantime which would be really really valuable. They could work to explore more of Earth, especially the oceans. Having just come back from a trip to USC's Wrigley Marine Ctr on Catalina Island where I met Chris Welsh and Loretta Whitesides, who are involved in the Virgin Oceanic deep-sea exploration project, I find it surprising that the New York Times article did not mention at all the need for more people to explore the depths of the oceans. Sure, it may not be quite as glamorous as space travel, but it is both difficult and very interesting. I do not personally think that space exploration and ocean exploration are mutually exclusive - we need to do both. But if there is a lull in space exploration for some time and people are looking for something to do - I would suggest they look down. Deep down. And while I am at it - I think the government should greatly expand deep sea exploration programs so we can learn as much about the oceans as we know about space.

A "work" trip to Catalina Island: USC, Wrigley, C-DEBI, dark energy biosphere, Virgin Oceanic, Deep Five, & more

Panorama of Catalina Island

Well, the last few days have been completely eye opening for me. I have been on a little trip to the USC Wrigley Marine Science Center near the town of Two Harbors on Santa Catalina Island. Alas, this has not been a vacation. This has been work trip. I was invited a bit ago to come to a workshop here by Bill Nelson, a friend and colleague of mine I used to work with at The Institute for Genomic Research (TIGR). Bill is part of a project called the Center for Dark Energy Biosphere Investigations (C-DEBI). The workshop he invited me to was to discuss evolutionary studies as part of this project.

I note this is a general post about the trip - I will post more about the individual science topics including C-DEBI and Virgin Oceanic later.

As is usual, I did not fully commit to going to the workshop immediately and I dragged out committing for a very long time (driving Bill I am crazy I am sure).  But eventually I accepted and then kept flip-flopping on exactly when I would go, but eventually settled on dates too.

What is C-DEBI:

When Bill first invited me to this workshop, I had no clue what this C-DEBI project was.  And Bill must have assumed I knew because he did not provide any detail about what C-DEBI was.  So of course, that is what that Google thing is for.  And what I found was quite intriguing:

A simple description comes from their web site:

Welcome to the Center for Dark Energy Biosphere Investigations (C-DEBI), a National Science Foundation (NSF)-funded Science and Technology Center on the deep biosphere. Our mission is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins. We are a multi-institutional distributed center establishing the intellectual, educational, technological, cyber-infrastructural and collaborative framework needed for transformative experimental and exploratory research on the subseafloor biosphere.

Compilation of links about my brother Michael's story on Amazon's $23million book about flies

Since I think it is pretty cool, I am compiling links to news stories and blog posts about my brother's recent posting on his "It is not junk" blog about Amazon’s $23,698,655.93 book about flies.  Basically, he tracked some sort of automated computer pricing feedback loop between Amazon and another site that led eventually to a very very very very high price for a book about Drosophila.

And the post has now been picked up by all sorts of places.  So I am compiling a list of some of the stories here.

• James Fallows from the Atlantic "Want to see how crazy a bot-run market can be?"
• How We’ll Know When the Machines are Taking Over (by David Post, from the Volokh Conspiracy"
• Gizmodo: How a Book Accidentally Gets Priced at $23 Million on Amazon ...
• Gawker: Why Amazon Charged $23698655.93 for a Genetics Textbook - Gawker
• Seattle Post: The perils of automatic pricing on Amazon
• CNN: Amazon seller lists book at $23698655.93 -- plus shipping
• MSNBC: Book about flies costs $23.7 million on Amazon
• PC Mag: Amazon Algorithm Price War Leads to $23.6-Million-Dollar Book Listing
• La estrambótica historia del libro más caro de Amazon
• Роботы-книготорговцы оценили книгу в $24 млн
• Boek voor ruim 1 miljoen euro
• 一本生物学著作是如何在Amazon网店上卖到200万美元的
• Algorithmes économiques fous
• Huff Post: Amazon's $23698655.93 Book About Flies (SCREENSHOT)
• Wall St. Journal Blog: For Sale: The Making of a Fly, Only $23698655.93 (Plus $3.99 Shipping)

Yolo Bypass area to reopen Saturday

FYI

The Sacramento Bee : Yolo Bypass area to reopen Saturday

Wanted - best/funniest/strangest Acknowledgements sections from papers

I was reading a paper recently which had an awkward acknowledgements sections and I thought it might be fun to make a collection of papers with unusual such sections. So I am putting out a call here - do people know any good examples of strange or funny or exceptionally long or otherwise interesting acknowledgement sections from papers? Please post them here or on twitter/friendfeed and I will eventually post a list

Amazon’s $23,698,655.93 book about flies

OK I realize I am not objective here since this is from my brother, Michael Eisen, but his post about a book on Drosophila that is for sale for > $23 million is fascinating. See
Amazon’s $23,698,655.93 book about flies.

Microbes do some strange things: splitting and permuting tRNAs

Figure 1 - Predicted secondary structures of trans-spliced and permuted precursor tRNAs

(a) Mature tRNAAsp(GUC) in A. pernix and T. aggregans are formed by joining the 5′ half and the 3′ half at position 37/38 after splicing at the bulge-helix-bulge (BHB) motif. (b) The 5′ half and the 3′ half of trans-spliced tRNALys(CUU) in S. hellenicus and S. marinus join at position 30/31, same as the previously identified split tRNALys(CUU) in N. equitans [5]. (c) Circularized permuted tRNAiMet(CAU) and tRNATyr(GUA) in T. pendens have the 3′ half located upstream of the 5′ half separated by intervening sequences represented in green. The two fragments join at position 59/60, same as the T-Ψ-C loop permuted tRNAs in the red alga C. merolae [9]. Pre-tRNAAla(UGC) in C. merolae is shown for comparison. 5′ half of tRNA transcripts are represented in blue, the 3′ halves in orange. Black arrows indicate positions of splicing. Anticodons are boxed in light blue.

I was woefully unaware of some of the tRNA shenanigans going on in microbes until reading this paper: Genome Biology | Abstract | Discovery of permuted and recently split transfer RNAs in Archaea from Patricia Chan, Aaron Cozen and Todd Lowe. Life is pretty weird and wacky sometimes, even in components of cells that are considered "core" parts of the machinery of life. Go figure. It is worth a read ...

Hospital acquired infections - NY Times raising level of attention w/ editorial

Just a quick one here.  The New York Times had an editorial Sunday on hospital acquired infections: Hospitals Shouldn't Make You Sicker.  I couldn't agree more.  The Times discussed some recent studies published in the New England Journal of Medicine as well as plans by the Obama Administration to fund some work in this area.  It would be good I note if some of the funding focused not on infections per se but on the microbial ecology of hospitals, which we know very little about.  Focusing just on hand washing and transmission of nasty pathogens is not enough. 

Boston, Bioinformatics & Ben Franklin Award wrap up from #BioIT11

Photo by Mark Gabrenya

Well, just got back from Boston where I went to the BioIT World convention to pick up the "Benjamin Franklin Award" for contributions to Open Science from Bioinformatics.Org.  A quick round up of the trip:

Interesting PLoS One paper on local assembly from short reads by "tagging" DNA via restriction enzymes

Quick one here. Interesting paper from Paul Etter et al. from Eric Johnson's lab at U. Oregon in PLoS ONE: PLoS ONE: Local De Novo Assembly of RAD Paired-End Contigs Using Short Sequencing Reads

Here is the abstract:

"Despite the power of massively parallel sequencing platforms, a drawback is the short length of the sequence reads produced. We demonstrate that short reads can be locally assembled into longer contigs using paired-end sequencing of restriction-site associatedDNA (RAD-PE) fragments. We use this RAD-PE contig approach to identify single nucleotide polymorphisms (SNPs) and determine haplotype structure in threespine stickleback and to sequence E. coli and stickleback genomic DNA with overlapping contigs of several hundred nucleotides. We also demonstrate that adding a circularization step allows the local assembly of contigs up to 5 kilobases (kb) in length. The ease of assembly and accuracy of the individual contigs produced from each RAD site sequence suggests RAD-PE sequencing is a useful way to convert genome-wide short reads into individually-assembled sequences hundreds or thousands of nucleotides long."

Hmm - How did I miss this paper discussing RFAM, Wikipedia & community annotation #cool

Edits for Wikipedia articles on RNA families. The cumulative number of edits since 1st January 2007 for the 733 Wikipedia articles that are associated with Rfam entries is shown in black. The total number of edits that were reverted or labeled as vandalism is shown in red. To mid-2010, there were just 106 of these. However, some reverted edits may have been well-intentioned but were deemed inappropriate for Wikipedia. From http://nar.oxfordjournals.org/content/39/suppl_1/D141.long

Very interesting discussion in this paper on Rfam about community annotation: Rfam: Wikipedia, clans and the “decimal” release. In the paper the authors (inlcuding Alex Bateman, Sean Eddy, Paul Gardner and others) discuss the use of Wikipedia for Community Annotation of biological databases. They report:

Given our positive experiences, we can highly recommend other curation efforts turning to Wikipedia for their annotation

I am not sure how I missed this paper when it came out recently.  But it is definitely worth a look.  The last line hints at future developments

We look forward to working with the wider community to develop these new tools and techniques.

It seems that they have bought into the Wikipedia based annotation system as having enormous potential.  I generally agree though I am not sure how this is best done.   

Nice review/commentary on challenges in phylogenomic analysis in PLoS Bio by Philippe et al. #fb

This one is definitely worth a read for phylogeneticists and phylogenomicists (is that a word?) out there: PLoS Biology: Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough. Philippe et al. discuss some important issues in using genomes to infer phylogenies of species in this commentary/review paper.  They discuss in particular some recent studies of animal evolution but they cover a lot of useful ground here and include a good review of terminology and some of the basic issues at play.  I am personally going to have to read it in more detail to help deal with some of the issues in our recent study of novel sequences in metagenomic data.

Richard Branson getting into microbial diversity (a little bit)

Just a quick one here. For those interested in the deep-sea and microbial diversity you might want to check out this article: Richard Branson launches Virgin Oceanic: deep-sea exploring submarines - Boing Boing. It discusses how Branson will be working with Katrina Edwards, Doug Bartlett and others to study microbial diversity in the deep sea as a component of his project to make dives in his personal submarine.

Request for #UCDavis affiliates to help Japan from Chancellor Katehi

Just got this email from the Chancellor of UC Davis Linda Katehi and thought I would share

To the UC Davis Community,

The crisis and devastation in Japan following the March 11 earthquake and tsunami continue, and as with any natural disaster of this magnitude, healing will be neither simple nor immediate. Our thoughts and hearts are with the Japanese people and with their many loved ones who are teaching and learning on our campus and in our community.

Inevitably, the disaster will fall from the headlines, but the UC Davis community will not look away. We will continue to reach out in comfort and with assistance to honor those who are hurting and in respect for our deep connection to Japan. Nearly 200 Japanese residents are currently studying at UC Davis, and this year, we have more than 50 Japanese faculty members visiting our campus. Our students were also at five universities in Japan at the time of the disaster, including in areas with heavy damage, and we are grateful that all are safe.

There is still much to do, and you can help, too. Please see this link for a variety of charities aiding the Japanese people:

http://www.charitynavigator.org/index.cfm?bay=content.view&cpid=1221

UC Davis has a compassionate spirit, and I thank you for proving that once again.

Linda P.B. Katehi
Chancellor

- Posted using BlogPress from my iPad

My twitter wrap up of the Joint Genome Institute User Meeting #JGIUM

Off to another meeting so don't have time to write up details of the JGI User Meeting that just ended.  But I am posting my tweets and some related tweets here.  Also, apparently videos of the talks will be available soon. Will try to clean up the style of the posts ASAP but on the road ...

Why #badomics words can also be very good: a case in study with museomics #JGIUM

Well, my snarky blog style with some of my awards comes with some risks. Today I experienced one of them. Stephan Schuster gave me some serious major grief over a post I wrote a few years ago. In the post I gave him an award for "Worst new omics word" for the word museomics. I gave this award because, well, I don't like the word. I stand by my complaints about the word. But Stephan did highlight ( in his comments to me in the back of the room at the JGI User Meeting) that the word has been remarkably useful at getting money and attention for museum based genomics studies.

The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb

Well, here goes.

This is a post about a paper that has been a long long time coming. Today, a paper of mine is being published in PLoS One. The paper is titled "Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees" and is available at http://dx.plos.org/10.1371/journal.pone.0018011. (or if that link does not work you can get a copy here). This paper represents something I started a long time ago and I am going to try to describe the story behind the paper here.

I note - we are not doing a press release for the paper, for a few reasons. But one of them is that, well, I am starting to hate press releases. So I guess this is kind of my press release. But this will be a bit longer than most press releases. I note - my key fear here is that somehow in my communications with the press or in our text in the paper or in this post I will overstate our findings. Here is the punchline - we found some very phylogenetically novel forms of phylogenetic marker genes in metagenomic data. We do not have a conclusive explanation for the origin of these sequences. They may be from novel viruses. The They may be ancient paralogs of the marker genes. Or they may be from a new branch of cellular organisms in the tree of life, distinct from bacteria, archaea or eukaryotes. I think most likely they are from novel viruses. But we just don't know.

UPDATE: Am posting some links here to news stories/blogs about our paper

• Glimpses of the Fourth Domain? by Carl Zimmer at his always stellar "The Loom" 
• Biology's 'dark matter' hints at fourth domain of life by Colin Barras at the New Scientist 
• 21st century science publishing will be multilevel and multimedia by PZ Myers 
• German Radio Story
• Chinese news report
• PLoS One Blog Pick of the Month for March 2011 by Brian Mossop 
• Brazilian news story from @info
• There might be at least one other, previously hidden, domain of life by Francis Martin 
• Pronađen potpuno novi "domen" života
• Craig Venter's study of marine DNA finds new branches on the tree ... Telegraph article #1 
• Scientist finds a whole new 'domain' of life - Telegraph article #2 
• Scientist stumbles on new class of living things - Zee News 
• A new domain of life: Plenty more bugs in the sea from The Economist 
• DNA Analysis Hints At a Fourth Domain of Life - Slashdot
• Check out the video story from Newsy.Com

I know - Ego Blogging is so 2010 - But I won. I won. I won. (The Ben Franklin Award ...)

OK so the title is a bit much. But I am really happy that I won this years Benjamin Franklin Award, given out by the Bioinformatics Organization. For more on this see ...

• UC Davis’ Jonathan Eisen Wins 2011 Benjamin Franklin Award - Bio-IT World
• BioMed Central Blog : Jonathan Eisen: 2011 Benjamin Franklin Laureate
• Jonathan Eisen named 2011 Benjamin Franklin Laureate - DOE Joint ...

I found out a few days ago and am rearranging some things to go to Boston April 13 for the award ceremony at the Bio-IT World Conference and Expo.  

From the Bioinformatics Organization web site:

Benjamin Franklin (1706-1790) was one of the most remarkable men of his time. Scientist, inventor, statesman, he freely and openly shared his ideas and refused to patent his inventions. It is the opinion of the founders of the Bioinformatics Organization, Inc. that he embodied the best traits of a scientist, and we seek to honor those who share these virtues

The Benjamin Franklin Award for Open Access in the Life Sciences is a humanitarian/bioethics award presented annually by this organization to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences.

J. Craig Venter Institute, UCSD, Beyond the PDF, #UCDavis leadership, all in one trip

A wee bit late but thought I would give an update on a recent trip.  In January I went on a little trip to Southern California.  The trip started with a simple plan - Susan Golden invited me to give a talk at UCSD.  After my usual complications in planning, I finally agreed to a date (1/19) after finding out the Phil Bourne, Editor in Chief of PLoS Computational Biology was helping organize a meeting starting 1/19 entitled "Beyond the PDF" to discuss the future of scientific publishing.  So this seemed like a perfect mix.  Go down to UCSD for one thing and stay for another.  Short flight and easy to change.  Seemed ideal

Of course I had to make it more complex so I contacted some friends at the J. Craig Venter Institute to see if they would be around and unfortunately my friend Jeff Hoffman was not going to be around.  But he connected me to Craig Venter and his wife Heather Kowalski and though what I really wanted was to just see if they would be around for a visit or dinner - I ended up getting roped into giving a talk there on the 18th.

Please help keep the pressure on Nature Publishing Group to restore free access to genome papers #opengate

Well, I realize of course some things take time, but I cannot imagine it is that hard to restore free access to all papers reporting genome sequence data.  Nature had promised to do this when many papers were published but recently I noticed that this was not being done.  For some background see:

• Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess
• Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail
• On science blogs this week: Evolution | ScienceWriters (www.nasw.org)
• The Tree of Life: Nature's publishing machine really wants you to pay for stuff even if it is supposed to be free.

So today I browsed around to see if access had been restored to these genome papers.  And alas they had not for many. For example, the Plasmodium genome paper is not available

Upcoming conference: DOE-JGI User Meeting: Energy, Genomes, Environment, Microbes, Trees and more ...

Just got this email I thought would be useful to share (with a few edits)

Still time to register for JGI "Genomics of Energy & Environment" 6th Annual User Meeting

The DOE Joint Genome Institute (JGI) hosts the "Genomics of Energy & Environment" 6th Annual User Meeting (March 22-24, 2011):
Here

Explore the agenda of presentations, poster sessions, and valuable hands-on workshops (see below).

Interesting take (though not completely convincing) take on NEJM farm microbe story

There is an interesting take in Forbes on a recent study NEJM on microbes and people growing up on farms.

Not totally convinced of the opinion of the writer, but with a look.


- Posted using BlogPress from my iPhone

Calling for Nature Publishing Group to return all money charged for articles that were supposed to be free #OpenAccess

Well, in case you did not see, yesterday I got really pissed off at Nature Publishing Group.  Short summary - many articles of mine that were supposed to be freely available on their journal sites were not.  For more information see

• Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail
• The Tree of Life: Nature's publishing machine really wants you to pay for stuff even if it is supposed to be free.
• On science blogs this week: Evolution | ScienceWriters (www.nasw.org)

People from Nature Publishing Group have responded quite quickly saying they will look into this and try to fix it and indeed they have fixed many if not all of the mistakes in accessibility I found yesterday.  Glad they responded so quickly.  However, their response raises quite a few questions.  Like "what happened?" - as in - why did access get closed off?  And why were they charging to for article use when they should not have been?

It would be good for Nature to publish / post a full description of what went wrong.  And perhaps they will.  Apparently, it was just a glitch in the system.  Whatever the cause however, almost certainly some people paid for access for articles that were supposed to be freely available.  I am calling on Nature here to audit their systems and return all money that was paid for such access.

Today is a day to be annoyed with Nature (Publishing Group that is) #NatureFail

Yuck.  Am getting really pissed off right now.  It is 1:30 AM.  I am tired.  And I am now angry.  I was writing a post about a recent trip, and wanted to link to an article I was a coauthor on.  The article was the paper on sequencing and analysis of the genome of Arabidopsis thaliana.  So I googled "Arabidopsis Genome Initiative" and found the link to the paper at Nature.  And much to my surprise I found this waiting for me:

Why is that a surprise?  Because the genome paper is supposed to be freely available to all forever, under a policy Nature developed for papers reporting new genome sequence data.  I am tired or I would write more about the history of this.  But another time.

So then I looked for other genome papers I have published in Nature.  And so I looked for the Plasmodium genome paper.  And I got this:

Grand.  That one was supposed to be free forever too.

And so I looked at many others.  And for most, I got the same thing.  Not freely available.  If I were not at home, I would not have noticed this because I have access at work.  And I could get access at home by setting up the UC Davis library VPN system.  But fortunately I do not do that or I would not have discovered that Nature, not for the first time mind you, has turned articles that were supposed to be freely available forever into charge for access articles.  I know.  I know.  This is probably just some glitch in their system.  They really do seem committed to trying to make these available.  But clearly, the system either does not work well.  Or they are not committed to it.  Either way this is really annoying.  In some cases, the papers were sold to communities of scientists in part with the "These will be freely available to all forever" line as part of the sell.  I am deeply worried about my recent Genomic Encyclopedia paper which is also supposed to be freely available forever.  Right now it still is, which is good.  But how long will that last?  And I note, though Nature people have said they would try and fix it, Nature still incorrectly claims Copyright to that article on the PDF.  Personally, I like most of the people I know at Nature Publishing Group and like many of the things NPG does.  But this is getting really annoying.  And it just goes to show - the ONLY way to go it seems is full, complete Open Access which the journals cannot magically then take away.

Norman R. Pace visit to #UCDavis; discussing microbiology of the built environment #microBEnet

Norman R. Pace, from UC Boulder, gave a talk at UC Davis last week about microbial diversity.  In his talk he discussed some of his recent Sloan Foundation funded work on “microbiology of the built environment” including studies of shower heads, indoor swimming pools, water supplies, and hospitals.

Pace is one of the pioneers of DNA based studies of microbes in the environment.  His initial work on studies of ribosomal RNA from uncultured organisms (started more than 20 years ago) helped launch the field.  For more information on his work see his lab page here

If you are interested in the microbes that are found in showerheads, his PNAS paper on this (which can be found here) on this from 2 years ago got a lot of press.  See for example this Science Friday
and this New York Times article by Nicholas Wade.

Pace was at UC Davis as part of the Storer Major Issues in Modern Biology Lecture Series.

I note, I have written about Pace before a few times including this:
Here's hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

I note we have a new project as part of this Sloan program to facilitate communication and networking and sharing information as part of this project.  My lab is creating something called "microBEnet" - the microbiology of the built environment network.  We are just getting our real site up and running.  For now you can find out some information at a temporary page http://microbenet.blogspot.com/

Arsenic revisited: discussing arsenic story with a #UCDavis biology writing class next week

Well, this could be fun. Next week I am making a guest appearance in a Writing class at UC Davis. The class focuses on writing in Biology and the instructor invited me to come in as a guest to coordinate a discussion of the arsenic paper and the coverage of it.

When the instructor asked for reading assignments I said they should read:

• The paper: A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus 
• Any one (or more) of the following
• Ed Yong's post
• Rosie Redfield's critique
• Carl Zimmer's wrap up

I think I probably should have suggested they read Zimmer's excellent full write up here.  Going to suggest that now but may be too late.

Any other pointers to good write ups of what has happened since the first week after the paper would be appreciated.

-------------
Some suggestions coming in from twitter:

• BoraZ Bora Zivkovic 

  @ 
  @phylogenomics I like this meta-post http://bit.ly/gUW0R8 also more to choose from here: http://bit.ly/dNlorL

The Microbe Project - A Portal to Federal Efforts in Microbial Research #microBEnet

For those interested in what the US Government is doing in areas relating to microbiology, there is a useful site to check out called "The Microbe Project". The goal of this project is to "to maximize the opportunities offered by genome-enabled microbial science to benefit science and society, through coordinated interagency efforts to promote research, infrastructure development, education and outreach." There is a lot of information there on different agencies and their funding opportunities.

A bit upset by @NYTimes article on twitter>>blogging so I posted 140 characters to my blog

A recent NYTimes article discusses how twitter/facebook are on rise vs. blogs-the key isn't to pick one over others but to use each smartly.

Some quick notes on mini trip to DOE-JGI & UCSF

Well, just got back from a very brief trip to give a talk at UCSF.  I was invited by graduate students via the following email message

The students in the DeRisi Lab at UCSF are thrilled to invite you as our selection for the California Institute for Quantitative Biosciences (QB3) and Integrative Program in Quantitative Biology (iPQB) Invitational Speaker Series!  This is a new type of speaker series at UCSF where students from a laboratory directly nominate and invite speakers from outside UCSF to deliver lectures about cutting-edge topics in quantitative biology.  All nominations are discussed by a QB3/iPQB student committee, and a speaker list is compiled from many outstanding nominations.  The invited speakers are scientists who gathered especially strong support from their nominating lab and the QB3/iPQB student committee, and who have an outstanding record in delivering exciting research talks grounded in quantitative methods. As our selected nominee, your travel, lodging and food expenses will be covered by funds from QB3/iPQB.

It was impossible to say no - I am always thrilled to be invited by student groups.  It took a bit to coordinate when I would come (I am notoriously bad at planning and answering such invitations).  But eventually, with a little prodding, I answered and we picked a date. I of course then asked to change the date and we settled on February 17.

Some things to read in light of reported human DNA in bacterial genomes vs. contamination

Well, there is an interesting few papers out there relating to human DNA and whether or not there have been some recent lateral transfers of it into microbial genomes.  See for example

• this paper in mBio that suggests there has been lateral transfer of LINE elements from humans to Neisseria species
• but then see this paper suggesting massive contamination of sequence databases with LINE elements (PLoS One paper on contamination)

So what is going on?  Not clear.  If you want more detail about these papers I suggest reading one of the following

• Mark Pallen: Human DNA in bacterial genomes? Yes? No? Maybe?
• Ed Yong: Gonorrhea has picked up human DNA (and that’s just the beginning)
• Hannah Waters: Contaminated genomes
• Hannah Waters: Transitioning into “real” science journalism

There were other stories out there ... but since Hannah and Ed interviewed me, I am a bit biased about which ones are worth reading.  Here are some others to read though

• Gonorrhea Steals DNA From Humans
• Scientists find human DNA in gonorrhea bacteria
• Gonorrhea has picked up human DNA

Personally, I am a bit skeptical of the LGT claim because most of the evidence they present relies on amplification (ie PCR).  But without getting into too many of the details myself I thought I would just post some background reading connected to some of my past work in this area for anyone interested in this type of thing

Information about claim of HGT into humans from bacteria that was in the Lander et al Human Genome paper:

• Link Between Human Genes and Bacteria Is Hotly Debated by Rival ...
• Salzberg et al. 2001. No bacterial to human HGT. Science.

One use of finishing genomes: helping rule out contamination

• You get what you pay for

A short story I wrote in 1998 about, well, contamination in genome databases

• HYG101

My colleagues assembling of nearly complete bacterial genomes from the raw sequence reads from fly genome projects

• Three Bacterial Genomes Found Lurking Inside Recently Sequenced ...

Complete mitochondrial genome(s) found in Chromosome II of Arabidopsis.  Was very difficult to sort out which reads came from nuclear genome and which from mitochondria

• Lin et al 1999. Arabidopsis chromosome II. Nature.

End of Sequence Read Archive (SRA) - some quick notes

Well, it seems that the Sequence Read Archive (SRA) is going away sometime in the near future.  I posted about the SRA last week and in the discussion someone posted an email message that supposedly was from David Lipman of the NCBI saying that the SRA is going to be closing.   This has now been confirmed and I thought I would just post some links discussing this

• SRA Home reports that NCBI will not support the SRA. See here also. 
• EMBL EBI says it will continue to support the SRA
• Unpopular genomic database faces budget axe
• Short Read Archive Canned - SEQanswers
• Short Read Archive Canned
• NCBI to End Support for Sequence Read Archive as Federal Purse ...
• Confirmed | The Daily Scan | GenomeWeb

Open Access Pioneer Award: George Garrity for his work on Standards in Genomic Sciences journal

A few days ago I got a message that made a big impact on my publication record in PubMed Central.  My number of publications there went up by 85 in one fell swoop (see below for the list ...).  Did I publish 85 new papers yesterday?  No.  But a journal in which I have been a co-author on many papers recently finally showed up in Pubmed Central.  The journal is called Standards in Genomic Sciences.  The journal's scope is:

The goal of SIGS is to serve as an open-access, standards-supportive publication for rapid dissemination of concise genome and metagenome reports that comply with the emerging MIGS/MIMS standards, detailed standard operating procedures, meeting reports, reviews and commentaries, data policies, white papers and other gray literature that is relevant to genome sciences but currently absent from the scholarly literature.

Lots of jargon, I know.  But you can ignore that.  The reason I am writing here is that this journal is a place to publish what could be called "genome sequencing data reports."  These reports are a way for data producers to describe, in a formal manner, their sequencing project - and to share - in a formal manner - not only the data but also metadata about the organism(s) sequenced and the methods used.  As sequencing gets cheaper and easier, we need places for people to publish these types of "data papers" to both produce a citable unit with a DOI relating to the data, and to also share the details of the data production in a way that a simple Genbank entry does not.

One aspect of the papers in this "SIGS" journal is that they are being done in a way that is compliant with sets of standards for sharing metadata about the organism and the project.  I confess, when I first heard about these standards developments, I was bored almost to tears.  But now I realize that this is a very important aspect of getting the most out of genome data.  If people who sequence a genome not only release the sequence data, but also a table of information about the project, such as information about the organism (e.g., aerobic vs anaerobic, location of isolation) and about the data production (e.g., sequencing methods used) then people will be able to do high throughput analyses of these features.  Then we will not just be looking at sequence but also connecting these sequences to organismal features.  Right now that is very hard to do since genome data is rarely accompanied by machine usable information about the organism that has been sequenced.

Anyway - long story short - there will be a paper published in this journal for each genome being produced as part of the "Genomic Encyclopedia of Bacteria and Archaea" project that I have been coordinating at the DOE Joint Genome Institute in collaboration with the DSMZ.

Today I am writing to recognize the people connected to this movement - the people who created the standards, the people who created and run the journal, and the people writing papers for this journal.  All of them are to be commended for their vision and their dedication to openness.  Thus I am giving George Garrity the EIC of SIGS  my "Open Access Pioneer Award" for creating SIGS, making it an open access journal,  for keeping it running and for getting its papers into Pubmed Central and soon Pubmed.   Many others should be recognized too for their contribution to SIGS (see the whole list of founding members here).  I also should recognize Nikos Kyrpides from the DOE JGI who helped coordinate the writing and submission of these papers along with Hans Peter Klenk from the DSMZ.  Without them, these papers would never have gotten out there.  Plus I think some credit goes to Michigan State University and the Department of Energy which apparently are sponsors of SIGS


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Checking out Davis Life Magazine

Just a quick post here - haven't posted to my Davis blog in a while but have been looking at Davis Life Magazine and like it a lot. Worth a look for Davisites out there.

STAMPS: good course for those interested in molecular surveys of microbial diversity

This looks like a good course to take for those interested ion molecular studies of microbial diversity

STAMPS: Marine Biological Laboratory

Though I generally love NCBI, the Sequence/Short Read Archive (SRA) seems to have issues; what do others think?

Well, here goes. Hope to not get people from NCBI too pissed off here. Overall, I think NCBI is invaluable: GenBank. PubMed. PubMed Central (PMC) (well, I have some complaints about that but let's not get into those here -- I still like it), BLAST (Basic Local Alignment Search Tool) and a plethora of other tools, databases and resources. Generally, money well spent.

However, one database from NCBI is driving me a bit wacky these days. This is the Sequence Read Archive (SRA). Known to some as the "Short Read Archive" this database is supposedly for storing "sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Life Technologies AB SOLiD System® , Helicos Biosciences Heliscope®;, Complete Genomics®, and Pacific Biosciences SMRT®."

It certainly seems to be used for that function. But alas, storing sequence is not the only need here. Recovering sequence and making use of it is really the key. And this is the area I have been having trouble with (especially related to environmental studies like rRNA PCR and metagenomics). Rather than go on about my particular issues here (and thus possibly biasing the discussion too much), I am wondering what others think of the SRA? Usability? Ease of deposition? Ease of extraction? Missing features? Things it does or does not do well? Do we need a new system for environmental projects?

Any and all comments welcome here or on twitter or on Friendfeed or wherever. See Friendfeed stream below:

Here are some comments so far from twitter

• digitalbio Sandra Porter I agree. RT @phylogenomics: Though I generally love NCBI, the Sequence/Short Read Archive (SRA) seems to hav… (cont) http://deck.ly/~XM75A
• lswenson Luke Swenson @phylogenomics I was JUST trying to navigate the SRA! There's no help section to be found, and forget about depositing sequences!
• audyyy Davis-Richardson @phylogenomics I can never tell if my submission went through without emailing support. Also, no FASTQ support?
• cabbageRed Rich C .@phylogenomics I agree, the SRA doesn't seem to be the easiest repository to search with what I believe to be "typical" NGS queries

Is it time to refer to mitochondria as bacteria?

Any time a scientific article has in the summary a sentence like the one below, I am attracted to it:

"Here, I playfully explore the arguments for and against a phylogenetic fundamentalism that states that mitochondria are bacteria and should be given their own taxonomic family, the Mitochondriaceae."

So how could I not want to read this: Trends in Microbiology - Time to recognise that mitochondria are bacteria?:

Well, one reason is that it had been unavailable outside of the TIM paywall. However, the author, Mark Pallen, with a little prodding from me, managed to get the Editors to feature it as a "free" article on their website for at least some time. So everyone, download this paper and distribute it to as many as you can (legally). Oh, and read it, it is definitely worth a read.

In the article Pallen argues for giving mitochondria their own family w/in bacteria. I think that would be a good idea as they are really just a highly reduced form of bacteria. We give endosymbionts, even those with tiny genomes, their own groups. So why note organelles that are derived from bacteria? After all - phylogenetically they are bacteria.

Pallen even goes so far as to suggest rethinking of mitochondria as bacteria will help with efforts to engineer mitochondria in various ways. That is an interesting notion.

I suppose one could push this to an extreme position and argue that the nucleus and all the genes associated with it are really just a shell around a mitochondrial core. And then I guess all eukaryotes could be considered bacteria. But I do not want to confuse the issue too much here. Overall, I really really like this paper. I wish it were in an OA journal, but since it is free for now I think it is worth checking out. In the long run, it would be better (hint hint Mark Pallen) to publish such thought provoking pieces in places everyone can access ....

So I guess this paper, along with all the "microbiome" stuff means that humans are really just carrying vessels for bacteria.

Is it time to refer to mitochondria as bacteria?

Any time a scientific article has in the summary a sentence like the one below, I am attracted to it:

"Here, I playfully explore the arguments for and against a phylogenetic fundamentalism that states that mitochondria are bacteria and should be given their own taxonomic family, the Mitochondriaceae."