Saturday, April 28, 2012

Dear Frontiers Journals - I am sick of your SPAM and I want nothing to do with you

Dear Frontiers Journals

Repeated unsolicited emails with no means to unsubscribe oneself (such as the one excerpted below) are SPAM. I like some aspects of the Frontiers journals but your email system has to be changed. I will not submit to or review for your journals until you make some commitment to stopping SPAMMING scientists.
Dear Dr Eisen, The article submission deadline for the Frontiers Research Topic, for which you received a call for participation, is approaching. If you are planning to submit a manuscript and you anticipate any delay beyond the deadline, please inform the Topic Editors and the Frontiers Editorial Office so they can manage the delay. If you have not yet responded to the call for participation or have not yet committed to a submission and you are planning to submit a manuscript, please let us know by responding to this message.
PS - the article alerts also have to stop. For F#*$@( sake clean up your act.

Friday, April 27, 2012

Phylogenetic analysis of metagenomic data - Mendeley group ...

Just a little plug for a Mendeley reference collection I have been helping make on "Phylogenetic and related analyses of metagenomic data." If you want to know more about such studies you can find a growing list of publications at they group collection.

Phylogenetic and related analyses of metagenomic data is a group in Biological Sciences on Mendeley.

Thursday, April 26, 2012

Nice use of PacBio sequencing to characterize methyltransferase specificity

Figure 1.

Rich Roberts just pointed me to this cool paper on which he is a co-author: Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing.  The paper was published in Nucleic Acids Research and is from Robert's group at New England Biolabs and Jonas Korlach's and others at Pacific Biosciences. What is cool is that they used the timing of the real time DNA sequencing to identify bases in particular DNA fragments that were methylated.  And this then allowed them to determine the specificity of particular methyltransferases (first tested on ones with known activity and then on ones with unknown activity).  This highlights one of the unique features of PacBio sequencing - because the method watches DNA replication in real time - if something alters the timing of the replication process - this can possibly be leveraged to detect alterations in DNA chemistry (e.g., methylation, DNA damage, etc).  Folks at PacBio have been promoting the methylation detection capabilities of their system for some time but I guess I did not get that interested in it because I viewed it is analogous to many other tools to quantify methylation.  But with this paper I now realize that the PacBio approach (and perhaps those of other methylation detection systems) are not just about quantifying methylation status on average across a set of DNA pieces, but can also be very specific as to exactly which bases are methylated.  And this in turn can be used to define specificity for a variety of unknown methyltransferases. ResearchBlogging.org Clark, T., Murray, I., Morgan, R., Kislyuk, A., Spittle, K., Boitano, M., Fomenkov, A., Roberts, R., & Korlach, J. (2011). Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing Nucleic Acids Research, 40 (4) DOI: 10.1093/nar/gkr1146

Twisted tree of Life Award #13: Press release from U. Oslo on new protozoan


Wow.  Just got pointed to this press release Rare protozoan from sludge in Norwegian lake does not fit on main branches of tree of life (hat tip to Bill Hooker).  It is a long PR.  And it is riddled with many examples of evolutionary mumbo jumbo - each of which on their own could win a Twisted Tree of Life Award here.  And together, well, I am just going to give it one award - the Twisted Tree of Life Award #14.

Here are some statements that are, well, dubious, and/or painful.

  • Biologists all over the world have been eagerly awaiting the results of the genetic analysis of one of the world's smallest known species, hereafter called the protozoan, from a little lake 30 kilometer south of Oslo in Norway.
    • Wow - really?  All over the world?
    • And why not tell us what the F#&$# it is?  Where is the name of the organism?  WTF?
  • When researchers from the University of Oslo, Norway compared its genes with all other known species in the world, they saw that the protozoan did not fit on any of the main branches of the tree of life. The protozoan is not a fungus, alga, parasite, plant or animal.
    • That is right.  There are five main branches on the tree of life.  Fungi.  Alga.  Parasites.  Plants. And animals.  Uggh.
  • His research group studies tiny organisms hoping to find answers to large, biological questions within ecology and evolutionary biology, and works across such different fields as biology, genetics, bioinformatics, molecular biology and statistics
    • Yes, and I study tiny organisms to answer small questions.
  • Life on Earth can be divided up into two main groups of species, prokaryotes and eukaryotes. The prokaryote species, such as bacteria, are the simplest form of living organisms on Earth. 
    • Yup, two main groups.  As of 40 f3$*@# years ago.
  • The micro-organism is among the oldest, currently living eukaryote organisms we know of. It evolved around one billion years ago, plus or minus a few hundred million years.
    • OMG.  This is a MODERN ORGANISM.  It did not evolve a billion years ago.  It is no older than ANYTHING ELSE ON THE PLANET.  AAAAAARRRGH.
  • The tree of life can be divided into organisms with one or two flagella
    • What?
    • The tree of life can also be divided into organisms with one or two penises.  
  • Just like all other mammals, human sperm cells have only one flagellum. Therefore, humankind belongs to the same single flagellum group as fungi and amoebae.
    • I don't even know what to say here.
  • The protozoan from ├ůs has four flagella. The family it belongs to is somewhere between excavates, the oldest group with two flagella, and some amoebae, which is the oldest group with only one flagellum.
    • Wow - no prior description of the major groups of eukaryotes and now we use excavates (kind of technical) and amoebae (not technical).  Translation error?
    • But even w/ translation issues still very strange.
  • Were we to reconstruct the oldest, eukaryote cell in the world, we believe it would resemble our species. To calculate how much our species has changed since primordial times, we have to compare its genes with its nearest relatives, amoebae and excavates," says Shalchian-Tabrizi.
    • What?  Their species has been around since primordial times?  What?  That is one really old cell. 
  • The protozoan lives off algae, but the researchers still do not know what eats the protozoan. 
    • Why does something have to eat it?
  • The protozoan was discovered as early as 1865, but it is only now that, thanks to very advanced genetic analyses, researchers understand how important the species is to the history of life on Earth
    • Very advanced?  Like, what? Sequencing?  
  • The problem is that DNA sequences change a lot over time. Parts of the DNA may have been wiped away during the passing of the years. Since the protozoan is a very old species, an extra large amount of gene information is required
    • What?  Since it is old they need more DNA? What?
I could go on and on.  I won't.  But I will say one last thing that drives me crazy.  There is no paper attached to the press release in any way I can tell.  So all we are left with is this very very very very bad PR.  Ugh.

Saturday, April 21, 2012

Best #openaccess figures: happy baby, sad baby

From J. Integrated Omics. DOI: 10.5584/jiomics.v2012i2012.76

One of the greatest things about open access papers in my mind is the ability to use the figures for blogs, classes, etc, without having to consult lawyers and other paper pushers. So I am starting a new series here where I highlight some fun/good figures from various open access papers.

The one shown above is from "How has the recent high-throughput sequencing revolution improved our knowledge of infant microbial colonization and health. J. Integrated Omics. DOI: 10.5584/jiomics.v2012i2012.76. By Adrien Fischer, Katrine Whiteson, Vladimir Lazarevic, Jonathan Hibbs, Patrice Francois, Jacques Schrenzel

Tuesday, April 17, 2012

One giant tweet for @MishaAngrist talk at #UCDavis from 3/8

When Misha Angrist visited in March I took notes for his talk on ... paper ... because my phone was dead ... so here is one big tweet for his talk.

Sunday, April 15, 2012

Storification of my talk (and responses to it) at #TEDMED

I made a "storification" of my talk at TEDMED.

Sunday, April 08, 2012

Crowdsourcing some facts for my upcoming #Tedmed talk on #microbes on #humans

OK all I am looking for some help here is finding out some latest pieces of information about the microbes that live in and on people for my Tedmed talk next week Some things I could use


  • 1. What is the number of species of microbes found on one person across their entire body (gut, skin, mouth, etc)? 

  •  2. What is the number of species of known human pathogens (that are microbes) 

  •  3. What human ailments are now thought to be possibly caused by disturbances in the microbiome? 

  •  4. How many viruses (kinds and numbers) are found in the human microbiome? 



  •  5. What is a good source of open (e.g., creative commons) images of the microbes found in / on people? 


 I am going to post these each as a comment below so people can respond to each one ... Thanks
UPDATE 6/4/2012 - Embedding the talk I gave for TEDMED




Tuesday, April 03, 2012

Video of Carl Zimmer's talk from the DOE-Joint Genome Institute User meeting

I really love this world of sharing and openness in science.  Here is a video of Carl Zimmer's Keynote talk from the DOE Joint Genome Institute User meeting.


I note - before his talk I took Carl out to lunch.  Since of course I cannot do anything in a standard way, I bought some sandwiches and some drinks and snacks and took him to the top of Mt. Diablo which is nearby Walnut Creek.  Alas, it took a LONG time to drive up to the top and it was very very windy.  And as I started to get a bit queasy from all the turns I think Carl probably was wondering what I was doing.  But the view from the top was nice (even though the firggin' visitor center and their nice viewing area was closed).  We did see some snow which was also nice.


And then we headed back down, down, down, down, down.  So- I am telling you this because we got back about 1.5 hours before his talk so he did not have much time to recover from the long and windy road.  And yet, I loved his talk.

For his talk I took "visual" notes using my iPad.  I made these using Notability and then it exports as a PDF which was awkward and then I took that an converted to JPGs since Blogger won't deal with PDFs.

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.

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).

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.

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 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.