Category: Misc.

Nature new PLoS One like journal "Scientific Reports"

Just a quick post here. Interesting news from Nature on the Open Access front: Press release archive:
Nature is starting a new open access journal “Scientific Reports”. Some detail from their press release:
All articles published in Scientific Reports will be open access and subject to an article-processing charge (APC). The 2011 APC rate will be US$1350/GB£890/ EURO1046 per accepted manuscript*
…
NPG will make an annual donation to Creative Commons equivalent to $20 per APC paid for publication in Scientific Reports
…
Scientific Reports will publish original research papers of interest to specialists within a given field in the natural sciences. It will not set a threshold of perceived importance for the papers that it publishes; rather, Scientific Reports will publish all papers that are judged to be technically valid and original. To enable the community to evaluate the importance of papers post-peer review, the Scientific Reports website will include most-downloaded, most-emailed, and most-blogged lists. All research papers will benefit from rapid peer review and publication, and will be deposited in PubMed Central.
Wow – sounds remarkably like PLoS One, even though they do not mention PLoS One in the announcement. Good news all around I think – the more OA we have out there the better.
H/T to Tom Sharpton and Katie Pollard for pointing this out.
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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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Taking a much needed blogging/twitter/etc break for a few weeks

Well, am on Winter Break here at Davis and am going to be taking at least a few weeks off of blogging/twitter/etc.  And trying to ignore email too.  I know – probably some irony in posting about taking a break, but whatever … am really taking a break.

Best wishes to all out there and see you next year ….

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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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NASA arsenic story – let’s lay off the personal attacks on all sides

I have many thoughts about the recent NASA – arsenic – microbe story.

Quick summary

  1. NASA announced a major press conference
  2. at the conference they discussed a new Science paper claiming to show the discovery of a microbe that could replace much/some of its phosphate with arsenic
  3. initial press coverage of the paper was very positive and discussed the work as having profound implications for understanding of life in the universe – though some scientists in some of the stories expressed skepticism of the findings
  4. subsequently many science bloggers further critiqued the paper and/or the press coverage
  5. NASA and the scientists have now refused to discuss the criticisms of their work and press interactions
  6. News stories have now come out summarizing the blogger criticisms and also discussing the unwillingness of NASA / the authors to discuss their work
As I said above I have some strong opinions about the published paper and about the actions of many of the people involved.  For example I think NASA handled this whole thing very poorly.  And I think the unwillingness of the authors and NASA to discuss the work by saying such discussion should be done only in the “peer reviewed literature” is really unwise.  
But that is not what I am here to write about today.  I am here to beg for people to calm down on the personal criticisms and attacks of any of the players involved.  I have seen so much out there about the failings of the paper reviewers, about the intelligence of the authors and the bloggers critiquing the authors, and a whole lot of uneducated guesswork about why some of the things associated with this story happened the way they did.  I think it is perfectly fair to express opinions about the original paper, about the press releases and conferences and about the actions of any of the players here.  But I do not think it is reasonable to go beyond that and to attack the people themselves.  Let’s try and make this an open discussion of science and science reporting and not a venue to spout derogatory comments about the people involved 
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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 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:

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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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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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