Guest post from Antarctica: Joe Grzymski (@grzymski) on "The Story Behind Nitrogen Cost-Minimization"

Well, this is getting really fun. I have been doing "The Story Behind the Paper" posts for my own papers for a while and recently opened this up to guest posts. And the one today is coming to us from the true wilds - Antarctica. Joe Grzymski (aka @grzymski on Twitter) is out there doing field work (yes, microbiologists have the best field sites ...). For more on the field project see the Desert Research Institute's "Mission Antarctica" site. Joe responded to my request for more guest posts and wrote up a really nice discussion of a recent open access paper of his from the ISME Journal. If anyone else is interesting in writing a guest post on an open access paper or an issue in open access, let me know ... without any further ado -- below is Joe's post

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I thoroughly enjoy reading Jonathan’s posts detailing – far beyond what can possibly be included in published papers – the who, what, where, when, why and how of science. The story behind the potential fourth domain of life article in PLOS ONE provides great detail about how science is done. After reading Matthew Hahn’s insightful history and commentary on his ortholog conjecture paper I was happy to reply to the request for more "stories" and am chiming in from Antarctica (where I am currently doing field research) to discuss the story behind our recent paper in ISME J, "The significance of nitrogen cost minimization in the proteomes of marine microorganisms". I hope it will provide another example of how a lot of science is lost in final, streamlined, published versions. Also, it is work that was largely done by an undergraduate and was vigorously and carefully reviewed – the improvements and expansion of ideas because of great reviewers highlights the best of the review process. What started out as a short two-page paper morphed into a larger piece of research – not things you can properly detail in a manuscript.

Story behind the paper: small RNAs in diatom (interview w/ Andrew Allen)

Here is another "Story behind the paper".  This one focuses on the following paper: Norden-Krichmar, T.M., Allen, A.E., Gaasterland, T., Hildebrand, M.  (2011) Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana. PLoS ONE 6(8): e22870. doi:10.1371/journal.pone.002870

I wrote some questions up for Andrew Allen, one of the authors.  I note I did this before my "new" system of inviting authors to write guest posts directly themselves.  Not sure which approach is better but guest posts are certainly easier for me so I will probably do that more.

1.     What is the history behind this work?  How did it start?  Why did you do it?

These studies on small RNA in diatoms are the result of collaboration between my group at the J. Craig Venter Institute (JCVI) and Mark Hildebrand’s group at Scripps Institute of Oceanography (SIO). Each lab group is interested in the ecology, evolution, and physiology of diatoms. More specifically we would like to know more about how diatoms sense and respond to environmental signals. Therefore we are interested in mechanisms of transcriptional regulation in diatoms and other microalgae. An earlier study suggested that cytosine methylation is an important mechanism for repression of transcriptional activity of retrotransposons, and associated mobility, in diatoms. In response to stress, nitrogen stress especially, long terminal repeat retrotransposons (LTR-RTs) display decreased levels of cytosine methylation (hypomethylation) and elevated transcriptional activity.

Blast from the past: video of a talk I gave in 2006 #metagenomics

Just re-found this video and posted it to youtube.  It is from a talk I gave in 2006 at the first "International Metagenomics Meeting" in 2006.

I think one may still be able to view videos from the CalIT2/UCSD page here. But I thought it might be better to have this talk on YouTube than at the CalIT site so I posted it ... hope they don't sue me.

Note - I wrote a blog post about the meeting here:
The Tree of Life: Metagenomics 2006

Once again, using nice "Tree of Life" video from Yale Peabody Museum for #UCDavis Course

I think I have written about this before but here goes again.  There is a nice "Tree of Life" video from the Peabody Museum that is now on Youtube and also their web site that is definitely worth a look for people interested in phylogenetics and the tree of life. It includes Michael Donoghue, Scott Edwards, David Hillis, Tandy Warnow and Charles Davis.

Crosspost from http://microbe.net: A very misleading “bacteria in buildings” advertisement presented as “news”

Am crossposting this from http://microbe.net where I posted it earlier. See original post here: A very misleading “bacteria in buildings” advertisement presented as “news”

Wow this “story” (which is really an ad) is just so incredibly bad I do not know what to say: Dangerous Bacteria Isolated in Healthcare HVAC Evaporator Coils. I do not even know where to begin with criticism so I will just go step by step through some of the advertisement.

1. Title: Dangerous Bacteria Isolated in Healthcare HVAC Evaporator Coils

There is no evidence that the bacteria being looked at here are dangerous.

2. First sentence ”A recent study suggests that doctors may want to monitor the environmental condition of their air conditioners evaporator coil before surgery to help prevent the spread of bacterial infections”

No evidence is presented anywhere that monitoring AC coils has any even remote potential value here.

3. Second sentence: Dr. Rajiv Sahay, Laboratory Director at Environmental Diagnostics Laboratory (EDLab) and his colleagues sampled evaporator coils in healthcare air handling systems and isolated Pseudomonas aeruginosa a known noscocomial pathogen.

Well, Pseudomonas aeruginosa is indeed a known pathogen.  However, there is no evidence presented that all the things they detect are indeed pathogenic/virulent.  In fact, later in the article they report their results as being for “Pseudomonas sp” which suggests that their typing was very broad.  It is very possible that many of the cells they detected are not pathogenic.

4. Ignore the middle part.  It is just saying that Pseudomonas aeruginosa can be nasty in compromised patients.

5. They then go on to discuss their study more “In the study, over 560,000 colony forming units (CFU)/gram of Pseudomonas sp were isolated from deep within the evaporator coil system.”

What study?  No data is presented.  No methods.  No results.  Nothing.

6. They then say “Potential aerosolization of these micro-organisms from the infested coil is immense due to a discharge of air stream with 6 miles/hours (commonly observed) across the evaporator coils”

Not so sure about that.  Would have been much better to study ACTUAL aerosolization.

7. Then we find out that they person who conducted the study Dr. Rajiv Sahay is also the one selling the cleaning service to clean your air coils.  That does not instill confidence in me.

So a person selling HVAC cleaning reports unpublished results that they claim suggest if you do not clean your HVACs in hospitals you put all your patients at risk.  I am on board with the need to study microbes in hospitals more.  I am on board with the potential risks of microbes in AC systems.  I am not on board with not presenting data, and with getting the science wrong.

Special Guest Post & Discussion Invitation from Matthew Hahn on Ortholog Conjecture Paper

I am very excited about today's post.  It is the first in what I hope will be many - posts from authors of interesting papers describing the "Story behind the paper".  I write extensive detailed posts about my papers and also have tried to interview others about their papers if they are relevant to this blog.  But Matthew Hahn approached me recently about the possibility of him writing up some details on his recent paper on the functions of orthologs vs. paralogs.  So I said "sure" and set up a guest account for him to write up his comments and details of the paper.  


For those of you who do not know, Matt is on the faculty at U. Indiana.  He was a post doc at UC Davis so I have a particular bias in favor of him.  But his recent paper has generated some controversy (I posted some links about it here).  So it is great to get some more detail from him.  In addition, I note, I am also using this approach to try and teach people how easy it is to write a blog post by getting them guest accounts on Blogger and letting them write up something with links, pictures, etc.  So hopefully we can get more scientists blogging too.


Anyway - without any further ado - here is Matt's post:

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Following Jonathan’s excellent example of how explaining the history of a project helps to illuminate how the process of science actually happens, I thought I’d start by giving a bit of history behind our study, and the paper that we recently published in PLoS Computational Biology (http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002073). And then I’ll address the critics…

How this all got started

It all started a bit more than three years ago, in the summer of 2008. Pedja (as Predrag Radivojac is known to friends) was giving a talk to a group of us on protein function prediction that he also presented as a tutorial at the Automated Function Prediction SIG at ISMB 2008. Pedja and I had already collaborated on a small project involving the evolution of phosphoryation sites, but I really had no idea about his work on function prediction, and little idea in general about how function prediction was done. Reviewing different ways to accomplish transfer-by-similarity, he eventually got around to evolutionary (phylogenomic) approaches. Here is what I remember of this specific exchange during his talk:

Interested in sex? How about in bacteria? Then these #PLoSGenetics papers are for you

Well I was torn about this. Should I title the post " ICE, ICE, Bacterial BABIES" or say something about sex? I settled on sex, but not sure if that was wise.

Anyway - quick post to say that there are two papers from PLoS Genetics last month that caught my eye. They are

• PLoS Genetics: The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EPC (2011) PLoS Genet 7(8): e1002222. doi:10.1371/journal.pgen.1002222 
• PLoS Genetics: A Broad Brush, Global Overview of Bacterial Sexuality Achtman M (2011) PLoS Genet 7(8): e1002255. doi:10.1371/journal.pgen.1002255 

The latter is a "review" paper linked to the first one which is a research paper. The papers together provide both a good background and a window into modern studies of "ICEs" or integrative conjugative elements in bacteria.

I like the summary from the first paper:

Some mobile genetic elements spread genetic information horizontally between prokaryotes by conjugation, a mechanism by which DNA is transferred directly from one cell to the other. Among the processes allowing genetic transfer between cells, conjugation is the one allowing the simultaneous transfer of larger amounts of DNA and between the least related cells. As such, conjugative systems are key players in horizontal transfer, including the transfer of antibiotic resistance to and between many human pathogens. Conjugative systems are encoded both in plasmids and in chromosomes. The latter are called Integrative Conjugative Elements (ICE); and their number, identity, and mechanism of conjugation were poorly known. We have developed an approach to identify and characterize these elements and found more ICEs than conjugative plasmids in genomes. While both ICEs and plasmids use similar conjugative systems, there are remarkable preferences for some systems in some elements. Our evolutionary analysis shows that plasmid conjugative systems have often given rise to ICEs and vice versa. Therefore, ICEs and conjugative plasmids should be regarded as one and the same, the differences in their means of existence in cells probably the result of different requirements for stabilization and/or transmissibility of the genetic information they contain.

That should be enough to get people started. And that is alas all I have time to write about here.

Put down what you are doing & read this article: Amy Harmon "Autistic & seeking a place in an adult world"

Some people out there complain about the death of great scientific and medical writing. Well, I say to them "What exactly have you been reading?" Sure there is crummy stuff out there. But there are some masterpieces. And yesterday night I found one - Amy Harmon has an article that was released online last night and published in the Sunday New York Times Today: Autistic and Seeking a Place in an Adult World.

It is a spectacular piece of work - captivating, heartbreaking (in ways), inspiring (in others) and just brilliant in many ways. I have just read it for the third or fourth time. And probably about to go back for another look. I recommend everyone and anyone give it a look.

Researchers seeking volunteers who have had HAPE (high altitude pulmonary edema)

Just a mini post here. If you have ever had high altitude pulmonary edema (HAPE, also known as altitude sickness  which they refer to as "a devastating form of altitude sickness") or know someone how has please check out: Altitude.org | Join the International HAPE Database. A group of researchers are seeking people to register in their HAPE database for future scientific studies of HAPE.

And so as to not have a post with just text I am putting in some pics of me in semi-high places (never gotten HAPE myself)

At Breckenridge

Atop Pico Bolivar in Venezuela

On top of Gothic Mountain in CO

Assemblathon 1 paper out, includes many #UCDavis folks, though @vsbuffalo name backwards

Quick one here. A new paper is out from many folks, including Aaron Darling from my lab as well as a few other UC Davis folks. It is a cool paper: Assemblathon 1: A competitive assessment of de novo short read assembly methods

One minor issue - seems they got Vince Buffalo's name backwards - he is listed as Buffalo Vince on the Genome Research page, though in the PDF they have his name correct. Will have to see what he has to say about that.

Can I just say I love Biomed Central #OpenAccess

Well, I have given Biomed Central a bit of snarky grief the last few days over a few things. First, I posted about to my Posterous site (but not here) a little comment about how their web site looks weird in safari:

Then I posted to this blog a little ditty about how I did not like some parts of a phylogenetic tree they use in marketing:No award to give out but here are some lessons in using Google's image search to find an image source

My main complaint was the poor treatment of microbes in the tree. In that post I discussed how I used google image search to trace the tree

 to a few sites and discovered that they recognized it was a bit of a biased tree.  And I noted they had fridge magnets that had the tree and how I wanted one.

Umm - thanks for the invitation but, umm - not going to go to this meeting

Wow.  I get a lot of what one could call "Conference SPAM" with invitations to meetings that seem like nothing more than feedlots.  But this one really takes the cake:

Dear Dr. Eisen JA.
It is with great pleasure that we invite you to attend the EPS Montreal International Gene Conference to be held November 3-4, 2011 in Montreal, Quebec, Canada. The conference will provide a forum for researchers in Genetics and Genomics to present cutting edge research and learn about the latest breakthroughs and technologies.
We would like to welcome you to our Conference as our valuable speaker and present your recent work and ideas of Environmental shotgun sequencing: its potential and challenges for studying the hidden world of microbes. that were published in PLoS Biol.. Please visit our website at www.epsglobal.ca  and www.epswordlink.com for program details. 

Montreal International Gene Conference is organized by EPS Global Medical development Inc. Professor Massaro, the editor-in-chief of the journal Cell Biochemistry and Biophysics (CBB) will be present at this event and call for submission of papers in this field. All of the papers presented in the conference may have a chance to be published in a special issue of Cell Biochemistry and Biophysics (CBB). 

EPS Global Medical Development Inc. is a Canada-based biomedical consultant agency that promotes continuing academic education, knowledge transfer and scientific exchange through life sciences-oriented conferences. We are delighted to host the EPS Montreal International Gene Conference in Montreal in order to foster and promote excellence in Genetics and Genomics through education and research, and to provide leadership in promoting development of evidence-based clinical genetics and genomics as well as the basic research that supports these clinical advances. 

We look forward to meeting you in Montreal and wish you all an enjoyable time. 

Warmest regards,
Yao Lu, MD, PhD

Executive Chair of Montreal International Gene Conference 2011
President of EPS Global Medical Development Inc.

They are inviting me to present about a "recent" commentary paper I published in 2007.   Umm - no thanks.

C-DEBI Research Support > Request for Research Proposals

Katrina Edwards on the Atlantis

I have always been fascinated by life in extreme places on the planet. And somehow I have managed to do projects on microbes from places like Antarctica, boiling hotsprings in Yellowstone and Kamchatka, acid pools, and more. The extremes are fascinating to me because they tell us a lot about the limits of life as well as indirectly about life in "normal" places.

And of course, I am not alone. Many many scientists are fascinated by life's extremes. But not everyone ends up studying life in extreme environments of course. One reason for this is that many extreme environments that might be of interest are kind of hard to study. Consider the deep sea. Not so easy to do work there and just getting samples can be a massive undertaking.

Just imagine though. What if there were a way to "tag along" on an existing project studying life's extremes at no cost to you or your grants? Even better what if there were a way to get extra funds to not just tag along on a project but to carry out detailed research at the same time?

Well, amazingly, there is such a chance right now. The C-DEBI "Center for Dark Energy Biosphere" project is calling for proposals. C-DEBI Research Support > Request for Research Proposals

John Madden discussing his dog's surgery at #UCDavis on #KCBS this AM

John Madden on KCBS this AM discussed taking his dog to UC Davis for surgery.  Go Ags.

Great paper showing the potential power of comparative and evolutionary genomics in #PLoS Genetics

There is a wonderful paper that has just appeared in PLoS Genetics I want to call people's attention to: PLoS Genetics: Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria

In the paper, researchers from CNRS and Aix-Marseille in France used some nice comparative and evolutionary genomics analyses along with experimental work to characterize the function and evolution of gliding motility in bacteria.

Their summary of their work:

Motility over solid surfaces (gliding) is an important bacterial mechanism that allows complex social behaviours and pathogenesis. Conflicting models have been suggested to explain this locomotion in the deltaproteobacterium Myxococcus xanthus: propulsion by polymer secretion at the rear of the cells as opposed to energized nano-machines distributed along the cell body. However, in absence of characterized molecular machinery, the exact mechanism of gliding could not be resolved despite several decades of research. In this study, using a combination of experimental and computational approaches, we showed for the first time that the motility machinery is composed of large macromolecular assemblies periodically distributed along the cell envelope. Furthermore, the data suggest that the motility machinery derived from an ancient gene cluster also found in several non-gliding bacterial lineages. Intriguingly, we find that most of the components of the gliding machinery are closely related to a sporulation system, suggesting unsuspected links between these two apparently distinct biological processes. Our findings now pave the way for the first molecular studies of a long mysterious motility mechanism.

Basically, they started with some genetic and functional studies in Myxococcus xanthus.  They analyzed these in the context of the genome sequence (note - I was a co-author on the original genome paper).  And then they did some extensive comparative and evolutionary analysis of these genes, producing some wonderful figures along the way such as:

Figure 2. Taxonomic distribution of the closest homologues of the 14 genes composing the G1, G2, and M1 clusters, and genetic organization of the core complex. (A) For a given gene, the number of homologues in the corresponding genome is indicated by the numbers within arrows. The relationships between the species carrying the different homologues of the genes are indicated by the phylogeny on the left. Based on their taxonomic distribution, the 14 genes can be divided into Group A (grey background) and Group B (white background). (B) In all non Deltaproteobacteria and in Geobacter, the Group B genes clustered in a single genomic region.  doi:10.1371/journal.pgen.1002268.g002  

Panel from Science Online London (SOLO11): Linking with the Literature – the Arsenic Story

Video from the panel that I skyped in to last week from my garage at 2:30 AM is now available. The detail is found at River Valley TV: Panel #1 : Linking with the Literature – the Arsenic Story | River Valley TV

Or see it here:


Fortunately for all I did not do skype video chat - just audio - since I was in my garage in my pajamas: Garage science: why skyping in to a meeting at 2:30 AM can be, well, interesting #SOLO11

Sharing what I have been learning about sharing audio synched to slides for talks #Slideshare #Youtube #SciVee

As many of you must know, I like to share. Sort of an open science thing. Sort of an ego thing. But I like to share my papers, and data and even my talks. Going about sharing ones talks is not completely straightforward alas. A few years ago I started using a really nice tool called Slideshare which is one of many site/systems out there for sharing slides from talks. I have I posted many presentations on slideshare over the years and continue to do so. It has some nice embed functions for example and thus I can put a little flash version of my talk from a few days ago right here in my post

DNA and the hidden world of microbes

View more presentations from Jonathan Eisen

And they have some social features there which are also really nice. But slides are, well, just slides. Much better would be to include audio along with slides.

Storification of my notes/tweets from #UCDavis CLIMB Symposium "The infant gut microbiome: prebiotics, probiotics and establishment"

I made a Storify posting for the CLIMB Symposium I participated in yesterday. First I am reposting my summary of what the symposium was about which I posted the day before the meeting:

There is a symposium tomorrow at UC Davis organized by a undergraduates in the CLIMB program.  CLIMB stands for "Collaborative Learning at the Interface of Mathematics and Biology (CLIMB)" and is a program that emphasizes hands-on training using mathematics and computation to answer state-of-the-art questions in biology.  A select group of undergraduates participate in the program and this summer the students had to do some sort of modelling project.  Somehow I managed to convince them to do work on human gut microbes.  And they have done a remarkable job.  

As part of their summer work, they organized a symposium on the topic and their symposium takes place tomorrow.  Details are below. 

The Infant Gut Microbiome: Prebiotics, Probiotics, & Establishment 

• Jonathan Eisen, UC Davis “DNA and the hidden world of microbes”
• Mark Underwood, UC Davis “Dysbiosis and necrotizing enterocolitis”
• Ruth Ley, Cornell University “Host-microbial interactions and metabolic syndrome” 
• CLIMB 2010 cohort “Breast milk metabolism and bacterial coexistence in the infant microbiome”
• David Relman, Stanford University “Early days: assembly of the human gut microbiome during childhood" 
• Bruce German, UC Davis

The only major issue for me is I am losing my voice.  So we will see how this goes.  Though I note I have gotten some very sage advice on how to treat my voice problem via the magic of twitter.  If I do not collapse I will also be tweeting/posting about the other talks during the day. 

More on the Bioweathermap project #NotAboutWeather #ItsAboutMicrobes #AndMoney #CitizenMicrobiology

Just a mini post here about Bioweathermap.  I had posted a mini post about this project in July: Desperate to know what microbes are on your money? This project is for you (with some cool side science benefits).  I got reminded about this by this PLoS Blog: DIY Science at #SciBarSpace 2 | The Official PLoS Blog.  The PLoS blog discusses a talk by Jason Bobe about Bioweathermap.

Bioweathermap is not the most accurately named project but it is pretty cool.  From their site:

The BioWeatherMap initiative is a global, grassroots, distributed environmental sensing effort aimed at answering some very basic questions about the geographic and temporal distribution patterns of microbial life. Utilizing the power of high-throughput, low cost DNA sequencing and harnessing the drive of an enlightened public we propose a new collaborative research approach aimed at generating a steady stream of environmental samples from many geographic locations to produce high quality data for ongoing discovery and surveillance. Our approach will provide a unique opportunity to engage the public in the scientific research process while we address fundamental questions such as “How diverse is the microbial life around us?” and “How do microbial communities in different habitats change over time?” and “How can advanced sequencing technologies best be utilized to address issues in biodiversity, public health, and biosurveillance?”

In other words, it is about microbes (suggestion to them - it might be good to have something about microbes in the title of the project - maybe "microbioweathermap" or something like that).  Anyway, to do the project they have been collecting dollar bills from various people:

From PLoS Blog.

And then characterizing the microbes on those bills.  I note - Jason collected the bill from me when we met at the book launch party for Thomas Goetz's "The Decision Tree".  Anyway - in essence this is a citizen microbiology project and it is worth checking out.  For more on it see:

• The Bioweathermap Sees The Germs Around Us - Forbes
• The Bioweathermap Facebook page
• Some of their videos on Vimeo

Seems to me there are more and more Citizen Microbiology projects out there.  For some other posts of mine about CM projects (got to give them an abbreviation) see:

• What microbes are lurking in your fish tank? 
• More on citizen microbiology project from @Penn_State & @NASA on thermophiles in water heaters via @scicheer @Sci4Cits
• Citizen Science
• Share the thermophiles lurking in your basement

Go microbes.  Go citizens.  Go citizen microbiology.

No award to give out but here are some lessons in using Google's image search to find an image source

Was going to blog about the distorted tree of life that BMC Biology used for an ad in the Scientist (note - I am a big fan of both BMC Biology and the Scientist, but the ad still irked me).  But I was not really sure where the image came from since the ad does not say much of anything about the source.  So I used a new trick I learned last week.  I scanned the ad:

As all of you should be able to see, this tree does not do such a good job with microbial diversity.  And as an official Guardian of Microbial Diversity, I was offended.  So the question now was - from where exactly did this tree come?  And could I find BMC Biology saying something important about the figure so that then I could snark about them in my blog and give them a Twisted Tree of Life Award.

Last week in response to an email from some folks at ASM about tracking down the source of an image, I discovered a cool new trick which I used here.  I went to Google's image search page:

Coming Monday at #UCDavis "The Infant Gut Microbiome: Prebiotics, Probiotics, & Establishment"

Just a little announcement here.  There is a symposium tomorrow at UC Davis organized by a undergraduates in the CLIMB program.  CLIMB stands for "Collaborative Learning at the Interface of Mathematics and Biology (CLIMB)" and is a program that emphasizes hands-on training using mathematics and computation to answer state-of-the-art questions in biology.  A select group of undergraduates participate in the program and this summer the students had to do some sort of modelling project.  Somehow I managed to convince them to do work on human gut microbes.  And they have done a remarkable job.

As part of their summer work, they organized a symposium on the topic and their symposium takes place tomorrow.  Details are below.

The Infant Gut Microbiome: Prebiotics, Probiotics, & Establishment

Monday, 12 September 2011, 9am-4pm

Life Sciences 1022

UC Davis

9:00-9:10 Introduction

9:10-9:40 Jonathan Eisen, UC Davis

“DNA and the hidden world of microbes”

9:40-10:40 Mark Underwood, UC Davis

“Dysbiosis and necrotizing enterocolitis”

10:40-10:50 break

10:50-11:50 Ruth Ley, Cornell University

“Host-microbial interactions and metabolic syndrome”

11:50-12:00 general discussion

12:00-1:00 lunch

1:00-2:00 CLIMB 2010 cohort

“Breast milk metabolism and bacterial coexistence in the infant microbiome”

2:00-2:10 break

2:10-3:10 David Relman, Stanford University

“Early days: assembly of the human gut microbiome during childhood"

3:10-3:40 Bruce German, UC Davis

3:40-4:00 next steps

The only major issue for me is I am losing my voice.  So we will see how this goes.  Though I note I have gotten some very sage advice on how to treat my voice problem via the magic of twitter.  If I do not collapse I will also be tweeting/posting about the other talks during the day.

Email phishing - does anyone still fall for these? #SPAM

Got this email this AM

from Western Union st104624@ait.ac.th
reply-to westernunion.organization@yahoo.com.hk
to date Sun, Sep 11, 2011 at 4:02 AM
subject Dear Customer.
mailed-by ait.ac.th
hide details 4:02 AM (2 hours ago)

Dear Esteemed Customer,
You have been awarded with the sum of $50,000.00 US Dollars
by our office, as one of our customers who use Western
Union in their daily business transaction.
This award was been selected through the internet, where
your e-mail address was indicated and notified. Please
provide Mr. David Palmer with the following details
listed below so that your fund will be remitted to you
through Western Union immediately.
* Full Name:
* Sex: Age:
* Martial Status:
* Nationality:
* Country:
* Direct Address:
* Mobile Number:
* Office Number:
* Occupation:

Just wondering - does anyone still fall for this type of phishing.  I mean, some phishing attempts out there are subtle and tricky.   This one, however, is not.  Anyone know - do these really obvious ones ever work?  Or are they just part of the "chatter" that eventually will disappear by natural selection of phishing strategies?

Germophobia: wanna get people in the mood for "Contagion" movie about killer virus - grow harmless microbes in public #microbialart

Well, this story is pretty cool in many ways. David Coil, who works on my "microBEnet" project posted an entry on our blog: Microbial art in the built environment: bacterial billboard goes viral which called my attention to the story.

Seems that the folks promoting the microbe-focused movie "Contagion" came up with a fun marketing idea. They created a living billboard with microbes on it



It is pretty cool. Just watch how the letters come out and the billboard becomes 3D. It would be fun to do this with some event at UC Davis .. will have to think about it. But overall, I think this idea is really cool and very very well executed.

However, I do want to note some of the reporting on it has gotten a few details a bit off. For example, in the Washington Post: ‘Contagion’ bacteria billboard is exactly what it sounds like (Video) - Celebritology 2.0 - The Washington Post they write

"A YouTube video shows the process in which “two large Petri dishes were inoculated with live bacteria including penicillin, mold and pigmented bacteria.” The result is the most amazing, creepy and literal viral marketing campaign in recent history"

O Na Na; Chemistry fun from the Women's Leadership Program at GWU; oh, and my mom

You go mom ... and her students ...

A Forest (Rohwer that is) on Black Reefs, Shipwrecks and Coral Reef Conservation

Well Forest Rohwer is at it again.  He just is always doing something I find worth paying attention to.  

First, he does fascinating and pioneering science on viruses in the environment.  For example, consider that he was one of if not the first to do random shotgun metagenomics from environmental samples.  See his lab's 2001 and 2002 papers on the topic (Production of shotgun libraries using random amplification and Genomic analysis of uncultured marine viral communities) which I note came out before the Sargasso and Acid Mine Drainage papers which most cite as the first environmental shotgun sequencing pubs.  

Second, he studies incredibly interesting topics that take him all over the world, mostly to coastal locations.  See for example - Comparative metagenomics of microbial traits within oceanic viral communities and Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis and Viral and microbial community dynamics in four aquatic environments and Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico and more.

Third, he also develops useful bioinformatics approaches to studying metagenomes.  See Phylogenetic classification of short environmental DNA fragments and Power law rank-abundance models for marine phage communities and FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries and others.  

In fact, you could say in many ways we do very similar work, except he focuses on viruses.  Not that we always agree mind you. I once gave a talk after him at a meeting and I changed my title to "Seeing the Forest and Missing the Trees" in a little dig at his not using phylogenetic methods and in his approach to metagenomic analysis.  But I digress. 

What I want to write about today is a new paper from his lab: Black reefs: iron-induced phase shifts on coral reefs.

Attention - all interested in synthetic biology - DARPA is interested, big time

For those interested in synthetic biology, check out the new DARPA call for proposals: Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms (ATCG) - Federal Business Opportunities: Opportunities

And check out the "teaming" site trying to bring together groups and people with diverse backgrounds and interests. Kudos to Alicia Jackson at DARPA and DARPA in general for recognizing the importance of synthetic biology.

I note - Alicia Jackson's announced this push at the Synthetic Biology meeting at Stanford earlier in the summer:

• Twitter / Jonathan Eisen: Alica Jackson from DARPA announcing DARPA is getting into synthetic biology in a big big big way w/ "Living Foundries Program
• The Tree of Life: Some quick notes on #Synbio5: Synthetic Biology ...
• Check out video from the Synthetic Biology meeting where this was announced:

For some other information about this see:

• DARPA's Living Foundries Concept
• DARPA Wants Artificial Lifeforms - Technology Review
• SOLICITATIONS - Defense Advanced Research Projects Agency
• DARPA's Microsystems Technology Office launches Living Foundries

Figuring out FigShare (@FigShare) & Digging into Digital Science (@digitalsci) #OpenData

Just got pointed to this post: Welcoming FigShare, an open data project, to the Digital Science family - DIGITAL SCIENCE: Applications and services for researchers

Digital Science I do not really know much about but am learning because, well, a big supporter of open science, Kaitlin Thaney (who I note, is also a friend), moved there relatively recently and I want to figure out what she does and what they do.

Digital Science has some detail in the "about" section on their home page. Some key points:

Digital Science provides software and information to support researchers and research administrators in their everyday work, with the ultimate aim of making science more productive through the use of technology. As well as developing our own solutions, we also invest in promising start-ups and other partners, working closely with them to help them realise their full potential.

We are a business unit of Macmillan Publishers Ltd. and our activities build on the reputation for editorial and technological excellence of its sister company, Nature Publishing Group (NPG).

So basically they partner with and/or acquire companies that are playing with new technologies for communicating science. OK. I can wrap my brain around that at least for now. Whatever Digital Science does is not the point of my post here though. FigShare is.

Garage science: why skyping in to a meeting at 2:30 AM can be, well, interesting #SOLO11

Well, that was in a way fun.  I was a part of a discussion panel for the Science Online London 2011 meeting.  However, I did not go to London ... I did it from my garage.  More about this below:

I got an email many months ago inviting me to participate in a panel discussion for a Science Online Meeting in London.  The discussion was to focus on the NASA arsenic life story and how this related to open science issues.  Now even though the one and only Kaitlin Thaney invited me, I alas said "it's going to be hard for me to get to London at that time" and eventually we settled on the idea of me skyping in for the panel.

And I sort of forgot about this for a bit.

What is a nice chloroplast like you doing in a parasite like that?

Cool new paper from Joe Derisi's lab: PLoS Biology: Chemical Rescue of Malaria Parasites Lacking an Apicoplast Defines Organelle Function in Blood-Stage Plasmodium falciparum. by Ellen Yeh and Joseph L. DeRisi. doi: 10.1371/journal.pbio.1001138

In it they use some experimental techniques to try and track down the elusive function of the apicoplast in Plasmodium falciparum, the causative agent of malaria.  The apicoplast is an organelle that is evolutionarily derived from chloroplasts (and thus derived originally from cyanobacteria).  Due to it's cyanobacterial origins many have thought that it might serve as a good target for drugs to try and kill Plasmodium species because in theory such drugs if specific should not have significant detrimental effects on hosts like humans due to our lack of known important cyanobacterial associates.

Here is their abstract:

Plasmodium spp parasites harbor an unusual plastid organelle called the apicoplast. Due to its prokaryotic origin and essential function, the apicoplast is a key target for development of new anti-malarials. Over 500 proteins are predicted to localize to this organelle and several prokaryotic biochemical pathways have been annotated, yet the essential role of the apicoplast during human infection remains a mystery. Previous work showed that treatment with fosmidomycin, an inhibitor of non-mevalonate isoprenoid precursor biosynthesis in the apicoplast, inhibits the growth of blood-stage P. falciparum. Herein, we demonstrate that fosmidomycin inhibition can be chemically rescued by supplementation with isopentenyl pyrophosphate (IPP), the pathway product. Surprisingly, IPP supplementation also completely reverses death following treatment with antibiotics that cause loss of the apicoplast. We show that antibiotic-treated parasites rescued with IPP over multiple cycles specifically lose their apicoplast genome and fail to process or localize organelle proteins, rendering them functionally apicoplast-minus. Despite the loss of this essential organelle, these apicoplast-minus auxotrophs can be grown indefinitely in asexual blood stage culture but are entirely dependent on exogenous IPP for survival. These findings indicate that isoprenoid precursor biosynthesis is the only essential function of the apicoplast during blood-stage growth. Moreover, apicoplast-minus P. falciparum strains will be a powerful tool for further investigation of apicoplast biology as well as drug and vaccine development.

My science communication hero/heroine of the month - Dr. Kiki @drkiki

Been working on revising my lab's web site and was looking for some videos of talks I have given online to post there.  And I discovered/rediscovered this video of an interview I did for Dr. Kiki's Science Hour.  Here it is:

NOTE - AT LEAST TEMPORARILY REMOVING THE VIDEO DUE TO MALWARE INFECTION OF TWIT.TV SITE

Now I know - this is over a year old. But I just watched the full video. Not so bad I think.

As many of you know, I like to talk.  And talk.  And talk.  But I would like to say that as an interviewer, Dr. Kiki is pretty frigging awesome.  Don't know how she does it.  But I am going to post this video on the new lab page and point people to it if they want to know what my lab does and what I am interested in.

But enough about me.  I want to thank Dr. Kiki for this great interview by saying a little bit about her.  Or, well, her work in science communication.

Fun with Pubmed central - first paper describing #HeLa cells - Note @rebeccaskloot

Last year, Rebecca Skloot came to Davis to talk about her book "The Immortal Life of Henrietta Lacks".  Note - if you have not read the book - what f*$ing rock have you been hiding under?  It is in my opinion the best non fiction book I have ever read.  Seriously.  Not the best science book. The best non fiction book of any kind.  And I am not alone in this feeling as it has won a bazillion positive reviews and awards.   In summary - it tells three stories - the story of the isolation of HeLa cells, the story of the woman from whom those cells came, and the story of Skloot learning the other two stories.

Anyway - I somehow managed to get her to come to UC Davis to give a talk last year just as the book was going viral.  In preparation for Skloot's visit I decided to do some sort of "open access" schtick and looked into how many papers about HeLa cells were in Pubmed Central.  Pubmed Central is a database of papers for which the full text is available at no charge.  After this mini-research and after interacting with Rebecca over the last year and seeing the well deserved recognition of her book, I have been a bit fascinated about how much of the literature surrounding studies of HeLa cells is openly and/or freely available.

So today I decided to see what was the earliest HeLa paper that was freely available on PubMed Central.  And I managed to find a good one: Studies on the propagation in vitro of poliomyelitis viruses. IV. viral multiplication in a stable strain of human malignant epithelial cells (strain hela) derived from an epidermoid carcinoma of the cervix. William F. Scherer, Jerome T. Syverton, and George O. Gey.  J Exp Med. 1953 May 1; 97(5): 695–710.

I believe this was the first full paper published discussing HeLa cells.  Nice short title by the way. Anyway - good to see it in Pubmed Central.

Calling all authors, bloggers, reporters - please help with aggregating discussions of scientific papers

There has been a lot of hand wringing over whether we should and if we should how should we link discussions about scientific papers with the papers themselves.  For example, if someone writes a news story about a paper in BMC Genomics - should the online version of the paper show links to the news story?  I think so, as so many others.  If someone writes a blog post discussing the paper, should there be a tracked link on the journal site?  Again, I think so.  I think this is even more important in social media discussions of papers, which I find fascinating much of the time.   Very few people go to journal sites and post comments and open up discussions of papers.  But lots of people post comments to twitter, facebook, and other social media sites.  So why not bring those posts into the fold?

Now there are lots of efforts out there to collect comments about papers.  Faculty of 1000.  The Third Reviewer.  Research blogging. And much more. For other discussions of the issue see:

• Science in the Open » Blog Archive » The future of research ...
• Implementing the “Publication as Aggregation” - Cameron Neylon
• Aggregating, Tagging and Integrating Biodiversity Research
• How to Publish a Scientific Comment in 1 2 3 Easy Steps
• Soft peer review: Social software and distributed scientific evaluation
• and much much more

I am not really going to get into a discussion of all the ideas out there in this area.  Some are good.  Some are bad.  Some are probably both.  I personally think aggregation is going to be a very useful tool in post publication sharing and discussion and searching.  But that is not per se what I am here to talk about.  What I am here to talk about is what anyone can do right now to help with this in a very simple way.

My simple suggestion:
If you see ANY online discussion of a paper - a news story - a blog - even some smaller thread somewhere.  Find the journal article online and use the comments function is the journal has one to post  a comment saying "There was a news story discussing this paper in the New York Times.  See ...."  Or something like that.  And presto, people who go see the paper online will also have potential to find the link you post.

I have been doing this for a while.  It is relatively easy for PLoS Papers.  For example for my paper on "Stalking the Fourth Domain in Metagenomic Data" I posted all sorts of links using the PLoS One comment function.  I posted links to my blog.  I posted links to positive news stories.  I posted links to critiques.  Anything I could find.

And this worked out pretty well.

More on 'phylogenomics' - as in functional prediction w/ phylogeny

There is a new paper out: Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium in Briefings in Bioinformatics.

The paper is interesting and presents a new general approach to using phylogeny for functional prediction of uncharacterized genes. I am interested in this for many reasons including that I was one of, if not the first to lay this out as a concept.  In a series of papers from 1995-1998 I outlined how phylogenetic analysis could be used to aid in functional prediction for all the genes that were starting to be sequenced in genome projects without any associated functional studies (at the time, I referred to all these ESTs and other sequences as an "onslaught" - little did I know what was to come).

My first paper on this topic was in 1995: Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions.  The abstract is below:

The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.

Some links on "ortholog conjecture" paper and critiques of it

Recently a paper by Matt Hahn was published in PLoS Computational Biology entitled "Testing the ortholog conjecture with comparative functional genomic data from mammals."  The paper created a bit of a stir as some aspects of it call into question some of the standard assumptions made in comparative genomic analysis.

I alas do not have time to go into all the details but fortunately others have tackled this and I am posting some links here:

• Comments at Faculty of 1000 (currently available for free but not sure for how long).
• Of mice and men and meta analyses (Richard Grant discussing Michael Galperin's F1000 dissent)
• The 'Ortholog Conjecture' | The Daily Scan | GenomeWeb
• Of Mice and Men or: Revisiting the Ortholog Conjecture (Iddo Friedberg)
• Friendfeed discussion: http://friendfeed.com/erickma... (see below)

Playing around with CloVR - cloud computing bioinformatics system

Nice new tool/resource available out there for metagenomic and genomic analysis called CloVR: CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

It is available at http://clovr.org and it should be useful to many people out there doing genomics and metagenomics if you want to make use of cloud computing resources.

CloVR is brought to us by Florian Fricke and Owen White and Sam Angiuoli and others from the University of Maryland (full disclosure - many of the authors are ex-colleagues of mine from TIGR).

Not only is Clovr available openly and freely but they even have a Clovr blog: http://clovr.org/category/blog/ ... though it does not seem to be heavily used.  Kudos to this team for producing and releasing this software for others to use.  And kudos to NSF, USDA and NIH for funding its development -- I have a feeling many people will use it.

I think that I shall never see - metagenomic analysis as lovely as a tree #PhylogenyRules #PLoSOne

Figure 2. Phylogenetic tree linking
metagenomic sequences from 31 gene
families  along an oceanic depth gradient
 at the HOT ALOHA site

I am a co-author on a new paper that came out in PLoS One yesterday.  The paper is PLoS ONE: The Phylogenetic Diversity of Metagenomes and the full citation is Kembel SW, Eisen JA, Pollard KS, Green JL (2011) The Phylogenetic Diversity of Metagenomes. PLoS ONE 6(8): e23214. doi:10.1371/journal.pone.0023214.

The first author is Steven Kembel, a brilliant post doc at the University of Oregon.  You can follow him on twitter here. This paper is a product of the "iSEEM" "integrating statistical, ecological and evolutionary approaches to metagenomics" collaboration between my lab and the labs of Jessica Green at U. Oregon and Katie Pollard at UCSF.  For more on iSEEM see http://iseem.org.  iSEEM was supported by the Gordon and Betty Moore Foundation.

Mendelspod interview with, well, me, discussing science, pranks, evolution and more

Here is an interview with me produced by Mendelspod. It was filmed in my office at UC Davis on Mendel's birthday.
 
Stalking the Fourth Domain with Jonathan Eisen, Ph D from mendelspod on Vimeo.

Some links of relevance to this interview:

• Freeing my father's publications part 5: near completion of PDF collection at Mendeley (h/t @David_Dobbs)
• The story behind the story of my new #PLoSOne paper on "Stalking the fourth domain of life" #metagenomics #fb
• Scientist Reveals Secret of the Ocean: It's Him- New York Times
• The Tree of Life: What kid would want to study bacterial evolution ...
• Confessions of an April Fool and the Dope on Brain Doping

Guardians of microbial diversity: some follow up links re species counting

Just some follow up links regarding counting species which I wrote about recently:

• Bacteria & archaea don't get no respect from interesting but flawed #PLoSBio paper on # of species on the planet by me 
• How Many Species on Earth? It’s Tricky - by Carl Zimmer 
• How many species are there? My latest for the New York Times - by Carl Zimmer 
• Ed Yong on Google Plus
• Don’t forget to count microbes - Bonnie Bassler and David Hooper letter in the Washington Post 
• How Many 'Kingdoms' of Life Are There? (Christopher Shea at the Wall Street Journal Blog) 
• A general lack of specificity by Jess Davenport 

Oh and I am working on some T-shirts if you want to advertise your microbial loyalty

Structures, structures, and structures: Structural genomics of infectious disease drug targets: the SSGCID

Cool new data set available for those studying infectious disease.  See the paper: Structural genomics of infectious disease drug targets: the SSGCID

This is a large scale effort to determine crystal structure of importance for infectious disease studies.  And there is a whole series of papers coming out in "Acta Crystallographica Section F Structural Biology and Crystallization Communications"

Plus all the papers about these structures are freely available (though I note - they refer to these as "Open Access" but really they mean "Available at no charge"

Examples of papers include:

• Gene design, cloning and protein-expression methods for high-value targets at the Seattle Structural Genomics Center for Infectious Disease
• Immobilized metal-affinity chromatography protein-recovery screening is predictive of crystallographic structure success
• Structures of phosphopantetheine adenylyltransferase from Burkholderia pseudomallei
• Structures of a putative -class glutathione S-transferase from the pathogenic fungus Coccidioides immitis

And many more.  

Also see their press release here.