Author: Jonathan Eisen

I am an evolutionary biologist and a Professor at U. C. Davis. (see my lab site here). My research focuses on the origin of novelty (how new processes and functions originate). To study this I focus on sequencing and analyzing genomes of organisms, especially microbes and using phylogenomic analysis

Guest Post on Viruses from Claudiu Bandea

From here.

Guest Post Today from Claudiu Bandea .

Claudiu wrote to me after my paper on “Stalking the Fourth Domain” came out.

He wrote

Jonathan,

I posted a comment on your ‘PLoSOne paper’ blog, but I thought of sending you this mail. 

You might be interested in taking a look at the attached paper presenting a fusion model for the origin of ‘ancestral viruses’ from parasitic or symbiotic cellular species, and its implication for the evolution of viruses and cellular domains, which I’m attaching here (you can see the entire series, including comments, at: http://precedings.nature.com/documents/3886/version/1). Possibly, the novel sequences you discovered belong to such ‘transitional forms’ between the cellular domains and the viral domains.

I know it’s a lot of material, but you might want to focus on Fig. 4 and the related discussion about TOLs from the perspective of the current hypotheses on origin and evolution of viruses. Because of your interest in TOL, I want to ask your thoughts on the difference between the concept of TOL based on the line-of-descent, the ways it was historically intended, and the current approaches of using (mostly) sequences which, as you know, due to LGT might not necessarily reflect the line-of-descent relationships.

Best, 

Claudiu 

After a bit of a back and forth I offered to let him write a guest post on my blog about this. He accepted my offer.  I note – I am not endorsing any of his ideas here and to be honest I have not read his papers he refers to – I have skimmed them and the seem interesting but have not had a chance to read them.  I also note – I am a bit uncomfortable with the fact that I cannot seem to find any Web Profile / Web Site / Blog / etc. with more detail about him and his work.  On one hand – ideas are ideas and they can and should stand on their own.  On the other hand context is useful in many cases and I feel like I am missing some context here.  He works at the CDC but I am not sure what he actually does there.  But in the interest of open discussion of ideas and since, well, not having a web site is certainly not a crime, his post is below.

The most efficient way of silencing ideas is not by criticizing them but by pretending they don’t exist. The antidote might be the blogging world.


A couple of decades ago, I published a novel model on the evolutionary origin of ancestral viral lineages. Recently, I updated this model and integrated it into an ambitious unifying scenario on the origin and evolution of cellular and viral domains, including the origin of life; well, that might have just buried it so deep that it’s gone for good even for those with an open mind and noble intentions.


So, I would like to ask you the favor of reviewing and criticizing this model. As a primer, you might want to read a comment I posted last summer on a book review by Robin Weiss. The book was Carl Zimmer’s A Planet of Viruses and the review by Dr. Weiss, one of the most distinguished contemporary virologists, was entitled Potent Tiny Packages, which symbolizes our century-long perspective on the nature of viruses as virus particles. If we have reasons to call Earth a planet of viruses, as I think Carl successfully made the point, then viruses require our full attention, including the right to be correctly identified and to be included in the Tree of Life.


I know, this is a lot of material, but I hope you’ll find it interesting, and I would be thrilled to address your questions and listen to your ideas.

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

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More fun w/ WordClouds: Cloud of Talk Titles for #TedMed

Well, getting more and more excited about speaking at TedMed next week.  The list of speakers and talk titles is quite impressive and unusual.  So – rather than list the details I thought I would make a word cloud using Wordle.  I think it captures the spectrum of talks pretty well. Here is one from just the talk titles (link to Wordle version here).

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

——–

With Twitter I can unfollow, With Facebook I can UnFriend, How Does One "Uncollaborate"?

So – I have this friend who is in need of help.  Suppose you have a collaborator who, well, it is just not working out with.  At one point you were sympatico.  You were friends with scientific benefits (i.e., you worked together well and were friend too).  (No it is not you dear reader – it is someone else).  What do you do now?  How does one break off a relationship with a collaborator.  You might be Co-PIs on a project.  You might share students.  Or you might study the same system.  You might share space or equipment or jointly run some project.  But now you just can’t bear the sight of them.

But the problem is – they still love you.  And they don’t know how you feel.  What do you do?  How do you break off the relationships when there is no “unfriend” or “unfollow button”?   I don’t know (really, it has never happened to me, I swear and no it is NOT you dear reader).

I have looked for an Ann Landers or Dear Abby for scientists but have no found one.  So perhaps we need a new blog or site for people to “break up” as collaborators.  Something like IBreakUp or one of these other services.  But I think de-collaborating is more complex – more like a divorce than a breakup.  Anyone out there know of services to help scientists de-friend a collaborator?  Anyone know of stories where someone had to do this and it became complicated?  Please post – I have even opened up anonymous commenting in case someone wants to use such a function.

——–
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.

——–

More phylogeny fun from Rod Page: TreeBase -> Genome Browser

More phylogeny fun from Rod Page.  Been reading up on his blog post: iPhylo: Browsing TreeBASE using a genome browser-like interface.  Seems very cool.

——–
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.

——–

This looks useful: Online Phylogeny Course from Rod Page

If you have an interest in phylogeny then this is definitely worth checking out – Rod Page has an online phylogeny course: Phylogeny.  It has some nice links in there to other online resources, some videos of talks, and various phylogeny resources.

——–
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.

——–

Reminder: Genome Center & SOM Faculty Recruitment Chalk Talk

Please post and distribute

The Genome Center and School of Medicine would like to present faculty candidate:

Justin Siegel, Ph. D

University of Washington, Seattle

“Metagenomic Enzyme Design”

Friday, April 6, 2012

12:00-1:00 p.m.

4202 GBSF

Siegel search flyer 2 [Read-Only] [Compatibility Mode].pdf

Continued fun with Ligercat

LigerCat Pubmed Cloud of my papers http://ligercat.ubio.org/articles/1365086.cloud

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

——–

My kids tampered w/ the @nytimes Sports section to secretly do April 1 joke on me

P83 P82 P81

See the full gallery on Posterous

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

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In case you haven’t seen it …

For those who read this blog but don’t follow me on Twitter or elsewhere just thought I would share my new project with you: The Eisenome.  Please join in.

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

——–

Nature Precedings – a preprint server for biology akin to arXiv – shutting down as of April 3

Just got this email regarding Nature Precedings.

Dear registrant:

As you are an active user of Nature Precedings, we want to let you know about some upcoming changes to this service. As of April 3rd 2012, we will cease to accept submissions to Nature Precedings.  Submitted documents will be processed as usual and hosted provided they are uploaded by midnight on April 3rd.  Nature Precedings will then be archived, and the archive will be maintained by NPG, while all hosted content will remain freely accessible to all.

Be assured that Nature and the Nature research journals continue to permit the posting of preprints and there is no change to this policy, which is detailed here.

Nature Precedings was launched in 2007 as NPG’s preprint server, primarily for the Life Science community.  Since that date, we have learned a great deal from you about what types of content are valued as preprints, and which segments of the research community most embrace this form of publication.  While a great experiment, technological advances and the needs of the research community have evolved since 2007 to the extent that the Nature Precedings site is unsustainable as it was originally conceived.

Looking forward, NPG remains committed to exploring ways to help researchers, funders, and institutions manage data and best practices in data management, and we plan to introduce new services in this area.  We have truly valued your contributions as authors and users to Nature Precedings and hope that you will actively participate in this research and development with us.

Interestingly, there is no announcement at the Nature Precedings site itself.  I assume the email I received is real (it really looks real) though you never know these days.  It’s too bad.  I like the concept of a preprint server for biology.  Interestingly, one of the alternatives to NP is FigShare (which is pretty cool) which recently became part of the Digital Science group which is a sister group to Nature.  Hmm … wonder what the conversations at joint tea parties between Nature and Digital Science group are like.  Could be fun.

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

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