Category: Misc.

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 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.

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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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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.

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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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Why is the paper behind "The Pill Led to Increased Women’s Wages" story free to .GOV but not others?

There is an interesting story going around the web.  An example of the coverage is here at the Huffington Post: Birth-Control Pill Helped Boost Women’s Wages, New Study Shows.  As for all stories I read about new scientific findings, for this one I looked for the research paper or report behind the story.  The Huff. Post story seemed a bit strange in this regard reporting “Bailey and her colleagues report in a National Bureau of Economic Research working paper due to be published in July in the American Economic Journal: Applied Economics.”  Weird – to be published in July.  Why report on it now?  So I sniffed around at other news stories about this topic and found one that said the working paper was published online.  So a little more sniffing (i.e., Googling) led me to the National Bureau of Economic Research (a private non profit entity).  And there, eventually, I found

The Opt-In Revolution? Contraception and the Gender Gap in Wages 

Martha J. Bailey, Brad Hershbein, Amalia R. Miller
NBER Working Paper No. 17922
Issued in March 2012

When I tried to get the paper I discovered it was $5.  Not so bad.  I prefer of course, free and open publication.  Especially if the research and salaries of the authors were paid for by Government grants.  But I did not have the zeal to dig into the funding behind the work.  And 5$ really is not much money.  So I decided WTF – let’s buy it. Alas, then I discovered that I could not just buy the paper but that I had to create a user account of some kind, and I stopped at that point.  Too complicated for a bit of a whim.  So much for buying the paper.

Then I saw further down on the page

Information about Free Papers 

You should expect a free download if you are a subscriber, a corporate associate of the NBER, a journalist, an employee of the U.S. federal government with a “.GOV” domain name, or a resident of nearly any developing country or transition economy.

Most of this makes sense to me except the .GOV part.  Why exactly do they make articles available for free to those who work for the US Federal Government but not for others, like, say, the taxpayers who pay for the US Federal Government?  Again, I get that publishers have to make a living somehow and I was even ready to pay for this article because the fee was low and it seemed interesting.  But I am a bit perplexed and annoyed that people that have a .GOV domain address get stuff for free.  This smells funny to me.  You can’t even give pencils to some people working for the US Federal Government due to gift rules.  But apparently you can give away research papers that are not available to others.  What is the logic behind this?  Aargh.  Well.  Maybe I will download the paper when I within a .GOV domain.  But it will feel icky in some way.

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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: nice review on de novo genome assembly

Just a quick post here.  There is a nice review by Monya Baker on de novo genome assembly in Nature Methods: De novo genome assembly: what every biologist should know : Nature Methods : Nature Publishing Group.  It is currently freely available though not sure if that is permanent or not …

Love the start which quotes my colleague Ian Korf

Asked how mature the field of genome assembly is, Ian Korf at the University of California, Davis, compares it to a teenager with great capabilities. “It’s got bold assertions about what it can do, but at the same time it’s making embarrassing mistakes,” he says

The paper is definitely worth a look …

——–
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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Calling on Nature Publishing Group to return all money received for genome papers and article corrections

Well, let’s see if Nature Publishing Group actually does the right thing here.  A few days ago I showed that they were charging for access to “genome sequencing” papers that were supposed to be freely available (see Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers? #opengate #aaaaaarrgh).  And in researching this I then discovered that Nature Publishing Group has been charging for access to corrections of articles (see Nature’s access absurdity: Human Genome Paper free but access to corrections will costs $64 and Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?).  

Multiple people from NPG have posted on my blog and twitter that they are working on “fixing” these issues.  By which I think they mean “We will make these freely available again.”  But this is not a full fix.  NPG really needs to do a self audit and return ALL money that anyone has paid for access to these articles.  Charging for something that is supposed to be free is not a good thing … and if they want to really fix the issue they need to give any money they got for these papers back.  Note – I already called for them to do this last year when I wrote about the genome papers not being free.  But I never heard back.  Please help put the pressure on them to do the right thing this time.
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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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Corrections Scamming at Nature: Tantalizing clues, to see errors just pay more money #Seriously?

So – after finding out that “corrections” for freely available papers at Nature cost money to get access to I decided to snoop around at Nature Publishing Group’s archives to see how they have handled corrections.

If you search for “Corrections” in Nature Publishing Group’s journals, you see that many / most are labelled as “free” and in fact, they do seem to be free.  That is until about 5 years ago.  As far as I can tell, most “Corrections” published prior to September 2007 are not freely available.

For example see this correction where we are told

“In the News & Views article “Chemical biology: Ions illuminated” by Christopher J. Chang (Nature 448, 654–655; 2007) an error crept into part a of the accompanying figure.”

Tantalizing.  To find out more you need just pay $18.

Or in this correction:

“In the News & Views article “Organic chemistry:A tuxedo for iodine atoms” by Phil S. Baran and Thomas J.”.  

Not so tantalizing.  But nevertheless the full correction can be yours for just $18.

Or this one:

The story ”That’s no laser, it’s a particle accelerator” (Nature 443, 256; 2006) incorrectly stated that the device described could accelerate electrons to 0.15% of their initial speed.

This is one of my favorites:

“A misleading statement appeared in the News and Views article “Cardiology: Solace for the broken-hearted?” by Christine L.”

Want to know what was misleading?  $18.

How about this one:

In Karim Nader’s News and Views article “Neuroscience: Re-recording human memories” (Nature 425, 571–572; 2003) the citation of reference 6 was unclear. The reference concerned — Siegel, J.

How about this one: 

“On page 875 of this Article, there are some typographical errors in the equations used in the computer model. The errors are in the third and fourth full paragraphs on this page.” 

Some don’t even have any clues.  For example in this one we just know the problem is in an article on Transatlantic robot-assisted telesurgery.  Or in this one the issue is with ancient homes for hard-up hermit crabs.

I could go on and on and on.

The corrections one needs to pay to see go back to the 1800s.  For example in 1893 J. J. Walker wrote:

“The next two paragraphs will require slight modifications accordingly; and the last will, of course, be unnecessary. I owe this correction to a correspondence with which Prof. W.”.  Alas, we can’t know the rest without – wait for it – without paying $32. 

I think we should have a context.  Find the correction for which the free part is the most absurd or tantalizing.  I don’t know if other closed access journals do the same thing but it would be great to know …

UPDATE: Some more fun stuff from Nature.  There is a paper from Nature in 2005 “Making sure corrections don’t vanish online“.  It is, of course, available for just $18.

——–
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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Nature’s access absurdity: Human Genome Paper free but access to corrections will costs $64

Ahh – the saga continues.  Though I peripherally noted this in a previous post this deserves a post of it’s own.  Nature Publishing Group has a policy of making genome sequencing papers freely available.  Alas, not all such papers have in fact been made freely available (see Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers?  and A Solution to Nature Publishing Group’s Inability to Keep Free Papers Free: Deposit them in Pubmed Central for more on this).

But I have discovered a just painful though funny absurdity with NPG’s money making machine.  They have in fact made the Lander et al. Human genome paper from 2001 freely available.  But there is an Erratum to this paper.  And if you want to get it (and without getting it there is no way to know what is being corrected), you have to pay $32: Access : erratum: Initial sequencing and analysis of the human genome : Nature.  Oh, and in addition a Correction “We have identified several items requiring correction or clarification in our paper on the sequencing of the human genome” for this paper also costs $32.  So the incorrect version of the paper is free but the corrections will cost you $64.

I wonder, for papers for which people pay $$, if there are corrections do they get them for free?

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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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A Solution to Nature Publishing Group’s Inability to Keep Free Papers Free: Deposit them in Pubmed Central

Well, tick tock tick tock.  I am still awaiting some explanation for Nature Publishing Group once again charging for access to genome papers that they promised would be available for free.  See my last post for more details: The Tree of Life: Hey Nature Publishing Group – When are you going to live up to your promises about “free” genome papers? #opengate #aaaaaarrgh

In the meantime I have come up with a solution even if NPG folks cannot figure one out.  It is very simple.  How about Nature Publishing just deposit’s all genome papers in Pubmed Central and thus even when the money making machine of Nature switches some setting and makes the papers not freely available at the Nature web site(s) for some time, the papers will  still be officially free in Pubmed Central.  I think this is probably the only solution I would trust given that this is at least the third time this has happened.

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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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