Category: Misc.

Any method allowed for presentations at ASM meeting, as long as you use Powerpoint on a PC.

Just got this email from ASM linking to a message about my presentation at the upcoming ASM meeting in San Francisco.

Here is the message.

Ugggh.

I highlight some parts that I find disappointing at best.  Basically- they say “You can do your presentation is any way.  As long as you convert it to PowerPoint for a PC.”  Never mind other tools to do presentations.  Like Keynote.  Or Prezi.  Or, well, anything else.  Never mind people who use Macs.  Or Linux computers.  Or iPads.

I have NEVER had a problem doing a presentation off of my Mac or iPad.  I have had MANY problems when I have converted my Keynote or PDF files or other material to Powerpoint for a PC.

Oh, and forget about modifying your presentation in response to anything going on in the session (which I do frequently).  I try to tune my slides to the actual crowd.  No longer possible.

Maybe I should use no slides, like I did at TEDMED.  Or maybe I should do a Ross Perot and have charts.  Maybe I will bring my own projector and set it up just before my talk …  who knows … but I hate it when meetings say “Trust us – you won’t have any problems with our system”.

May 9, 2012

Dear Jonathan Eisen;
Thank you for participating as a speaker at asm2012, ASM’s 112th General Meeting in San Francisco, June 16-19, 2012. As a speaker, we kindly request that you consider the following guidelines as you finalize your PowerPoint presentation in the session listed below and also take note of some of the new requirements and changes for asm2012.

Session Details
Session Date/Time: 6/17/2012 3:00:00 PM – 6/17/2012 5:30:00 PM
Session Title: The Great Indoors: Recent Advances in the Ecology of Built Environments
Presentation Title: microBEnet: The Microbiology of the Built Environment Network (If your presentation title is not listed or incorrect, please provide this information to xxxxx immediately.
Length of your Personal Presentation: You are allotted 30 minutes for your presentation or lecture unless otherwise notified by the convener of this session.


New this Year
In order to provide the highest quality experience for our attendees, ASM now requires that all speakers upload their presentations at least four hours before their session begins (if you have a morning session, we recommend you upload your slides at 2:00 p.m. the afternoon before).

Speakers will no longer be permitted to use personal laptops during their presentations. The General Meeting began experiencing a greater number of technical issues as more and more speakers relied on using personal laptops from which to present. This contributed to unique technical situations during individual presentations as well as awkward transitions between speakers. The General Meeting will be utilizing the Presentation Management System for all speakers and our talented and dedicated set of technicians will be well-prepared and equipped to ensure all presentations are presented in the way they are intended and there are smooth transitions between speakers.

asm2012 will feature a networked presentation submission system, called our Presentation Management System. The tips below will help ensure that little, if any, editing will need to be done on-site, allowing you to quickly review your presentation and then attend other sessions in progress. However, ASM strongly recommends that you visit the Speaker Ready Room in Room 120 to test your slides before your session begins to ensure that they run properly on the Presentation Management System. The Presentation Management System can accommodate both Mac and PC based presentations.

The tips below are for both Windows and Mac users. As all the provided computers will be PCs, Mac users should additionally review Considerations for Mac Users at the bottom of this document.

· Building Your Presentation

Movies:
Please take steps to compress your videos. Uncompressed videos will take longer to upload and load within your presentation, and will not be better quality than a modern MPEG-4 codec. We can only accept movies created as MPGs, WMVs, or with the following AVI codecs: MPEG-4 (Divx, Xvid, or WMVs), Cinepack, Techsmith. Flash content (SWF) is fully supported.

Note: It is important your movies do not completely fill the screen. In the meeting room you will only have a mouse to advance your slides. You can only advance your PowerPoint with a mouse by clicking on the slide, not the movie itself.

DVDs:
If you plan to play a DVD as part of your presentation, please notify a technician in the Speaker Ready Room so arrangements can be made for assistance in your meeting room.

Fonts:
We only supply fonts that are included with Office 2010. If you need a specialized font, it should be embedded into your PowerPoint presentation. For instructions on this process, please click on the following link: http://support.microsoft.com/kb/826832/en-us

· Before you Depart

Advance Submission:
You may submit your presentation starting on Friday, May 18. You will receive a notification on May 18 that will provide you with the link to upload your presentation.

Multiple Presenters:
Please do not combine multiple presenters’ PowerPoints into one file and then submit under one name. The Presentation Management System manages presenters individually and any co-presenter will not be able to logon to edit the combined presentation.

Backup:
Please bring a backup copy of your presentation along with you when you depart for your meeting. Copy your PowerPoint and all movies to a folder on a USB drive or CD. PowerPoint does NOT embed movies, and therefore, they must all be placed in the same folder as your PowerPoint.

· At the Meeting

Speaker Ready Room:

Speakers should review their presentation in the Speaker Ready Room prior to their scheduled presentation. The Speaker Ready Room will be staffed with technicians that can assist with any compatibility or formatting issues within your presentation. The computers in the Speaker Ready Room will be configured with hardware and software exactly like the computer in the meeting rooms.

Be sure to use the mouse to advance your slides, not the keyboard, as you will only have a mouse at the podium to advance your presentation. Left click advances the slides; right click goes back. Once you are comfortable that your presentation is complete, confirm the date, time, and room for your session. Be sure to click the green “save/logout” button on the top of the screen.

Speaker Ready Room: Room 120

Hours of Operation:

Friday, 6/15/12: 8:00 a.m. – 5:00 p.m.
Saturday, 6/16/12: 7:00 a.m. – 7:00 p.m.
Sunday, 6/17/12: 6:00 a.m. – 7:00 p.m.
Monday, 6/18/12: 6:00 a.m. – 7:00 p.m.
Tuesday, 6/19/12: 6:00 a.m. – 3:00 p.m.

· Considerations for Mac Users

Pictures:
If you use a version of PowerPoint prior to 2008, please be sure any embedded pictures are not TIFF format. These images will not show up in Windows PowerPoint. With PowerPoint 2010 for the Mac, this is no longer an issue, and any inserted image will be compatible.

Keynote Users:
Please export your presentation as a PowerPoint Presentation. If you are having any issues please notify Mac support at XXXXX for additional help.

By following the guidelines above, your presentation will go smoothly. Should you have any questions not addressed in this document, please feel free to email XXXX.

If you have any questions regarding the scientific program or session details, please contact Janet Mitchell at XXXXXX.

Sincerely,

Janet M Mitchell, M.S.
Program Manager, General Meeting

——–
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.

——–

Dueling microbial diversity talks at #UCDavis on May 2 #symbioses #microbiology

Here is a storification of the dueling microbial diversity talks that happened at UC Davis on Wednesday May 2.
http://storify.com/phylogenomics/dueling-microbial-diversity-talks-at-ucdavis.js?template=slideshow[View the story “Dueling microbial diversity talks at #UCDavis” on Storify]

——–
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.

——–

Draft of a Proposal for a UC #OpenAccess policy – comments wanted

Just got sent this email

Dear Colleagues, 

On behalf of the Academic Senate Library Committee (ASLC), I am asking for your comments on the attached proposed Open Access Publishing Policy for the University of California.. All faculty, including Academic Federation members are invited to post their comments on the Academic Senate web-forum site at http://academicsenate.ucdavis.edu/Forums/index.cfm?Forum_ID=67. Please go to this site to submit your feedback. 

Briefly, the issue is this: the faculty of the University of California, in conjunction with the University Committee on Libraries and Scholarly Communication (UCOLASC), is proposing a new OPEN ACCESS PUBLISHING POLICY that will apply to the dissemination of all scholarly work. UCOLASC is seeking feedback from all campuses on this issue in order to inform a final version of the policy which will be presented to the Universitywide Academic Senate sometime this calendar year. 

The ASLC would appreciate your comments by Wednesday, May 9, 2012. Your ideas will then be shared with UCOLASC in time for its May 25th meeting. The web-forum will remain open substantially past May 9, and we will endeavor to include as many comments up to May 25 as possible. 

Sincerely, 

Brian H. Kolner 

Academic Senate Library Committee

The relate to a draft of a proposal for a new Open Access Publishing Policy being circulated at the University of California. The draft of the proposal can be found here.

UC Davis (and I presume other UCs) are now soliciting comments on the proposal. I would love to here / read comments from anyone. Personally, I think the policy is way to weak as it allows exceptions to be granted …

——–
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.

——–

Social Networks and Scientists: Chronicle for Higher Education Article

Quick post here.

There is a new article in the Chronicle for Higher Education in which I am quoted: Social Networks for Academics Proliferate, Despite Some Scholars’ Doubts

The article discusses many connected topics relating to the use of social media by scientists – though it does not make clear how everything is connected perhaps.  Anyway the author talked to me about Mendeley and various uses of Mendeley and I told her about an effort to create a Mendeley collection of my father’s papers.  The article also discussed LinkedIn, Academia.Edu, Twitter and other social media systems.

Some quotes

Jonathan A. Eisen, a professor of medical microbiology and immunology at the University of California at Davis, used Mendeley to distribute the research papers that his father, Howard J. Eisen, a researcher at the National Institutes of Health, published before he died, in 1987. After struggling to free papers locked behind pay walls, Jonathan Eisen compiled the articles and posted nearly all of them on a Mendeley page he had created for his father. 

Mr. Eisen, a self-described “obsessed open-access advocate,” described the impact in a blog post last year: “Thanks to the social features of Mendeley, more and more people will see and have access to those papers, thus ensuring that they do not wallow in never-never land but continue to have some potential impact on science and society.”

Perhaps most important from my point of view – I love the picture of me taken by Max Whittaker.

——–
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.

——–

Summary of responses to question about metrics for density in phylogenetic trees

I posted a question to Twitter and Facebook about metrics for assessing density in a phylogenetic tree. Here is a “Storification” of the responses. Thanks for the help all.
Any other suggestions welcome in comments … http://storify.com/phylogenomics/metrics-to-quantify-density-of-taxa-sampling-in-a.js?template=slideshow[View the story “Metrics to quantify density of taxa/sampling in a phylogenetic tree” on Storify]

——–
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.

——–

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. http://www.mendeley.com/groups/1152921/_/widget/29/10/

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

——–
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.

——–

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

——–
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.

——–

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 Ås 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.
——–
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.

——–

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

——–
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.

——–

Happy birthday brother Mike

——–
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.

——–