Category Archives: PFP14S

Higher education for todays life after PhD

When ever I talk to relatives or friends outside academia, I get the feeling that I am considered a complete nerd incapable of any “real world thinking”. Even some employers avoid hiring PhDs because they are viewed as too theoretically oriented and too expensive. In some field this might be true. And it should not be. The higher education system should serve the community.

There are not enough positions in academia for all graduate students anyway. And all graduate students don’t desire those positions. We need to prepare students for the whole world,  not only for academia. The info graph below describes the faith of biology PhDs. If 15 and 20% of post-doctoral researchers go to tenure track or non-tenure track faculty positions, it is actually under 23% of all students who receive PhDs. We cannot afford to only cater for the 22.6% percent who will become faculty.

Offering options and softer skills needed to survive in industry or as an entrepreneur for example would make any graduate program more attractive to students.  Virginia Tech’s certificates and transformative graduate education are a great help for career planning. But we could be doing more to help future PhDs to apply their degree outside academia.

Offering instruction in “soft skills” can help students build a suitable degree for non-academic workplaces. Simple accounting can help any academic to hold the lab’s funding in order, and leadership classes will help future workers deal with other people at their work place, where ever they end up at. Some of these are already offered and just need to be marketed better for students as well as their mentors. Contacts to industry will help engineering students and biology students alike. Internships care a great option for students with the time and their adviser’s blessing to take time off their research. But mentoring is useful for everyone.

Having a great mentor can make your career. But finding a great mentor can be very tricky. Virginia Tech does a great job supporting undergraduates as they come to the university. Even new faculty can get mentoring. PhD student’s mentor should ideally be their adviser. But that adviser is embedded in academia. Every PhD student should have a mentor outside academia to offer thoughts on possible career moves outside the university system. They could be part of the PhD student’s committee, or just an extra support.

In the future, I would like to see a larger number of PhDs to find jobs outside academia with confidence that they can make it in this environment.

Faculty LOLing and Trolling

Can anyone imagine a world without Facebook on our fingertips and course materials on-line? Social media has penetrated our world via Facebook, Twitter, internet dating, chatting, and professional networking sites. It has become our front porch, cafe, and living room to converse with people in a setting we modify to match our personality and mood. What are some of the great and not-so-great aspects of these web-based tools?



Twitter goes through 500 million 140 character micro blogs or “Tweets” every day. The mission of Twitter Inc. is “to give everyone the power to create and share ideas and information instantly without barriers”. This sounds great and has been used in university classes to activate students. Professionals use it to follow interesting news in their fields, and everyone can use it to have an online presence and personal channel for connection to friends and acquaintances. I have found it useful to keep up on cutting edge science publications, that cause public conversation among scientists.

This can be used in unkind ways too. Without realizing both students and faculty can be very offensive in an extremely public and immediate environment. Teachers of a Los Alamos high school read tweets about themselves to remind students what they share on the internet can be read by anyone. This January In university of Illinois at Urbana-Champaign, twitter comments on chancellor’s decision to  keep classes in session, when cold weather hit the campus, got very offensive. This was reported in Inside Higher Ed news section. It seems university students also need a remainder on how the internet works.

Professional networking sites® and many other sites have profiled themselves as professional Facebook. Indeed the mission statements of LinkedIn and Facebook are very similar.

The mission of LinkedIn is to connect the world’s professionals to enable them to be more productive and successful. To achieve our mission, we make services available through our websites, mobile applications, and developer platforms, to help you, your connections, and millions of other professionals meet, exchange ideas, learn, make deals, find opportunities or employees, work, and make decisions in a network of trusted relationships and groups.

Founded in 2004, Facebook’s mission is to give people the power to share and make the world more open and connected. People use Facebook to stay connected with friends and family, to discover what’s going on in the world, and to share and express what matters to them.

Facebook offers more personal sharing environment and LinkedIn® concentrates on the professional advantages it can offer. This sort of networking could be more comfortable for the introverts in any field. Activity within the social media is still required for it to benefit you, but you can plan and form a strategy to best present yourself. And there is a lot to plan for; Summaries, CV items, and skills.

With today’s wide variety of social networks, this one can be forgotten easily when you are working. But as soon as you need to find a new job, you wish you were more active in the networking social media. If you don’t take this seriously and make it just another Facebook page, the benefits will be non-existent and the sloppy public profile can even hurt your professional image. When our students start using these networks, they really need to make a difference between the professional site and Facebook profile. Even if it is tempting to accept all invites to connect, one should be careful what kind of professional picture is presented by choice of contacts.


wordpress-logo-stacked-rgbBoth faculty and students can benefit from blogs. They can offer a creative outlet or be a professional front for anyone. The content posted can be visible to anyone or even just the class contributing to it. The benefits are usually connected to improvement in writing skills and sense of ownership for one’s work. The need to be careful in framing blogging as student activity cannot be emphasized too much. Requirement of certain number of blogs will give you exactly that. Number of posts to get it done. And words on screen that do not engage, written by someone not interested in writing them.

The best sort of blogging is engaging to the writer and audience. An example of that are the Harvard faculty blogs. What a great way to build an online presence of the whole university and bring it all together under the institution. It can lead to professional discussions as well as offer a source for future students looking for mentors. It can also harm one’s online reputation, if care is not used on what is shared.

In the end, the greatness and the pitfalls of any social media we use as faculty or students comes down to thinking what you post and do on-line. On twitter the best advice for students would probably be the Wheaton’s law: “Don’t be a dick”. It is simple and easily understood in many contexts. As future faculty, student, teacher, or a parent, one must consider the consequences. I find it helpful to think any writing I post as a presentation to a large group of people including your co-workers, relatives, and all minorities. You don’t want to needlessly offend anyone. And since your boss is listening, you don’t want to loose your job.

Telling people to use social media responsibly is like telling them to drink responsibly. Most will do it, but there can be temptation to go overboard. Having an internet troll tweeting offensively is like listening to an obnoxious drunk…

Are PhDs prepared to run their own labs?

One reason why I chose Virginia Tech to do my PhD is the transformative graduate education program. It provides extra preparation to ones future career after graduation. It is not perfect yet, but what really is?

In the fields of biological sciences faculty has to run a laboratory efficiently. But the standard PhD education does not necessarily address how a primary investigator (PI) does it. Are we expected to absorb information on day-to-day lab managing skills from the stuffy air of our offices? And students are really busy with research, to the point of sacrificing sleep and human contact. Some labs have technicians running parts of the lab. Most primary investigators don’t involve students in the management side of things unless the student brings in their own grant.

There are consulting companies, like hfp, giving courses on how to manage a lab. Commonly these sorts of courses are offered for fresh primary investigators. But how can a graduate student really understand what they are getting into as they embark on a career path leading to a tenured primary investigator. I think these courses should be available to graduate students for them to make informed decisions about their future.

Leonid Schneider's comic in

Leonid Schneider’s comic in

A resource to alleviate the lack of these kinds of courses is produced by Howard Hughes Medical Institute in their resources for early career scientists. The “Making the Right Moves” manual offers advice for all levels and layers of starting as a primary investigator starting from applying the position, to hiring staff, and managing the projects you might have. I found this document to have a lot of useful information about a post graduation career for PhDs. I don’t want to be blindsided when I have to fire staff, balance a budget, and hire new people suddenly.

To help graduate students make career decisions I think courses and discussions involving everyday lab management issues. The life of a primary investigator is different from a laboratory work intensive graduate students life. And we really don’t want to buy a “pig in a bag” for a career.


  • Laursen, Lucas (2014) Learning to Lead a Lab, Science Careers.
  • Making the Right Moves: A Practical Guide to Scientific Management for Postdocs and New Faculty, (2006) by the Howard Hughes Medical Institute and Burroughs Wellcome Fund. Accessed 4/22/2014 at

Limited access to journals in Greece

In a last years Nature News article, the financial situation of Greece was brought up in connection to science by Varvara Trachana. The government is dealing with six years worth of recession and pulling the nations belt tighter on everything. This includes science. The salaries and funds for reagents are frozen, leading to young scientists leaving the country. One devastating consequence of decreased funds in science, is the lack of access to subscription journals. Since the government does not pay for the subscriptions, university scientists are left without the information they need.

I found this highly problematic. For example when preparing all the necessary paperwork for animal experiments, one has to research all possible alternatives to use of animals and make sure the experiment has not already been done. What if you cannot have access to the journals the relevant literature is published in? This situation underlines the need for open access journals. Having all research publications open access as soon as they are published could improve the science done around the world.

“Many Greek researchers, unable to afford personal subscriptions to their favourite journals, are already considering reviving a practice that was common a decade or so ago — contacting friends and colleagues in foreign research centres and asking them to fax or e-mail articles.”                                            -Varvara Trachana, (2013)

The quoted statement above is a bit troubling to me. It seems like requesting the subscription journal articles to be sent by ones colleagues could be the only option for Greek scientists. Could one get into trouble like Aaron Swartz did over making the subscribed content available to others for free? Are there any rules about this?


  • Trachana, V. (2013). Austerity-led brain drain is killing Greek science. Nature 4967445:271 (
  • Khier Casino (2014) New Details Surface About Events Leading Up To Prosecution Of Aaron Swartz, in Design and Trend (accessed 4/17/14 at

Sabotage of scholarly integrity

Science relies on integrity and trust between scientists, between scientists and public, as well as universities and their employees. The public needs to trust us to not waste their tax-money and to produce information that serves them. Universities need to trust that the employees don’t misrepresent the institution. The university employees trust the universities treat them fairly in employment and their bosses treat them fairly.

A case from the office of research integrity brought up a situation where primary investigator suspected falsification of data by a technician. A duplication of a result of an experiment was presented as a separate set of results. A method for detecting radiolabeled proteins by exposure to films was used. The duplication was detected as the method used results in varying imperfections in each film due to air bubbles, dust, or other artifacts on film. The two films were identical. That does not happen in this technique.

The technician was confronted by the primary investigator twice and denied the duplication at both times. The results were viewed by other scientists per request of the primary investigator and confirmed as copies. The case seems straight forward at first, but when you start thinking of the severity of consequences the parties face if action is taken, the “what if”s start to appear. What if the technician truly believes the results are from two separate experiments and does not knowingly lie about it.

The primary investigator takes on a huge amount of responsibility if the case goes forward. Their responsibility as a mentor to the technician would be to prevent the possible misconduct, by making them aware of the types of scientific misconduct and the consequences. As a result of misconduct the primary investigators integrity could be brought to question. The consequences for the technician could include sanctions like loosing their job. Also their integrity would be questioned and they might not be able to work in a laboratory again.

There are proper channels to go through for this kind of suspicion of misconduct. University research integrity office (ORI) is the first place to contact. Since there is physical evidence, it should be handled carefully as instructed by ORI. Since the technician is not a student, the case does not go through honor court system, but directly to  research integrity officer. The following graphic simplifies how Virginia Tech research integrity office processes misconduct allegations:

Misconduct handling. Modified from

Misconduct handling. Parties are requested to review reports from inquiry and investigation committees. Appeal of decision is made to university president and dismissal of charges is followed by restoration of reputation. Modified from

But what if this type of misconduct procedure does not apply? This was the case at University of Michigan in 2010. A postdoctoral researcher sabotaged a graduate students laboratory work by killing her cell cultures. The case was reported in Nature news in 2010 by Brendan Maher. Sabotage does not apparently fit the federal definition of misconduct (plagiarism of work, cooking up data, or falsifying data), and therefore won’t be addressed by any of the federal funding agencies.

From the article:

The graduate student had to go to the police to report the case as a crime. After the campus police had first interrogated her and performed lie detection test, they started investigation. The day after installing cameras to record the cell culture space, the postdoc was caught. Court ordered him to pay for lost reagents and court fees ($9400), serve probation and 40 hours of community service. His visa however prevented him from staying in the country after losing his job. Further hearings along with greater damage payments did not go through. Punishment did not reach its full scale. And the graduate student lost her trust in scientific community as mutually respective for a while. (Maher, 2010)

The investigated person leaving the country to either escape or to avoid immigration problems, is an additional issue. It is related to research as many researchers are in US on some kind of a visa with strict rules to allow them to stay in the country. This is just an extra layer of trouble on top of the core issue of ethical misconduct.

To me it is unbelievable, that sabotage is not considered research misconduct. It violates ethical codes of universities, hinders research on purpose, and in the end shakes everyone’s trust in scientific community in the long run. Could the federal definition be changed to include sabotage? And how would one formally document those cases, if acquiring physical evidence could potentially damage individuals rights (eg. filming without subject’s knowledge)? Do we have to involve the police in a clearly research related ethical issue? Or does that route actually provide harsher punishments for the perpetrators?


  • Maher, Brendan. 2010. Sabotage!, Nature 467, 516-518 | doi:10.1038/467516a (
  • Office of Research Integrity website, RCR casebook, (accessed 4/7/2014 at
  • Research Integrity Office website of Virginia Tech, (accessed 4/7/2014 at

Open access to disease and other research – PLoS Pathogens

The appearance of open access journals is something I personally applaud. Having current research available for everyone with internet connection and understanding of English language, seems fair as some of the research is supported by tax money. This was also pointed out in Richard Van Noorden’s article “The true cost of science publishing” in Nature (2013) (1). To my mind it highlights, that my research is accountable to the general public instead of just my peers. Paying for my research to be distributed widely instead of to only the ones with access to high impact scholarly papers seems like a responsible thing to do.

PLoS is perhaps the most widely known open-access journal family with a good reputation. It concentrates on biological and life sciences. It has a very appealing web interface and is indexed in all the major archives we use in biological research to find articles like PubMed, MEDLINE, Web of Science, and Scopus.

PLoS stands for US Public Library of Science. The online journals of PLoS family include PLoS ONE, PLoS Biology, PLoS Medicine, PLoS Computational Biology, PLoS Currents, PLoS Genetics, PLoS Pathogens, and PLoS Neglected Tropical Diseases. I will concentrate on the PLoS Pathogens for now to illustrate the PLoS family of journals. PLoS is a non-profit organization. In 2001 it announced to start publishing electronic open-access journals, after an attempt to persuade other publishers to release their journals for the public for free after a delay (2-6 months post first publication of the issue) (2). The goal of PLoS is to provide the public access to research, not depending on financial resources. PLoS Pathogens has been published as a separate journal since 2005, as evident from the journal’s archives.

Scope of PLoS Pathogens include research on bacteria, fungi, parasites, prion, and virus related diseases which impact medical, and agricultural fields, and economies everywhere. The study of this microbial world gives insights into basic functions of cells and organisms, expanding basic science knowledge. Due to the impact of pathogens in everyday life, I find it appropriate that this publication is open-access. A separate issue arises to enhance the general public’s understanding of these scientific texts. Should we have a separate abstract to the public outlining the results? Or should scientific community present their information more aggressively in other mediums like blogs, tweets, and forums?

Notice the easy access tabs to metrics and comments, and subject areas tags.

PLoS Pathogens, like all PLoS journals, adhere to Creative Commons Attribution license (CC BY). This means that authors still own their research, but anyone can copy, modify, reuse and reprint the articles as long as the researchers are cited. You don’t have to ask for publishers or authors permission. This seems fair compared to the publisher obtaining the rights to the work. Taylor however in his article in Scripted- A Journal of Law, Technology and Society, calls for a balance between the copyright practices (3). He points out, that the copyright is mostly on the side of the author. His point of view also includes the academic publishing done in book form, which to me is a whole different animal compared to publishing in research journals.

PLoS Pathogens has the impact factor of 8.14. Compared to non-open-access journals with long history and high prestige like Nature Immunology’s 26.2, or Cell Host and Microbe’s 12.6, it seems a bit low. When comparing to other open access journals like BMC Immunology’s 2.61 it is rather good.  However impact factor is not the best statistic to evaluate a journal. To me the width of the scope a journal presents affects my appreciation of the journal. Ones that take in articles from varied fields of research tend to select articles that have the  WOW-factor. Journals specializing to a topic seem to take in articles, that don’t necessarily have the WOW-factor, but are important in bridging the research to that future WOW! moment.

Part of Jorge Cham's PhD comic about rivalry between Nature and Science magazines.

Part of Jorge Cham’s PhD comic about rivalry between Nature and Science magazines.

The following quote from Van Noorden (1) shows the opposition from subscription journal publishers.

“The costs of research publishing can be much lower than people think,” agrees Peter Binfield, co-founder of one of the newest open-access journals, PeerJ, and formerly a publisher at PLoS. But publishers of subscription journals insist that such views are misguided — born of a failure to appreciate the value they add to the papers they publish, and to the research community as a whole. They say that their commercial operations are in fact quite efficient, so that if a switch to open-access publishing led scientists to drive down fees by choosing cheaper journals, it would undermine important values such as editorial quality.

Maybe I don’t know enough about the publishing industry, but to me the extra value gained from editorial quality is not clear. The open-access journals, like PLoS Pathogens, use peer-review and have very nice e-publication formats. The publishing in them is less expensive too, and the research can be seen by more people than the subscription based publications. Does anyone know exactly what the editorial quality refers to? I would really like to know what extra value I would get compared to open-access.


1. Van Noorden, R. 2013. Open access: The true cost of science publishing. Nature 495:426-9.

2. Vicki Brower, 2001. Public library of science shifts gears. EMBO reports. Nov 15, 2001; 2(11): 972–973.

3. K Taylor, “Copyright and research: an academic publisher’s perspective”, (2007) 4:2 SCRIPTed 233 < >

Finnish higher education system

The Finnish higher education is divided to two branches. The actual universities offer Bachelor’s, Master’s and PhD programs in all fields. Universities of applied sciences offer more practical studies and only Bachelor’s degrees in specified fields like nursing, engineering, arts like dance, and media production.

Flow chart of the Finnish school system. No tuition required at any step.

Flow chart of the Finnish school system. No tuition required at any step.

Students who opted out of high school and went to vocational school can apply to both as long as they meet the requirements. Usually they go to the applied sciences institution first and then apply to university. High school is a faster track to university, but students also go to the applied sciences institutes from there. I really appreciate the flexibility of the system. You are never shut out from higher education.

Students apply directly to the department, to a certain major. Your school grades are taken into account as well as the matriculation exam (high school students), and the main requirement is the entrance exam specific to the major. Each entrance exam can be based on one or more books and contains application of the learned material to answer problems. For applied sciences, entrance exam is based on high school courses, but some fields like nursing might require psychological testing as well as group interaction tests.

Universities in Finland. Modified from

Universities in Finland. Modified from

There are no core courses required in the university. Only compulsory non-major classes are language classes (English and Swedish). All the general knowledge classes are taken at high school level. Minors can be used to widen one’s education. For example marketing, biology, chemistry, and microbiology are popular minors for biochemistry major. In retrospect, maybe having some sort of common core could have been beneficial and allowed introduction to more varied minor choices. Students have the freedom to not show up in most classes as long as they acquire the information on their own, return any homework required, and pass the exams. This is expected to change as teaching methods are developed to more student centered.

All higher education in Finland is tuition free at the moment. Administrative fees (includes student health care and dental fee) are low, around 90 euros ($125) per year in my old university. For citizens of Finland there is an automatic stipend to cover living expenses and support for renting an apartment as we have no dorms. Most students avoid loans like they are the plaque. The meals on campus have student discount pricing and consist of quite healthy home cooked style fare (side salad, bread, warm main, milk or water). Students take care of buying their books when needed, but libraries commonly carry enough books for most students to use during the semester. I bought around 6 books during undergrad.

Student housing ( and student life at University of Oulu

Student housing ( and student life at University of Oulu

Recently we have started several master’s programs completely taught in English. For example at the University of Oulu master’s degrees offered in English are from Business and economic, Education, Engineering and architecture, Health sciences, and Natural sciences. These have attracted students from Europe, Africa, and Asia.

The higher education system is flexible in Finland and students financed well by the government. It is not a perfect system by any means and faces many of the same problems as other higher education systems in Europe and US. Keeping the higher education available for all qualified students is still a priority and is seen as a way to enhance equality. As Finland is a small country with limited natural resources, our economy depends on highly skilled people.

Some of us rather deal with bacteria than people

There is no love lost between science and politics in my experience. The general population overall seems to have a level of distrust for both. The nature of politics showing as people pleasing, backstabbing, and a bit dirty to younger generations, has possibly deterred individuals interest in politics. Some of us rather deal with bacteria than people.


Luke Jerram with glass E. coli (

How ever this can lead to serious problems in decision making in politics and isolation of science from society. Luckily there are scientific advisers at many levels of governing. An enlightening article in Nature by Peter Gluckman, the scientific adviser of New Zealand’s prime minister, paints a positive picture of this position. His comment on the advisers role in policy making underlines that we can’t just barge in to politics:

The role of the science adviser is often less about providing direct technical expertise than it is about nudging attitudes and practices to enhance both the demand for and the supply of evidence for public policy.

The preparation of policies is not about bringing up great science and implementing policies only driven by raw science. The society has other parameters, that need to be taken into account like economy, traditions, and social structure. Scientists need to be aware of these parameters as much as policy makers need to understand science.


HIV in glass by Luke Jerram (

Cutting edge science can be extremely difficult to grasp. Nature News has put out a helpful list of tips for evaluating scientific claims for non-scientists. It has twenty core principles of evaluating scientific data explained. There is also a 20 point tip list for scientists to understand the making of policies in the Guardian written in response to the Nature’s list. Putting these lists to use in policymakers and scientists interactions could make a positive impact on the whole process and bring the two groups together. Not to mention increase the trust of public for both politics and science.



Student organizations in Finland – the system of guilds

As part of positive psychology on campuses Frank Shushok Jr. and Eileen Hulme bring up positive organizations for students to belong to. According to their paper “What’s right with you: Helping students find and use their personal strengths” in About Campus, they describe these organizations as communities where students can use their strengths and feel empowered.

In higher education in USA this can be clubs connected to hobbies, sororities and fraternities, service groups for the community, or special interest clubs like the Dairy Club. Some of these communities require application or being chosen to be part of it. What if you are not accepted as part of the group? What if the application and initiation processes are too daunting for some people to even try?

In Finland this is solved by having “guilds” based on your major. And you are automatically accepted to the guild as you get your acceptance letter to the university to study the major. These are student run communities designed to serve the students. For example during my undergraduate days the biochemistry “guild” arranged parties for undergraduates, master’s students, PhD students and post graduates together. We got to know basically everyone in the department and could get peer support for every single class we had from the older students. Sports events were very casual. You did not even need to know the rules to come and play football, floorball, volleyball, or anything else.

This kind of environment offered a safe space for discussions on the topic of our major –biochemistry- as well as general thoughts about higher education and even politics surrounding it. The community would lend a helping hand also outside of academic life readily. It is not uncommon to have the guild help with moving for example.

What would be a better way to build an active community than the all-inclusive relaxed guild? One drawback of this system however is the exclusion of other majors. Some parties were arranged with other guilds and friends from other guilds are always welcome to join in on the activities, but it was rare for people with no personal ties to the guild to join in with sports or other activities.

I would be interested to know, if these kinds of systems work or could work in the US. Or is the exclusive nature of clubs an advantage in the higher education generally, and in building up your CV?


Do you want to ride a unicorn?

A recent article in chronicle of higher education on the perils of scientists in academia caught my attention immediately. It reflected my feelings on academic career “nicely”. The main data graph is attached to the end of this post for anyone brave enough to look.

Press and academic publications have been piling up messages on dwindling grants, too many PhDs, and dissatisfaction in working conditions. The data indicates that over 40% of primary investigators surveyed are encouraging students to leave the ship, 80% expect to see more discouraged PhD students and Post-docs, and over 20% have encouraged students to leave US for their next career step.

To lull oneself into the false security of this happening to just starting level scientists is foolish. The piece in the Chronicle of Higher Education gave stark examples of even established scientists leaving the field, or the country, to survive. No wonder I feel like staying in academia seems implausible, I am not good enough, and landing a tenured position seems as likely as finding an unicorn under the lab bench.


Some days leaving science and finding work at a grocery store seems like the easy way out. But then I see my PI and she seems to find the unicorns and ride them with success. What made her able to do that? Was it just a completely different environment ten or so years ago? Sure. But maybe it is actually about the ability to see the unicorns in the first place, that allows her to ride them. The current financial situation, which will change, makes it just harder to see these magical creatures. And maybe the people leaving academia have found that they would rather ride a Pegasus with wings, or they see the unicorn elsewhere.

Possibly the goal of our higher education is first to consider the existence of unicorns and then finding ways to get to them, where ever they are. Or maybe the stress has just made me delusional… I have finally cracked an it manifests as hallucinations of unicorns.