Tuesday, December 12, 2017

Retroblogging 1990s talk by James Childress on deep-sea & hydrothermal vent symbioses

Not 100% sure when this talk was but ... here are my notes from a talk at Stanford by Jim Childress on hydrothermal vent symbioses.







Blast from past - Colleen Cavanaugh gets tenure in 1996 at @Harvard

Can't remember who sent this to me but thought I would share.  It is an article about Colleen Cavanaugh, my undergraduate advisor, getting tenure at Harvard in 1996.



Monday, December 11, 2017

Retroblogging seminars: Harry Noller 1993 Ribosomal RNA & Translation

I am going back to posting notes from talks I went to a long time ago ... I have scanned in notes form talks and am posting some of these.  It is something I call "retroblogging".

Here are notes from a talk I saw while at Stanford in Graduate School. The talk was by Harry Noller. 




Sunday, December 03, 2017

Another blast from the past - 1986 Maryland High School Mock Trial Competition Handbook

When I was in high school and in college I was interested in law.  This is why I worked at the Public Defender Service in DC the summer after my freshman year in college and why I still have a passion for things related to forensics.  I was digging through some old files and found by Mock Trail Competition handbook from 1986.  I thought some people might get a kick out of seeing it.









A blast from the wacky packs of the past (~ 1978)

So - I found an old binder of mine that was decorated with Wacky Pack and related stickers.  It is from 1978.  And, well, I thought I would share the pics since they brought back memories of my youth.  And, of course I should have known - lots of people sell versions of these or related ones - e.g., via Amazon.  I seem to remember them being more offensive but these ones seems to be mostly just kind of dorky.



Thursday, November 30, 2017

Good Twitter thread on phylogenetic methods

WMD Video w/ @edyong209: Wolbachia of Male Destruction adapted for fighting dengue, Zika

Another video from Tangled Bank Studios

 

Thursday, November 23, 2017

Temporary injunction against spammy, scammy OMICS publisher & associated groups

Big story: FTC Halts the Deceptive Practices of Academic Journal Publishers | Federal Trade Commission.

From the FTC press release with some bolding by me
A federal court has granted a preliminary injunction requested by the Federal Trade Commission, temporarily halting the deceptive practices of academic journal publishers charged by the agency with making false claims about their journals and academic conferences, and hiding their publishing fees, which were up to several thousand dollars.

The preliminary injunction against OMICS Group Inc., iMedPub LLC, Conference Series LLC, and their CEO, director, and owner, Srinubabu Gedela stems from a complaint the FTC filed last year that names Gedela and his three companies as defendants.

The defendants operate several websites, including OMICSonline.org, iMedPub.com, and Conferenceseries.com.  They advertise hundreds of online academic journals and international conferences for scientists and medical professionals

According to the complaint, the defendants deceptively claim that their journals provide authors with rigorous peer review and have editorial boards made up of prominent academics when in fact, many articles are published with little to no peer review and many individuals represented to be editors have not agreed to be affiliated with the journals.

The FTC’s complaint alleges that the defendants do not tell authors submitting papers for publication that, after their online journals accept an article, the defendants charge the authors significant publishing fees and often do not allow authors to withdraw their articles from submission, making their research ineligible for publication in other journals.

The FTC also alleges that, to promote their scientific conferences, the defendants deceptively use the names of prominent researchers as conference presenters, when in fact many of those researchers had not agreed to participate in the events.

The FTC’s complaint charges the defendants with multiple violations of the FTC Act’s prohibition on deceptive acts or practices.

The preliminary injunction entered by a federal district court in the District of Nevada prohibits the defendants from making misrepresentations regarding their academic journals and conferences, including that specific persons are editors of their journals or have agreed to participate in their conferences.  It also prohibits the defendants from falsely representing that their journals engage in peer review, that their journals are included in any academic journal indexing service, or any measurement of the extent to which their journals are cited.  It also requires that the defendants clearly and conspicuously disclose all costs associated with submitting or publishing articles in their journals.
Some related posts by me:




Monday, November 13, 2017

Of possible interest: Science-Corps "to teach science to underserved students and build science capacity globally. "

Just got an announcement about this from a colleague and thought it might be of interest:



Science-Corps

Providing an opportunity for recent PhD graduates, as Science-Corps Fellows, to teach science to underserved students and build science capacity in the developing world
Finished, or finishing your PhD in a science, technology, engineering, or math (STEM) field? Interested in taking a six-month break from the research/academic track to work in a different part of the world and share your expertise where it is needed? Science-Corps has launched a new fellowship, which provides STEM PhD graduates the opportunity to teach science, design curriculum, and build scientific capacity abroad.

Science-Corps is recruiting STEM PhD students near completion and up to four years post degree completion for placement starting June of 2018. Applications are due by January 31, 2018.


If interested, visit science-corps.org


Great episode of "I Contain Multitudes" on Symbioses in Hydrothermal Vents

Love this - featuring Colleen Cavanaugh - the person who got me into microbiology ...


 


 Note - I have been a scientific consultant to this project.

Monday, October 30, 2017

Storify of #UCDmicroBOOmes Halloween Symposium at #UCDavis on #microbiomes

YAMMM alert: Yet another mostly male meeting - Frontiers in Microscopy at Janelia Farm

So I got invited to a meeting at Janelia Farm today. Alas I cannot go because it is while I am teaching in the Spring. But in pondering the meeting (which is not posted currently on the Janelia site) I decided to snoop around and see what their other meetings looked like. And, as I generally do, I also scanned the meetings to see if they seemed to have diverse participant pools. And, well, the first meeting on their Spring meeting list alas did not look so good from a diversity point of view.
This is the meeting: Frontiers in Microscopy Technologies and Strategies for Bioimaging Centers Network
This unique meeting will bring together directors of imaging centers and program leaders of open access infrastructures. Our goal is to create a platform to explore the frontiers in imaging technologies, discuss common challenges, and strategize how the global imaging community can build a common network to tackle the era of “big data” as well as rapid technological advances in microscopy.
First glance did not look great so I dug into it a bit more. I tried to infer the gender of the people listed on the site by looking for their personal web sites or other descriptions of them to see what gender pronouns were used. When that was not available I guessed based on name or appearance. I know this is not ideal / perfect but it usually does a decent job of estimating gender balance for a meeting.

Here is what I inferred (and color coded). 
  • Male
  • Female

Organizers
  1. Teng-Leong ChewJanelia Research Campus/HHMI 
  2. Antje Keppler, European Molecular Biology Laboratory 

Ok that is good. It has been shown that having a good gender balance of organizers can help lead to a good balance for a meeting. 

Invited Participants
  1. Holly Aaron, University of California, Berkeley
  2. Pablo Ariel, University of North Carolina at Chapel Hill
  3. Richard Cole, NY State Department of Health, Wadsworth Center
  4. Hunter Elliott, Harvard Medical School
  5. John Eriksson, Turku BioImaging
  6. Scott Fraser, University of Southern California
  7. Jeremy Freeman, Chan Zuckerberg Initiative
  8. Ronald Germain, National Institute of Allergy and Infectious Diseases/NIH
  9. Gary Greenburg, Gordon and Betty Moore Foundation
  10. David HoffmanJanelia Research Campus/HHMI
  11. James Jonkman, Advanced Optical Microscopy Facility
  12. Luke Lavis, Janelia Research Campus/HHMI
  13. Jennifer Lippincott-SchwartzJanelia Research Campus/HHMI
  14. Elisa May, University of Konstanz
  15. Robert Price, University of South Carolina
  16. Joshua Rappoport, Northwestern University
  17. Jean Salamero, Institut Curie
  18. Hari Shroff, National Institute of Biomedical Imaging and Bioengineering/NIH
  19. Robert Singer, Albert Einstein College of Medicine
  20. Jason Swedlow, University of Dundee
  21. Aaron TaylorJanelia Research Campus/HHMI
  22. Paul Tillberg, Janelia Research Campus/HHMI
  23. Jean-Yves Tinevez, Institut Pasteur
  24. Michael Unser, École Polytechnique Fédérale de Lausanne
  25. Jennifer Waters, Harvard Medical School
  26. Simon Watkins, University of Pittsburgh
Well, this is pretty skewed.  That comes to 22:4 male; female.

Or 85% male.

The meeting I was invited to had a pretty good gender balance of invited participants.  So maybe this microscopy meeting is an anomaly.  But it made me wonder - does HHMI or Janelia Farm haver a diversity policy for meetings?  I could not find anything in Googling around or looking at their web sites.  If they do not have one, I think they should consider developing one.  I did find many examples of what seems to be a commitment to supporting diversity in STEM by HHMI.  But this meeting is definitely not doing a good job of that.  HHMI can do better.


Thursday, October 26, 2017

Really excellent article on "Imagining the Open University" by Erin McKiernan

This is definitely worth a look:



Imagining the “open” university: Sharing scholarship to improve research and education



Abstract



Open scholarship, such as the sharing of articles, code, data, and educational resources, has the potential to improve university research and education as well as increase the impact universities can have beyond their own walls. To support this perspective, I present evidence from case studies, published literature, and personal experiences as a practicing open scholar. I describe some of the challenges inherent to practicing open scholarship and some of the tensions created by incompatibilities between institutional policies and personal practice. To address this, I propose several concrete actions universities could take to support open scholarship and outline ways in which such initiatives could benefit the public as well as institutions. Importantly, I do not think most of these actions would require new funding but rather a redistribution of existing funds and a rewriting of internal policies to better align with university missions of knowledge dissemination and societal impact.

Sunday, October 15, 2017

From Google Scholar: Follow Related Research for Key Authors

This seems like it could be useful:



Google Scholar Blog: Follow Related Research for Key Authors


Scholar provides several ways to keep up with research in your area. You can set up keyword alerts, get recommendations related to your publications and follow your colleagues’ profiles.

Today, we are adding another approach to stay up to date in areas of your interest. Now, in addition to following articles by and citations to an author, you can follow research that is related to her work. 
To follow related research for an author, simply go to her public profile, click “Follow” and select “New articles related to this author’s research”. Scholar will automatically scan all new publications for articles related to her research and will send them to you as an email alert. 
This is particularly useful if you are a graduate student or an early stage researcher. By following related research for your advisor, your thesis committee and possibly a few key faculty members in your department, you would be able to see the research landscape from their experienced vantage point.

It is also useful if, like myself, you are an industry or medical professional who isn’t active in the research realm but would like to keep up. By following related research for leading scholars, you will be able to quickly view relevant articles in key areas.
The astute reader has no doubt guessed that this can also be used to get email alerts for research related to your own work -- go to your public profile, click “Follow” and select “Recommended articles”.

Monday, October 09, 2017

Offensive overselling of the #microbiome in breast cancer from the Cleveland Clinic





This is just sickening to me.

I saw a news story that smelled funny:  Breast cancer: Bacterial deficiency linked with onset. And I went and found the scientific paper and then the press release from the Cleveland Clinic that the news story seemed based on.  And, well, the press release turns out to be ridiculous.

The paper showed something somewhat interesting but very limited.  Here is the abstract with key parts bolded and underlined by me
It has long been proposed that the gut microbiome contributes to breast carcinogenesis by modifying systemic estrogen levels. This is often cited as a possible mechanism linking breast cancer and high-fat, low-fiber diets as well as antibiotic exposure, associations previously identified in population-based studies. More recently, a distinct microbiome has been identified within breast milk and tissue, but few studies have characterized differences in the breast tissue microbiota of patients with and without cancer, and none have investigated distant body-site microbiomes outside of the gut. We hypothesize that cancerous breast tissue is associated with a microbiomic profile distinct from that of benign breast tissue, and that microbiomes of more distant sites, the oral cavity and urinary tract, will reflect dysbiosis as well. Fifty-seven women with invasive breast cancer undergoing mastectomy and 21 healthy women undergoing cosmetic breast surgery were enrolled. The bacterial 16S rRNA gene was amplified from urine, oral rinse and surgically collected breast tissue, sequenced, and processed through a QIIME-based bioinformatics pipeline. Cancer patient breast tissue microbiomes clustered significantly differently from non-cancer patients (p=0.03), largely driven by decreased relative abundance of Methylobacterium in cancer patients (median 0.10 vs. 0.24, p=0.03). There were no significant differences in oral rinse samples. Differences in urinary microbiomes were largely explained by menopausal status, with peri/postmenopausal women showing decreased levels of Lactobacillus. Independent of menopausal status, however, cancer patients had increased levels of gram-positive organisms including Corynebacterium (p<0.01), Staphylococcus (p=0.02), Actinomyces (p<0.01), and Propionibacteriaceae (p<0.01). Our observations suggest that the local breast microbiota differ in patients with and without breast cancer. Cancer patient urinary microbiomes were characterized by increased levels of gram-positive organisms in this study, but need to be further studied in larger cohorts.
That is it.  Barely significant finding of some clustering of the microbiomes of breast cancer patients versus those of patients without breast cancer.  And yet, this turned in the press release into cancer causing bacteria that they will be fighting with nanotechnology.  Seriously.

The press release title and subtitle is semi OK:
Cleveland Clinic Researchers Find Link Between Bacterial Imbalances and Breast Cancer. Study compares bacterial composition in healthy vs. cancerous breast tissue
But it goes way way way downhill from there.  Here are the parts with problems
  •  In our wildest dreams, we hope we can use microbiomics right before breast cancer forms and then prevent cancer with probiotics or antibiotics
    • Sure, in my wildest dreams I would cure cancer too.  
  • In addition to the Methylobacterium finding, the team discovered that cancer patients’ urine samples had increased levels of gram-positive bacteria, including Staphylococcus and Actinomyces. Further studies are needed to determine the role these organisms may play in breast cancer.
    • Umm.  No. Further studies are needed to see if these organisms play ANY role of any kind in breast cancer.
  • Co-senior author Stephen Grobymer, M.D., said, “If we can target specific pro-cancer bacteria, we may be able to make the environment less hospitable to cancer and enhance existing treatments. Larger studies are needed but this work is a solid first step in better understanding the significant role of bacterial imbalances in breast cancer.
    • Noooooooooooooooooooooooooooo.  You have not shown anywhere that there are "pro cancer" bacteria and this quote clearly implies that you have. 
  • The study provides proof-of-principle evidence to support further research into the creation and utilization of loaded submicroscopic particles (nanoparticles), targeting these pro-cancer bacteria. 
    • What?  This study does not provide ANY proof of principle of this sort.  You have not shown there are any pro-cancer bacteria.  This is ridiculous and offensive.  
No wonder the news stories imply that this study is about preventing breast cancer.  The press release from the Cleveland Clinic is deceptive.  It makes claims about the work that are irresponsible, misleading, and potentially dangerous. The Cleveland Clinic should be ashamed.

And thus the Cleveland Clinic is the winner of this edition of the Overselling the Microbiome Award.


UPDATE 10/16/17

And so the deceptive PR from Cleveland Clinic is now leading to claims of "Antibiotics May Prevent Breast Cancer" See


Friday, October 06, 2017

This week in Science SPAM

I would love it if I could just ignore my Gmail Spam folder.  Alas, every once in a while I find important emails in Gmail Spam.   So alas I cannot ignore it. While digging through today I found a collection of "Science Spam" - that is Spam emails that have some science-y theme.

Here are the ones from this week in my Gmail Spam folder that I identified as being Science Spam.   Most are invites from Spammy journals.  Some are invites from Spammy conferences.  A few are other things.  Do other people get this much science Spam?






Monday, September 25, 2017

Nature Publishing Group continues to deceive about #OpenAccess to genome papers

I was reminded today about the wonderful history of Nature in it's claim that it would make all papers reporting a new genome sequence freely and openly available. I wrote about how this was, well, not the truth, in 2012: The Tree of Life: Hey Nature Publishing Group - When are you going to live up to your promises about "free" genome papers? #opengate #aaaaaarrgh. And today I decided to recheck this.

So I searched for "Genome sequence" on the Nature site

And, well, I found a doozy of an example of a paper that is supposed to be openly available but is not. Initial sequencing and analysis of the human genome



That's right.  The "public" human genome paper is not freely or openly available.  It is $4.99 to rent or $20 to purchase.  Is this Nature's way of saying "We think the Lander et al. paper did not actually report on a genome?" and that the Venter paper truly won the race?  I don't think so.  I think this is a way of Nature saying "How can we make money off of our past papers? Which one gets a lot of looks? What? It is freely available? Change that." or something like that.

Want to bet they will say this is a mistake?  Want to bet they will not refund anybody's money who paid for this?

Here is a simple solution for everyone out there.  Do not trust Nature Publishing Group to make something available even if they say they will.


UPDATE 9/25 1 PM

But wait - there is more.  The Plasmodium genome paper, which I wrote about in 2012 not being available and which Nature promised to fix is again behind a pay wall










And more



UPDATE 10/16/17

Nature has apologized and said they fixed the issue and will refund any money people spent to buy these articles



Friday, September 01, 2017

Trip to Chaa Creek Lodge in Belize - Day 1

Note - writing this with some help from my daughter.

My family and I went on a trip to Belize in early August 2017 and I am posting some notes and pictures from the trip here.

We chose Belize for a few semi - random reasons.  First, we had wanted to go to Europe but we really only could travel just the week before school started for my kids and we felt like Europe was (1) too far (2) would involve too much jet lag and (3) would involve too many Real Madrid fans.  So we started looking around closer to home.  We wanted to go out of the country (out of the USA - not just out of California, though it really is it's own country).  So - well - we looked at Mexico.  And Central America.  And we settled on Belize.

We decided to spend the whole week of our trip at one place and, since we have been going to Hawaii a bit recently, we decided we did not want to spend our time in a beach-like setting, so we looked for places in the inland rainforesty areas.  My wife spent quite a lot of time searching for possible places and she came up with some candidates and after discussions on the pluses and minuses of all the places and after also asking Twitter and friends and such we settled on Chaa Creek.  An ecolodge of sorts with a slight upscale angle.

More on the place and such later.

Right now I really want to start to get some pictures posted.  So here are some from our travel day.

SMF to Dallas to Belize.

On the plane
I did not take too many (well, more than one) pictures on the actual trip.  But suffice it to say we flew on a plane.


An interesting shirt at a shop at the airport

Waiting for our ride while all the local taxi drivers, well, tried to offer us rides in ways I found to be, well, dubious. 

The ride to Chaa Creek was about two hours long.  I took some pics along the way.  Here are some of them.  Oh - and our driver, Edward, was an FC Barcelona fan.  Yay.

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek

On the road to Chaa Creek 
On the road to Chaa Creek 
On the road to Chaa Creek 
Off to the reception building 
Off to the reception building

Off to the reception building

Off to the reception building

We settled in, got some dinner, and were very hot.  Like really very hot.  Like really really warmer than warm.  It was beautiful.  And interesting.  And hot.  Really really hot.  Or, more relevant.  It was hot and really really humid.  I mean, I grew up in the Washington DC area so I know hot and humid.  But I live in California now, where hot and humid usually do not go together.  We get hot in Davis.  Really really really hot.  But dry. Like really really dry. .