Eisen Lab Blog

Brooke Borel at #UCDavis 6/4 Discussing her New Bed Bug Book “Infested”

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Brooke Borel

“Infested: How the Bed Bug Infiltrated Our Bedrooms and Took Over the World”

Thursday June 4, 2015

10:00 AM – 11:30 AM

UC Davis Memorial Union – MU II

Host: Jonathan Eisen

Brooke Borel is a science writer who is a Contributing Editor at Popular Science and has written for Slate, Aeon, PBS’s Nova Next, and many other publications and sites.  Her first book has just been published by the University of Chicago Press.  The book is   Infested: How The Bed Bug Infiltrated Our Bedrooms and Took Over the World and it is getting praise from all over the place (see some reviews below). She will be at UC Davis on June 4 to discuss the book and some of the fun, interesting, scary and wonderful things about bed bugs.

Some reviews of the book below:

New York Times Book Review (by Marlene Zuk)

“A book about bedbugs is, by necessity, a book about nearly everything: about travel and adventure, about our ­relationship to nature, about how scientists solve problems, about trust and whether we view strangers as friends or foes. It is a book about what people will do under extreme circumstances, and about environmental politics, and art and mental illness. It is even a book about kinky sex. Borel deftly takes us through this arthropod microcosm of the universe, as she traces the culture and biology of a resurgent scourge.”

Carl Zimmer, author of A Planet of Viruses

“Our encounters with bed bugs used to be limited to wishes for a good night’s sleep. But now they’re everywhere—in hotels, apartments, and even subways. In her fascinating book Infested,  Borel chronicles the renaissance of this frightful insect and leaves us marveling at their remarkable biology.”

Maryn McKenna, author of Superbug: The Fatal Menace of MRSA

“In an odyssey that begins with understandable loathing and ends with surprising sympathy, Borel takes us on a smart, subtle, witty journey through the biology and history of the bed bug—an insect that has been our companion for hundreds of millennia, yet one that we barely understand and have no clue how to control. Borel captures the persistence of the bug, the obsessiveness of its foes, and the eagerness of entrepreneurs to turn a quick profit with no thought for the long consequences. It is impossible to read Infested without experiencing fascination, respect—and just maybe, a phantom itch.”

Seth Mnookin, author of The Panic Virus: The True Story Behind the Vaccine-Autism Controversy

“Borel has done the seemingly impossible: written an absolute page-turner of a book about bed bugs. Infested is as engaging as it is erudite, as fun as it is informative. This is popular science writing at its best.”

Dan Vergano, National Geographic

“A fun, wild romp through the wily world of bed bugs and the folks hunting them down. Borel travels from Brooklyn bedposts to Bohemian benches on the trail of this burgeoning pest, itching for the reader as she goes. Infested unveils the secrets of these frankly weird bloodsuckers, right down to their unlikely sex lives, and introduces readers to the obsessives looking to stop their march into your own bed. A terrific science book.”

Guest Post: 5 Things You Probably Didn’t Know About Jonathan Eisen

5 Things You Probably Didn’t Know About Jonathan Eisen 

  1. He doesn’t know how to play Minecraft
  2. He mailed grass when he was a little kid
  3. His new phone is “precious” to him
  4. He loves Let it Go and Taylor Swift
  5. He has very ugly pink boots 
by his bored daughter A. I. Eisen
——–
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.

——–

Overselling the mcirobiome award: Dr Roizen’s Preventative and Integrative Medicine Conference

Just got an email announcement for “Dr. Roizen’s Preventative and Integrative Medicine Conference” in Las Vegas in December 2015.

The announcement did not start of well for me with the gender balance of the key speakers

But since I spoke at this meeting in 2013 and since there was a good gender balance at that meeting, I decided to give the benefit of the doubt and keep reading (though I note – not trying to say this 5:0 gender ratio is a good thing).

And this is when it got worse – here are the bullet points for what one should learn from attending this meeting

  • The key concept about optimal aging that Dr. Roizen learned from 56 million people who took the RealAge® test
  • Smart tips about changing you and your patient’s microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging
  • How you can affect the role of the GI tract in chronic disease
  • How to understand the clinical utility of TMAO testing for monitoring cardiometabolic risk
  • The tricks about measuring your microbiome’s effects
  • Why some choose a plant based diet and why you might not
  • What supplements do you and your patient’s need with a plant based diet to decrease inflammation and improve your microbiome
  • Clarify how a systems-based approach can effectively treat illness and promote wellness
Now – I don’t know much about Dr. Roizen or his optimal aging claims in his books (I am skeptical). But the microbiome stuff in here is silly.
Let’s start with: “Smart tips about changing you and your patient’s microbiomes and what to do for your microbiome to promote weight loss and how it inhibits aging“.  I wonder how he will give these smart tips when as far as I know there is nothing actually known about this.  How the microbiome inhibits aging?  Really? Is this going to be a summary of future research not yet done or even imagined?
What about “The tricks about measuring your microbiome’s effects.”  So – there are 1000s of scientists studying this, they mostly say it is very very very hard to study the effects of the microbiome and Roizen and crew are going to solve this with a few “tricks”?  So is he saying everyone in the field is incompetent since they can’t measure these effects but he knows how to with a few tricks?
Dr. Roizen seems like a smart person and some of what I have heard from him sounds reasonable.  These microbiome claims from him here are a clear example of “Overselling the microbiome” and buying into the hype and not staying with the science. Maybe he was not paying attention for my talk for this meeting in 2013 when I discussed overselling the microbiome

I hope he tones down his claims in the future … but for now he is a winner of a coveted “Overselling the Microbiome Award”.  For other “winners” see here.
——–
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.

——–

Blind trust in unblinded observation in Ecology, Evolution and Behavior (Guest Post by Melissa Kardish)

This is a guest post from Melissa Kardish – a PhD student at UC Davis – writing about a recent paper from work she did at her prior position.  The citation for the paper she is writing about is below:
Kardish MR, Mueller UG, Amador-Vargas S, Dietrich EI, Ma R, Barrett B and Fang C-C (2015) Blind trust in unblinded observation in Ecology, Evolution, and Behavior. Front. Ecol. Evol. 3:51. doi: 10.3389/fevo.2015.00051
Here is her post.

Blind trust in unblinded observation in Ecology, Evolution and Behavior

We recently published our study in Frontiers in Ecology and Evolution where we found that a remarkable number of studies that could be affected by observer bias didn’t indicate whether or not they blinded their research. In fact only 13.3% of studies reported this:

We tried to make this a very transparent study. In addition to journal level data in the main article, we include in our supplemental material a table with the score for every article we read for this study (a summary of these scores per journal can be found in Figure S2 included here). If anything, our results under-represent the amount of studies that could have been scored blind (the real underreporting/underuse of blind observation is probably less than the 13.3% we report). For instance, we did not assess that there was potential for bias in the scoring of microsatellite markers (scored as unlikely to have observer bias). However, we did identify one study which was based on data from microsatellites which did blindly score their markers and report this scoring in their methods (and was therefore scored as “blind” in our study).  We also considered a study blind in its entirety for the purposes of our scoring if only one aspect is reported even if other experiments could also have been influenced by observer bias (Check out our supplemental methods for more ways we conservatively scored in our study).


We recognize that not all EEB studies can be blinded due to a variety of logistical or hypothesis driven reasons; however, we encourage such studies to accurately report this rationale and consider and attempt to minimize observer bias when designing experiments.
Thus far we have had a great response from the surveyed journals. Many of them have notified their editors about the lack of blind observation that we found reported in their journal. One journal has even notified us of plans already in place to address this issue at their next editorial board meeting.
We’re excited to have this work out there and hope this will inspire people to blind their studies and accurately report the science they are doing. We’re also excited to have the study published in an open-access format where we hope the encouragement for blind observation can reach all levels of science. Finally, as reporting of science in our fields improves in the coming years, we hope this study can serve as a template to address other potential concerns in experimental design and reporting.
For our article check out:  http://journal.frontiersin.org/article/10.3389/fevo.2015.00051/full
For our supplemental text and methods: http://journal.frontiersin.org/file/downloadfile/10238/octet-stream/Data%20Sheet%201.PDF/711/2/142945
For our data table with each of the articles we surveyed: http://journal.frontiersin.org/file/downloadfile/10235/octet-stream/Table%201.XLSX/711/1/142945
——–
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.

——–

6/10 at #UCDavis: Workshop on “The Social Life of Medical Data”

The Social Life of Medical Data

A one-day workshop on sharing, pooling and appropriating medical information

http://icis.ucdavis.edu/?tribe_events=workshop-the-social-life-of-medical-data

Wednesday, June 10, 10 am to 5 pm
UC Davis campus (location TBA)

Once digitized, medical information – such as data, images, standards, and codes – travels across different spaces and communities. Smartphones produce and transmit data coming from our bodies, which is shared and discussed in social media platforms and then gathered and analyzed in data centers. Medical information intended for professional use can be appropriated, circulated and used to create communities of caring or participate in biomedical research. At the same time new power asymmetries can emerge, as public institutions and private corporations claim control over increasingly valuable health data.

In this one-day workshop we will analyze the trajectories of digitized medical data. We will discuss how patient communities, care providers, social activists, governments and corporations are designing, fostering and managing alternative approaches to healing and increasingly look towards open source, distributed, and participatory research to do this. Data created from bodies has the potential to expand our understanding of health-related research and scholarly communication practices.

In addition, we will explore different ways of including patient communities in participatory design of tools that assist in the management and analysis of health data. We aim to foster a discussion amongst anthropologists, media scholars and biomedical researcher about the emergent forms of sociality and the politics of health and illness in our digital era.

Speakers include:

Nick Anderson, UC Davis
Carlos Andres Barragan, UC Davis
Dav Clark, UC Berkeley
Alessandro Delfanti, UC Davis
Joe Dumit, UC Davis
Allison Fish, UC Davis
Marina Levina, University of Memphis
Hélène Mialet, UC Berkeley
Kim Surkan, MIT
Orkan Telhan, University of Pennsylvania

Detailed program TBA

Lunch will be served. Please RSVP at this link if you plan to attend http://bit.ly/1PxzbQ6

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UC Davis Innovating Communication in Scholarship
icis.ucdavis.edu

Post-doctoral position in Human Microbiome Research and Women’s Health

POSTDOCTORAL POSITION BIOINFORMATICS & HUMAN MICROBIOME RESEARCH

The Institute for Genome Sciences at the University of Maryland School of Medicine encompasses an inter-disciplinary, multi-departmental team of collaborative investigators with a broad research program related to the genomics of infectious diseases, human microbial metagenomics, functional genomics, and bioinformatics.

TWO POSTDOCTORAL FELLOW positions are currently opened at the Institute for Genome Sciences for collaborative projects between Drs. Jacques Ravel and Rebecca Brotman. Qualified candidates will be enthusiastic, highly motivated and interested in studying the role of the human microbiome in relation to women’s health. The research in this position will focus on how the vaginal microbiome provides protection from sexually transmitted infections (STIs) and in the development of bacterial vaginosis (BV). Projects will apply computational, statistical and bioinformatics approaches on multi-omics’ datasets such as genome sequences, metabolomics, metagenomics, and metatranscriptomics.

The ideal applicant will possess a demonstrable understanding of bioinformatics and computational biology with a background in molecular biology, microbial ecology, statistics and/or molecular epidemiology. The candidate will have a doctoral degree in Genetics, Biology, Microbiology, Computer Science or a related field. Programming and statistical skills in languages such as Perl, Python, C/C++ and R, though not essential, are a plus.

Postdoctoral fellows at IGS benefit from a community of interactive research labs, bioinformatics experts and a variety of state of the art sequencing, and computational resources in a world-class institute dedicated to genomic, basic, and translational research.

To apply, please send a CV, a statement of research interests (2 pages maximum), and contact information for three references to IGS-jobs.

Additional inquiries about the position can be sent to Drs. Jacques Ravel and Rebecca Brotman

jravel@som.umaryland.edu
rbrotman@som.umaryland.edu

Ravel Brotman bioinformatics postdoc description.pdf

CPB Seminar at #UCDavis today: Environmental gradients and interactions with soil biota shape adaptation in teosinte

CPB Spring Quarter Seminar Reminder – Tuesday, May 19, 2015 – 4:10pm – 1022 Life Sciences

May 19: Anna O’Brien
Graduate Student, Population Biology Graduate Group, UC Davis
Title: “Environmental gradients and interactions with soil biota shape adaptation in teosinte”

Nice story from Dan Potter on KQED about Women Science PhDs

Nice story on KQED from Dan Potter: Women Getting Science Ph.D.s Still Face Gender Barriers    

http://blogs.kqed.org/science/files/jw-player-plugin-for-wordpress/player/player.swf

——–
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.

——–

At #UCDavis today Sam Diaz-Munoz, 11:15 am

Department of Microbiology & Molecular Genetics Recruitment Seminar

Samuel Diaz-Munoz, Ph.D.
(NYU)

"The Evolution of Viral Social Interactions"

Monday, May 18, 2015

11:15 am*


197 Briggs*

*note time and location

Diaz-Munoz Seminar 5-18-15.doc

Talk at #UCDavis today: Michael Fischbach on Small molecules from the human microbiota – GBSF noon

Seminar today

“Insights from a global view of secondary metabolism: Small molecules from the human microbiota”

Michael Fischbach, Ph.D.

Assistant Professor, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco

Friday, May 15, 2015 12:10 – 1:00 PM

Genome and Biomedical Sciences Facility Auditorium (GBSF 1005)

Fischbach.pdf