Tag: Misc.

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

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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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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.

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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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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

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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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Twisted Tree of Life Award #9: Nature News on the "Marsupial" platypus

OK, though this is not as bad as printing the wrong form of DNA on the cover Nature has another faux pas. In a recent Nature News story discussing a recent paper on the characterization of venoms in the platypus, Ewen Callaway reports in Poisonous platypuses confirm convergent evolution : Nature News:

By some accounts, being poisoned by a platypus could qualify as punishment in one of Dante’s circles of hell. In one case report2, Australian doctors described their treatment of a 57-year-old man a few hours after he grabbed one of the small marsupials while fishing. The pain was “so bad I started to become incoherent” the man said, and far worse than the shrapnel wounds he took as a soldier. Ibuprofen and morphine provided no relief, and one finger was swollen and ached more than 4 months after the run-in.

The only problem with this is that the platypus is a monotreme, not a marsupial.

From http://kaboodle.nescent.org/?q=node/594

Fortunately Nature does get this correct on the headline for the story “Genome analysis shows that the monotremes and snakes have similar venoms” but the damage is done in the middle.

The mistake in the middle of the article may seem a very minor thing to most of you out there.  But @an_dre_a is calling for action on twitter from the monotreme antidefamation league.  And I am now posting here and giving Nature my coveted “Twisted Tree of Life Award” (the ninth) to bring attention to this horrendous horrendous offense to monotremes everywhere.

Hat tip to @recher_she on twitter who called my attention to the Nature article because it mentions the “venome” a really #badomics word that I will be writing about later. 
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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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Twisted Tree of Life Award #7 #8: Alroy on "Changing the rules of evolution"

Twisted Tree of Life

Every once in a while I give out an award here for bad discussions of evolution in the media or scientific publications. I call this the “Twisted Tree of Life Award.” And here is a doozy. It comes from a recent paper in Science: The Shifting Balance of Diversity Among Major Marine Animal Groups — Alroy 329 (5996): 1191 — Science

The paper is actually pretty interesting. But the last line of the abstract. OMG. It is beyond awful. Here is the full abstract:

The fossil record demonstrates that each major taxonomic group has a consistent net rate of diversification and a limit to its species richness. It has been thought that long-term changes in the dominance of major taxonomic groups can be predicted from these characteristics. However, new analyses show that diversity limits may rise or fall in response to adaptive radiations or extinctions. These changes are idiosyncratic and occur at different times in each taxa. For example, the end-Permian mass extinction permanently reduced the diversity of important, previously dominant groups such as brachiopods and crinoids. The current global crisis may therefore permanently alter the biosphere’s taxonomic composition by changing the rules of evolution.

That last line saying that the current extinction crisis may change the rules of evolution really really really bugs me. Changing the rules? Please. If they are rules, then, just how, exactly do they change? If they do change, perhaps they should not be rules no?
And as an aside, what is up with Science not printing the full first name of authors? Does that really save space?
Anyway – not much to say here other than that J. Alroy is the winner of my the 8th “Twisted Tree of Life Award” for suggesting that the evidence presented in this Science paper changes the rules of evolution. And a half award goes to the editors of Science for letting this BS get into the abstract.
Previous recipients of this award are
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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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Here’s hoping molecular classification/systematics of cultured & uncultured microbes wins #NobelPrize in medicine

From Wu et al. 2009. A phylogeny driven genomic encyclopedia of bacteria and archaea. Nature 462, 1056-1060 doi:10.1038/nature08656  http://bit.ly/8Y8xea

Well, I am always hopeful.  Every year when the Nobel Prizes come around I am alway hoping that one of them goes to someone involved in studying microbial diversity in some way.  And really, there is a potential Nobel Prize in Physiology or Medicine out there in this area.  Sure they do not give out a Nobel in biology, or evolution or ecology.  But I think a good argument could be made for giving out a Nobel Prize in Physiology or Medicine to those who have worked on molecular systematics of cultured and uncultured microbes.

Why should this attract the attention of those giving out the Nobel Prizes?  Well, without molecular systematics of microbes we would be completely lost in a sea of microbial diversity.  And with such molecular systematics we can not only make much more sense out of the biology of cultured organisms, but we can go to environments and determine who is out there by sampling their genes.  And this type of work has undoubtedly revolutionized medicine, from determining what antibiotics are most likely to be useful in infections, to tracking emerging infectious diseases, to studying the vast diversity of microbes we have not yet cultured in the lab.  Certainly with the growing importance of the human microbiome in medical studies and the growing application of molecular systematics (e.g., rRNA surveys) to all sorts of aspects of microbiology, the time is ripe for an award in this area.

And who would get an award if one was given.  Well, certainly one of the people should be Carl Woese, who pioneered the use of comparative analysis of the sequences of rRNA genes to the study of systematics of microbes.  Woese of course was responsible for proposing the existence of a third branch in the tree of life – the archaea.  And even if you do not personally believe that the “three domain” tree of life is perfectly correct, Woese and colleagues (e.g., George Fox, who was a coauthor on some of the pioneering papers) were responsible for making microbial systematics a much more rigorous science than it had been.

And I think a good argument could be made for including Norm Pace in this Nobel as he was the one mostly responsible for pushing the sequencing and analysis of rRNA genes for studying microbes in the environment (though I note, others like Mitch Sogin also helped pioneer this field).  There is a direct path from Woese through Pace to much of modern molecular studies of microbes in the environment, including the latest approach – metagenomics.  In fact, there has even been a Nobel Prize already given that depended on much of this work – the one in 2005 to Barry Marshall and Robin Warren for discovery of the role of Helicobacteri pylori in causing stomach ulcers.

Anyway – just a short post about this – maybe more later.  But I sincerely think this would be a well deserved area in which to hand out one of those Nobel Prizes.  Not holding my breath, but always hopeful.

Here some potentially related things that I have written that may be useful to read:

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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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BIS002C "Biodiversity & the tree of life" Lecture2&3 more on phylogeny & trees

Well, tomorrow is going to be a bit crazy for me.  I teach four lectures tomorrow for “BIS002C – Biodiversity and the Tree of Life” and UC Davis.  Well, actually, I do each of two lectures twice.  This happens for two reasons.  First, there are two sections for the class and the way we do it, each faculty gives each lecture for which they are responsible twice.  Second, on Mondays, we do two lectures for each section.  In total there are four lectures per week and our schedule is as follows

Section A:  MWF 11-12 M 6-7
Section B: MWF 3-4 M 7-8

So tomorrow at 11 AM I give Lecture 2 for the class to Section A.  Then at 3 PM I give Lecture 2 to Section B.  Then at 6 PM I give Lecture 3 to Section A.  Then at 7 PM I give Lecture 3 to Section B.  Well, enough trying to make it seem like I am working hard.  Especially after PZ Myers gave me a little grief about this on twitter since, well, my teaching load is not actually that big compared to many.

Anyway – back to the class.  I am going to be posting about the class here as much as I can.  To give people an idea of the whole course this is the general highly simplified schema:

Lectures 1-5 Phylogeny (me)
Lectures 6-13 Microbes (Bacteria, Archaea, microbial euks) (me)
Lectures 14-21 Plants and relatives (Jim Doyle)
Lectures 22-24 Fungi  (Jim Doyle)
Lectures 25-36 Metazoa (Susan Keen)
Lectures 37-38 Wrap up, symbioses, etc (Susan Keen)

I do Lectures 1-13 and possibly 37-38.

For the first week or so I am introducing the students to various aspects of phylogeny and phylogenetic trees.  We do this in part because the rest of the class is oriented around using phylogenies and phylogenetic trees so it is important that the students really understand them.

To that end, tomorrow here is the plan:

Lecture 2 will focus on (a) the components of a phylogenetic tree and what they mean plus (b) taxa and groups in trees.  Among the topics we will cover are rooted trees, rotating trees (e.g., vertical vs. horizontal), rotating branches in trees, monophyletic groups/clades, non monophyletic groupings, outgroups vs. ingroups and more.  Oh in addition we will show the awesome Tree of Life movie that we did not get to on Friday. See below

Lecture 3 will then focus on characters and on tracing character evolution on trees.  Among the topics we will cover include traits vs states, homology, ancestral vs. derived, synapomorphies, and the many faces of homoplasy.  Am planning to start posting slides from the class after lecture hopefully starting soon.  But I keep refining them so not going to post before I am close to done ….

Any comments or suggestions welcome …

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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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Quick Tip: if you want someone to share job ads, announcements, etc, send links to web sites not attachments

OK I have had it. I have had it with people who send me job ads and meeting announcements and other things they want me to “share” with colleagues or students. I got six such requests today – two for job ads, two for course announcements and two for meeting announcements.

But this rant may not be what you think. I am not annoyed that they want me to share something. I actually like doing this. What I am annoyed with is how people do this. 95% of the time people send these email requests with an attachment and expect me to forward this on to all who might be interested. And much of the time these attachments are big files, sometimes written in programs that only some people can open.

Does this work some of the time? Sure. Do I sometimes forward these on? Sure. But that approach is so 2005. Here in 2010 there are better ways than email blasts to people who mostly just click delete. In my opinion, the best way to get someone to share something like this is to post your announcement on the web somewhere and then send people a link to the web site. Include a brief summary in the email you send around and if people want more information they can go to the web site. Not only does this save some bandwidth and not clutter up peoples email servers, but it also allows those of us who share via Twitter and Friendfeed and Facebook and so on to more easily send the announcement around. I am sure many people prefer the attachments, but I for one get 50+ attachments a day, almost all of which do not get looked at.

UPDATE 9/23/2012
So – the post above was written two years ago, almost to the day.  And not much has changed.  Excepted perhaps the way people share links (I mention Friendfeed above — I guess I that could be replaced by Google+).

What is an easy way to post a document and then send people a link?  There are many ways to do this including

  • Post as a Google Doc/Presentation in Google Drive and send the link
  • Upload to Dropbox or another such site and, well, share the link
  • Post as a blog post (if you have a blog) or friggin start a blog and post it there
And of course many many other ways.  But please please please stop sending all these files around.  For a while I was posting them to my blog (I can autopost by forwarding email messages to the right address).  But I am sick of doing this for other people and am going to stop.
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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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Probiotic use spreading, lots of money being made, known benefits still murky

A little news report from last week prompted me to write this mini post.  The report (Global probiotics market approaching $30bn by 2015: Report) indicates that the use (and purchase) of probiotics is spreading globally.

I find the whole thing pretty interesting actually. I personally think that at some point we will be able to figure out how to use “good” microbes to manipulate and manage human health and performance in all sorts of ways.  And there is more and more evidence that in some cases probiotics can have positive effects.  So in a way it is not surprising that more and more people are buying and using probiotics.

On the other hand, the evidence showing that probiotics are actually beneficial is still limited.  I note, this is why I have started giving out an “Overselling the microbiome and probiotics award” here.  So far, the best simple site I have found discussing probiotics is from NCCAM – the National Center for Complementary and Alternative Medicine.  This may come as a surprise to some (as it did to me), since NCCAM has been severely criticized by many for its support of pseudoscience (e.g., see here).  I note I am not even remotely trying to defend much of what NCCAM does here.  I am simply pointing out that they have a decent resource on probiotics.

For more on the science of probiotics see “Probiotic Microbes: The Scientific Basis” from ASM.  The report references above clearly seems to overstate the potential of probiotics by suggesting that they are being targeted for use in all sorts of health situations without presenting the caveats that these health benefits are not that well established.

Anyway, given that the evidence for benefits of probiotics is still pretty sparse, the fact that their use is spreading very rapidly is I guess a little bit disconcerting.  I would be willing to wager that a lot of the spread has to do with deceptive marketing practices by probiotic suppliers.  But there is a silver lining to this.  I think over the next few years we will see many new discoveries relating to where and when probiotics can help people and animals and such.  And the fact that the notion of “good microbes” is spreading is a good thing since we certainly need to reduce the “kill all microbes” mentality that has pervaded in some circles (consider the use of antibiotics in all sorts of materials).

Anyway, just a little post here about the spread of probiotic purchasing.  One thing I will end with – the report referenced above mentions that probiotics are being put into all sorts of new foods including “chocolates, cheese, muffins, and sausages”.

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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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Can’t wait for this meeting on Microbial Communities as Drivers of Ecosystem Complexity

I truly can’t wait for this meeting: Keystone Symposia Conference | Microbial Communities as Drivers of Ecosystem Complexity – Program

Organizers: Jacques Ravel, Vincent B. Young, Mitchell Sogin and Trina McMahon. March 25 – 30, 2011 • Beaver Run Resort  •  Breckenridge, Colorado

The current program is listed below.  Still time to register.  Oh, and it is in Breckenridge, CO, which is kind of nice.  If you are interested in microbial communities, especially molecular studies of said communities, this could be the place to be …

  • Norman R. Pace, University of Colorado at Boulder, USA 
    Molecular Analysis of Microbial Communities – Historical Perspective
  • Mitchell Sogin, Marine Biological Laboratory, USA Long-Tailed Microbial Communities
  • Susan Lynch, University of California, San Francisco, USA Microbial Community Analysis Using the PhyloChip
  • Jonathan A. Eisen, University of California, Davis, USA Phylogenetic and Phylogenomic Approaches to Metagenomic Analysis
  • Joseph Petrosino, Baylor College of Medicine, USA Sequencing Technologies Applied to Studying Microbial Ecology
  • Patrick D. Schloss, University of Michigan, USA Developing and Validating Tools for Computational Microbial Ecology
  • Rob Knight, University of Colorado, USA Quantitative Insights into Microbial Ecology
  • Jed Alan Fuhrman, University of Southern California, USA Integrating Molecular and Environmental Data to Evaluate Community Patterns
  • John Heidelberg, University of Southern California, USA Metagenomic Analysis of Marine Microbial Communities
  • Peter J. Turnbaugh, Harvard University, USA Metagenomic Analysis of the Human Gut
  • Susannah Tringe, DOE Joint Genome Institute, USA Bioenergy Metagenomics
  • Stanislav Dusko Ehrlich, Institut National de la Recherche Agronomique (INRA), France A Human Gut Microbial Gene Catalogue Established by Metagenomic Sequencing
  • Trina McMahon, University of Wisconsin-Madison, USA Functional Genomics of Polyphosphate Accumulating Bacteria: ‘Eco-Systems’ Biology for Wastewater Treatment
  • Gregory J. Dick, University of Michigan, USA Talk Title to be Determined
  • Robert L. Hettich, Oak Ridge National Laboratory, USA A Proteogenomic Approach for Characterizing the Molecular Activities of Gut Microbiomes
  • Brendan Bohannon†, University of Oregon, USA Environmental Microbial Ecology
  • Claire Horner-Devine, University of Washington, USA Biogeography of Microbial Communities
  • Thomas Schmidt, Michigan State University, USA Ecologic Strategies of Environmental Microbes
  • Margaret Riley, University of Massachusetts Amherst, USA Antibiotic-Induced Changes in the GI
  • Jacques Ravel, University of Maryland School of Medicine, USA The Temporal Dynamics of the Vaginal Microbiota
  • Forest Rohwer, San Diego State University, USA RNA Virus Communities Associated with Human
  • Zoe G. Cardon, Marine Biological Laboratory, USA Soil Microbial Ecology
  • David A. Stahl, University of Washington, USA Metabolic Modeling of a Mutualistic Microbial Community
  • Jay P. Tiesman, Procter & Gamble, USA Microbial Community Analysis from a Systems Biology Perspective
  • Edward F. Delong, Massachusetts Institute of Technology, USA Systems Biology of Planktonic Marine Microbial Communities
  • David A. Relman, Stanford University, USA Perturbation of the Human Microbiome: Unrest at Home
  • Julie Segre, NHGRI, National Institutes of Health, USA The Skin Microbiome
  • Vincent B. Young, University of Michigan, USA Integrating Human Microbial Ecology in a Clinical Setting
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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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