The Tree of Life

New #openaccess paper in G3 from my lab w/ many others on 'Programmed DNA elimination in Tetrahymena' #CiliatesRule

2012-02-11T08:21:00.000-08:00

A new paper in which the lab was involved has been published recently (just found it though it is not in Pubmed yet): Genome-Scale Analysis of Programmed DNA Elimination Sites in Tetrahymena thermophila. It was a collaboration between Kathy Collins, multiple Tetrahymena researchers, the Eisen lab, and the UC Davis Genome Center Bioinformatics core (Joseph Fass and Dawei Lin). The paper is in G3, an open access journal from the Genetics Society.

This stems from the project I coordinated on the sequencing and analysis of the macronuclear genome of the single-celled ciliate Tetrahymena thermophila. This organism, like other ciliates, has two nuclei - one called the micronucleus and one called the ~~micronucleus~~ macronucleus. In essence you can view the micronucleus as the germ line for this single-celled creature and the ~~micronucleus~~ macronucleus is akin to somatic cells. The micronucleus is reserved mostly for reproduction. And the ~~micronucleus~~ macronucleus is used for gene expression. In sexual reproduction, haploid versions of the micronuclear genomes from two lineages merge together just like in sexual reproduction for other eukaryotes. After sex the offspring then create a macronuclear genome by taking the micronuclear genome and processing it in a variety of ways - going from 5 chromosomes for example to hundreds. Plus many regions of the micronuclear genome are "spliced" out and never make it into the macronuclear genome. Our new paper focuses on trying to better characterize which regions of the micronuclear genome get eliminated.

For more on our past work on Tetrhymena genomics see here which includes links to much more information including to my 2006 blog post about our first paper on the project.

Note - the work in my lab on the sequencing was supported by grants from NSF and NIH-NIGMS.

New publication from members of my lab (e.g., @ryneches) & lab of Marc Facciotti on ChIP-seq based mapping of archaeal transcription factors

2012-02-10T00:51:00.000-08:00

New publication from members of my lab and the lab of Marc Facciotti on a workflow for ChIP-seq based mapping of archaeal transcription factors. The paper includes a description of new software from Russell Neches in my lab called pique for peak calling.

See: A workflow for genome-wide mapping of archaeal transcription factors with ChIP-seq

Russell's pique software is available on github here: https://github.com/ryneches/pique.

Figure 3.

The Pique software package processes ChIP-seq coverage data to predict protein-binding sites. Strand-specific coverage data are output as tracks for the Gaggle Genome Browser, and putative-binding sites (peaks) are output as ‘bookmark files’. (A) Screenshot of data browsing in the Gaggle Genome Browser. Green box outlines the navigation window for clicking through bookmarks of predicted binding sites. Details of each site can be displayed (inset). The Gaggle toolbar (shown with black arrow) can be used to broadcast selected data to other ‘geese’ in the gaggle package, programs such as R, cytoscape, BLAST or KEGG. (B) Schematic overview of bioinformatics workflow.

New York Times "Insight Panel" - SPAM? SCAM? or just LAME? cc: @nytimes

2012-02-10T00:26:00.000-08:00

Just got this email below regarding the "New York Times Insight Panel." Seems like a scam to me. If it is real, then it seems pretty, well, lame. Anyone know anything about this?

Dear New York Times Subscriber,

We would like to invite you to become a member of our community of engaged New York Times readers by joining The New York Times Insight Panel and sharing your opinions with us.

This important panel is made up of readers like you who are interested in giving us feedback on a variety of topics, including their involvement with The Times. Here's a quick overview of the benefits of being a member:
...... READ MORE .......

Wanted - input on voting for resolutions for the #UCDavis Academic Senate #OccupyUCDavis

2012-02-09T20:21:00.000-08:00

Well today I am finally getting around to voting on some UC Davis Academic Senate resolutions relating to the Occupy UC Davis pepper spray incident. For those not familiar with this - first - I offer you my undying love - second - here are some of my previous posts on the theme:

I wrote a lot about the pepper spray incident here and on twitter - I felt in many ways like I had to report on what was going on for the outside world. Here are some of my key posts:

And then Winter break happened and things calmed down a bit at UC Davis. Plus, I got busy and needed to go back to running my lab and doing some work. Not that nothing happened during this time. Lots did in fact. The best place to find out about what happened is the Davis Enterprise which continued coverage of everything going on (see list on the right side of this page).

Catching up to today - now the issue (for me and other faculty/members of the Academic Senate) is that we have to vote on some resolutions regarding the pepper spray incident.

Below are the three for which I am supposed to vote. I am asking anyone out there for input on these. All of them seem pretty, well, lame to me and I am inclined to vote no on all of them. But I am reserving judgement and looking for feedback from others out there. Any comments / suggestions welcome.

Interesting 2011 pub on origin of multicellularity in cyanobacteria

2012-02-09T11:03:00.000-08:00

Just a quick one here. There is an (openaccess) publication I thought people might find interesting: The origin of multicellularity in cyanobacteria. Schirrmeister BE, Antonelli A, Bagheri HC. BMC Evol Biol. 2011 Feb 14;11:45.

In particular it has some very nice figures on phylogeny of cyanobacteria and the evolution of phenotypes in the group.

Figure 1. Phylogenetic tree of 1,254 cyanobacterial species.

Figure 4. Phylogenetic tree of a cyanobacterial subset.

Some of the same authors also have a paper on the need for better phylogenetic sampling of genome data in the group:

Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches. Schirrmeister BE, Anisimova M, Antonelli A, Bagheri HC. Commun Integr Biol. 2011 Jul;4(4):424-7. Epub 2011 Jul 1.

Though I note, I am a bit annoyed and surprised they did not cite my "Phylogeny driven genomic encyclopedia" paper in this pub ...

Still wondering -can UC force me to sign "patent amendment" that is "not a change in patent policy" ????

2012-02-07T23:04:00.000-08:00

Just got an annoying email regarding patents that is a follow up to one I wrote about previously (Wondering – can UC force me to sign new patent agreement?). I have appended the text of the email below. I am still wondering if the University of California can actually force me to sign this agreement. In addition, I am wondering about the competence and/or honesty of the people behind this amendment as it is pretty clear it is a major change and not as they claim in essence no change at all. If it is really in essence no change - then what is the point? If it is a major change why was there little if any discussion prior to the edict?

For other comments and questions about the UC attempt to force employees to sign this agreement see UC Patent Amendment: To Sign or Not to Sign? by my brother (I did not know until a Google search that he had written this post in December ... I guess we need to talk more) and this post Sample language for my UC friends and
UC Patent Amendment: To Sign or Not to Sign? | UC San Diego ... and Davis Faculty Association » Blog Archive » UC's Patent Amendment ...

UPDATE: someone thought the email might have been a PHISHING attack: Fwd: PLEASE SIGN NOW: UC Patent Amendment - Micronet at UC ...

I find the style and tactics of UC on this to be obnoxious and bullying. I fight for many many things for UC and UC Davis. Being bullied into signing a amendment that is claimed to not be any change even though it is clearly a big change - not something I can support.

Here is the email, which I note, had as the header a big seal of the University of California - I assume to try and intimidate me into signing.

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Converting repeated emails into FAQs: Today's = How to Get Figures/Details from 2009 GEBA paper

2012-02-07T18:03:00.000-08:00

OK I am now officially completely driven insane by email. As part of my attempt to reduce email communication with people I am going to start posting some of the emails I get often into FAQs.

Today's email relates to the 2009 paper on a "Phylogeny driven genomic encyclopedia of bacteria and archaea" for which I was the senior and corresponding author. The email is asking for higher resolution figures that were published in the paper. This person and many others have asked for a higher res. version of our "genome tree" which was Figure 1. Here is the version from the paper

But alas, as a JPG when you zoom in you can't see the text very well. And about 30 or so people, maybe more, have asked for a higher res. version. Well, the simplest way to get this figure with legible fonts when zoomed in is to get the PDF of the paper and zoom in on it. But that may not be for everyone - so here is a link to the PDF of the figure that I posted on postures (Blogger does not allow PDF uploads). I also posted PDFs of the other figures.

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New openaccess paper from my lab on "Zorro" software for automated masking of sequence alignments

2012-02-07T07:58:00.000-08:00

A new Open Access paper from my lab was just published in PLoS One: Accounting For Alignment Uncertainty in Phylogenomics. Wu M, Chatterji S, Eisen JA (2012) Accounting For Alignment Uncertainty in Phylogenomics. PLoS ONE 7(1): e30288. doi:10.1371/journal.pone.0030288

The paper describes the software "Zorro" which is used for automated "masking" of sequence alignments. Basically, if you have a multiple sequence alignment you would like to use to infer a phylogenetic tree, in some cases it is desirable to block out regions of the alignment that are not reliable. This blocking is called "masking."

Masking is thought by many to be important because sequence alignments are in essence a hypothesis about the common ancestry of specific residues in different genes/proteins/regions of the genome. This "positional homology" is not always easy to assign and for regions where positional homology is ambiguous it may be better to ignore such regions when inferring phylogenetic trees from alignments.

Historically, masking has been done by hand/eye looking for columns in a multiple sequence alignment that seem to have issues and then either eliminating those columns or giving them a lower weight and using a weighting scheme in the phylogenetic analysis.

What Zorro does is it removes much of the subjectivity of this process and generates automated masking patterns for sequence alignments. It does this by assigning confidence scores to each column in a multiple seqeunce alignment. These scores can then be used to account for alignment accuracy in phylogenetic inference pipelines.

The software is available at Sourceforge: ZORRO – probabilistic masking for phylogenetics. It was written primarily by Martin Wu (who is now a Professor at the University of Virginia) and Sourav Chatterji with a little help here and there from Aaron Darling I think. The development of Zorro was part of my "iSEEM" project that was supported by the Gordon and Betty Moore Foundation.

In the interest of sharing, since the paper is fully open access, ~~I am posting it here below the fold~~. UPDATE 2/9 - decided to remove this since it got in the way of getting to the comments ...

Fun visit to the #UCDavis Bohart Entomology Museum w/ my daughter's Daisy Troop (led by my wife)

2012-02-05T09:00:00.000-08:00

Kudos to the UC Davis Bohart Museum of Entomology for the tour they gave to the Daisy Troop my daughter is in (which is run by my wife and a friend of hers). I got there a little late and embarrassed myself by thinking one of the dads was one of the museum workers and introducing myself (even though I know the dad pretty well). Oh well, live and let learn. The visit went great - the kids got to play with bugs, got to open the stacks and even pull out drawers of various bugs (note - the general term, not the Homoptera). The museum staff were wonderful and the museum itself is very nice. A great kids activity in Davis and good for adults too. Always great to see passionate science education and outreach.

Next up for Science in Congress: HR3433 - the Grant Reform and Transparency Act

2012-02-04T09:26:00.000-08:00

Just got pointed to this by Mark Martin. There is a new bill making its way through congress - HR 3433 - the Grant Reform and New Transparency Act of 2011. It has a subtitle apparently of "To amend title 31, United States Code, to provide transparency and require certain standards in the award of Federal grants, and for other purposes."

The full text of the bill and other information is available here.

I personally don't know much about this bill but found some discussion of it here:

I have not formed an opinion of the act but thought I would share the information since it does not seem to be getting much attention but seems like it could have impact. I note - one group that I respect deeply supports the act: the Sunlight Foundation which involves people like Ester Dyson and Lawrence Lessig. Any opinions or insight on the bill would be welcome.

Stop deifying "peer review" of journal publications:

2012-02-04T03:57:00.000-08:00

Peer review. It is a critical part of scientific research and scientific progress. Without it, science as a field might look like Fox News Stories or postings on Jenny McCarthy's web site, where ideas people have are given gravitas regardless of how ludicrous they are. But somehow, many in the public and press, and many many scientists alas, have deep misconceptions about peer review.

The most recent example of such misconceptions involves the arsenic life saga. If you are not familiar with this story - here is a summary (for some fine scale details on the early parts of the story see Carl Zimmer's post here).

In November 2010 NASA announced that in a few days they would hold a press conference discussing a major finding about life in the universe. On December 2, 2010, they held their press conference and discussed a paper that was in press in Science from multiple NASA funded authors including Felisa Wolfe-Simon. The paper was of interest because it claimed to have shown that a bacterium was able to replace phosphate in its macromolecules, including its DNA, with arsenic. The press conference made claims that were very grandiose, like that textbooks would have to be rewritten, and the study of life on Earth and elsewhere would have to be completely rethought.

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Interesting new metagenomics paper w/ one big big big caveat - critical software not available "

2012-02-03T07:23:00.000-08:00

Very very strange. There is an interesting new metagenomics paper that has come out in Science this week. It is titled "Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota" and it is from the Armbrust lab at U. Washington.

One of the main points of this paper is that the lab has developed software that apparently can help assemble the complete genomes of organisms that are present in low abundance in a metagenomic sample. At some point I will comment on the science in the paper, (which seems very interesting) though as the paper in non Open Access I feel uncomfortable doing so since many of the readers of this blog will not be able to read it.

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2010 "Arsenic found in DNA", 2012 "We never claimed arsenic was in the DNA" WTF?

2012-02-02T00:20:00.000-08:00

Unbelievable. Check out this news story on some new results relating to the "Arsenic Life" story. The story discusses a paper from Rosie Redfield that has been deposited in arXiv. Rosie has been persistent in doing tests on the strain GFAJ-1 that Wolfe-Simon had isolated. One of their new results is that they cannot detect arsenic/arsenate in the DNA from this strain. Amazingly, in this news story Wolfe-Simon is reported to have said that they never claimed that arsenic was getting into the DNA:

Wolfe-Simon, who says she can’t comment in detail until Redfield’s results appear in a peer-reviewed journal, wrote in an email that her original paper never actually claimed that arsenate was being incorporated in GFAJ-1’s DNA, but that others had jumped to that conclusion. “As far as we know, all the data in our paper still stand,” she wrote. “Yet, it may take some time to accurately establish where the [arsenic] ends up.”

Wow. I recommend people go check out the original paper and see for themselves. And also check out the press conferences and news stories. The whole thing was about their claim that the arsenic was ending up in the DNA.

In their abstract, for example:

Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bio-elements may have profound evolutionary and geochemical importance.

Q & A about Elsevier, my blog retraction, and #OpenAccess

2012-02-01T23:25:00.000-08:00

Jop de Vrieze has written an article related to the Elsevier boycott for ScienceInsider:

Thousands of Scientists Vow to Boycott Elsevier to Protest Journal Prices

In the article, one of the things he discusses is my blog post (which I then "retracted) suggesting people ignore any papers published in Elsevier Journals: Boycotting Elsevier is not enough - time to make them invisible (UPDATED/RETRACTED).

In his article he wrote:

One scientist who strongly supports the boycott is Jonathan Eisen, a microbial genomicist at the University of California, Davis, and the Academic Editor-in-Chief of PLoS Biology, an open access journal. On Tuesday, Eisen urged readers of his blog to go one step further, by no longer paying attention to research published by Elsevier. "In essence, ignore them - consider them dead - make them invisible," he wrote. But after readers protested that no paper should be ignored just because of where it's published, Eisen quickly retracted the entire post, which he said had been written "at midnight, with a cat on my lap." "The response to my post helped make me realize that the semi-sarcastic attempted tone was not coming through correctly," Eisen writes in an e-mail to ScienceInsider.

de Vrieze did a good job of representing my point of view. But I thought it might be useful to all of the Q&A in the email with him. Fortunately, he said this was OK to do so ... here are my full answers to his questions:

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Scary and funny: functional researcher Peter Uhnemann on OMICS group Editorial Board #JournalSPAM

2012-01-30T10:42:00.000-08:00

OMG. This is both hilarious and terrifying.

Many out there know there are journals out there that border on SPAM. I have written about this often before (e.g., see For $&%# sake, Bentham Open Journals, leave me alone and Yet another SPAMMY Science publisher: Scientific and Academic Publishing and The Tree of Life: Really sick of Bentham Open Spam) as have many others (e.g., Open and Shut?: The Open Access Interviews: Matthew Honan and Academic spam and open access publishing - Per Ola Kristensson). UPDATE: forgot to include this link: Science SPAMMER of the month: OMICS publishing group

But this one takes the cake. There is a journal called "Molecular Biology" from the OMICS Publishing Group (for more on this publisher see Open and Shut?: The Open Access Interviews: OMICS Publishing ...). It seems new - as I cannot find any publications - but you never know - maybe they have been around a while and just have not gotten any submissions.

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Boycotting Elsevier is not enough - time to make them invisible (UPDATED/RETRACTED)

2012-01-30T00:32:00.000-08:00

Update: The original post here was written at midnight, with a cat on my lap. I thought this post conveyed some tongue in cheek aspect of this idea to ignore work in Elsevier journals. (one could view it as a midnight middle finger to Elsevier over some of their policies). But clearly, based on the responses I am seeing that did not come across. I accept the error of my ways. Drug Monkey is right - no work should be ignored - no matter where it is published. I could explain in more detail what I was trying to convey - but in the end that is like explaining a bad joke. Instead, I am therefore retracting my blog post. That is one for Ivan Oransky I guess. Now back to your regularly scheduled programs.

There has been much written in the last few days about multiple calls to boycott journals published by Elsevier due to Elsevier's generally problematic publishing policies and support of SOPA/ RWA, etc. People have called for people to not only boycott publishing in Elsevier journals but to also stop reviewing for them, editing for them, and also to try to get libraries to stop subscribing to them. Some good reading in this area includes:

I think these are good steps. But I also think they are not enough. I am therefore calling for people to go one step further - to stop helping promote articles published in Elsevier journals. Don't blog about papers in Elsevier journals. Don't tweet about them. Don't use Elsevier papers for journal clubs. In essence, ignore them - consider them dead - make them invisible. Not completely of course. Any work should be considered a contribution to science or math or whatever your field is. But there are LOTS and LOTS of things to do with your time. And if you like to share - to communicate - to discuss - it is easy to find non Elsevier articles articles for those purposes (even better - pick open access articles ..)

~~This may be a minor thing in the fight for more openness in publishing, but it should help. After all, for many scientists, the worst thing that can happen is to be ignored.~~

How are these @kejames re: #PLoSOne cc: @boraz @edyong209 @danielaphd

2012-01-29T16:59:00.001-08:00

Having lots of fun with my @Olloclip macro lens for my iPhone

2012-01-29T16:38:00.001-08:00

First "Guardians of microbial diversity" award to Rob Dunn #microbiology #GMDs

2012-01-29T13:40:00.000-08:00

Nice piece by Rob Dunn: Eating off the floor: How clean living is bad for you | Guest Blog, Scientific American Blog Network

For this I am awarding him the first of what will be many "Guardians of Microbial Diversity" awards here (we can just call these the GMDs). Not only will he get an award - I am going to send him a GMD gift from the various GMD doodads I am putting together.

Congratulations Rob. Now off to design some more diverse GMD doodads.

Dear #AAAS, I am NOT embargoing my own talk & I plan to record it and post afterwards #embargowatch

2012-01-29T08:02:00.000-08:00

Just got another email from AAAS regarding their big meeting in February in Vancouver where I am scheduled to talk:

----------------------------------------

This request for materials is from the AAAS media relations team and is separate from any you may receive from your symposium organizer or the AAAS Annual Meeting office.

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Dear AAAS Annual Meeting Participant:

Thanks to all of you who uploaded materials to the AAAS Virtual Newsroom by Jan. 16. For those of you who have not submitted materials or want to submit additional materials, you may do so right up through the meeting. The materials will be available online to reporters, although we can no longer guarantee that we'll be able to copy new
submissions at our expense for placement in the on-site library of speaker materials. We will try to include materials received in the next several days in our copy order, however.

One old, one new - a few phylogeny papers worth checking out

2012-01-29T07:24:00.000-08:00

Just a quick one here. A few days ago in my lab we were discussing some challenges with doing phylogenetic diversity (PD) measurements in very very large phylogenetic trees. PD is a measure of total branch length in a phylogenetic tree for a group of taxa ... and we use it for many purposes.

For many of our applications we have been using an algorithm described by Mike Steele "Phylogenetic diversity and the Greedy Algorithm". But alas, is is not keeping up with the massive tree sets we are dealing with. Fortunately Aaron Darling in my lab found a alternative paper with a perfect sounding title for us: Phylogenetic Diversity within Seconds from Minh, Klaere, and von Haeseler. This seems like it will do the trick. I note - Kudos to Systematic Biology for making some older papers freely available. Not sure of their general policies on this but good to see.

Anyway - back to the grind ...

A science birthday party for a five year old

2012-01-28T17:15:00.000-08:00

Some pics from my son's fifth birthday party - chemistry & geology focused (we may sample microbes later ...). For the geology part we cracked open geodes. For the chemistry part, we played with citric acid, baking soda, some dyes, and other things ...

Experimenting with Blogger's "Dynamic Views" format and a way to use with without changing my front page

2012-01-28T00:28:00.000-08:00

A while ago Blogger announced "Dynamic Views" for Blogger blogs (Dynamic Views: seven new ways to share your blog with the world). Some of these seem pretty near but I kind of like the non dynamic format for my blog and I am reluctant to jump into the new dynamic world.

Then I discovered a trick. Dynamic views are there and you do not have to switch over the front page for people to still play with with views.

To get to the dynamic views for this blog go to one of these links:

Seems like this may work for most blogger blogs too. Not sure whether this is on purpose by Blogger and/or whether they have written about it or not but I like that it is there to play with. If people have any opinions about the Dynamic Views let me know. I note - one you go to the dynamic views you can switch between the different views using the drop down menu on the left.

Notes on #UCDavis Citizen Microbiology Meeting #UCDCitSci

2012-01-27T10:48:00.000-08:00

We had a meeting at UC Davis on "Citizen Microbiology" from 1/23-1/24. It was a small meeting funded via my microBEnet project which itself is supported by a grant from the Alfred P. Sloan Fundation. The meeting was held at UC Davis - participants stayed at the new Hyatt on campus. We met in the new Conference Center. Participants at the meeting were me, David Coil (post doc in my lab), Paula Olsiewski (from the Sloan Foundation), Holly Bik (post doc in my lab), Darlene Cavalier (founder of ScienceForCitizens.Net), Dan Smith from Argonne National Lab, Denneal Jamison from UC Davis, Holly Menninger from NC State, Noah Feirer from CU Boulder, Josh Neufeld from Waterloo, Jason Bobe from The Personal Genome Project, Tom Bruns form UC Berkeley, Madhu Katti from Fresno State, Chris House from Penn. State, and Patrik D'haeseleer (from Lawrence Livermore National Lab).
Below is a "Storification" I made of the tweets and links from the meeting. ...... READ MORE .......

A conference where the speakers are all women?

2012-01-27T10:45:00.000-08:00

So - I was working on organizing a conference - a part of a series - and I was frustrated that prior conferences in the series had only or mostly male speakers. So I suggested for the new conference in the series we have only female speakers. Still working on pulling that off but probably won't quite happen. So then I posted to twitter and Google+ the idea - and asked a question about it. I made a "storification" of this which you can see below the fold:

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