Faculty position at NCSU on “Global Environmental Change and Human Well-Being”

NCSU_GEC Hire 2013- job ad 9_24_13.pdf

Seminar at #UCDavis, 9/26 4 PM, Mary Maxon: “Scientists, Sciences & Science Policy: From the Bench to the White House”

Scientists, Sciences & Science Policy: From the Bench to the White House

Mary Maxon, Ph.D.

4:00 – 5:00 p.m.

The Genome & Biomedical Science Facility (GBSF) – Auditorium, Room 1005

 

Mary Maxon is:

  • Current Head of Strategic Planning and Development for the Biosciences Area at the Lawrence Berkeley National Laboratory
  • Former Assistant Director for Biological Research, The White House Office of Science and Technology Policy, Washington DC
  • Former Deputy Executive Director, President’s Council of Advisors on Science and Technology, Washington DC
  • Former Marine Microbiology Initiative Lead, The Gordon and Betty Moore Foundation
  • Completely brilliant and awesome

MaxonSeminarFlyer_9-26-13_2.pdf

Fecal transplants as treatment for anxiety? Not so fast (but worth pondering)

 Just read this: Gut Bacteria Transplant: A New Treatment For Anxiety? | Psychology Today: calm vs. anxious.  On the one hand, I agree that the microbiome very well may have interesting effects on human behavior.  Well, actually, we know the microbiome does impact human emotion and behavior.  For example, I get pretty anxious when I have gut problems, and we certainly know that the microbiome has a major impact on gut health.  And of course, we know lots of examples of microbes affecting behavior of animals.  The latest on this that I am aware of comes from studies by Wendy Ingram in my brother’s lab at UC Berkeley – who has been looking at Toxoplasma and it’s effect on mouse behavior (e.g., see Toxoplasma infection permanently shifts balance in cat-and-mouse … and Cats, Mice and Toxoplasma Gondii Parasite Weird Love Triangle and Mice Aren’t Scaredy-Cats When Infected By Toxoplasma).

On the other hand, despite the apparent connections between microbes and emotion and behavior in some cases, this does not mean either that (1) microbes have a role in causing anxiety in people or (2) even if microbes CAUSE anxiety that microbiome transplants could treat the anxiety.  Anyway – I certainly think this is an interesting area of research but I urge caution before we go overboard in marketing fecal transplants for everyone with any issues connected to behavior or emotions …

Best evidence yet that we should do away with the "Candidatus" terminology used for uncultured microbes

Just got this email:

Dear Jonathan , I am relatively new to phylogenetics and have developed a keen interest in bacterial phylogenies. I read one the papers which you have published in Nature on the same topic. I needed some help. Thing is, I have constructed a bacterial phylogeny based on 16s rRNA and have found that Candidatus species differ by a really great extent from one another, and appear to be in completely different clades. I need some way to verify this and was wondering if you could send me the phylogeny you have created in order for me to verify. Thank you

I have been arguing for years that the use of the term “Candidatus” to describe microbes is a bad idea.  This email is exactly the kind of thing I worry about.  Candidatus is a term used “for well characterized but as yet uncultured organisms.” (A nice description of the history of the term is here).  The problem with Candidatus are many – including the confusion such as evidenced by this email – in that people who are not used to dealing with the term have no clue what it means.  But in addition, the constraint that one is not “allowed” to name things unless they have been cultured is silly, outdated, and damaging to the field.  But I can write about that some other time.  For now, this email will suffice …

Some examples of Candidatus names from http://www.bacterio.net/candidatus.html

ASU tenure-track search – 2 bioengineering faculty positions

Two faculty positions available at ASU:

  1. Synthetic/ Systems Biology
  2. Molecular, Cellular, and Tissue Engineering

Synthetic_Systems Biology.pdf

Advertisement_MCTB_Search_2013.pdf

Lovely – Entangled Bank conference not only only includes men, but has obnoxious FAQ about doing that

Just got pointed to this: These men would like you to kindly shut up about gendered conferences | Feminist Philosophers.  It discusses a painful example of Gender Bias associated with Science conferences.  In this example a charity “or, a supposed charity” is organizing a meeting featuring only male speakers.  And they included a FAQ on the meeting website to explain why there were only men:

Wow.  That is just horrendous.

More about this is available now on Jezebel.

Note – the same group organized another meeting also with only male speakers. http://www.entangled-bank.co.uk/dawkins-in-bristol.html

Guest post by Josh Weitz: IP vs. PI-s: On Intellectual Property and Intellectual Exchange in the Sciences and Engineering as Practiced in Academia


Today I am pleased to publish this guest post from my friend and colleague Joshua Weitz. He does some fantastically interesting research but that is not what he is writing about here. Instead he is focusing on intellectual property and sabbaticals …

Joshua S. Weitz
School of Biology and School of Physics
Georgia Institute of Technology

Preface:

This blog entry is inspired by a recent personal experience. However, I believe it serves to illustrate a larger issue that requires open discussion amongst and between faculty, administrators, and the tech transfer offices of research universities.

Context:

I am temporarily based at the U of Arizona (hereafter UA) working in Matthew Sullivan’s group where I am on a 9 month leave from my home institution, Georgia Tech (hereafter GT), spanning the term: August 15, 2013 to May 15, 2014. I arrived on campus and began the process of signing various electronic forms to allow me to use the campus network, get keys, etc.

The gateway to this process was a request to sign a “Designated Campus Colleague (DCC)” agreement: http://www.hr.arizona.edu/dcc. The DCC agreement is the official way the UA establishes an “association” with long-term visitors who do not receive any form of payment from UA (as applies in my case). I would be an Associate of the Department of Ecology and Evolutionary Biology, where the Sullivan group is based. The privileges of the DCC include receiving a UA email, keys to an office, a “CatCard” (Cat = short for Wildcats, the UA mascot) which enables me to access the building after hours, as well as other discounts. The DCC makes it quite clear that I am not an employee and that I will receive no form of payment whatsoever from UA. Indeed, all of this is rather immaterial to my real reason for spending 9 months here – to work in closer collaboration with the Sullivan group on problems of mutual interest. The obligations I must affirm are largely boilerplate (i.e., do no harm) but do include the following identified in Clause 11 of the DCC:

“11. INTELLECTUAL PROPERTY – Associate hereby assigns to the ABOR all his or her right, title and interest to intellectual property created or invented by Associate in which the ABOR claims an ownership interest under its Intellectual Property Policy (the “ABOR IP Policy”). Associate agrees to promptly disclose such intellectual property as required by the ABOR IP Policy, and to sign all documents and do all things necessary and proper to effect this assignment of rights. Associate has not agreed (and will not agree) in consulting or other agreements to grant intellectual property rights to any other person or entity that would conflict with this assignment or with the ABORs’ ownership interests under the ABOR IP Policy”

This clause is worth reading twice. I did. I then refused to sign the agreement. This clause, my refusal to sign the agreement, and what happened next are the basis for this blog entry.

Note that the template upon which my particular agreement is based can be found on the UA website. For those unfamiliar with intellectual property (IP) clauses that universities routinely request visitors to sign, here is a small (random) sample:

  1. U of Texas
  2. U of Maryland Baltimore
  3. Emory University
  4. Washington University @ St. Louis
  5. Northwestern University

It would be possible to collect many more such agreements that apply to both employees and to visitors of research universities.

The issues
The central issue at stake is one of ownership of future intellectual property. Presumably a visitor has decided to visit U of X because U of X is the best in the world and that new, monetizable discoveries will emerge as a direct result of the “resources” at U of X. This may be true. Or, it may not be. However, rather than try and chase IP after it has been created (a tenuous legal position), universities would rather have all visitors assign future IP immediately upon arrival and sort it out later (if and when IP is generated).

This language of “hereby assigns” (as quoted above) is not chance legal-ese. To the contrary, it is clear that the legal staff and upper administration at universities are concerned with respect to the repercussions of Stanford vs. Roche. If you haven’t read up on this case, I encourage you to do so. The key take-away message is that the Supreme Court has ruled that inventions remain the property of the inventor to assign as they see fit unless the inventor assigns inventions to a specific entity (e.g., an employer). As the U of California memo to faculty makes clear, the way that many universities want to deal with this problem moving forward is to reword their employment contracts so that employees immediately assign their IP to their university, rather than “agree to assign” their IP. “Agree to assign” (a clause meant to describe a potential future action) was the language found in Stanford’s prior IP agreement and represented one key component of Stanford losing their Supreme Court case to Roche, to the disappointment of Stanford, other major research universities and the federal government.

Figure 1 – Supreme Court decision on Stanford vs. Roche, remainder available here: http://www.supremecourt.gov/opinions/10pdf/09-1159.pdf

However, scientific visits to other institutions create a complex contradiction whereby institutions ask their visitors to sign agreements that they would never want their own employees to sign while visiting other institutions!

These agreements make perfect sense if only one university retains aggressive IP language (i.e., they grab all the IP of visitors who spend time on their campus and give none away when their own employees become visitors elsewhere). Of course, none of this makes sense once all (or many) institutions adopt such policy as is now the case. For example, how does someone from the U of California system visit UA? Or, as I asked myself, how can I “hereby assign” IP rights to the Board of Regents of Arizona when I have already assigned them to the Board of Regents of Georgia. Moreover, how can I affirm that I have “not agreed (and will not agree) in consulting or other agreements to grant intellectual property rights to any other person or entity that would conflict with this assignment”. Obviously, any faculty visitor already has a prior IP agreement with their employer! What should be done? Well, before I make some recommendations, let me point out that not all visits are the same. Instead of trying for a single blanket IP policy (the approach taken by most companies and apparently co-opted by academia), consider the following scenarios.

A few scenarios

  • Case 1: The visitor learning techniques. Many experimental groups routinely welcome visitors to learn new techniques and practice established techniques on new equipment. In many cases, such visits have a dual benefit: first, the visitor (often a student) learns a new method that they can apply to their research problem; second, the host helps to spread the use of some technique or method that they may have had a hand in establishing. There is a strong degree of cooperation here, one that is common in many, but not all, branches of science and engineering. The objective of such visits is not to perform a key experiment or test but to learn the basic steps that could enable their own advances at some future point. 
  • Case 2: The visitor performing research experiments. In some instances, collaboration requires visits to a peer institution. Such visitors may stay for short- (e.g., = 1 week) periods. The purpose is to generate new scientific data that may, in turn, represent novel IP. The performance of such experiments requires some resource at the host institution, however, it is almost certainly the case that resources (whether personal or material) are also being contributed by the visitor.
  • Case 3: The short-term collaborative visitor. Scientists and engineers routinely visit each other. Why? Perhaps because they like talking about science with their peers or because they like learning about what is happening at other institutions or because they like talking to (and recruiting) students at other institutions, and in many cases, all of the above! Visits may range from 1-2 days (while giving a seminar) to a week (while spending focused time visiting a group that may kickstart a scientific collaboration). I have used the 1 week threshold rather arbitrarily, but it is helpful to classify visitors as either short- (= 1 week). 
  • Case 4: The long-term collaborative visitor. Similar to Case 3, albeit on a longer scale, typically associated with sabbatical visits. Such visits need not involve any use of University resources in the sense that the visitor does not conduct experiments, does not utilize lab equipment, resources, reagents, etc. The purpose of such visits may be to experience a distinct intellectual environment, to stimulate a long-term collaboration, and/or to embark on a new research direction.

Before specifying recommendations that address these case, I simply want to point out that these are different cases. Trying to treat all visitors equally with respect to IP conflicts with both the spirit of open scientific exchange and reflects poorly on the extent to which the drafters of such policy appreciate what takes place during scientific visits. Hence, let me pause and ask you, the reader, to consider: what sort of guidelines would you recommend for each of these cases? And, while you’re busy considering that question, let me also propose a unified equation to try and shed some light on factors that suggest that IP policies are both self-contradictory and self-defeating.

An illustrative “equation” of the costs and benefits of aggressive requests for control of the IP of institutional visitors

I propose the following equation to quantify the total amount of money generated by a scientific visitor to a host institution:

$ = P * M * F

where

P = Probability of the invention taking place, as a direct result of the scientific visit
M = the Monetary value of the invention, accrued over its lifetime
F = Fraction of the dollar value assigned to the host institution.

Indeed, I believe it worthwhile to examine the effect that such policies have on each component, to the extent that university IP policies for visitors are aimed to increase incoming revenues to their institutions. First, how do policies affect the P, i.e., the probability of the invention. Second, do they affect the Monetary value? Finally, how do they affect the Fraction of accrued revenue generated by visitor-initiated IP? Of note: it is clear that when a university asks a visitor to “hereby assign” IP rights, then they are trying to position themselves positively with respect to the 2011 Supreme Court ruling in the Stanford vs. Roche case. In other words, they don’t want to become another Stanford and lose out on potentially significant inventions. However, the key word is potentially.

P: I think it fair to say that such policies are also likely to have negative effects on the P component of this equation. If a visitor knows that a visit to another institution is likely to involve giving up IP, creating conflicts with the IP policy of their own institution, or wasting many hours in trying to resolve such conflicts, are they more or less likely to spend the sort of time and energy necessary to create the IP in the first place? I am quite happy to visit the Sullivan group, but certainly far less happy to be spending time on visitor agreements (although I hope this blog entry may be of service to others). Perhaps others may feels similarly.

M: I don’t know whether such policies have a neutral or negative effect on the Monetary scale of invention (and its future monetization). But, I can’t imagine such IP policies act to increase the monetary scale of invention for which the inventor gives all claim to an entity other than his/her employer without surety of compensation! Moreover, whatever monetary return to the university might ensue, such agreements are also likely to lead to legal costs due to the conflicts that these agreements generate, thereby decreasing the return on the invention.

F: The IP clauses claim to do an effective job of increasing the Fraction of revenue a host institution will acquire. Indeed, they claim to protect 100% of the IP-related revenue. However, given the fact that any such clause is almost certainly in direct contradiction to the employee agreement of their visitor, then it is not so clear which clause of which agreement takes precedence.

In summary, I hope this formula and discussion have shed some light on the costs and benefits of aggressive IP policies. I contend that aggressive IP policies act to increase one aspect of potential revenue but are likely to decrease two other aspects. Whether the cumulative effect is positive or negative remains a topic for someone else’s blog (or study). In any case, the most likely outcome of visits is not necessarily IP but ideas. These ideas are much more likely to be shared in the public domain and perhaps even be the basis for collaborative research proposals to governmental and non-governmental funding groups. If at the end of the day, the university administration is counting $, irrespective of where it is generated, then it would be far more sensible to generate policies that would not favor one type of revenue stream (licensing derived from IP) over another (direct and indirect costs generated from grants). To reiterate: I suggest that aggressive IP policies are likely to negatively effect the probability that interactions occur that lead to monetizable ideas in the first place. Of course, such IP clauses may also have negative effects on the pursuit of knowledge, generation of knowledge, etc. (but wait, that was never the issue anyway).

Recommendations
I am not a lawyer. As such, the recommendations I lay out should not be mistaken for legal advice. Rather, I hope they are viewed as a few practical guidelines to avoid creating legal impossibilities and, in the process, diminishing rather than augmenting the likelihood that meaningful scientific exchange leads to the type of knowledge that will benefit society at large (and in some cases, stimulate revenues for institutions and individuals for whom this is important). These recommendations are meant to apply to instances where visitors from other US universities or the government do not receive a salary/stipend/benefits and therefore are not employees. Cases where a visitor is paid a stipend/salary/benefits suggest a form of employee-employer relationship that involve distinct contractual obligations. Cases of visitors from industry and/or foreign institutions may require separate treatment.

1. Clauses regarding partial/full assignment/protection of IP should not be considered a default standard in visitor agreements unless (i) the visitor will perform experiments and/or directly utilize laboratory equipment, reagents and materials; (ii) the visitor will discuss, view, or in any way interact with proprietary information/materials owned by the university. Identifying such cases could be addressed via simple online questionnaires when establishing the agreement.

2. In the event that language regarding assignment/protection of IP is necessary, such clauses in visitor agreements should not attempt to take primacy over the IP assignment that the visitor almost certainly has signed with their employee. Rather, they should specify their rights to ownership over their employee’s portion of IP generated as a result of the collaborative visit. At the end of the day, if IP is generated, then the scientists and engineers involved at both institutions will either come to a satisfactory division of percentage stakes or not. Technology transfer offices at major research universities routinely interact with each other and, I imagine, would be receptive to such a collaborative approach that they routinely practice, irrespective of the rules on the books that may have emerged from other administrative offices.
Thankfully, I believe that an excellent model for the default IP clause in visitor agreement already exists! It is part of the Visitor Agreement to the Kavli Institute of Theoretical Physics at UC Santa Barbara. I have highlighted the clauses that I think should become the new default:

“INTELLECTUAL PROPERTY – To the extent legally permissible and subject to any overriding UC obligations to third parties, your home institution may retain ownership of any patentable inventions or copyrightable software you may develop during your work at KITP while participating in a KITP program as long as: (1) you will be visiting KITP for less than one year; (2) you do not need to be entered into UCSB’s official payroll system; (3) any financial support provided to you by KITP is for travel, living expenses and other similar costs and not to support direct research activities/projects (participation in the KITP program is not considered a direct research activity); and, (4) your activities occur in KITP facilities, only. Please note that if you engage in any research-related activities outside of KITP facilities and programs, the UC’s standard intellectual property policies, which require the UC to own intellectual property developed by visitors using UC facilities, will apply”

Figure 2 – KITP, indeed why would you go elsewhere on campus if you were based here! http://www.kitp.ucsb.edu/sites/default/files/kitp/visitors/localarea/DSCN4997.JPG

The benefits of such a clause is that it assumes the default mode of a visit is for scientific collaboration. That is absolutely correct! Further, it does not try and replace the established agreement of visitors with their home institutions. Indeed, other institutions have tried (to some extent) to address this point, e.g., that of Stanford University which explicitly creates an alternative agreement if a prior employer agreement is already in place: SU 18A. A simple questionnaire could be used to help identify cases that require further discussion. The key here is simple, since creating yet another bureaucratic layer of complexity to visits is not what the scientific community wants nor needs. Indeed, a final recommendation should be:

3. IP agreements should not become an element of short-term visits where laboratory access is not needed (i.e., as part of seminars, symposia, mini-conferences, etc.).

Of course, some might argue: all of this is moot since universities should not be in the business of generating, retaining and fighting for IP that is created with tax dollars, but should give away access to all published inventions. That perspective is important and discussed extensively elsewhere. However, the issue at stake is that for some institutions, IP related revenue is a significant portion of income and this is a likely driver of the increasingly aggressive visitor IP policies that are unlikely to disappear.

In closing, I hope that this entry stimulates some discussion and perhaps even productive conversations to minimize the extent to which IP clauses act at cross-purposes with the visits of Principle Investigators, postdocs and students between peer institutions.

Postscript:

All parties, both at UA and GT, have been incredibly helpful and highly sympathetic as I explained my rationale for taking issue with the IP clause of my visitor agreement. Perhaps they were also surprised that I read the agreement. In the interest of expediting the process, I handed over my case to the appropriate representatives at GT and at UA. After some discussion, they found a way forward. Recall that the original IP clause in my visitor agreement includes a reference to claims of ownership under the “ABOR IP Policy”. The relevant ABOR IP policy applies to two types of individuals:

  1. Any intellectual property created by a university or Board employee in the course and scope of employment, and
  2. Any intellectual property created with the significant use of Board or university resources, unless otherwise provided in an authorized agreement for the use of those resources.”

The terms of my visitor agreement make it clear that I am not an employee. Hence case 1 does not apply Second, because of my situation as a theoretician, I do not plan on using any UA laboratories, equipment, materials, etc.. Moreover, all of my computational-based research will continue to be conducted on GT-owned or personally owned computers. Hence, the only “resources” I plan to utilize are: (i) an office; (ii) the internet. Both UA and GT agree that such activities do not cross the threshold for “significant use” of resources. Hence, case 2 does not apply. So long as my use does not change, then UA should not have standing to claim any IP and my signing of this agreement would not conflict with my employee contract at GT. This understanding now has a paper trail.

As of mid-September 2013 (one month or so after my initial refusal to sign the DCC), I have now signed the agreement and am now officially a Visiting Professor in the Department of Ecology and Evolutionary Biology at the University of Arizona.

Jerusalem Post on Allergy and Fecal transplants

Some interesting tidbits in this Jerusalem Post article: Health Scan: Ungluing the complexity of allergy | JPost | Israel News (a bit overenthusiastic too but just thought I would point some of these lines /quotes out):

  • Studies in adults show that more than 90 percent of patients are cured following such therapy and, experts say, they have every reason to believe the numbers would be equally impressive in children.” – not sure this is true (i.e., the 90% cured level).
  • In less than a decade, we’ll have lab-cooked poop that we can administer to restore balance in the guts of people with a wide array of conditions caused by the imbalance between good and bad germs.” OK – a bit overenthusiastic 
  • But this is my favorite: “The concept is hardly new. The method originated with ancient Chinese healers who gave their diarrhea-ravaged patients “yellow soup,” a concoction of fecal matter and water. Thousands of years later, the delivery approach has evolved” – So – I have been writing and talking about fecal transplants for a while now (e.g., see this) and have linked them to coprophagy and poo tea and such but never heard of the yellow soup thing.

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.

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

Dunn_MVZ