Sunday, September 14, 2014

Everything You Wanted to Know about the Lake Arrowhead Microbial Genomes meeting #LAMG14

The Lake Arrowhead Microbial Genomes meeting, which happens every other year, is starting tonight.  I love this meeting.  No bias here since I am now a co-organizer.  But I really love this meeting.  I am posting here some background information about the meeting for those interested.  We will be live tweeting the meeting using the hashtag #LAMG14.  This years program is here.

Posts of mine about previous meetings
Blog posts by others
Programs and notes from past meetings
Meeting Web Sites
I have uploaded slides from my previous presentations at the meeting

Friday, September 12, 2014

Fun read of the day: On whimsy, jokes, and beauty: can scientific writing be enjoyed?

This is such a fun paper: On whimsy, jokes, and beauty: can scientific writing be enjoyed? by Stephen Heard in Ideas in Ecology and Evolution 7: 64–72, 2014  I found out about it in an email from Heard, who sent it to me because he had earlier commented on a blog post I had written: The best writing in science papers part 1: Vladimir Nabokov in Notes on Neotropical Plebejinae (Lycaenidae, Lepidoptera).

Anyway - enough about me - what about this paper?  It has so many nuggets of interest I am not sure which to highlight so I will just go through some of it.  Oh - and it is published with a Creative Commons Attribution license (yay).
Abstract: While scientists are often exhorted to write better, it isn’t entirely obvious what “better” means. It’s uncontroversial that good scientific writing is clear, with the reader’s understanding as effortless as possible. Unsettled, and largely undiscussed, is the question of whether our goal of clarity precludes us from making our writing enjoyable by incorporating touches of whimsy, humanity, humour, and beauty. I offer examples of scientific writing that offers pleasure, drawing from ecology and evolution and from other natural sciences, and I argue that enjoyable writing can help recruit readers to a paper and retain them as they read. I document resistance to this idea in the scientific community, and consider the objections (well grounded and not) that may lie behind this resistance. I close by recommending that we include touches of whimsy and beauty in our own writing, and also that we work to encourage such touches in the writing of others.
OK - the title would have drawn me in anyway but the abstract definitely had me.
If scientific writers aren’t sure how to write better, it isn’t for lack of advice. Dozens of guidebooks discuss form, style, and goals in scientific writing (e.g., Montgomery 2003, Davis 2005, Day and Gastel 2006, Katz 2006, Matthews and Matthews 2007, Rogers 2007, Harmon and Gross 2010, Hofmann 2010, Pechenik 2010, Greene 2013, Heard unpubl.).
OK - I am going to have to look at some of these.

Heard documents a bit of a spat between Sprat and Boyle from the 1660s regarding scientific writing.  I especially like the Boyle quote:
To affect needless rhetorical ornaments in setting down an experiment...were little less improper paint the eyeglasses of a which even the most delightful colours cannot so much please the eye as they would hinder the sight...And yet I approve not that dull and insipid way of writing, which is practiced by many...for though a philosopher need not be solicitous that his style should delight his reader with his floridness, yet I think he may very well be allowed to take a care that it disgust not his reader by its flatness...Though it were foolish to colour...the glasses of telescopes, yet to gild...the tubes of them may render them most acceptable to the users (Boyle 1661:11-12, spelling and punctuation modern- ized).
Heard then goes through some different aspects of good scientific writing
  • Sightings (1): Playfulness in the scientific literature
  • Sightings (2): Beauty
Also - he then doscusses pushback against the "notion that whimsy, jokes, and beauty can have a place in our scientific literature." which I have also seen in many contexts.

He ends with suggestions and I quote the whole section with some highlights:
If you write papers that are crystal clear and thus effortless to read, you’ll have achieved the primary goal of scientific writing and your work will be among the best of our literature. But if you want to reach for even more, if you agree with me that we can also offer our readers some pleasure in reading, what can you do? To begin, you can try to write with small touches of whimsy, humanity, humour, and beauty—without, of course, compromising clarity; and even knowing that sometimes, reviewers will make you take them out. I am not suggesting writing in which art shares the stage equally with content (as can be true in the lay literature). Rather, the goal that’s within our reach is clear, functional writing punctuated with occasional nuggets of playfulness or glints of beauty—to extend Boyle’s metaphor, not a telescope of solid gold but one lightly gilded. 
You can also work to encourage pleasure in what your colleagues write, in two complementary ways. First, when you review manuscripts, you can suppress the reflex telling you to question any touches of whimsy, humour, or beauty that you find; you can even (gently) suggest some be put in. Second, you can announce your admiration of writing that has given you pleasure. Announce your admiration to the writers who crafted the passage, to editors who might be considering its fate, and to students or colleagues who might read it. If we choose to, we can change our culture to deliver, and value, pleasure along with function in our writing.
This is a must read paper.  And I really wish more people would endorse the idea that scientific writing can include more than just science.  Of course, there are many who already endorse this notion but for those who do not - give it a try.

Thursday, September 11, 2014

Kudos to Tedmed for the gender ratio of speakers for this year's event

Well done Tedmed.

Here are the speaker pages below.  Notice anything?

The gender ratio of speakers is actually well balanced.  Well done Tedmed.  Well done.

Tuesday, September 09, 2014

International Symposium on Subsurface Microbiology - where men tell us about deep things

Just saw this Tweet:
This refers to this meeting: Call for Abstracts for 2014 Ninth International Symposium on Subsurface Microbiology, Pacific Grove California

The plenary speakers for this meeting are all men
  • Peter Girguis
  • Terry Hazen
  • Rainer Meckenstock
  • Lars Nielsen
  • Aaron Packman
  • Karsten Pedersen
  • Timothy Scheibe
  • Jack Schijven
The last meeting was in 2011 and it was not much better - with one female keynote speaker.
  • Andreas Kappler
  • Karsten Pedersen
  • Christian Griebler
  • Ian Head
  • Frank Löffler
  • Babara Sherwood-Lollar
  • Bo Barker Jørgensen
  • Ken Takai
  • Kai-Uwe Hinrichs
  • Tori Hoehler
Apparently, only men can talk about deep things.  Fun times.

Sunday, September 07, 2014

Story behind the paper: Bonnie Baxter on "A tale of salt and gender" #STEMWomen #Halophiles

After posting A tale of salt and gender: participation of women in halophile research I sent the post to Bonnie Baxter, one of the authors of the article I discussed and I asked if she would be interested in writing a guest post about the "Story Behind the Paper" (for which I have a whole series).  I am so so pleased that she said yes.  I have followed Bonnie's work for many years but this is her first guest post here.  I hope there will be more.  She is a wonderful and brilliant scientist and educator.

Guest Post by Bonnie Baxter
Salty Sisters: The Women of Halophiles

Bonnie Baxter and Nina Gunde-Cimerman at the north arm of Great Salt Lake (2008)

I was drawn to the western US, the extreme landscapes, and ended up at the only liberal arts college in Utah. I had wanted a career doing science with undergraduates, and I set about exploring the microbiota of Great Salt Lake. Since few had studied this incredible spot, I quickly became the go-to person for studies on the lake, and these collaborations and grant projects eventually evolved into an organization I direct called Great Salt Lake Institute. We are dedicated to research, scholarship and education efforts on Great Salt Lake.

There had been no microbiology done on Great Salt Lake since 1979. This is why there was much excitement concerning our emerging data, and in 2004, I was invited to speak at the triennial International Halophiles conference in Slovenia. Halophiles are microbes that thrive at high-salt, and the people who study them maintain an interesting balance of field-work and lab work. I had been to large meeting on DNA repair, DNA replication, nucleases and the like, but I had never met a group who were centered on a theme that connected them around the planet. 

From my first Halophiles meeting (I’ve since attended 2007 in Colchester UK, 2010 in Beijing and 2013 at University of Connecticut), I felt an unusual level of support from the elders of this group. And I noticed that, unlike the NASA meetings or biochemistry meetings I attended, there seemed to be a nice balance of men and women. There were a group of folks who had participated for a long time, without a membership organization, and these people maintained the notion of mentoring in the field. It is this spirit that drew all of us younger folk to participate. 

Friday, September 05, 2014

Paperwork, paper pushing policies push people past pressure points

So I am going to make this simple here.  Paperwork at UC Davis is driving me batty these days.  One thing in particular does not make much sense to me. When I or anyone who works in my lab go on trips associated with work, we have to collect all the receipts for the trip and then these need to be submitted in an intemized way for reimbursement.  With a lot of people going on a lot of trips, this amounts to a lot of work for us, for my administrative assistant, for the UC Davis Genome Center administration, and for the UC administration.  At other places I have worked, and in other situations, people can get reimbursed using a per diem calculation.  Such calculations save an absurd amount of work for people even if they come with some "risks" such as people getting reimbursed for more than they actually spent.  Personally, I would take a 50% per diem to save everyone the trouble associated with all the reciepts and submitting them and checking them and such.

So - the reason I am writing is to ask - what happens at other institutions?  Does everyone have to submit all the receipts?  Or does anyone out there do per diems?

Thursday, September 04, 2014

Nice letter to the editor in the Davis Enterprise taking on school district's anti-science tone

I assume many people heard about the recently released report from the American Academy of Pediatrics where they recommended high school classes start later in the morning than most do right now.  See for example: Let Them Sleep: AAP Recommends Delaying Start Times of Middle and High Schools to Combat Teen Sleep Deprivation.  And this report was covered in all sorts of newsy and bloggy places.   See for example, Amy Graff's article in SFGate and Deborah Netburn in the LA Times.  Overall, the argument presented by the AAP makes sense and seems supported by scientific fundings.  And they go through a lot of scientific reasons for their recommendations.

Alas, Winfred Roberson, superintendant of the Davis, CA schools (also known as the DJUSD) told the Davis Enterprise that the schools here would not be making any changes in response to this report:

“While DJUSD won’t be modifying start times, our role as an educational institution can be to find ways to support our students by giving them the tools that will help them to think through, make adjustments and prioritize their competing forces that may be cutting into the recommended sleep time,” Roberson said. “These are life skills we are helping to build that will help students to function even after graduation.”
And I had missed out on this quote, thankfully, but became aware of it when my wife showed me this letter by Steve Carlip in the Davis Enterprise today:  Don’t ignore the science Davis Enterprise.   I quote from it below:

The superintendent’s response, as reported in Tuesday’s Enterprise, was to simply ignore the science. Instead, he said, the schools will help student “build life skills” to “prioritize their competing forces that may be cutting into the recommended sleep time.” 
Really? The high school is going to teach students to control their circadian rhythms? It’s going to give them the “life skills” to regulate the timing of their bodies’ secretion of melatonin? It will educate them to overcome biological sleep-wake phase delay by sheer force of will?
He completely nailed it here.  I hope Winfred Roberson and the Davis School district rethink their attitude towards scientific studies.

Tuesday, September 02, 2014

The US Postal Service Cares (actually this was kind of a nice gesture)

Well, this is a new one for me and my family.  We got some mail today.  My wife called me over this evening to tell me and said "it might make something good for my blog".  But it was very strange. From the US Postal Service.  In a plastic bag and the bag read "We care ..." see below:

And inside of this was half of a piece of mail.  A card.  It felt very weird.  Like someone was censoring us but most likely some machine just ate the other half.


Add caption
They easily could have just tossed this once it got damaged.  Glad they did this.  Now, mind you, I still detest all their junk mail / bulk mail policies, but this was nice ..

Science Journal SPAM of the Week: the Journal of HIV/AIDS from Sci Forschen

Well, got this email this AM.  It is yet another spammy journal (I don't work on HIV/AIDS).  I particularly like the part where I am called an "eminent personality".

Dear Dr. Jonathan Eisen,
Greetings from the Journal of HIV/AIDS,
We take great delight in inviting you to join the Editorial Board for the Journal of HIV/AIDS , which is an open access, peer reviewed journal managed by Sci Forschen.  Ensuring quality and accuracy for every submitted article is the top most priority for Sci Forschen, and we genuinely believe that someone with the knowledge and experience, such as yourself, can really make a huge difference for us.
Journal of HIV/AIDS , publishes cutting edge research work submitted by scholars from all over the world, and we believe that your presence will polished up with the help of illustrious experts in research field.
We are always striving to involve eminent personalities like you and your standing in the global community makes us confident.
Kindly let us know your valuable response and acceptance if possible with in 48 hours.
Please kindly submit your following particulars to update in our journal website

1. Updated CV
2. Passport Size Photo
3. Short Biography
4. Research Interest
Looking forward for your valuable and soon response.


Editorial Office
Sci Forschen Incorporation
913 Catkin Ct.
San Jose, CA 95128, USA.

Saturday, August 30, 2014

A tale of salt and gender: participation of women in halophile research

Interesting paper on women in science of direct relevance to my work: Frontiers | Salty sisters: The women of halophiles | Extreme Microbiology.  I have been working on halophilic archaea for many years (since introduced to them in graduate school) and published papers on this topic (e.g., see The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon and Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux and more coming).  However, I have never been to a meeting dedicated to the topic and confess I have not thought specifically about the gender of scientists in this field and at meetings in the field and such.  Thus I was pleasantly surprised to see this analysis from Bonnie Baxter, Nina Gunde-Cimerman and Ahoren Oren.  Their abstract is below:
A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.
As part of their paper they analyze participation of women at conference on halophiles:

This is a useful analysis and compendium and it would be great to see this done for as many fields as possible.