Eisen Lab Blog

The Saga of Howard Zochlinski, ex-#UCDavis PhD Student

I met with Howard Zochlinski last week at UC Davis.  His story is like none I have ever heard.  Howard does not have ready web access.  He has little money.  He needs to go to the library to check his email.  And he met with me to ask me to share his story.  And I readily agreed to.  I do not know ANY of the history personally.  I do not even know whether all of what he says is true or not.  But the story is worth putting out there in my opinion for people to make their own judgements.

To begin to get to know the details behind the saga of Howard Zochlinski you might want to start with the petition he just posted on Change.Org: Petitioning To The Honorable John G. Roberts, Chief Justice, and the Honorable Justices of the Supreme Court of the United States.

Other sources of information about Howard’s story are linked below:

The DavisWiki page summarizes some of the details on the saga and I have copied the current text from there below:

Howard Zochlinski has been the center of academic and judicial controversy within California and the UC System, including at UC Davis. 

When Howard was an undergraduate at UC Santa Barbara in the early 1970s he was arrested; none of the charges stuck. 20 years later he was a Genetics doctoral candidate at UC Davis and was arrested by the same policeman who had arrested him back in Santa Barbara. 

The arrests in Santa Barbara resulted in either dropped charges or were thrown out of court. All three of these arrests were made by the same two officers, John Jones and John MacPherson. Howard believes that these arrests were the result of his being a Vietnam War protestor. During his detainment he claims that he was sexually assaulted while in police custody and believes that officer Jones was instrumental in arranging it.
He transferred to UC Berkeley where four years later he graduated with a Bachelors degree. He then earned two Masters over the next six years from University of Hawaii and John Hopkins University. During this time officer Jones transferred from UC Santa Barbara to the UC Davis Police Department. 

In 1984 Howard was admitted to UC Davis as a PhD candidate. In 1992 officer Jones again arrested Howard, this time for stalking. Jones claims that there was nothing personal or targeted about the arrest; Howard claims that the arrest was the result of Jones holding a vendetta and being an anti-semite. This charge as well was dropped when the victim did not appear in court. Howard also maintains that Jones arrest report does not meet the legal definition for the charges that were filled against him. 

In 1993 he was arrested again, but acquitted in court. His defense attorney claimed that the police were not conscientious in the manner in which they handled the case. It does not appear that officer Jones was involved in this case. 

Shortly prior to the time of this last arrest after having been a PhD candidate for 9 years Howard was dismissed for not filling an acceptable thesis by the deadline his committee had assigned. 

Howard believes that the stalking arrest had prejudiced his department against him. Part of his feelings of persecution stem from having had a conduct hold placed on his academic record; one with an end date in the year 2099. Student Judicial Affairs says that this was a clerical error. Howard thinks that this contributed to his difficulty in landing a job.
Howard filed a lawsuit with the University in regards to his dismissal as a student. As of 2006, the details and status of this lawsuit are unknown. In 2005, the Academic Senate of UC Davis overwhelmingly ruled to re-admit Zochlinski as a student. Such a ruling by the Academic Senate is fairly unheard of, prompting University officials to question what would happen next. However Jeff Gibeling, Dean of Graduate Studies, ruled against readmitting Zochlinski on the basis that his predecessor had made the same ruling. As such, this case is still ongoing.

I am still trying to wrap my brain around the whole saga.  But if even a tiny fraction of it is true, which certainly seems to be these case, he has been pretty badly treated.  Again, I do not know all the details or what is the “truth” but I can say for certain that Howard continues to struggle and I cannot for the life of me see any reason not to allow him to be readmitted as a student.

——–
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 UC Berkeley 9-23 9:30 AM: Rob Dunn “Finding Discoveries in Biology from Our Homes and Bodies”

Dunn_MVZ

Faculty position in Microbiology at CSU San Bernardino

Got this by email and thought it would be of interest:

Tenure Track Faculty

Microbiology

The Department of Biology at California State University San Bernardino invites applications for a tenure track position at the rank of assistant professor in the area of microbiology. The successful applicant will develop an independent research program and is expected to excel in teaching courses related to microbiology, medical microbiology, microbial ecology, or immunology at the undergraduate and M.S. levels. Candidates must have a record of published research and show potential for developing and sustaining independent, externally funded research involving both undergraduate and M.S. students. Candidates must have a Ph.D., preferably in the biological sciences; postdoctoral experience is desirable. Application deadline is 1 November 2013, but applications will be accepted until the position is filled. Submit curriculum vitae, statement of research accomplishments and goals, statement of teaching philosophy, and three letters of reference to:

Dr. David Polcyn, Chair

Department of Biology

Attn: Microbiology Faculty Search

California State University

5500 University Parkway

San Bernardino, CA 92407

(909) 537-5305

Email: dreynold@csusb.edu

http://biology.csusb.edu

Really? Nature put the #HeLa genome paper behind a paywall? Time for Nature Publishing Group to return ALL money obtained from genome papers

This is just fucking ridiculous.  As I have written about many many times – Nature Publishing Group many years ago promised to make papers reporting genome sequence data freely available.  They do not generally live up to this promise well.  See for example

Today I discovered that not only are some important genome papers not freely available but one for the ages – the paper on the HeLa genome – reported with much fanfare recently as a triumph of an agreement with the family of Henrietta Lacks – is only available if you pay.

Once again I call on Nature Publishing Group to publicly disclose all financial gains that have come from people paying for the these genome papers and for the money to be returned.
——–
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.

——–

Faculty position at the Global Health Institute, EPFL, Switzerland in “microbiota of the gut”

Forwarding this:

Dear Colleagues,

Please find attached an announcement regarding an exciting career opportunity on the Microbiota at the Global Health Institute, EPFL, Switzerland.

I would be grateful if you would forward it to the members of your Institution.

With best regards,

Stewart Cole

Global Health Institute

EPFL, Switzerland

Faculty Position in Microbiota of the Gut.pdf

Can academics use the "copyright termination" system to recover academic works?

Heard an interesting story on copyright termination on NPR last night: Taking Back ‘Funkytown’: Songwriters Prepare For A Custody Battle  By Joel Rose.  This in turn led me to a New York Times article on the same general topic: A Copyright Victory, 35 Years Later – NYTimes.com.

The gist of these stories is that it turns out UC Copyright law has a “termination” provision which allows artists / writers / etc to terminate copyright agreements that they made for work they produced.  This is allowed 35 years after the copyright was assigned.  And many musicians are using this provision of copyright law to reacquire some works they made three and a half decades ago.

So – I am asking the world out there – could this same provision be applied to scientific or academic works?  Would this be a way to move a lot of material that is behind a wall back into the hands of authors and/or into the public domain?  I am looking into doing this with work published by my father as a test case (as part of my long struggle of  Freeing My Father’s Publications (since termination rights apparently transfer to family members if the holder passes away as my dad did in 1987).

So – anyone out there know if this termination has been used for scientific or academic works?

UPDATE: Other reading

——–
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.

——–

Story behind the paper guest post by Corey Nislow (w/ Metka Lenassi) on "Genomics w/o Borders"

Below is another in the “Story behind the paper” series of guest posts here.  This one is from Corey Nislow w/ Metka Lenassi.  If anyone else has published an open access paper on anything relating to this blog and would like to write a guest post on the Story behind the paper, please let me know.

Genomics without Borders: Genome Sequence of the Extremely Halotolerant Yeast Hortaea werneckii 

by Corey Nislow (with Metka Lenassi)

In this guest post (thank you Jonathan!) I wanted to tell the story behind a paper that my colleagues and I published two weeks ago in PLoS ONE. The story also offers an opportunity to talk about what role, if any, a middle author can play in a scientific study.

The story is set in Slovenia a beautiful country which was part of the former Yugoslavia and which is home to about 2 million inhabitants, 2400+ fungal species (thanks Wikipedia) and some very interesting environments. One of these environments is the Secovlje Salterns where one can find the yeast Hortaea werneckii.

A worker harvests sea salt in the Secovlje salterns, July 17, 2010. Some 2600 tons of salt is expected to be produced during the two and a half month season at the salterns.(Xinhua/Reuters Photo)

I hadn’t heard of Hortaea until I started googling around looking for a yeast extremophile that I can grow in the lab to dissect out its nucleosomes to ask questions regarding nucleosome occupancy and transcription in the face of extreme environments. Turns out it was not a crazy idea–

13 years ago a peculiar black yeast Hortaea werneckii was isolated from its natural habitat: waters containing so much salt, it would kill most living organisms instantly. Since then, two small (but enthusiastic) Slovenian groups have tried to understand its halotolerance. This demanded field trips to the beautiful Slovenian coast, but also a lot of hard work and inventiveness to optimizing protocols used for other organisms – and to do it on a low budget. The first important obstacle was actually cultural – to persuade the scientific community that such extreme yeast even exists in nature! You can see it below. We now have ample evidence as Hortaea has been isolated from many seawater-related environments, saline lakes, but also from surface layers of tropical microbial mats in salterns and even from spider webs in Atacama Desert caves. All these different Hortaea strains are now waiting in their freezer (the Ex culture collection) to be analyzed.

Hortaea werneckii growing happily on 2M salt.

The figure below summarizes what was known about halotolerance of Hortaea before the genome sequence was decoded. In brief, high salinity is detected by sensors of the HOG signaling pathway (green arrows), which modulate the expression of salt-responsive genes (underlined green). The expression of other genes also varies; genes with higher expression at high salinity are written in red, repressed genes in blue). The impact of a hyperosmolar environment is countered by increasing the energy supply to drive energy-demanding processes such as export of Na+ and H+, import of glycerol andthe synthesis of compatible solutes. Melanization of the cell wall reduces the leaking of solutes from the cells and restructuring of membrane lipids helps preserve the integrity of the cells. Read this paper if you want to know more: Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96 .

Gostinčar et al, Adv Appl Microbiol. 2011;77:71-96

This critter, as our recent paper reports, is as interesting genotypically as it is phenotypically. The full genome sequence reported in the PLoS ONE paper shows that genome size is 51mB quite a bit larger than its closest relatives, and given the number of gene models detected (20,000!), for all intents and purposes it looks like Hortaea underwent whole genome duplication last weekend!

Piquing my interest, I immediately started searching for the the genome sequence to have a reference to map nucleosome sequencing reads. Turns out, I had requested the strain from Metka years ago, only to find that one of our lab mates, Uros, with whom I was collaborating at the University of Toronto, had performed some of the groundwork on Hortaea for his PhD. But the network connections don’t stop here, I moved to the University of British Columbia last year, and as it happened Hortaea is popular in Vancouver too! Our new colleagues at UBC were working together with the Slovenian team on sequencing and analyzing the Hortaea genome. In fact, the collaboration started in 2005, catalyzed by a poster at the Budapest FEBS conference were Metka, at that time still a PhD student, and Ivan Sadowski started a discussion about the interesting phenotypic switch that Hortaea undergoes between yeast and filamentous forms. So, by virtue of a convergence of curiosity, good luck and generous collaborators I had the good fortune of being an active participant in the study.

So how does this have anything to do with what a middle author does or doesn’t do on a manuscript? And why do I care? 

Well, I recently re-read the comments section of a fellowship application, and ginned up the guts to read the “supervisor/training environment” section. The chief criticism was that I have a lot of papers on which I am not the senior author. So to the skeptics, I would say- even middle authors play important roles in bringing a study to an audience. In my case my self-interests guided my actions, but along the way, I had the chance to learn about an extraordinary critter, and an amazing group of Slovenian scientists. Yeah, I needed the genome sequence, but I was also excited to help drafting the manuscript, have our sequencing facility prepare additional libraries to close some gaps, and now to bring attention to this extraordinary critter.

The genome sequence offers an exciting new start in studies of Hortaea werneckii. Going forward, the Slovenians want to study its transcriptome and proteome in response to increasing salinity. Preparing knock-out mutants is also a must, to find key genes important for halotolerance. We definitely want to take a closer look at all those cation transporters and their functions. It would also be fun to find its mating partner in one of those frozen Hortaea samples. And now that the genome sequence is available to everybody, the research on this extremely interesting species may start to gain more appeal even to researchers beyond the two stubborn Slovenian groups.

Although I might not get to Slovenia in the foreseeable future, I wouldn’t be surprised if one of my graduate students will meet up with the group at an upcoming yeast meeting. This particular student is dragging our lab into evolutionary genomics by trying to see if he can’t get Hortaea to lose some of its genome in long-term culture (I can’t help but think of “Amadeus” where Salieri is telling Mozart that the composition is fine but it has too many notes….). I’m sure the results will be surprising, and am also encouraged to see what our future collaboration will bring.

——–
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 show on KQED on Inspiring Girls and Women to Code #Diversity #STEM

Listened to a nice show on KQED this AM on my bike ride in to work (note – I listen with one earplug in, and one ear free to hear the world around me, and I listed on relatively low volume …).  We still need to do so much to make STEM fields and related fields more diverse …

Inspiring Girls and Women to Code:

  http://www.kqed.org/assets/flash/kqedplayer.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.

——–

Bay Area Malaria Meeting (BAMM) – Tuesday 17 September

Bay Area Malaria Meeting (BAMM)

RSVP by phone: monroe

Come join the ‘updated’ local Malaria Meeting to share your research, policy work, ideas on eliminating malaria, etc. Make your voice heard, network, collaborate and have fun!

Date: Tuesday, September 17th, 2013

Location: Amyris Inc, 5885 Hollis St., Emeryville

Street parking available, accessible by Emery-Go-Round & Amtrak

Time: 6 – 8pm

Format :1- (30 min) Keynote, 2- (15 min) presenters, 30min network

The Key to Malaria Control and Elimination,

Roly Gosling,UCSF- GHG

The Effects of Deforestation and Climate Change on Avian Malaria, Ravinder Seghal, SFSU

Light Refreshments will be served

Sponsored by:

http://berkeley-oakland.mosquitosquad.com/

Families that share everything: Health2Fit video on brother helping sister by being a donor for a fecal transplant

I guess today is fecal transplant day. So why not a little news story from Health2Fit about families that share everything …

——–
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.

——–