Eisen Lab Blog

10 benefits (for my career) of blogging/tweeting/etc #fb

I was recently interviewed for a story in the Scientist by Bob Grant about blogging and related activities (see his story “You Aren’t Blogging Yet here). As preparation for this interview I made a top 10 list of ways that blogging had been beneficial to me. And I thought I would post my list here. I note, I made this list in about 10 minutes so I am sure there are other things I could add, but it was REALLY easy to make the list so I think w/o a doubt there have been many many benefits ….

10 ways blogging/microblogging has been beneficial to my career:

  • Collaboration. Many of my current projects have collaborators that have come about in part via interaction on blog/Twitter. 
  • Concentration. I concentrate more at meetings since I am either planning on writing something about it, or am actually live blogging the meeting. 
  • Personnel. Some of the recent recruits to my lab have come about via connections online. 
  • Crowdsourcing. Asking questions on twitter and my blog has been a great way to rapidly find out information about a particular area. 
  • Reduced travel. I have two little kids and do not like to travel much right now for this and other reasons. Blogging and Twitter and other social networking activities help peole find out about my work without me having to travel. 
  • Outreach. Blogging and related activities are a good way to interact with public and scientists in other fields. 
  • Keeping up with cutting edge (mostly via twitter). Following the right people is a great way of finding out about the latest in various fields 
  • Great practice for explaining/teaching. In my head, I could explain anything. But when I actually try to explain in writing, I realize how many assumptions we make and how much jargon there is. Trying to explain to a broad audience is great practice. 
  • Record of my thoughts/ideas. I forget a lot of things. I am sure others do too. But twitter and my blog provide a good record of some thoughts I had on various topics. 
  • New $$. I have recent gotten a new grant mostly due to my activities in the Science 2.0 world and I think my activities like blogging, etc also could in principle help get other grants where “outreach” is important. 

Anyway – just a little post about ways that blogging and tweeting have been helpful for my career. Other examples/areas that blogging and tweeting have helped people’s careers in science would be welcome here …

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

——–

Quick post – congrats to Jill Banfield, environmental #microbiology guru, for winning Franklin Medal & L’Oreal-UNESCO award

Very cool news from UC Berkeley.  Jill Banfield, one of the greats of environmental microbiology, is going to receive both the Benjamin Franklin Medal in Earth and Environmental Science and the L’Oreal-UNESCO “for women in science” award.

I am very happy to see this.  Jill has done some amazing work in multiple areas of environmental microbiology and continues to push frontiers in technology and science.  And since I am always on an Open Access crusade here, here are some links to some of her recent papers that are free in Pubmed Central:

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

——–

A very simple suggestion for scientists to increase their interactions w/ people in the humanities

Well, I have been inspired recently by some of my interactions with people in the humanities. In general I think that there need to be more professional interactions between scientists and people in the humanities. So here is a simple suggestion, that could be taken up by scientists.

When you go to give a talk at another place, and your hosts ask who you want to meet with, include someone from outside the sciences. Either find someone yourself or asks your hosts to do it. I am going to do this for all my future visits to other campuses. Not only might it help in terms of interactions across fields, but I know my brain hurts after a full day of meeting with only scientists, so this has got to be better …

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

——–

Another good paper, but bad omics word of the day: uniqueome

Wow. This is bad. Really not much to say here other than to point you to a new paper by Koehler et al in Bioinformatics:

The Uniqueome: A mappability resource for short-tag sequencing — Bioinformatics

Paper seems useful. The word. It is simply awful. And the winner of today’s “Bad omics word of the day“.  Hat tips to @leomrtns and @neilfws 

From “The Uniqueome: A mappability resource for short-tag sequencing
Ryan Koehler, Hadar Issac , Nicole Cloonan,*, and Sean M. Grimmond.” Bioinformatics (2010) doi: 10.1093/bioinformatics 

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

——–

One of my new favorite things: paleovirology

Just a quick post here about a paper that came out about a month or so ago: PLoS Biology: Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

This paper, by Clément Gilbert, Cédric Feschotte is quite cool.  In it they describe their work on “Paleovirology” where they look for viruses than have “endogenized” by inserting into the genome of some host species.  This endogenization is important in particular when the endogenous form becomes inactive and thus, in essence, trapped in the genome.  This in turn is important because many viruses evolve so rapidly when they are “free” that it is very hard to reconstruct their ancient history through comparative analysis.  But the endogenized viruses serve in essence as a molecular “fossil record” that aids in the comparison and phylogenetic analysis of various families of viruses.  As we get more and more genomes, this searching for and analysis of endogenous viruses will get much better.

Anyway, in the paper they report on endogenous viruses in the Zebra Finch genome that are in the Hepadnaviridae family.  Here is their summary:

Paleovirology is the study of ancient viruses and the way they have shaped the innate immune system of their hosts over millions of years. One way to reconstruct the deep evolution of viruses is to search for viral sequences “fossilized” at different evolutionary time points in the genome of their hosts. Besides retroviruses, few virus families are known to have deposited molecular relics in their host’s genomes. Here we report on the discovery of multiple fragments of viruses belonging to the Hepadnaviridae family (which includes the human hepatitis B viruses) fossilized in the genome of the zebra finch. We show that some of these fragments infiltrated the germline genome of passerine birds more than 19 million years ago, which implies that hepadnaviruses are much older than previously thought. Based on this age, we can infer a long-term avian hepadnavirus substitution rate, which is a 1,000-fold slower than all short-term substitution rates calculated based on extant hepadnavirus sequences. These results call for a reevaluation of the long-term evolution of Hepadnaviridae, and indicate that some exogenous hepadnaviruses may still be circulating today in various passerine birds.

Figure 4. Summary of the evolutionary scenario inferred in this study.

It is an interesting paper and worth a look if for those who have any interest in viral evolution. And I am becoming more and more fascinated by “Paleovirology” these days so I thought I would just post about this article here.  And I guess I am not alone in this opinion that the article is interesting (though I am late).  Here is some coverage of their paper:

Gilbert, C., & Feschotte, C. (2010). Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses PLoS Biology, 8 (9) DOI: 10.1371/journal.pbio.1000495

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

——–

Good paper but bad omics word of the day: drugome

Already tweeted about this but felt it had to be given more prominent status. There is a new, interesting paper in PLoS Computation Biology: The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications
But that word – drugome. Here is their definition

The resulting drug-target interaction network for all structurally characterized approved drugs bound to putative M.tb receptors, we refer to as the ‘TB-drugome’

I really do not think they need to make that into a “ome” word. Mind you, the study is cool and useful. But that word. It is not very good. And thus they are winners of my “Bad omics word of the day” award.

Figure 2. A protein-drug interaction network to illustrate similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red). From Kinnings SL, Xie L, Fung KH, Jackson RM, Xie L, et al. (2010) The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Comput Biol 6(11): e1000976. doi:10.1371/journal.pcbi.1000976 

Hat tip to @7T1 and @dgaston83 and @toranaga for pointing this one out.
——–
This is from the “Tree of Life Blog”
of Jonathan Eisen, an evolutionary biologist and Open Access advocate
at the University of California, Davis. For short updates, follow me on Twitter.

——–

YARFOA: Yet another reason for #OpenAccess: speeding innovation in aquaculture

Just saw this interesting paper arguing that open access to literature is critical for the field of aquaculture. The paper argues that open access to literature has accelerate innovation by promoting more partnerships with hobbyists and with others who might normally be outside the “inner circle.” Definitely worth a read and it fits under my “YARFOA” category – Yet Another Reason For Open Access.

The paper is “The importance of open access in technology transfer for marine ornamental aquaculture: The case of hobbyist-led breeding initiatives” from the Journal Aquaculture, Aquarium, Conservation & Legislation International Journal of the Bioflux Society.

It is is by Andrew Rhyne who is connected with the New England Aquarium and also at Roger Williams University.

I love the concluding paragraph by the way:

Opening the door to an open process. I would hope that others would join me in supporting the free flow of information by publishing their work in open access journals, and encouraging societies like the World Aquaculture Society, the American Fisheries Society, and European Aquaculture Society to go to an open access format. We should fully applaud blogging or posting on discussion forums in real time about efforts to rear new species or develop new live feeds. The dialog that occurs on MOFIB and other online forums can spark innovation that is not possible through traditional formats. I believe that open access is the key to faster breakthroughs, and to better translation between academia, hobbyists, and commercial industry. The Aquaculture field has an opportunity to become an exemplary model for all applied science fields: let’s seize it.

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

——–

Good omics word of the day: transcriptomics

As many of you know, I spend a lot of time bashing #badomics words.  Some have asked if I just hate all omics words.  And the answer is no.  First, I am only annoyed by words that use “omics” or “ome” in the sense of “genomics” or “genome”.  Thus words that use the “ome” suffix in the sense of a cellular complex (e.g., ribosome, proteosome, etc) are not on my radar.  And words that use “omics” in the sense of “economics” (e.g., Obamanomics”) are not my concern either.  My problem is those that in essence are latching onto “genomics” excessively.

And on twitter as well as in my blog I have bashed many such #badomics words including vaccinomics, waveomics, adversomics, bibliome, epitheliome, nutriome, transactome, N-terminome, miRNAome, modomics, tRNomics, variome, Speechome, connectome, negatome, material degradomics, and many more.  I even give out two types of awards here in this regard: Worst New Omics Word Award and bad omics word of the day.  And alas, I am sure I will give out more.

But today I thought it might be useful to be positive.  And thus I am going to discuss what I view as a good omics word.  Not great mind you.  But pretty good.  And this is “transcriptomics” and its relative “transcriptome”.  Both of these are pretty good words.

From Wikipedia here is the definition of transcriptome

The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells. The term can be applied to the total set of transcripts in a given organism, or to the specific subset of transcripts present in a particular cell type. 

This seems to be a perfectly reasonable and useful use of the “ome” suffix.  It is genomic in scale (i.e., all RNA in the cell – not like many badomics words which are too specific).  And it is broad in that it can be used to refer to all the RNA in an organism or cell or such.  The first use I have found is from this paper on yeast in 1997.    But there may be earlier examples.

Anyway – trying to be positive today.  And transcriptome to me is a good omics word.  

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

——–

The Story behind the Meeting: Lake Arrowhead Microbial Genomes 2010 #LAMG10

Well, I really wanted to write up some thoughtful piece about the Lake Arrowhead Microbial Genomes Meeting I just got back from.  But I am in the throes of prepping for beginning teaching a 700+ person class here at UC Davis and well, I just can’t put enough effort into the meeting write up as I would like.  So perhaps my live blog page may be all that I will post directly about the meeting (and at the bottom of this post I am re-posting my feed from Friendfeed).

And if you want to see my slides here they are

Jonathan Eisen talk at Lake Arrowhead Microbial Genomics Mtg #LAMG10http://static.slidesharecdn.com/swf/ssplayer2.swf?doc=eisen-100915032755-phpapp02&stripped_title=jonathan-eisen-talk-at-lake-arrowhead-microbial-genomics-mtg-lamg10&userName=phylogenomics

And here is a little write up of sorts – more about the history of the meeting than this 2010 meeting…..

First, some background.  The Lake Arrowhead Microbial Genomes meeting was, well, in Lake Arrowhead California.  This is both a town and a lake and is in the San Bernadino Mountains East of Los Angeles.

Fortunately for all of us who were there, UCLA has a conference center in Lake Arrowhead, just off the lake itself.  And for the last at least 12 years, every two years, there is a meeting in September at this Conference Center that focuses on microbial genomes in one way or another.  The meeting has changed names, and has gone through a few different major financial supporters, but has always been organized in a large part by Jeffrey H. Miller from UCLA.  Do not confuse him, please, with Jeffrey F. Miller, another microbiologist from UCLA.  That would be a bad thing.  Sort of like confusing me with my brother Michael.

Anyway, Jeffrey H. Miller has been the major force behind organizing this meeting and he has always done a bang up job on fostering a great atmosphere for both science and interaction.  I am not sure what it is he does, but it always seems to work.  One component is that Miller clearly believe that a conference is not only about hearing talks.  Too many times recently I have been to meetings that were overscheduled with speakers and no time for relaxation or discussion or other activities (the Open Science Summit in Berkeley comes to mind – at that meeting I had to actually stage a coup of sorts to prevent the organizers from skipping lunch and all breaks just to have more talks).  At the Arrowhead meetings, Miller always leaves a few hours in the afternoons free and then has poster viewing/reception time before dinner, plus reception time after evening talks.  It works out well.

The Lake Arrowhead Microbial Genomes meeting has a bit of an unusual history.  It is in essence part of a yearly meeting that used to be go by the name “Small genomes.” And every two years, it happens in Lake Arrowhead under the direction of Jeffrey H. Miller.  And since 1998 I have gone to this meeting each time it has come around: 1998, 2000, 2002, 2004, 2006, 2008, and now 2010.

It all started for me in 1998.  I originally signed up for the meeting to give a joint talk with A. John Clark.  I was finishing up my PhD at Stanford on Evolution of DNA Repair Genes, Proteins and Processes and had a post doc lined up to work with Clark at Berkeley.  John was the person who had discovered the recA gene many years before with his graduate student Ann Murgulies. Clark, Steven Sandler and others had been working on functional studies of archaeal homologs of recA and has recently turned their attention in collaboration with Norm Pace (who was then at Berkeley) to trying to use PCR amplification of the archaeal recA homologs to study uncultured archaea, much like Pace and others had done with rRNA. This was seemingly perfect for me as I had worked on both rRNA PCR of uncultured microbes and on evolution of recA (e.g., see here, here, and here) and on DNA repair in archaea.

Anyway, John was invited to give a talk at the Lake Arrowhead meeting and he asked if I would do a tag team talk with him where I could present the results of my phylogenomic analysis of DNA repair genes across the available genome sequences.  So I said sure.  I had no idea what I was getting into, but I went to the meeting.

Alas, there was some awkwardness there because after accepting the post-doc at Berkeley with Clark, I told him I was going to have to drop it.  That was because in the meantime I had finagled my way into going to a dinner with Craig Venter when he came to Stanford to give a talk.  At the dinner I proceeded to tell Craig that I thought some of the evolution stuff he was doing was sketchy and that the genome annotation at TIGR could be improved by phylogenetic analysis.  I drew on napkins, told him about some of my recent papers and eventually he invited me to interview for a job.  The interview went well and both I and my then fiancé now wife were both offered faculty jobs at Craig’s institute “TIGR”, which we accepted.

So here I was giving a joint talk with Clark yet had just told him I was ditching him for another job.  Well, we soldiered through – but the rest of the meeting went well.  I met all sorts of interesting people, developed multiple collaborations, and had a very good time.  Shortly thereafter I moved to TIGR and began life as a genome sequencer.  For more on the 1998 meeting, alas, there is not much out there on the web.  But I did find my meeting book and some notes and I scanned them in (see below).


So when I got an email in February 2000 inviting me to give a full talk at the 2000 Arrowhead meeting, I accepted immediately.  The 2000 meeting was good and so when I was again invited to talk in 2002 I said yes too.  And so it went.  Back in 2004.  And again in 2006. And again in 2008.  And now again in 2010.  If you want to learn about these past meetings, one way is to go to the meeting web pages.  Those from 2008 and 2006 and 2004 are still up.  Those from prior years are not, but I found two of them by going to the wonderful Internet Archive/Wayback Machine by entering the web address from the other years and changing the year in the http.  See 2002, 2000.  Still trying to track down the 1998 one.

But of course, meeting outlines on the web are not ideal for learning about past meetings.  I have scanned the programs for all the meetings as well as some of my notes, but those too are less than ideal.  I have been unable to find much of interest out there about the meetings before 2006.  But I did blog that 2006 meeting (see here) as well as the one in 2008 (see here and here) where some detail can be found.

It would take too much out of me to retroblog all these past meetings so I am just going to post links to the programs for the ones in 1998, 2000, 2002, 2006, and 2008 (still working on 2004).  I scanned these in, did OCR and converted to PDF.

But I note, perhaps my favorite part of these meetings have been the quotes. Many of these are in the slides from my talk embedded above but here goes

2004

  • Space-time continuum of genes and genomes
  • Gene sequences are the wormhole that allows one to tunnel into the past
  • The human mind can conceive of things with no basis in physical reality
  • Thoughts can go faster than the speed of light

2006

  • The human guts are a real milieu of stuff
  • You better kiss everybody
  • Microbes not only have a lot of sex, they have a lot of weird sex
  • This is how you do metagenomics on 50 dollars, and that’s Canadian dollars

2008

  • Antibiotics do not kill things, they corrupt them
  • There comes a point in life when you have to bring chemists into the picture
  • The rectal swabs are here in tan color
  • And there’s Jeffrey Dahmer
  • We are the environment. We live the phenotype.
  • If I have time I will tell you about a dream
  • A paper came out next year

2010

  • We have been using this word for many years without actually realizing it was correct
  • Another thing you need to know” pause “Actually you don’t NEED to know any of this
  • “I have been influenced by Fisher Price throughout my life
  • Don’t take that away from us
  • It takes 1000 nanobiologists to make one microbiologist
  • I am going to wrap up as I hear the crickets chirping
  • And we will bring out the unused cheese from yesterday
  • In an engineering sense, the vagina is a simple plug flow reactor
  • This is going to be ironic coming from someone who studies circumcision
  • A little bit about time, but I am going to spend a lot less time on time than on space

And with those I will close out my month – delayed posting about the Lake Arrowhead Microbial Genomes Meetings.  Looking forward to 2012.

————————-
Here are my tweets as captured by Friendfeed – click on the “View on Friendfeed” button to see the older ones.

Update 9/2012 – Friendfeed embed broken so deleted it.  But some other ways to see some of the notes

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

——–

Figuring out figures in scientific papers: new search / ranking method outline in PLoS One paper

Just a quick post here.  A colleague just sent me a link to her fascinating new paper in PLoS One: PLoS ONE: Automatic Figure Ranking and User Interfacing for Intelligent Figure Search

In this paper Hong Yu from the University of Wisconsin in Milwaukee describes a system for better automated characterization of figures from scientific papers.  The system is available through their webserver “Ask Hermes“.

If you want to learn more about the system I suggest you read the paper.  Or watch their video.

Basically the general idea is summarized in their background section of the abstract:

Figures are important experimental results that are typically reported in full-text bioscience articles. Bioscience researchers need to access figures to validate research facts and to formulate or to test novel research hypotheses. On the other hand, the sheer volume of bioscience literature has made it difficult to access figures. Therefore, we are developing an intelligent figure search engine (http://figuresearch.askhermes.org). Existing research in figure search treats each figure equally, but we introduce a novel concept of “figure ranking”: figures appearing in a full-text biomedical article can be ranked by their contribution to the knowledge discovery.

I particularly like that they also allow searching just for open access figures, which may be of significant value to people who want to do things like make a slide presentation with no copyrighted/protected material in it.  For example see the results of a search for open access figures using the keyword phylogenomics.

Anyway – definitely worth checking this out.

Yu, H., Liu, F., & Ramesh, B. (2010). Automatic Figure Ranking and User Interfacing for Intelligent Figure Search PLoS ONE, 5 (10) DOI: 10.1371/journal.pone.0012983

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

——–