GSC COMMITTEE & CLUB UPDATES: MARCH 2016

GSC Career Paths Committee

On February 13, 2017, the GSC Career Path’s Committee kicked off the year with a workshop learning the basics of the Prism Graphpad software. In the past, students had expressed interest in analysis of data using statistical software as well as graphing the data in a presentable fashion. Therefore, the GSC thought a workshop on PRISM would not only be very useful but also have a significant impact on the students’ research careers. The workshop was kindly guided by Dr. Dan Cox, a professor in the Neuroscience department, and it took place in the computer room in the Sackler library. There workshop was well-received, according to GSC representatives Vaughn Youngblood and Roaya Alqurashi. “(The workshop) was a successful one and from who attended they loved it too. The attendees loved how Dr. Cox explained each application you will need to use in Prism with an active learning experience” Roaya said. Vaughn mentioned “the Prism workshop was helpful!  It taught the fundamentals of using Prism along with how to represent different types of data.  Hopefully, we can bring Dr. Cox in for another session with another statistical program like R.” If time permits this year, the GSC Career Path’s Committee hopes to hold several more workshops like this with different analysis softwares (R, SAS, etc.).

Harder, Better, Stronger, Faster through CRISPR?

After a year-long intense and bitter dispute over the rights to patent use of CRISPR-Cas9 gene editing technology in mammalian cells, the US patent office ruled in February that “there is no interference” and that the patent belongs to the Broad Institute. Needless to say, effects of this verdict extended beyond the emotions of the scientists locked in the dispute, as the shares for Editas Medicine, established by Feng Zhang from the Broad, saw a 29% jump by the close of trading. What does this mean for other biotech companies looking to harness the power of this novel technology? It would mean that they can only license the use of Broad’s patents if Editas passes on a specific disease-related application since Zhang holds the patent for application of CRISPR for disease applications. However, this does not mean that Doudna and Charpentier, the two heavyweights from the losing side of this patent battle, are going to miss out on benefitting from their discoveries. UC Berkeley has already filed patent for application of CRISPR technology on all cells, which the Broad is not contesting. Biotechs who had invested in obtaining patents through UC Berkeley may actually be able to benefit regardless of the loss in the patent fight.

The promise of CRISPR-Cas9 in disease applications, while still in its nascent stages, is a real possibility. CRISPR has yet to enter human clinical trials en masse for such purposes, although last week a team of Chinese scientists reported successful editing of normal human embryos. This hasn’t deterred popular science news outlets from speculating whether the era of designer babies is finally within sight. This may have been compounded by the recent release of a report by an international committee convened by the U.S. National Academy of Sciences and the National Academy of Medicine that cautiously suggests germline editing of human embryos sometime in the future, albeit “only for compelling reasons and under strict oversight”. The panel also suggested that the genome editing can only be undertaken after much more research on its risks and benefits. This report appears to be a cautious first step towards unlocking the so far forbidden zone of germline editing, and a move away from the moratorium previously established in December 2015 by an international group of leading scientists.

Does this imply, then, that Gattaca or similar engineered societies are upon us? It is a possibility that heritable diseases may one day be cured, but scientists warn us that engineering complex traits such as intelligence are still a pipe dream. These utopian societies are based on the fantasy of engineering the human species to be “harder, better, stronger, faster”; however, they completely ignore the scientific evidence that such adjectives usually are applied to traits that require reciprocity between the genetics and the environment. While genetics play a part, the environment of the individual, along with other factors such as diet, lifestyle and socioeconomic status heavily influence such traits. Even making small changes in the genome has been a challenge, as shown by the efforts to “fix” the mitochondrial genome of babies using the three parent approach.

The question then becomes whether we can engineer designer babies or not, but rather should we be doing such a thing. It would help to note that this obsession with making human beings “better” is rooted in eugenics and racial supremacy, and history is rife with such examples. What the futurists or people who propagate such ideas are missing out on is that evolutionary changes are not meant to make any species more “efficient” as is understood in technological vernacular, but rather help the organism adapt better to the changing environment. This understanding perhaps would help shed more light on the role of the environment and pull us out of our obsession with genetic determinism. Maybe if we ARE to build better human beings, we should start by fixing our environmental problems, such as pollution, climate change, deforestation, the threat of extinction to a large variety of organisms, etc. The promise of genetic engineering should not blind us to what is more important at the moment. Like they say – “one bird in hand is better than two in the bush” and if we don’t do our part to save the environment, we won’t have any bushes or birds left.

On the Shelf…

For Work

Effective Data Visualization

Effective Data Visualization: The Right Chart for the Right Data, by Stephanie D.H. Evergreen

Location: HHSL Book Stacks, Sackler 5, P 93.5 E937 2017

This book shows you how to select the best type of chart for your data, design an easily readable chart, and create effective charts and graphs in Excel.

For Leisure

The Undoing Project

The Undoing Project, Michael Lewis

Location: HHSL Book Stacks, Sackler 5, WL 103.4 L675 2017

Michael Lewis, the author of The Blind Side and The Big Short, describes the working relationship between two psychologists, Daniel Kahneman (author of Thinking Fast and Slow) and Amos Tversky, whose work changed how we think about decision making, and catalyzed the creation of the field of behavioral economics.

PubMed Tip of the Month…Topic-Specific Queries

Topic-specific queries in PubMed are carefully constructed search strategies that can either be applied to a set of results as a filter or added to a search using ‘AND’.  Each of these searches has been created by an expert, tested to optimize sensitivity and specificity, and is periodically updated.  To view a complete list of the available searches, click the ‘Topic-Specific Queries’ link under PubMed Tools on the PubMed homepage.  This will bring you to the Directory of Topic-Specific PubMed Queries, where you can view the available subject searches, which include: AIDS, bioethics, cancer, health disparities, toxicology and veterinary medicine.  Clicking the link for a subject either limits your PubMed search to that subject area (i.e. applies a filter) or brings you to a page with the search strategy and additional resources.

Topic-Specific Queries
Topic-Specific Queries link on PubMed homepage.

Some of the searches can also be applied as filters from a search results page.  To do so, click the ‘Show additional filters’ link in the left-hand column of a PubMed search results page.  Check the box next to Subjects and click the Show button.  Select a link under Subjects to narrow your results.  If you do not see a particular filter, then click the ‘Customize’ link under Subjects to choose additional filters.  I don’t use topic-specific queries too often, but they can save you a lot of work if an appropriate search filter has been constructed for your topic.

Notes from the Library…Copyright

As both creators and users of copyrighted works, it is good to know a little about this topic.  Below, you will find a brief copyright primer.  For answers to copyright questions pertaining to your thesis, see FAQs for Dissertation & Thesis Writers from the Tufts University Libraries Scholarly Communications Team, where you will find answers to questions such as: Can I delay the release of my thesis?  What if I have already published part of my thesis as an article?  What if I want to reuse a graph created by someone else in my thesis?  What is open access?

What is copyright?

Copyright is a set of rights, which give the owner the exclusive right to do or authorize any of the following: reproduce the copyrighted work; prepare derivative works based on the copyrighted work; sell, transfer ownership of, rent, lease or lend copies of the work; publicly display or perform the work (17 U.S. Code § 106).

The authorization for copyright legislation goes back to Article 1, Section 8, Clause 8 of the United States Constitution.  The Copyright Act of 1976 provides the framework for today’s copyright law, which can be found in Title 17 of the U.S. Code.

What does copyright apply to?

Copyright applies to “original works of authorship fixed in any tangible medium of expression” (17 U.S. Code § 102).  This includes literary, pictorial, graphic, and audiovisual works.  Copyright does not extend to ideas, procedures, processes, methods of operation, concepts, principles or discoveries.  Patent, trademark or trade secret policy may apply to these forms of intellectual property.  For more information on these types of IP protection, see What Are Patents, Trademarks, Servicemarks, and Copyrights? and Trade Secret Policy on the U.S Patent and Trademark Office website.

How long does copyright last?

In general, for works created on or after January 1, 1978, copyright lasts for the life of the author plus 70 years (17 U.S. Code § 302).

Who owns the copyright to my thesis?

You do!  According to the Tufts Policy on Rights and Responsibilities with Respect to Intellectual Property: “Students generally own the copyright to the academic work they produce.  Academic work can include class papers, theses, dissertations…”.

ICYMI: Public Relations and Communications Essentials for Scientists

When it comes to reporting our scientific findings, we are trained to compose manuscripts that are measured, precise and objective. The mainstream media, however, take a very different approach to broadcasting scientific news: headlines designed to grab readers tend to be more sensationalized and the articles draw more conclusive and overarching statements. These contrasting approaches to reporting are appropriate in their respective fields and it is important that we as scientists learn to take advantage of mainstream journalism for the publication of our discoveries, not only for the reputations of our university and ourselves, but also to share with the public, whose tax dollars fund most of our work, what we have accomplished. Enter the Tufts Public Relations Office—a fantastic resource that allows us the opportunity to share our research with the community outside of our scientific world. The purpose of the seminar du jour was to inform the Tufts community on how the office works and how to best use it to our advantage.

The purpose of the seminar was to provide some information on how to work with the PR office when you are ready to publish work that you would like to broadcast beyond scientific journals. Kevin, the assistant director of the office, stressed that the earlier you get in touch with the PR office, the better prepared they will be to help you. The best time to contact them about publicizing a manuscript is when you are submitting your final revisions to the scientific journal that will be publishing the paper. You will be asked to share your manuscript with the office so that Kevin and members of his team, who are well versed in reading scientific literature, can familiarize themselves with your work. Soon after, they will meet with you to discuss the details of your study, get a quote, and draft a news release that your PI can edit and approve. From there on out, the PR Office works to spread the word on your research via prominent blogs, science, local, and potentially national media, depending on your work’s level of impact. The PR Office is also equipped to help you interact with reporters effectively: they can prepare you to talk about your science in layman’s terms to be more relatable and better understood by the general public.

By sharing your work with more mainstream media, you build your reputation as well as credit your university, your funding agencies, and the tax-paying public. Reach out to the PR Office for more information on communicating your science with the rest of the world and take advantage of the great opportunities they offer that can make you a more visible and effective participant in the science world!

One last tip for those of you interested in improving your science communication skills–keep your eyes peeled for more details on our upcoming joint Dean’s Office / TBBC / GSC Event, Sackler Speaks in April!  This is a competition for students to pitch their 3-minute flash talks in front of a panel of judges.  Besides critical feedback on presentation skills, there will also be cash prizes for winning presentations!

Contacts at the Tufts PR Office, Boston Campus:

Siobhan Gallagher, Deputy Director (Siobhan.gallagher@tufts.edu)

Kevin Jiang, Assistant Director (Kevin.Jiang@tufts.edu)

Lisa Lapoint, Assistant Director (Lisa.Lapoint@tufts.edu)

 

Reflections from AAAS 2017 – Research During the Trump Administration

The theme of this year’s American Association for the Advancement of Science (AAAS) meeting in Boston was “Serving Society through Science Policy.” As we move through the first few months of a new administration, this gathering could not have been more timely. While this conference is diverse with topics ranging from gene editing to criminology, the undercurrent of the meeting was anxiety over what will happen to research under the Trump administration.

What is science policy even? Most in this audience probably think of it as how much money research gets budgeted and occasional rule changes on whether fetal stem cell research can occur. Generally, science policy is the set of federal rules and policies that guide how research is done. Science policy can be split into two general frameworks: policy for science and science for policy. These can often feed into each other. For example, policy for science provides funds for climate research. The data and conclusions derived from that research could then inform new climate related policies. That would be science for policy. While science itself is an important input into the whole process, other considerations such as economics, ethics, budgets and public opinion are also inputs. As a scientist who considers science as a method of interpreting the world, my biases had not let me consider non-science inputs for science policy decision-making. It may seem obvious to some, but it was illuminating to realize that other concerns can be just as valuable and legitimate.

As funding is a major reason scientists are concerned, I was happy to learn a lot about the place of research in the federal budget. There are some out there who believe that research in Boston will be fine no matter who is in charge because of all the industry science in the area. It’s true; around two-thirds of research and development is funded by industry. However, industry is mostly concerned with development. Basic research is primarily funded by federal money. The federal budget is divided into mandatory spending and discretionary spending. Mandatory spending does not require congress to act for programs in it to be funded. These include the entitlement programs such as Social Security, Medicare and Medicaid. Dr. Josh Shiode, a Senior Government Relations Officer from AAAS, informed us that entitlement programs are considered “third-rail” discussions by lawmakers, meaning if you touch them, you die (an electoral death). In contrast, discretionary spending requires Congress to actively fund. Most of research and development spending falls into this category.

 

 

Due to changing (aging) demographics, the percentage of the budget that goes towards mandatory spending has been steadily increasing. 50 years ago, we spent around 30% of the federal budget on mandatory spending and now we are up to 70% and increasing. Research and development generally gets around 10-12% of the remaining budget left for discretionary spending. Traditionally, increases in discretionary defense spending will correspond with a parallel increase in nondefense discretionary spending. The Trump administration has proposed increases in military spending. Given likely tax cuts and reluctance to make changes to entitlement programs, it is unlikely nondefense discretionary funding will fare well. The good news is major research programs like the BRAIN Initiative, Precision Medicine Initiative and the Cancer Moonshot were funded through the bipartisan 21st Century Cures act during the lame-duck session. While NIH and biomedical research will likely have diminished profiles during this administration, both parties are against Alzheimer’s, diabetes and cancer. What is less clear is how research performed by the EPA and Department of Agriculture will fare although initial reports are grim. Finally, repeal of the Affordable Care Act will have rippling effects, as many research universities are also providers of healthcare. It is clear that there will be a shift in culture. Under President Obama, science was elevated and scientists were regularly consulted. As former senior science adviser to President Obama John Holdren said: “Trump resists facts he doesn’t like”.

There is reluctance for some scientists to get involved in the political theater, as some believe science should be apolitical. I would argue that science is already political as science can dictate policy and policy can dictate science. What science is and should be is nonpartisan. No party has an inherent monopoly on being allies of science and scientific thinking. So what can scientists do? All politics is local and personal. The majority of Americans say they don’t know a scientist. This is an easy thing to work on. Make sure you introduce yourself to others! Visit your lawmakers and let them know that you are funded by federal money. Politicians are most concerned about their own districts and so if you’re a transplant, you likely have connections to more than one district. Try to build a relationship with him or her by seeing if you could help with anything. Figure out if you can help your local community with anything by serving on committees. Speaking of committees, know what committees your representatives are on. When communicating, think carefully about what words you use. Former U.S. Congressman Bart Gordon opined that he never called it climate  change. Instead, he called it energy independence. While branding may sound like a trivial thing to worry about, targeted story telling is extremely important. We would love for our data to speak for itself but people connect best to stories, especially ones concerning things they can relate to or care about.

If you’re interested in science policy, there are a number of good resources available to get better acquainted. The Engaging Scientists & Engineers in Policy (ESEP) Coalition has a wealth of information and resources on their website (http://science-engage.org/). In fact, they host a local monthly science policy happy hour to network and engage those interested in science policy. If you are interested in learning more about the R&D budget, AAAS has an excellent resource with analyses of federal research and development funding (https://www.aaas.org/program/rd-budget-and-policy-program). There you can also find their data dashboard to look at funding for specific agencies for different periods of time.