Neglected Tropical Diseases: Challenges for the Post-2015 Development Era

This article is being cross-listed with the Harvard graduate student publication Signal to Noise, Special Edition on Infectious Disease.

Health equity is based on the idea that all lives, anywhere in the world, have equal value.

Neglected Tropical Diseases (NTDs) are a group of 18 infectious diseases – caused by parasites, viruses, or bacteria – that disproportionately affect the poor and cause significant health and financial burdens. NTDs are endemic – meaning that they regularly infect humans – in 149 countries, with over 1 billion people infected and 2 billion people at risk. These diseases are largely treatable and preventable through control of the insects that carry these diseases, improved water quality and sanitation, and the efficient delivery of drug treatments already donated by major pharmaceutical companies. The control and elimination of NTDs cuts across the United Nations’ eight Millennium Development Goals for 2015. Controlling NTDs would not only reduce disease burden but would also improve maternal health, reduce childhood mortality, reduce malnutrition, improve school attendance, and help to empower women. With just a year left on the Millennium Development Goals clock and these diseases still constituting a major burden, we are at a pivotal time for infectious diseases and global health. By defining a clear way forward in the post-2015 development era, we stand to make major progress toward the control, elimination, and eradication of NTDs and other diseases.

What are Neglected Tropical Diseases?

The World Health Organization (WHO) prioritizes 17 neglected tropical diseases (NTDs) (Figure 1) that affect over a billion of the world’s poorest people and pose a significant economic burden to developing economies (scabies was just added to the list in June of 2014, bringing the count to 18). NTDs are a heterogeneous group of infections caused by parasites, viruses, and bacteria. What makes NTDs different from non-neglected diseases is that these diseases are disablers rather than killers. Indeed, these infections are co-endemic: an individual may be infected with more than one NTD in addition to other well-known diseases such as HIV, tuberculosis, and malaria. For example, the parasite infection schistosomiasis can make women and girls more susceptible to HIV infection, saps micronutrients and iron from developing children to stunt their growth, and renders children less likely to attend school. A chronic helminth parasite infection known as lymphatic filariasis (LF) may reduce vaccine efficacy by broadly modulating the immune system. LF causes severe swelling (lymphedema) in 40 million people rendering them socially stigmatized and largely unable to work. In addition to schistosomiasis and LF, many more NTDs are characterized by chronic disabilities, increased susceptibility to infectious and non-infectious diseases, social stigma, and an economic burden on the individual, the family, and the country.

Figure 1

NTDs don’t just affect low- and middle-income countries, although their victims are often socioeconomically disadvantaged. Cysticercosis, echinococcus, toxocariasis, Dengue virus, West Nile virus, and Chagas disease all have appeared in the United States, disproportionately afflicting the poor. Peter Hotez of the Sabin Vaccine Institute and Baylor College of Medicine has estimated that half of the 20 million people living in poverty in the US are infected with at least one NTD.

How NTDs cut across the Millennium Development Goals

The Millennium Development Goals (MDGs), established following the Millennium Summit of the United Nations in 2000, are a list of 8 objectives aimed at lifting the world’s poorest countries out of poverty by 2015. MDG 6: Combat HIV/AIDS, malaria, and other diseases, most directly applies to NTDs, which fall into the “other diseases” category. The idea that NTDs fall under the “other diseases” umbrella is also now an old one, as NTDs have rightly gained much more attention over the past 10 years as a significant development burden.

The Global Network for Neglected Tropical Diseases issued a report outlining the contribution of NTDs to hindering progress on several other MDGs. With respect to MDG 4: Reduce Childhood Mortality, for example, a child infected with any of the helminth parasites will be anemic and malnourished with a compromised immune system, making it much more likely that that child will succumb to another infection. Children harboring one or more NTDs are also less likely to have regular attendance in school, contributing to MDG 2: Achieve Universal Primary Education. In fact, a study of schools in Western Kenya demonstrated that treating intestinal parasite infections by mass drug administration programs can improve school attendance by up to 25%.

One metric that captures the impact of diseases that disable rather than kill, like many of the NTDs, is the Disability Adjusted Life Years (DALYs) calculation. One DALY can be thought of as one lost year of healthy life to an individual, either by mortality or by disability. Estimates place the burden of Disability Adjusted Life Years (DALYs) lost to NTDs at 26.6 million in 2010, but this is likely a gross underestimate if we consider the secondary effects of NTDs. For example, NTDs contribute to an estimated 15-30% of lost productivity in endemic countries. The coordinated effort to control, eliminate, and eradicate NTDs is not only an issue of human health, but one of economic development.

Recent Progress: NTDs are a Big Bang for the Development Buck

In addition to improving human health and health equity, combating NTDs is a strong and cost-effective method of increasing economic growth. For example, the early results of the Global Programme to Eliminate Lymphatic Filariasis has generated a return on investment of $20-$60 for every US$1. Recognizing this opportunity, the US Congress committed funding support through USAID for the integrated control of NTDs in 2006, and in 2008 the UK Department for International Development also committed funding for NTD eradication. The Bill and Melinda Gates Foundation and the World Bank have also committed significant aid to fighting NTDs over the past decade, followed more recently by other international aid funds.

The First WHO Report on Neglected Tropical Diseases published in 2010 brought NTDs to the forefront. The WHO released a follow-up report in 2012, closely followed by the 2012 London Declaration to control, eradicate, or eliminate by 2020 ten NTDs (lymphatic filariasis, trachoma, soil-transmitted helminths, onchocerciasis, schistosomiasis, leprosy, guinea worm, visceral leishmaniasis, Chagas disease, and human African trypanosomiasis). The London Declaration has been notably effective in kick-starting a strategic and directed effort in the battle against NTDs. It brought together global health leaders including the Gates Foundation and the CEOs of ten pharmaceutical companies to guarantee the donation of an unlimited amount of medicines for these 10 NTDs for the foreseeable future.  The NTDs agenda has been characterized by these strong public-private partnerships, which will be key for continuing progress.

Uniting to Combat NTDs, the coalition of partners and individuals formed during the London Declaration, issued their second progress report in 2014. The report highlights a large upwelling in political will in countries where one or more NTDs are endemic. For instance, demand for drugs for NTDs has increased by 35% and has been matched by industry donations, and there has been an increase in mass drug administration programs. Funding for NTDs has also increased, led by USAID, the UK Department for International Development (DFID), the World Bank, and the Bill and Melinda Gates Foundation. New rapid diagnostic tests for Human African Trypanosomiasis will streamline diagnosis and treatment, and there is now a new pediatric formulation of praziquantel to treat childhood schistosomiasis.

We have effective drugs for most NTDs. The major challenge, and the cost, is effectively and efficiently delivering those drugs to endemic regions. We are now in the position to ask, “What kind of mass drug administration (MDA) regime might lead to local eradication? And can we coordinate the delivery of multiple drugs for multiple diseases at the same time? With the end of 2015 only a year away, we must also ask, “What’s next?”

Looking Ahead: Innovation for NTD Elimination and Control

Since the London Declaration, some successes indicate that control and eradication are possible. Colombia recently became the first country in the world to eradicate onchocerciasis. Niger, Nigeria, and the Ivory Coast have also recently eradicated Guinea worm. Twenty-three countries treated at least 75% of children at risk for soil-transmitted helminth infections,  and a massive disease mapping program of blinding trachoma using mobile technology has cut the unmapped regions of the world for this disease in half.

However, we still have a long way to go. It has been estimated that of all the drugs approved for distribution, only 65-75% are reaching the people who need them. Implementation and operational research on how to carry out mass drug administrations effectively must be a priority. Even when control programs go well, they can be quickly derailed by political unrest, natural disasters like Superstorm Haiyan, or even epidemics like the ongoing Ebola outbreak that have overwhelmed the existing health systems in Liberia and Sierra Leone. Furthermore, disease boundaries for mosquito-transmitted diseases are especially sensitive to changing temperature and precipitation patterns due to climate change.

Last November in his keynote address to the American Society of Tropical Medicine and Hygiene, Bill Gates highlighted a need for global health innovations, citing the example of the new diagnostic test for human African trypanosomiasis. Gates urged the community to take the digital revolution and apply it to disease surveillance to determine where to concentrate disease-fighting efforts The Bill and Melinda Gates Foundation is a strong proponent that “big data” health care informatics solutions must be apart of efficient disease control programs, and this will represent a burgeoning area of global health research in the near future.

As the clock on the 2015 Millennium Development Goals runs out, planning for the post-2015 Sustainable Development Goals. is well underway. What do you think are the biggest issues facing human development today and in the near future?  You can take a look for yourself to see if NTDs will make the cut by reviewing the proposals for the Sustainable Development Goals using the Overseas Development Institute’s

Rachel Cotton is a PhD student in the Harvard Immunology Program, with an interest in infectious disease, global health, and science policy. Her past research has included the immunobiology of parasitic diseases. Follow her on Twitter @RachCotton.

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ISCB Student Council – Documenting the efforts of student organisation volunteers

A guest post by: Geoff Macintyre, Thomas Abeel, Magali Michaut

In July 2014 the International Society for Computational Biology Student Council will celebrate it’s 10th anniversary. Over its ten years of operation, the Student Council has grown to over 2000 members thanks, in a large part, to its constituent of innovative and enthusiastic volunteers. These volunteers have worked hard to uphold the Student Council’s mission of “promoting the development of the next generation of computational biologists”. While many of the volunteers have not received any direct recognition for their contributions, each and every one of the Student Council members will attest that the reward lies in the skills and experience gained in being part of organising an event or activity.


However, to ensure that both the efforts of these student volunteers did not go unnoticed, and that their collective experiences could be shared with others, the Student Council put together a series of article documenting various aspects of the Student Council initiatives that PLOS Computational Biology is publishing in conjunction with ISCB. Many of the articles are now published and have been launched as a PLOS Collection.


The first article is a great source of information regarding the series and the Student Council. But as a supplement to the series, we thought we would use this post to demonstrate the benefits of being involved in the Student Council by explaining the story behind the creation of the article series. For us personally it was a tremendously rewarding experience and taught us as much about collaborative writing as it did about differences in education backgrounds and culture of our co-authors.


The story

While the Student Council has had the opportunity to share proceedings from the annual Student Council Symposium in the past (1-7), there were only a handful of examples of Student Council initiatives being shared with the broader community (8). To rectify this, in early 2012 Nelson Ndegwa and Magali Michaut, both active members of the Student Council, put a call out to all members to see if they would like to share their experiences organising and running events in a paper. The response was overwhelming with many of the leaders from the Regional Student Group program sharing their successes (and failures) in organising initiatives for students from their home country. Originally the collaborative writing environment of WikiGenes was used but, after the expansion to a second page and over 20 authors, this quickly became unwieldy. The other problem was that, with so many stories demonstrating different experiences, different themes, and different writing styles, it was becoming near impossible to condense it all down into one body of writing representing the essence of the Student Council volunteer experience. At the time, Geoff was Chair of the Student Council and had contributed some stories from his time in the Australian Regional Student Group. Seeing the potential arising from this writing effort he took the project to his colleagues in the Student Council executive team and they agreed to set up a small team to oversee and coordinate the writing efforts which included Magali Michaut, Thomas Abeel and Geoff Macintyre.


Initially, we attempted to extract some of the abstract concepts from the stories to see if we could write an overarching piece. However, we realised that a lot of the personal nature and details of the experiences were lost. The only way to capture details and write a relatable story was to split up the monolith into many small focused stories. At ISMB 2012 we approached PLOS Computational Biology and the ISCB Publications Committee with a plan to write 12 short articles to document the efforts of Student Council members in various endeavors and hopefully entice others to get involved. After some discussions, and early support from committee members Scott Markel and Olga Troyanskaya, it was agreed that the ISCB pages as part of PLOS Computational Biology would be a good fit for the article series. Needless to say we were rather excited by this news, but then we faced the challenge to coordinate the writing of these articles!


Much time was spent on Skype to develop a strategy to deliver twelve high quality articles in a timely manner. We wanted to give every member an opportunity to contribute to the series, but we wanted to ensure no-one was simply along for the ride. We therefore decided to have one person as a lead author on each article (selected from those who initially contributed to the stories) and one of us to oversee each article. Each lead author had to select passages of text from the original stories collected on WikiGenes which were relevant to their article and invite the author of that text to be part of their article. An additional announcement was put out with the description of each article and any students who wished to be involved had to submit to the lead author a short piece of writing relevant to the article. This process resulted in an average of four potential authors per article – we made it clear that authorship would be determined based on contributions after the article was written.


We opted to use Google Docs for the writing of each article as it allowed simultaneous editing of the articles and the ability to track the edits. Initially, the authors were required to provide an outline of the article which had to be discussed amongst all authors via Skype. Once this was done, we provided additional feedback and writing could commence. Naturally each article went through a number of drafts with all authors working on different aspects of each article. Once the final drafts of the articles started to trickle in, they were sent out to previous Student Council members who volunteered their time providing ‘peer review’ feedback on each article. Their comments were taken into account and each article was revised accordingly. With the articles in a final draft form, we discussed with the lead authors the contributions of everyone involved and authorship was jointly decided – a process that went surprisingly smoothly.


At this stage, the articles were ‘nearly’ ready for submission. The only problem remaining was that the articles lacked flow or clarity in parts. This was likely a byproduct of having authors from different countries writing in conflicting styles and for quite a few of the authors it was the first journal paper they ever wrote. To overcome this, and drawing on the inspiration of the astounding volunteer efforts of the Student Council members, we sought out students from another discipline – in this case professional editing students – to see if they would volunteer their time in editing the article to improve readability. To our delight, Stephanie Holt, from RMIT University agreed to put forward our articles to her Advanced Manuscript Editing students, as a group exercise in practicing their editing skills. As such, we received a collection of suggested changes which dramatically improved some of the articles.  The articles were finally ready for submission.


Since then, we have submitted each article sequentially, which are now being published with the help of the teams at PLOS (currently up to article 10 of 12). Overall the experience was immensely rewarding. The process of having to coordinate the collaborative writing efforts honed our planning and time management skills, made us realise the benefit (and limitations) of using collaborative writing software, and helped us get more familiar with the process of taking an idea through to publication. However, most interesting for us, was the insight into cultural and educational differences between our co-authors from around the globe, including Africa, Europe, South and North America. For example, different authors had different ideas about how and what they could talk about when critically analysing their own education experiences. No-doubt these insights will help us in future collaborations during our scientific careers.


Looking back on some of the articles that have been published, we hope that many of the Student Council members feel proud that their volunteer efforts have been shared with the broader community. But more importantly, it will be exciting to see if the articles in this series can inspire other students to see the benefits in volunteering in student organisations and contributing to their scientific community.



1. Gehlenborg N, Corpas M, Janga S (2007) Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology. BMC Bioinformatics 8: I1. doi: 10.1186/1471-2105-8-s8-i1


2. Peixoto L, Gehlenborg N, Janga S (2008) Abstracts of the Fourth International Society for Computational Biology (ISCB) Student Council Symposium. Toronto, Canada. July 18, 2008. BMC Bioinformatics 9 Suppl 10: I1–P6. doi: 10.1186/1471-2105-9-s10-i1


3. Abeel T, de Ridder J, Peixoto L (2009) Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. BMC Bioinformatics 10 Suppl 1: I1 doi: 10.1186/1471-2105-10-S13-I1.


4. Klijn C, Michaut M, Abeel T (2010) Highlights from the 6th International Society for Computational Biology Student Council Symposium at the 18th Annual International Conference on Intelligent Systems for Molecular Biology. BMC Bioinformatics 11: I1. doi: 10.1186/1471-2105-11-s10-i1


5. Grynberg P, Abeel T, Lopes P, Macintyre G, Pantano Rubiño L (2011) Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology. BMC Bioinformatics 12: A1. doi: 10.1186/1471-2105-12-s11-a1


6. Goncearenco A, Grynberg P, Botvinnik O, Macintyre G, Abeel T (2012) Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012. BMC Bioinformatics 13: A1. doi: 10.1186/1471-2105-12-s11-a1


7. Di Domenico T, Prudence C, Vicedo E, Guney E, Jigisha A, Shanmugam A (2014) Highlights from the ISCB Student Council Symposium 2013. BMC Bioinformatics 15(Suppl 3):A1  doi:10.1186/1471-2105-15-S3-A1


8.  Gichora NN, Fatumo SA, Ngara MV, Chelbat N, Ramdayal K, et al. (2010) Ten Simple Rules for Organizing a Virtual Conference—Anywhere. PLoS Comput Biol 6(2): e1000650. doi: 10.1371/journal.pcbi.1000650



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Mechanization, Automation, and the Future of Biological Research

Much like a bicycle leverages mechanical advantage to propel a person much faster and further than on his or her own, automation machinery is amplifying both the speed and accuracy with which biological research can be conducted. Machines are precise and do not fatigue, unlike their human counterparts. For this reason, machines are slowly being adopted for laborious, repetitive, and tedious laboratory tasks.

Some automation machines, like the flow cytometer seen here, have already become widely used pieces of laboratory equipment.

There are two ways of thinking about machines in the modern scientific community: physical, mechanical machines and laboratories, institutes, and facilities to which experiments can be outsourced. The former of these are often tailored to a single specific task. Tasks can include phenotypic screening, liquid transfer, and even laboratory organism maintenance. Mechanical machines are perfect for performing repetitive, tedious lab work inside the laboratory. Many of these machines offer sensors that can detect and measure traits that would be otherwise immeasurable by hand. When utilized properly, mechanical machines can greatly increase precision, efficiency, and reproducibility while reducing overall workload. Mechanical machines, while massively advantageous when working properly, often lack the ability to sense their surroundings or steps in their mechanical processes. Therefore, it is nearly impossible for these machines to adapt to conditional changes or for certain segments of the machine to provide feedback to other segments, either to adjust processes or alert their human keepers to an issue.

Great strides must be made in the design and engineering of experimental machinery so as to reduce innate variability of experimental setup and screening. Human’s, sentient beings, can sense and adjust to errors made mid-experiment. If too much of a solution is added to a reaction, a person can adjust the rest of the protocol on the fly or, at worst, begin the reaction over again. If the same error is made by a machine, it may go unnoticed until the output data are collected. Even worse, it may go completely unnoticed, presenting false data that are interpreted as correct upon analysis. Likewise, if the error is due to the improper functioning of a device, such as a pipette in the above example, a human is more likely to notice the error in the first place as we are equipped with sensors, i.e. eyes, that can detect that the volume transferred does not match the volume desired. Such sensors and feedback networks are currently not available on many of the mechanical machines being utilized in experiments.

The second way to think about machine automation in science is through the outsourcing of experiments to external research labs, institutions, or facilities. These organizations will take, as input, reagents or experimental parameters and return the output reagents or data back to the experimenter. These organizations can be thought of as automation machines because they take input and serve output from and to experimenters without any further involvement or work from the experimenter. The most common example of this process is that of DNA sequencing. While DNA sequencing has become a routine task in many modern laboratories, only a small minority of labs own and operate their own sequencing machine, either due to financial cost or lacking an operator with the requisite expertise and experience. Instead, most laboratories outsource this process to external organizations that specialize in DNA sequencing.

Perhaps the greatest advantage of the utilization of automation machinery is the ability

In the future , labs may use mechanical arms to transfer experiments between machines like incubators and flow cytometers. Labs may more closely resemble car assembly lines than the labs of today.

to pipeline experimental segments into one another. For example, laboratories can now outsource the creation of a specific reagent, the utilization of the reagent in a specific experiment, and the measurement of the outcome of the experiment all without conducting any work in their own laboratory. While the jury is still out on whether this pipelining technique will ever lead to any “virtual laboratories” where investigators simply dream up experiments, outsource their execution, then analyze the data, it is important to note that the modularization of experiments will almost certainly lead to increased efficiency in much of modern science. Instead of spending money on training and technicians to run repetitive short-term experiments, researchers now have the capacity to outsource these experiments to either mechanical machinery in their own lab or external research organizations for a fixed, per-experiment cost.

Automation can increase the productivity of a single individual by orders of magnitude. Machines do not tire or vary innately in their performance of a task; however, machines can break, suffer inaccuracy or variability in their measurements, and not detect faults when they may be blindingly apparent to a human. For these reasons, great care must be taken in protocol derivation and maintenance scheduling when utilizing any form of automation equipment.

When utilizing machinery in the design and/or execution of an experiment, the most important variable to consider is the trustworthiness of the data at each individual step. If unnoticed, systematic biases in data collection resulting from measurement error of machinery can lead researchers astray. Additionally, variability between experimental runs must be considered. One sign of data trustworthiness is reproducibility of the data. If the same experiment is replicated under the same conditions, the data resulting from each round of the experiment should be, at best, identical or, at worst, comparable. Although automation machinery has the incredible upside potential to streamline and parallelize experimental workflows, scientists must be careful to thoroughly validate results, both data and reagents.

 TylerShimko_HeadshotTyler Shimko is an undergraduate studying and conducting research in biology at the University of Utah. You can follow him on Twitter @TylerShimko

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Ebola Immunopathology and the Outbreak in West Africa

Ebola virus (EBOV) is a highly virulent pathogen, resulting in death by Ebola hemorrhagic fever in up to 90% of people who contract the virus. There are no drugs to treat it, and no vaccines yet to prevent it.

There is an Ebola outbreak in West Africa, and it has been ongoing for several months, since the first death occurred in December 2013. The most recent counts from the World Health Organization include 328 cases, with 208 deaths, in Guinea so far, with additional cases in Liberia and Sierra Leone. Between May 29 and June 1 alone, there were 37 new reported cases and 21 deaths.

Cases of Ebola are occurring throughout Guinea, Sierra Leone, and Liberia. Credit: E.Ervin/CDC

Cases of Ebola are occurring throughout Guinea, Sierra Leone, and Liberia. Credit: E.Ervin/CDC

By April, Médicins Sans Frontières  (Doctors Without Borders), which has been the lead aid organization for the outbreak, was calling the epidemic  ‘Unprecedented’. What makes this epidemic different, in addition to the fact that this is the first outbreak of Ebola in West Africa, is that cases are not geographically isolated. Cases have been occurring throughout Guinea, and now Sierra Leone and Liberia as well. Senegal even closed its borders to Guinea in April for fear of spread of the virus.

Ebola virus is carried by fruit bats, and is transmitted to and among humans and other primates by blood and bodily fluids at skin and mucosal surfaces. The most common routes of exposure for humans are handling infected bushmeat, contact with the remains of an individual who has succumbed to the virus, or occupational exposure to health workers by needle-stick.

The strain causing the present epidemic has been sequenced and characterized, and was published in the New England Journal of Medicine in April. It represents the emergence of a new clade of the virus – unique, but related to Zaire ebolavirus, an extremely virulent strain that has caused epidemics in the Democratic Republic of the Congo and Gabon.

So what makes Ebola virus so deadly? And why do some individuals progress to Ebola hemorrhagic fever and death, whereas others recover?

Ebola Immunopathology

Ebola immunopathology is characterized by uncontrolled inflammatory responses by monocytes and macrophages in the early stage of infection, coupled with immune suppression and the destruction of several cell types including dendritic cells (DCs) and endothelial cells in the later stages of infection. This ultimately leads to the collapse of the vascular system, shock-like symptoms, uncontrollable hemorrhaging, and death.

Compared to those who recover from Ebola infection, victims exhibit high viral loads, an absence of cytotoxic CD8 T cell activation, below-normal numbers of T cells, and high nitric oxide production, a sign of macrophage activation. Furthermore, recovered individuals have detectable levels of anti-EBOV antibodies in the blood at the onset of symptoms, whereas susceptible individuals do not. Those who succumb to the virus mount a robust but ineffective innate inflammatory response, followed by a failure to induce adaptive immunity. Viral replication and cell death continue, unchecked.

How is it that the innate response is both strong and ineffective?  This paradox can be explained by differential effects of ebola virus on macrophages and DCs. While strongly activating monocytes and macrophages, ebola-infected DCs are inhibited in activation and function.

Ebola activates monocytes and macrophages

Virus-activated monocytes and macrophages secrete an abundance of proinflammatory cytokines and chemokines like tumor necrosis factor (TNFa), IL-1β, macrophage inflammatory protein-1a, and reactive oxygen and nitrogen species, and large numbers of infected macrophages undergo activation and apoptosis. However, this is insufficient to deter viral spread. Macrophage apoptosis recruits more monocytes and neutrophils that further the inflammatory response and provide new host cells for the virus.

The unchecked production of pro-inflammatory mediators is cytotoxic to the surrounding tissue, and likely contributes to the hemorrhagic pathology of Ebola infection, by increasing vascular permeability. That is not to down-play the effects of the virus itself, which has a particular tropism for innate immune cells and endothelial cells, and induces cell lysis in most if not all cells it infects.

Ebola virus virion.  Colorized transmission electron micrograph (TEM) Credit: Cynthia Goldsmith/CDC

Ebola virus virion. Colorized transmission electron micrograph (TEM) Credit: Cynthia Goldsmith/CDC

Ebola impairs and co-opts dendritic cell function

Dendritic cells (DCs) serve as the bridge between innate and adaptive immunity. When functioning normally against infection, DCs internalize a pathogen or a piece of it, and then process and present signatures of that pathogen to T cells in the lymph node. Dendritic cells also secrete activating cytokines like interferons (IFNs) and IL-12, and express co-stimulatory molecules to further induce responses from cells of the adaptive arm. Ebola virus, however, inhibits dendritic cell function by several mechanisms. Ebola-infected DCs fail to secrete IFNs and other pro-inflammatory cytokines, fail to upregulate  costimulatory molecules, are impaired in antigen presentation and processing, demonstrate increased expression of inhibitory molecules, and are in all poor activators of T cells. These effects are dependent on the Ebola envelope glycoprotein.

A particularly interesting feature of Ebola, is that its sticky! The virus binds C type lectins on the surface of a number of cell types, including the lectin DC-SIGN which is highly expressed on dendritic cells. The benefit of this for viral pathogenesis is unclear, but may facilitate viral entry into DCs and other cells, or may simply allow the virus to hitch a ride through the lymphatic system and disseminate infection.


The immune response to Ebola virus gets only half-way there in fatal cases. The innate immune system is alerted and activated, but then the virus inhibits the initiation of an adaptive response by DCs.  The unchecked innate response only contributes to the vascular permeability and tissue damage that proves fatal. In short, there is a lot that we don’t know about Ebola immunopathology, but it is clear that those who recover are able to initiate a T cell response and the production of antibodies.

A vaccine for Ebola is still 5 years away or more, and is being actively pursued by researchers at the National Institute of Allergy and Infectious Diseases (NIAID) and Thomas Jefferson University. BioCryst Pharmaceutical in Durham, NC is pursuing a drug candidate, and Mapp Biopharmaceutical in San Diego is currently developing a monoclonal antibody cocktail in partnership with the Public Health Agency of Canada.

None of the above leads will help in the present epidemic. The current strategy is to provide medical care to and observation of those infected, and attempt to contain the spread of the virus any further.


Rachel Cotton is a Senior Biological Sciences major in the Eck Institute for Global Health at the University of Notre Dame, where she conducts immunology and infectious disease research. She is Co-Editor in Chief of the undergraduate research journal, Scientia


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Lessons in Online Learning

Massively open online courses, or MOOCs, are rapidly revolutionizing the face of higher education, but this may not be a good thing when it comes to instruction of the physical sciences. A MOOC is a class created by an expert in a particular field (often a university professor) that is posted online and open to the public. The number of MOOCs available has increased dramatically from roughly 100 in 2012 to more than 1,200 at the beginning of 2014.  Over 200 universities have contributed courses, and it is estimated that more than 10 million students have signed up for these free online classes so far. MOOCs allow students to learn at

A student completes coursework outside on her laptop.

A student completes coursework outside on her laptop.

their own pace, from anywhere where they can find an Internet connection. Several universities in the United States are even beginning to offer credit for online courses, allowing students to replace in-person lectures with time behind the computer. While many are hailing MOOCs as the future of higher education, it can be argued that hands-on, real-life science education can never truly be replaced by virtual learning.

According to the Oxford Dictionary, science is the “intellectual and practical activity encompassing the systematic study of the structure and behavior of the physical and natural world through observation and experiment.” The physical sciences are unique among other disciplines in that they describe the principles that govern our world. These mechanisms surround us, and the only way to understand them is to witness and experience them. No number of online simulations or lengthy descriptions can substitute for feeling the heat from an exothermic reaction in a chemistry lab, or measuring for yourself the flow of electricity through a circuit that you have constructed. As an undergraduate science major, I used to mope and groan when I had additional required lab time in conjunction with all of my chemistry, physics, and biology courses while my friends in business and arts and letters majors were free from study outside of their normally scheduled lecture times. By the end of my four years, however, I came to appreciate how essential these hands-on experiences

Young students gain first-hand knowledge of basic chemical principles.

Young students gain first-hand knowledge of basic chemical principles.

were in cementing and clarifying abstract scientific principles.

If online courses cannot sufficiently replace face-to-face class time, how can online learning platforms improve science education? The smartest application of MOOC technology to education in the physical sciences is to implement a “flipped classroom” approach. In this course structure, students watch lecture videos in advance in order to learn a lesson’s fact-based material before meeting with their instructor.  The flipped-classroom approach permits the most efficient use of one of the scarcest resources amongst students and professors: time. It allows class time to focus on demonstrations and applications of those principles instead of the recitation of background information that students can master on their own. Students are free to do a good deal of their learning online at their own convenience, while still gaining practical understanding of the principles in their textbooks through in-person classroom experiences.  This greatly increases the value of classroom and lab experiences, allowing greater depth of education and improving the retention of information and experience. So, while online courses should not be a replacement for classroom education, they can serve as a way to augment students’ work in the classroom, improving and accelerating education in partnership with traditional approaches.

Rebecca Marton is a senior Biological Sciences major at the University of Notre Dame and co-Editor in Chief of Scientia, the undergraduate journal of research for Notre Dame’s College of Science. She studies retinal regeneration in the adult zebrafish and plans to pursue a Ph.D. in stem cell biology. 

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“Synthetics” – Berkeley Scientific’s Spring 2014 Issue

BSJ Synthetics

Berkeley Scientific publishes undergraduate research, features articles, and interviews with UC Berkeley professors spanning many areas of science. In the Spring 2014 issue of Berkeley Scientific Journal, we explore how recent technological and biomedical developments have advanced our understanding of “synthetics” in science. We are constantly surrounded by synthetic science— manmade technological advancements that enable us to communicate faster, manipulate genes, and progress toward cleaner energy. UC Berkeley professors and other members of the academic community are currently researching cancer immunotherapy, genome editing, and solar energy among other topics. These accomplishments among many others have garnered global attention. Now is the perfect time to dedicate the current BSJ issue to “synthetics.”


This semester’s issue is filled with high quality research, features articles, and an interview with an award-winning Cal professor. For an understanding on how synthetic science works on a microscopic level, read our feature articles about DNA as building blocks of nanotechnology, magnetoelectric materials, and “lab on a chip.” Departing from micro-scale technology, explore interesting articles on “Manufactured Memories,” artificial heart devices, and “Bright Ideas in Solar Energy.” Additionally, Berkeley Scientific had the opportunity to interview Jan Rabaey, a professor of Electrical Engineering and Computer Science about his research on neural prosthetics and their future applications. I invite you to read the second issue of Berkeley Scientific Journal’s eighteenth volume, filled with fine articles and undergraduate research papers on the topic of synthetics.


Prashant is a senior undergraduate student studying biochemistry and molecular biology at the University of California, Berkeley. He currently is Editor-in-Chief of Berkeley Scientific Journal, where he became interested in science journalism and its propensity to motivate general audiences.  Read the current issue here. Follow BSJ on Twitter.


Category: Artificial Intelligence, Bacteria, Clinical Trials, ethics, Interviews, Medicine, Memory, Neuroscience, PLoS, PLoS Biology, PLoS Blogs, PLoS Medicine, ResearchBlogging, Science Journalism, Students, The Student Blog | Tagged , , , , , , , , | 1 Comment

What can you do with that PhD?: FAQs about non-academic jobs

As the school year winds to a close, another class of students nears graduation and will be asked the inevitable question: “So, what’s next?” This year, I’m one of those students, and like 61% of STEM PhDs, I’m leaving the tenure-track career path.

I’ve noticed a difference in how people react to my career plans versus those of my friends who are moving on to postdocs or professorships. When asked about their post-grad plans, my friends on the traditional path receive a quick congrats and the topic of conversation moves onto something else. On the contrary, I’ve found that people ask a lot of follow-ups about my career plans. If you’re interested in alternatives to traditional academic careers, read on for my answers to some of the most commonly asked questions.

Why are you leaving?

People mean well when they ask this, but it’s a very personal question; I don’t recommend asking unless you know the person well. Often, I’ve found that the asker wants to commiserate with you about the state of the academy. While I do think that there are major issues with the culture and structure of academia (the leaky pipeline faced by women in STEM and replication issues, among others), I’m grateful for the knowledge and skills I’ve gained through my graduate school experience.

Contrary to popular belief, students do not always leave the academy because they are disillusioned or have “failed” at finding an academic job. Many have genuine interest in consulting, outreach, starting a company, working on Watson, hiking the Pacific Crest Trail, starting a bakery, or whatever it is they go on to do. Research is only one facet of life, and it need not be the only one. I’m leaving because I have always had other interests, and I want to explore those opportunities. During my time in grad school, I discovered that the part of my work I found most rewarding and enjoyable was communicating cutting-edge research to the public, so I’m trying out a career in science writing and outreach.

Condoleezza Rice, former U.S. Secretary of State, has a Ph.D. in Political Science. She didn’t stay on the academic track, but she’s doing just fine.

Did you tell your advisor? How did it go?

To be honest, I dreaded having this conversation with my advisor. My fear – which is a common one – was that she would be disappointed, angry, or even “give up” on me by providing fewer lab resources and less guidance. I waited to tell her until I was sure I wanted a non-academic career. After that conversation, I felt like a weight had been lifted, and I wished I had done it sooner.

Advisors can be a great resource to connect you with others who have been in your position before. Plus, you may find that you and your advisor work better together if you’re honest about what you want – for instance, if you and your advisor both know that you’ve got your heart set on consulting, you may decide together that those five exploratory follow-up studies that would have made you a more competitive academic job applicant are no longer a productive goal.

I feel lucky that my advisor has been supportive of my decision, but unfortunately, not every advisor will be supportive of students who choose a non-academic career path. In that case, seeking out a faculty member who will support you can be helpful.

But what can you do with that degree?

I’m usually asked this question by students in my field who have been thinking about leaving the academy, and are hopeful I will mention some magical, previously undiscovered career path. Consider instead: what do you want to do with your degree? Sure, your degree may confine your choices to some extent – sadly, as a psychology PhD, it’s pretty unlikely I’ll ever be an astronaut – but students routinely underestimate the general skills they learn as a PhD that apply to most jobs. All those studies you’re juggling? That’s project management. The RAs you’ve trained to run your studies? That’s leadership and team management. Submitting manuscripts and writing endless emails? Communication skills.

A longitudinal study from the Bureau of Labor Statistics found that between the ages of 18 and 46, the average person has 11 different jobs. Your job as a graduate student is just one of many you’ll have!

How did you find out about career options?

Narrow down the qualities of your ideal job. Do you enjoy teaching? research? working with people? Do you want something with flexible hours and projects, or do you do better with structure and deadlines? Do you prefer to work on teams or alone? These are just several questions to consider; if you’re at a total loss, check out AAAS’s MyIDP to help you start asking the right questions.

I’m also fortunate to work with Beyond Academia, a career education conference at Berkeley. We had our second annual conference in February, where we invited former PhDs talk about their experience transitioning from academia to the “beyond”. There were panels featuring speakers from a variety of industries (e.g. technology, science communication, and entrepreneurship) and workshops where students worked on specific skills (e.g. narrowing in on a career path, or how to create a personal brand). It was a great learning and networking opportunity, and students on other campuses are now lobbying their universities to hold similar events. Your campus may have a similar career education program, or at least a career fair. If not, consider starting one!

There are also a variety of online resources that can help you begin your search. Most universities’ career centers have websites with resources for students, though not all have sections specifically dedicated to post-PhD careers. Beyond Academia has begun compiling a list of resources here, which can be a good starting point.

Eric Schmidt, Google executive chairman and former CEO, is another former Ph.D. who has done quite well off the academic track.

What helped you in finding your career path?

Reaching out to others who understand your position can be both inspiring and educational. Take advantage of your personal network – talk to recent graduates from your department, or friends and faculty in your department to see if there’s anyone they know who has the type of job you’re interested in. Also remember that your university’s career center could be helpful for resources or alumni connections.

If you don’t have personal connections to your chosen field, the internet can be a massively powerful tool. Set up a LinkedIn profile and see if there’s anyone in your extended network who has your dream job. Twitter and blogging are also a good way to connect with strangers in your field. (On a personal note, I found out about a fellowship through Twitter and got a job interview due in large part to a blog post I wrote. The internet is a magical place!)

Also, be sure to try out what it is you want to do. Do you want to be a consultant? Join your campus consulting club. Your campus doesn’t have a consulting club? Start one! Other options to consider are summer internships, conferences, and workshops.


If you’re considering an alternative career, get acquainted with your options as soon as you can. Start right now, if you feel so inclined. Use those time management skills you’ve learned in grad school to set aside a couple hours a week for career exploration. Like completing a dissertation, career exploration is a marathon, not a sprint; incremental steps toward your goal will get you there. Admittedly, seeking out these opportunities in addition to your duties as a grad student can be tiring, but finding the right career for you is a worthy reward!

If you have any additional resources to suggest, please leave them in the comments below.


jane hu

Jane Hu is a Ph.D. candidate in the psychology department at University of California, Berkeley. Her research focuses on social cognition and learning in preschoolers. She is also an editor of the Berkeley Science Review and an organizer of the Beyond Academia conference. Follow her on Twitter @jane_c_hu, and check out her science blog:

Category: Academia | Tagged , , , , , , | 10 Comments

NASA to SpaceX: the Space Race Privatized

Over the several decades that have passed since the Space Race there has been a dramatic decrease in federal support for the nation’s intergalactic sense of manifest destiny. However, it is not that the nation suffers from a lack of curiosity or a decrease in intellectual prowess. The ultimate factor lies within our infrastructure. Changes in the national political climate have made for a tumultuous history for large scale scientific projects. Our lunar touchdown was the product of an efficiently focused national effort during a time when our status as an ingenious and powerful nation was threatened. Today, the idea of space travel and research has become significantly less of a priority, illustrated through the cuts in the NASA budget over the past years. This year, the federal NASA budget is set at $17.7 billion, a decrease of approximately $50 million from the initial 2012 plan. While this budget is enough to sustain several major projects, such as the James Webb Space Telescope, NASA has had to cut and reduce many promising programs, thus relying on partnerships with other countries, especially Russia and China, in transporting American crew and payload to work at the International Space Station.

Russian Soyuz spacecraft docking on International Space Station. (Image Credit: NASA)

Russian Soyuz spacecraft docking on International Space Station during Expedition 37. (Image Credit: NASA)

As a junior physics major hoping to pursue a career in astrophysics research, I have noticed an underlying theme in the variety of opinions on NASA’s current funding levels. That is the lack of full understanding of the organization’s contributions to immediate technological and medical problems. Much of the technology developed to break the earth’s atmosphere and operate properly in space, has led to several “spinoffs” on earth. For example, the technology used in the space shuttle fuels pumps inspired NASA and heart surgeon Dr. Michael DeBakey to design the miniaturized ventricular assist pump, which is now undergoing European clinical trials and has been successfully implanted within 200 people . Furthermore, technology developed to test the effects of a Martian climate on wind power resulted in 200 NASA-derived Northern Power wind turbines and a decrease in annual carbon emissions by 50,000 tons. Also, much of the data used to monitor the earth’s climate, which is invaluable during emergency situations, originates from NASA. In fact, such geospatial data is now available via the Cloud, due to an agreement with StormCenter Communications. Within the past ten years, the work done by the space agency has resulted in approximately 18,000 jobs created, 444,000 lives saved, and $5.1 million in revenue.

NASA has a strong focus on inspiring and promoting wonder within the general public. Space naturally appeals to the innate childlike curiosity we possess when looking up at the stars. With one child enchanted by a spectacular image of the Milky Way Galaxy, a passionate scientist can evolve. Without this process, how could the nation maintain a strong footing in solving the difficult problems space exploration presents? Yet, last year the sequestration forced NASA to suspend all aspects of their outreach program, causing a ripple of anger amongst much of the public. Though a minute amount of funding is now available, it does not correlate to the realistic amount needed to reach the millions of students within the country, and certainly not to depths the agency is capable of.

My passion and situation in physics are ultimately due to an internship I had at NASA Goddard Space Flight Center. During the summer of 2011, I worked in the heliophysics division studying the magnetic interactions between the sun’s interplanetary magnetic field and the earth’s magnetic field. The experience was humbling and slightly overwhelming, as one can imagine. Earlier that year President Obama cancelled the Orion and Antares projects meant to facilitate human low orbit shuttling with the assumption that private space companies would grow large enough to fulfill these needed rolls. The morning of the final mission launch, STS-135, my mentor picked me up at 4:00AM to view it live from campus. As a rising college freshman, it was easy to become fixated on the sadness and disappointment of the ending of something so iconic. Yet, the atmosphere within the auditorium was not mournful, rather, celebratory and hopeful. Every astronaut I met that summer emphasized how their passion began with something they experienced as a child. Now a junior, I often imagine the amazing feeling of fulfillment and excitement one has when achieving a dream so deeply seeded, which motivates me to withstand the trials of college.

Since the retirement of the shuttle program there have been several major changes within the environment of space exploration. First, NASA’s reliance on other countries, especially Russia, has grown. In order to reach the ISS, a join flight must be sent including Russian and American payloads. However, the current Ukrainian conflict and rising international tension with Russia has caused several figures, namely NASA director, Charles F. Bolden Jr., to emphasize the need to eliminate dependence on Russia. In fact, the agency recently declared that it plans to pause “the majority of its ongoing arrangements” but will continue to collaborate at the ISS.

In light of these political events impeding the advancement of space science and technology, it is difficult to envision a prolific future for NASA. This is where, I believe, the second change enters. In recent years, privatized space companies have risen to new heights in rocket development. However, the path to these promising developments is one not free of failure. In 1996 NASA funded Lockheed Martin to design, build, and fly the X-33 rocket with the intention of improving space travel. However, the failure of this program caused monetary losses of approximately $922 million and $357 million for NASA and Lockheed Martin, respectively. After more than a decade, the objective to produce successful privately funded space crafts was achieved. In 2008, NASA announced the results of the second round of their Commercial Orbital Transportation Services program, thus signing agreements with SpaceX and Orbital Sciences, out of the more than twenty firms that applied, to fund their proposals focused on transporting crew and cargo to the ISS. With the development of Falcon 9 and Dragon, SpaceX became the first private organization to successfully launch a spacecraft to rendezvous with the ISS. While this was a major success for the state of human space exploration capabilities, the program also highlighted the heavily competitive environment of the market. In the past many firms have failed to develop innovative and successful designs, resulting in massive losses for the owners as well as their respective funders. It clear that the market for privatized space transportation is high risk but high reward.

SpaceX, founded by Elon Musk, has proven to be a major, if not the most important, player in the market now, with a history of efficiency and innovation. Though the Falcon 9 and Dragon were not able to transport a crew during the initial launch, the design of the rocket and spacecraft are exceptional. The two stage rocket is propelled by the 9 Merlin engine octaweb, which is capable of producing a power equal to more than five 747s at full power. In order to separate the two segments, Falcon 9 relies on a pneumatic system rather than the traditional pyrotechnic method, thus allowing for more control. During the second stage, only one engine is used; however, it includes the unique and innovative ability to restart periodically, making maneuvering Dragon from different orbits more manageable and efficient. SpaceX is currently working on the adjustments needed to make both suitable for transport of a crew per the NASA agreement.

Falcon 9 carrying Thaicom 6 at Cape Canaveral on January 6, 2014. Image Credit: SpaceX

Falcon 9 carrying Thaicom 6 at Cape Canaveral on January 6, 2014. (Image Credit: SpaceX)

International Space Station fastening onto Dragon. (Image Credit: SpaceX)

International Space Station fastening onto Dragon. (Image Credit: SpaceX)

Branching out from the initial Falcon 9 design, the Falcon Heavy is the world’s most powerful rocket boasting a liftoff thrust equal to fifteen 747s at full power. This is achieved through three 9 Merlin engine octawebs, which also provide the ability to maintain proper flight even after one engine shutdown. It is capable of carrying a payload of 53,000 kg to low earth orbit, which is more than twice the amount a NASA space shuttle can transport. The regular use of this rocket will provide the U.S. Air Force, NASA, and others who can afford it with unprecedented cost efficient and reliable transportation.

The Falcon Heavy is the world's most powerful rocket, capable of carrying 53,000 kg. (Image Credit: SpaceX)

The Falcon Heavy is the world’s most powerful rocket, capable of carrying 53,000 kg. (Image Credit: SpaceX)

During a visit to GSFC, I was able to meet with Nobel Laureate John Mather Ph.D and inquire as to how he felt about the rise of privatized space companies. His response emphasized a strong support for such firms, as ultimately, NASA spends an extraordinary amount of money on rockets, around $1.6 billion per flight. If SpaceX can develop a standard, cost efficient, design space exploration would only become easier. Per flight, the costs of Falcon 9 and the Falcon Heavy are $56.5 million and $77.1 million-$135 million (geostationary transfer orbit), respectively. Yet, the impressive company has already started work on designing a reusable rocket. The Grasshopper, the experimental 10-story Vertical Takeoff Vertical Landing vehicle, reached its highest distance of 744m altitude on October 7th, 2013. Afterwards, it was able to hover and land successfully. Living in a community where reusing materials is the go to method of maintaining environmental consciousness, the development of reusable rockets is a major leap towards achieving a balance between advancing human knowledge and being proactively conscious of the state of our environment. It is an enormous challenge to produce rockets and spacecraft that are reliable, efficient, and dramatically cheaper than traditional costs; however, SpaceX has managed to operate well on that thin line of success. Perhaps the firm’s ultimate goal of providing humans with the ability to inhabit other planets will be achieved sooner than estimated.

Grasshopper during test flight. (Image Credit: SpaceX)

Grasshopper during test flight. (Image Credit: SpaceX)

With this I am reminded of the late Steve Jobs and his famous saying, “one last thing”. It is exciting and inspiring to see this same visionary outlook. As a college student I have noticed a strong need to constantly think ahead. Remaining with the pack is useless, but forcing ahead, taking risks with confidence and creativity is essential for success. The world and its environment are constantly changing and we must be prepared to adapt with them.

Before I end this rather long post, I would like to make a remark on another benefit of privatized space companies. While thousands of jobs have been lost as a result of the NASA budget cuts, communities surrounding the launch sites of SpaceX plan on greatly benefiting from these projects. The latter will create hundreds of jobs, provide internships for students, and attract other major, up and coming, companies. The potential Falcon 9 launch site, Brownsville, TX, is extremely excited but equally focused on confirming their selection. If you would like to read more on this, please refer to their local newspaper, the Valley Morning Star. In a previous post I highlighted the benefits of astrophysics research, beyond the romanticized visions of space. I hope that this post will provide clarity on the current standing of NASA both budget and research wise. The agency has been the pinnacle of human space exploration abilities and continues to conduct extraordinary work on the spatial objects. Its concentration on the earth’s dynamics have provided invaluable data as we learn to adapt our lifestyles. Due to recent political events, there is certainly a need for privatized space companies and it is clear many firms are meeting this challenge. The continued partnership between NASA and companies like SpaceX and Orbital Sciences will lead to major advancements in space exploration. As an aspiring physicist, with research experience in astrophysics and nanotechnology, I look forward to combining both areas to develop technology that can build upon this powerful and incredible progression.


  1. Jones, John. (2011, May 01). Space shuttle spinoffs. Retrieved from
  2. SpaceX. (n.d.). Capabilities and services. Retrieved from
  3. SpaceX. (n.d.). Dragon. Retrieved from
  4. SpaceX. Falcon 9. Retrieved from
  5. SpaceX. (n.d.). Falcon heavy. Retrieved from
  6. Turnbough, L. (2012, March 02). Commercial crew and cargo. Retrieved from
  7. United States. National Aeronautics Space Administration.Budget for Fiscal Year 2014. Web. <>.
Category: Physics, Technology, The Student Blog | 7 Comments

The Final Steps of Your Undergraduate Research Experience: Peer Review and Publishing

Conducting research is quickly becoming an integral part of the undergraduate STEM curriculum. The benefits of self-directed research early in an undergraduate education is echoed by my colleagues at The Student Blog (notably, Sarah Bhattacharjee, Rachel Cotton, Sean Lim) and large advocacy groups like the Council on Undergraduate Research. On paper, the increase in student research has very little to show, even with the developing trend of undergraduate-only research publications. Too many students and their faculty advisors are failing to recognize that the research is not complete until it is peer reviewed and presented to an audience. While undergraduate research journals have existed for some time, (for example, the Beloit Biologist for over 30 years and the Journal of Young Investigators for 17 years) the awareness of these opportunities is still lacking. When I speak with my peers, few of them are aware of the many opportunities for undergraduates to publish their research. The most common forum for young scientists to present their research is through conferences such as the Beta Beta Beta Conventions, MCMS Symposia, and NCUR. While these fantastic opportunities can contribute greatly to the development of a young scientist’s career, I believe that undergraduate-only refereed research journals provide an invaluable platform for the student research, well beyond other media.

Charles Darwin, who presented his research on leech eggs as an undergraduate

Charles Darwin, who presented his research on leech eggs as an undergraduate

Why you should try to publish as an undergraduate

1. Active and individualized feedback will help improve your scientific writing

Undergraduate STEM students are huge consumers of scientific literature. Students are introduced to primary research articles within the first few classes of their education. Many of these articles are poorly written. In a recent blog post, my fellow blogger, Jahlela Hasle, posed a very important idea; she said, “Why is the [scientific] writing so bad? Simple. We scientists aren’t trained to write.” Sure, we have all written countless lab reports, but in most cases, we are never asked to improve and revise our writing. Professors and TAs simply do not have the time to offer individualized feedback about their students’ writing. This is where peer review comes in. Many universities have implemented aspects of peer review and mock-publishing activities as part of their curriculum, with much success (and little additional work for the faculty). For example, at the University of South Carolina, the use of peer review contributed to the advancement of students’ writing skills and scientific reasoning abilities as measured by objective tests. Not surprisingly, the students agreed! Eighty-three percent of students involved in the peer review reported that it improved their writing, editing, researching, and critical thinking skills. Unfortunately, the implementation of peer review within formal coursework is still too uncommon.

The unfortunate destination of far too many undergraduate research papers [Wikimedia Commons]

The unfortunate destination of far too many undergraduate research papers [Wikimedia Commons]

2. It will professionalize your education

While most educators emphasize the importance of student-directed research projects, they must also recognize that a research experience isn’t complete until it is published. Peer review and peer assessment are an unavoidable component of a professional science career. Most research projects are bookended by peer review—first through proposal evaluation, then through publishing.  In order to professionalize an undergraduate science education, research experiences should be designed in a similar manner. Engagement in publishing is encouraged in many other disciplines, such as art, journalism, and creative writing yet it is unnecessarily avoided in the sciences.

3. You can get excited!

In my own experience, my first time publishing in an undergraduate-only research journal was an incredibly exciting experience. Not only did it give me confidence in what I can do, but I learned to communicate like a professional. Just as importantly, I have evidence that I can communicate! Now, I have a better idea of what to expect in graduate school and beyond. One of the most cited benefits of having journal-quality work as an undergraduate is that it provides evidence of a student’s gumption, independence, and ability to communicate clearly.

An undergraduate student realizing his dreams

Criticisms of Undergraduate Research Journals

Despite the apparent benefits of undergraduate-only journals, some oppose the idea. Critics argue that undergraduate publishing will “up the ante” and put unnecessary pressures on both students and their faculty advisors. Interestingly, the negative reaction to undergraduate journals often come from those who value undergraduate mentoring in their own labs. Many of the criticisms are along the lines of what Scott F. Gilbert argues, “If the research is good enough, it should be published in a ‘real’ journal.” By extension, if undergraduate-only research journals publish only “sub-par” research, who will read them?

What these arguments fail to recognize is that undergraduates, especially those who perform self-directed work, have much less time, money, and resources than research faculty. This disadvantage should not limit their ability to have their work peer reviewed and published. This is why undergraduate-only research journals primarily benefit the authors, and only secondarily benefit the readers.

To those who think that publishing should not be the status quo in a serious undergraduate STEM education, I pose the question: What is the purpose of an undergraduate education?

How to get involved in undergraduate publishing

It is extremely easy to get involved in peer review and publishing as an undergraduate. The Council on Undergraduate Research compiled a list of undergraduate journals. Many of these journals use undergraduate students as reviewers, editors, programmers, and designers. The journals span subjects from religious studies to physics. Some notable nation-wide journals include the Journal of Young Investigators, BIOS, Stanford Undergraduate Research Journal, and EvoS. In addition to these, an increasing number of undergraduate colleges are starting their own institutional journals.

[Credit: Grace Gockel]

Nathaniel Omans is a recent graduate of Beloit College where he founded the Beloit Undergraduate Research Journal. He plans to pursue his interests in neuroscience and education at Columbia University in the fall.


Category: The Student Blog | Tagged , , , | 2 Comments

Communicating Science Through Hip Hop

The Student Blog has talked a lot about ways to communicate research, from eliminating zombie nouns to “sacrificing truth for understanding.” But how about summarizing your findings in a rap?

We tracked down the Perlstein Lab, and asked Ethan Perlstein a few questions about his lab’s recent research remix.

Q: So, why a hip hop remix of your research?
Ethan Perlstein: The Evo Pharma Remix started out life as a more conventional video animation that I commissioned from a Canadian production company called Stone Canoe in the summer of 2012. (The genesis of the 2013 Ted-Ed video is unrelated even though it also deals with the topic of membranes). I decided to repurpose the original video animation after I crowdfunded Baba Brinkman’s 2013 Indiegogo campaign. The perk for my donation was a custom rap. Baba has released several science-themed rap albums, eg The Rap Guide to Evolution, and I’m a huge fan. I thought he would be uniquely suited to understand the basic science underlying evolutionary pharmacology and to parlay this understanding in rap form.

I knew that folks were blending science and hip hop in creative ways. That includes Baba’s oeuvre, but also Tom McFadden, an innovative science teacher whose students produced a hip hop tribute to Rosalind Franklin, the scientist who produced the historic images of double-helical DNA that Crick and Watson analyzed; and Chris Emdin, a Columbia professor who teaches science through hip hop. Science outreach is usually done by writers and bloggers who act as translators, but there’s no reason this outreach has to be in prose.

I basically just emailed Baba a link to the original video animation, which I had narrated, and he did all the rest! Including enlisting his musical partner Jamie Simmonds, who created a catchy, head-bopping beat.

Now imagine them remixing. [Citation: Chen J, Korostyshevsky D, Lee S, Perlstein EO (2012) Accumulation of an Antidepressant in Vesiculogenic Membranes of Yeast Cells Triggers Autophagy. PLoS ONE 7(4): e34024. doi:10.1371/journal.pone.0034024]

[Credit: Chen J, Korostyshevsky D, Lee S, Perlstein EO (2012)  doi:10.1371/journal.pone.0034024]

Briefly describe the research highlighted in the video.
EP: The Evo Pharma Remix is based on my former Princeton lab’s 2012 PLOS ONE paper. In broad strokes, we used yeast as a simple experimental model for studying how a complex drug works at the cellular level, an approach I dubbed evolutionary pharmacology. Specifically, we uncovered a novel mechanism of action of the antidepressant Zoloft involving its accumulation in membranes and ensuing cellular adaptations. We proposed that this drug accumulation plays a role in the human response to antidepressants, a hypothesis that still needs to be tested.

 Are you hoping to do more in the future?
EP: My biotech startup Perlstein Lab is focused on orphan disease drug discovery, and I would love to commission an entire album of orphan disease hip hop explainers. Not only to raise awareness of orphan diseases, but also to explain their underlying biology, their clinical history, and their patient advocacy efforts. And I couldn’t think of anyone better to do it than Baba Brinkman.

If you could remix one scientific paper from any time in history, what would it be and why?
EP: That’s a tough question because I think every seminal paper in the history of science should be immortalized and popularized in rap form. Someone needs to call Kanye’s or Eminem’s agents and see if they’re interested in bringing science to the masses. There are lots of papers to go around!

If Lady GaGa is more your tune, see our Q&A with the Lab Grammy-nominated DLab follies. Also, check out this PLOS ONE paper about the relationship between listening to hip hop and learning words. 

Category: The Student Blog | 2 Comments