10 professional abilities you develop by doing science

By Lilian Pavani
English edit: Lídia Paes Leme and Katyanne M. Shoemaker

Original here

   Those who have done scientific research know how hard it is to explain what you do. Since your work is not an internship or a job, research is typically first done in the position of a student, as either an undergrad, masters, or doctoral student. Is there a researcher among us who has not heard the phrase “do you work too, or only study?” Contrary to common belief, yes, you work and work hard!

   Mislead are those who think that work within science is a cinch. Research goes beyond reading articles and books, it involves the construction of new knowledge. On this ardent path, scientists are forced to learn many things that are valued in the “real world.”

   When I was doing research I didn’t have any idea of the skills I had learned along the way, but when I started to work in the business world, I realized how many abilities I had due to my undergrad and masters studies in marine ecology. Regardless of the subject you research, you’ll likely find the following to be true for yourself:

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1- You know how to use Word and Excel

You may need a bundle of complicated software to analyze specific aspects of your work, but there will never be a time you’ll forego the simplicity of making a datasheet and quick graph in Excel. One of the first skills we teach ourselves in data analysis is how to transform a pie chart to a bar graph and change the colors of data series’ until we find what best represents our results. And if you’re applying to a scholarship, presenting results, or formatting a thesis, you’ll – pardon me the pun – learn Word “write.” You insert tables, images and references without losing sight of the format of paragraphs, margins, or footers.

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2- You know how to make nice presentations in PowerPoint

Who hasn’t made a poster to present in a conference? Or a presentation for a class in your undergrad or to defend your thesis? Research has helped you almost certainly develop a good aesthetic sense: knowing how to pick the best background color and font, and how to symmetrically distribute the elements of your slide. By now, we all know a picture is worth a thousand words, and wordy slides are the downfall of an otherwise good presentation. Powerpoint helps us master the art of presenting the important information in the available time, be it five, 20 or 50 minutes.

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3- Project management is something natural

Your desire to do research likely started with a question you wanted to answer, a need you identify – the initiation step. To answer the question, you needed to write a research proposal, so you to gathered information, defined the necessary activities to your study, and estimated the necessary resources and deadlines – the planning step. With a research project approved, you developed the defined activities – the execution step. And while your project was being developed, from time to time some activities and processes were reviewed, adjusted and made better – the control and monitoring step. By project completion, you presented the final results in a report or article that went through a rigorous evaluation by your adviser and others – the finalization step. There you go, you may have never heard of a PMBOK or MS project, but you know all about project management!

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4- Quality is mandatory

The level and rigor and requirements in the academic field can be stratospheric. I’ve seen people kicked out of graduate programs because their scores didn’t meet the level desired by the program. Even if your work is a good contribution to the field, an unsatisfactory abstract alone may prevent you from presenting your work at a conference. If your article is not well structured, it likely won’t be published in any journal. Peers evaluate everything and screen your work for any minor slip; therefore, it is imperative to always make sure the work is well done.

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5 – You become judicious

Because of the obligation to quality, the more thoughtful you are in the development of your work, the greater the chance that it will be well done. This habit is acquired without notice.

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6 – Knowing how to argue is a necessity

In order to discuss your results, apply for funding, or convince your advisor, you need to know how to defend, support, and prove your point of view.

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7 - You learn how to deal with people

During your research, you need to deal with several different people in varying positions of power. At the very least, you have an advisor and maybe a co-advisor. If you are at masters or doctorate level, you will have collaborators alongside you and new students below you to train. There will also likely be the need to connect to other members of the your home department, especially professors. Those who even only minimally understand academia know that the academic field is an ego war, and you are caught in the crossfire. You must learn to do whatever is possible to keep things going without damaging the pace of your research.

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8 – You understand deadlines are important and you abide by them

If you’re on a scholarship you’re always aware of the deadlines for filing reports and funding forms. If you don’t have a scholarship, you’ll be following program deadlines and keeping track of when to submit a new proposal. If you want to present your work at a conference, you have deadlines for abstract submission (sometimes organizers can extend the deadline date, but in general, people use that just to review the abstract sent).

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9 – Financial management is part of it

In general, most scientific grants and scholarships have a technical reserve -- money that does not go to the researcher but towards the acquisition of equipment, books, field research, and other items needed to the development of the research project. This pool of money is often small, so you learn to manage the financial resources by looking for the best value. In some cases, you may learn to manage many different project funds, to buy common materials that will benefit multiple projects and other in the lab.

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10 – You realize that your success is totally up to you

The academic field can be a hostile environment, demanding a lot of dedication. Because of that, people tend to qualify themselves as much as possible and are always in search of improvement. So, if you intend to leave the academic career and follow an alternate path, remember your own self value! You have a lot to offer! ;)

About Lilian Pavani:

Lilian is a biologist, with a masters in ecology and specialization in environmental engineering from the State University of Campinas. She is a lover of sponges and other marine invertebrates, especially the colorful ones. After sailing through sponges, amphipods and petroleum, the current and winds took her literally down other roads, where she worked studying run-over fauna, doing environmental management and supervision of railroad construction. She has many diverse interests, including education, writing, innovation, cooking, playing the flute in an amateur group of antique musicians, and bird watching. Anyway, she lives with her feet in the sand and kind of in the tides.

Challenges faced by women in science

By Catarina Marcolin

English edit by Katy Shoemaker

A debate at the Institute for Advanced Studies (IEA-USP) recently got my attention, entitled “Women in the University and Sciences: Challenges and Opportunities.” If you can understand a bit of Portuguese, it is worth watching the entire video (it is only available in portuguese). The debate lasts around an hour and consists of three female scientists telling incredible statistics and surprising facts about women’s participation in the academic world, and some of these facts are really hard to believe.

So this week, I want to discuss some of the facts included in this debate. To do that, I searched for more data so we can go deeper into the subject. First of all, I was happy to find out that women represent about 50% of the undergraduate students in Brazil. We are even the majority in some areas. However, when we look only at the sciences and engineering, women make up less than 40%. At the University of São Paulo, USP, a paltry 15% of the students enrolled in engineering courses are female.

Extending beyond undergraduate education, there are also as many women as men in graduate and postdoc positions in Brazil. In fact, in 2010, more women earned Masters and Ph.D. titles than men. But again, that is not the reality in science and engineering. There is still something hampering our inclusion in these areas, including oceanography.

Number of scholarships per area in 2014. Source CNPq. Women: Feminino; Men: Masculino.

The most shocking numbers are those related to the distribution of specific research grants called PQ grants. These grants are awarded to researchers for research excellence, and they determine the distribution of funding to research projects in the country. Therefore, PQ grants directly affect our performance as researchers. PQ fellowships are tiered, and women's participation decreases as we go up each level. Note that women receive no more than 38% of these grants, even at the lowest level.

PQ research grants per level in 2014. Level 2 is the lowest category that a researcher can apply for, whereas SR is the highest level. Source: CNPq. Women: Feminino; Men: Masculino.

It is clear from these two plots that there is both horizontal and vertical segregation of men from women. Women appear to be concentrated in certain careers (horizontal), but within a career, there is a vertical separation of power, with women having low representation in the highest positions.

We find more examples of vertical segregation when we analyze leadership positions in large research groups. In Brazil there are currently 126 National Institutes of Science and Technology (INCTs). Well, 109 of those INCTs are run by men and only 17 by women. There are 6 INCTs focused on oceanography/marine science, and only one of those is lead by a woman (Antarctic Environmental Research - INCT-APA).

An all too common scenario can be seen in the Brazilian Academy of Sciences (ABC). The following data was presented by the physicist Carolina Brito (Federal University of Rio Grande do Sul) in the debate I mentioned at the beginning of this post. For a researcher to join ABC, he/she is nominated by an ABC member and a committee decides whether or not that researcher will enter. This committee is massively comprised by men, and as you can imagine, the result is not at all encouraging for female scientists. There is a list of the current ABC members on their website. There are 795 men and 122 women in ABC. From these, 15% of the men are below the 1A level in the CNPq, and only 1% of the women are below level 1A researchers. A fast interpretation we can make is this: if you want to be a member of ABC, and if you are a woman, it is almost mandatory to be a level 1A researcher or higher. For men, this standing does not have the same impact.

Unfortunately, this reality does not seem to be getting any better. In 2008, 20% of the deans in universities were women, and 8 years later, this number dropped to 10%. Although 48% of the Ph.D. holders are women, only 23% of them occupy teaching positions in our public universities. In a previous post we have addressed some of the reasons for why women quit the academic career at a higher rate than men (When to add children to the academic timeline).

So, what can we do to change that picture?

1 - The data presented here is limited. We need numbers, we need more indicators.

2 - We need training on gender issues. In France, curriculum was recently modified to discuss gender in all undergraduate courses. That sounds like a good start.

3 - We need to fund women's projects, provide scholarships, and reward them. We have very few initiatives, but these have incredible effects. Check out the post Finding self-confidence as a woman in science to see Deborah's testimony on the importance of being recognized in her area.

4 - We need role models. Young female scientists do not see people like themselves in power positions regularly enough. Socially, girls are still discouraged to pursue scientific careers that are considered "hard." From a very young age, we are overwhelmed with ancient cliches telling us how to take care of the house, how to be good wives, mothers, true ladies of our homes. We have to give girls the opportunity to fall in love with science and make them confident that this relationship can work. The L'Oreal Foundation recently conducted an opinion poll that demonstrated how Europeans feel about the role of women in science. Five thousand people were heard (men and women), and 67% said that women are not qualified to hold positions of high responsibility. The main reason being that "women would suffer from lack of perseverance, lack of practical spirit, scientific rigor, rational, and analytical spirit."

All I have to say about this is: It’s time to get to work! At the VII Brazilian Congress of Oceanography there was a round table discussion on the subject, with a crowded room of people eager to speak. Although it was an excellent experience, there is still so much to discuss. So I want to invite you all to continue this discussion. Let's talk about gender in the spaces we occupy, spread this idea! Organize an event and call everyone you know. Share your experiences with us!

References on statistics:

http://cnpq.br/estatisticas1

http://memoria.cnpq.br/estatisticas/bolsas/sexo.htm

http://inct.cnpq.br/institutos/

Misadventures in Research

By Yonara Garcia
English edit: Lídia Paes Leme and Katyanne Shoemaker

Illustration by: Caia Colla 

   As I was finishing writing my thesis, I started to consider all of the challenges that I went through in the two years of my Masters education in order to deliver such a perfectly rounded piece of work. My feelings were mixed because I was obviously happy to finish this step in my life, but I realized that this document didn’t contain even a third of all the misadventures that got me to this point. In my opinion, the thesis was missing a chapter; there should have been a chapter on “the making of” the research, just to explain how much went wrong and what it really takes to deliver good work. 

   When starting a Masters course, you must submit a proposal, which includes your research objectives, the hypothesis, and how you plan to answer that hypothesis. Wow! It was so easy so far! You just follow a previously described method and you understand what your results will look like and how they should be treated. This is all based on previously done work on a similar subject, which of course you know all about after reviewing the relevant literature. Two years to finish this project? No problem! …or at least that is what I thought. For me, it was not this easy, so I am going to tell you a little bit about my many misadventures during my masters.

   My work was a behavioral study of marine planktonic organisms in a 3D system. To build the system, I got together with a crew of post-graduate students who would also be using the experimental tank. This is where the soap opera began. We believed that we could build our system based on previous studies, but we quickly noticed that several components were not correct. There were issues with the magnification, color of LED lights, and the shape and positioning on the table. Everything had to be disassembled and reassembled to incorporate the necessary changes. The entire system had to be rebuilt 4 times because with each assembly we noticed new flaws. After months of arranging and rearranging pieces, and with the help of specialists in the area of optics, we finally reached a working system. 

   Ok, that took a few more months than expected, but now I could finally perform my tests, generate results, and graduate, right? Wrong. My work required filming the trajectories my target organism takes in the water column. However, the software for the two cameras we had would only film for 20 seconds at a time, which was not a long enough time span to get a valid representation of swimming behavior. We increased the computer’s memory, but that was not the issue. Thankfully, a student in our lab was proficient with computer science, and he became a key contributor to this project’s success. The filming software was completely replaced with software he developed. This new program didn’t have a time limit, however it could not utilize two cameras at once, so two computers had to be used. Having the two computers meant we could be introducing human error in timing; no matter how hard I tried, I cannot click the mouse at the exact same time on two computers. The solution for this problem was to use two microcontrollers that were activated by a potentiometer. Finally, we had a working system with a program that could be modified according to our needs!

   Onto the experiments! One of the primary challenges of working with living organisms is that you depend on them to be present in a certain collection spot at a given time of year. Unfortunately for me, by the time the experimental system was set up, we could not find enough individuals to run the experiments. It took several months of daily sampling to have enough individuals to perform all of my experiments, but I finally finished. 

   After video collection, the next step of the project was to use a computer program to find coordinates and relevant numerical data on the trajectories of the organisms. Given the topic of this post, it may not be a surprise to say something went wrong in this part too. As it turned out, the program that was originally going to be used could not compare the long videos that we fought so hard to attain. Once more, we turned to our computer science hero, and he developed software that could give us the organisms’ trajectories independent of video size. Let me take a moment to point out that software development is not an easy task; it took several iterations to get it to the point we needed it.

   With data in hand, I could finally analyze them and get my results. Data analysis is never easy, but given what I had already gone through, the challenges seemed minor in comparison. I had no idea how far off that initial Master’s plan would end up being, or that I would face so many challenges. I also didn’t expect how much this project would shape me. I had to be more than a biologist for this work; I learned how to solder, make electrical connections, understand physics, be a computer technician, and learn a little about programming. 

   Beyond all of the research obstacles, you still have to live your own life. This may be the most complicated part of the whole project. I often felt defeated and like I couldn’t carry on as I was faced with problem after problem. I know many others have lived through much bigger issues with their graduate research, but no matter the size of the problem, it shakes you to the core, and it can often be debilitating. 

   But, if you can push through these setbacks and fears of failure, you will eventually reach the end with a huge sense of accomplishment, as I did. It is important for me to share these misadventures in research with you to show what it actually takes to do research—it involves many tries and more wrongs than rights, but in the end, you publish a beautiful piece of well-crafted work. Even with all of the pressures and obstacles I faced, I still love what I do. Through all of the challenges, I grow more certain that I made the right choice.

   What challenges have you faced in your research? Comment below to share a little of your story with us!

POP(s) – and we are not talking about a music genre

By Juliana Leonel
English edit: Katyanne M. Shoemaker

Persistent organic pollutants, commonly known as POPs, are a group of compounds that are very resistant to degradation. These compounds bioaccumulate, can be transported far from their source through atmospheric and oceanic currents, and can have adverse impacts on living organisms, including humans.

In 2001, representatives from various countries signed an agreement called the Stockholm Convention with the aim of reducing and controlling the production and use of POPs. This treaty went into effect in 2004 with 151 signatory countries. Initially, 12 compounds were classified as POPs, and the participating countries agreed to ban the use of nine of them. Additionally, the use of DDT (we have a post on DDT here) was limited to only malaria control, and the unintentional production of dioxins and furans was to be reduced.

The first 12 POPs were all organochlorine compounds (organic compounds formed by C, H, and Cl), which were divided into three groups according to their use and production. The first group consists of pesticides and herbicides: compounds used to fight agricultural pests such as insects and weeds, which are harmful to the production or storage of grains, fruits, vegetables, wood, etc. The second group includes compounds used in industrial processes, such as polychlorinated biphenyls (PCBs) that were mainly used to cool engines, generators, and transformers. Finally, the third group consists of the dioxins and furans, which are compounds unintentionally produced by some industrial processes. This third group contains  by-products of processes (e.g. metallurgy and steel manufacture) and are not produced for a specific purpose. Over the years, during the Conference of the Parties, another 17 compounds or groups of compounds have been added to the list of POPs.

From left to right: o,p'- DDT, cis-chlordane, PCB 153, perfluorooctane sulfonate, PBDE99

To deal with each of these compounds, they were classified into three annexes. Annex A: compounds that must have their use and production eliminated; Annex B: compounds whose use and production should be restricted and only allowed in specific cases; and Annex C: compounds in which (unintentional) production must be controlled and, where feasible, must be phased out.

Each signatory country is responsible for carrying out inventory of stocks, production, and use of POPs in its territory. In addition, these countries must implement measures to reduce or eliminate the release of both intentionally and unintentionally produced POPs. In some cases, it is possible to request an exemption, to use one of the POPs in exceptional cases for a pre-determined amount of time (Ex: DDT use in case of malaria infestations). Signatory parties are also responsible for conducting systematic monitoring studies to assess whether measures are being effective in reducing the environmental levels of POPs.

Brazil approved the Convention’s text through Legislative Decree No. 204 on May 7th, 2004, and promulgated it via Decree No. 5472, on June 20th, 2005. Implementation of the Convention in Brazil is coordinated by the Ministry of the Environment (MMA) through the Secretary of Water Resources and Environmental Quality.

Although POPs are mainly used on land, their transport to the ocean is quite effective, whether through atmospheric transport, urban drainage, or effluent released directly into coastal regions. In this way POPs have been detected in a wide variety of environments and animals (water, air, soil, sediment, birds, fish, marine mammals, etc.). They have been found at the peak of great mountains and in the depths of the oceans, from the equatorial region to polar regions (see an example here: http://batepapocomnetuno.blogspot.com.br/2017/05/pesticidas-e-aves-marinhas.html).  POPs are a not-so-subtle reminder that environmental contamination has no borders, and it is a problem and responsibility of all the world’s citizens. 


Stockholm Convention Text:
http://www.mma.gov.br/estruturas/smcq_seguranca/_publicacao/143_publicacao16092009113044.pdf
Stockholm Convention - Brazil - MMA
http://www.mma.gov.br/seguranca-quimica/convencao-de-estocolmo
Stockholm Convention Home Page:
http://chm.pops.int/

Big Bang to the Dawn of Life: A Brief History - Part II and III

By Amanda Bendia
English edit: Katyanne M. Shoemaker

Part II: Ideal conditions for the origin of life (as we know it)

Artist's conception of early Earth. Font

Earth's first 400 million years were hostile and desolate: temperatures of over 200 oC liquefied the crust, and volcanic gases, especially CO2, were released in large quantities into the forming atmosphere. As the Earth cooled, the crust solidified and the lower temperature allowed liquid water to remain on the surface. This cooling was a key factor in the emergence of life.

In addition, organic molecules, generated in the nebula that gave rise to our solar system, underwent chemical reactions. This resulted in more complex organic molecules, composed especially of Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus and Sulfur. These were the building blocks for the first biological molecules.

Another important event that allowed the development of life was our planet’s impact with a celestial body the size of Mars, which resulted in the formation of our Moon. It is curious to think that a collision with 100 million times more energy than the impact that killed the dinosaurs was pivotal in the establishment of life on our planet. The gravitational force of the newly formed Moon stabilized the incline of the Earth's axis. Without this stability, major climatic changes would occur, and complex life forms would likely not have developed.

Origin of the Moon: Artist's conception. Font

Other features of our planet were also fundamental to the emergence and maintenance of life, including the presence of a metallic nucleus, which generates a magnetic field and acts as a protective shield against cosmic radiation. Additionally, the presence of a mantle and its movement below the crust promotes tectonic activities such as volcanism and continental shift. Volcanism was very important in the emergence of life, since its gaseous emissions provided the compounds (CO2, H2S, etc.) that may have been used for energy by the first unicellular organisms. Volcanoes also help maintain the planet's climate and help recycle carbon back to living organisms.

Part III: Our chemical origins: the formation of biomolecules

An incredibly rare set of conditions (see Part II) allowed life to arise on our planet from organic molecules and chemical reactions. Today, all of Earth’s living organisms are composed of biomolecules such as proteins, nucleic acids, polysaccharides and lipids.

These biomolecules consist of small units interconnected with one another, called monomers. The biomonomers that form proteins, nucleic acids (DNA and RNA) and polysaccharides are respectively the amino acids, nucleotides and monosaccharides. We now know that most biomonomers can be produced spontaneously when given the necessary conditions.

Miller-Urey experiment, 1953. Font

One of the first attempts to produce biomolecules in the laboratory was done by Stanley Miller and Harold Urey in 1953. They were based on studies conducted by Alexander Oparin and J.B.S. Haldane who suggested that biomolecules and life would have emerged in a “primordial soup,” an atmosphere rich in methane, ammonia, hydrogen, and water vapor.

The Miller-Urey experiment attempted to simulate these primitive Earth conditions described by Oparin-Haldane. In a sealed system, gases were introduced to create the primitive atmosphere described above, a heat source and liquid water were added, as well as electric discharges. Under these conditions, a number of biomonomers, such as the amino acids glycine and alanine, and other organic compounds such as urea and formic acid were produced.

Although recent studies indicate that the composition of the primitive atmosphere was not exactly as Oparin and Haldane proposed, the importance of Miller-Urey's experimental results revolutionized our concept of the origin of life by solidifying the idea of a chemical origin for all living organisms.

Types of biomolecules. Font

The next step in the emergence of the first living cells was the polymerization of these small structural biomonomers. How did  amino acids, monosaccharides and nucleotides form protein chains, polysaccharides, or the complex structure of DNA and RNA? Unfortunately we still do not have all of the answers to these questions, and the hypotheses that have been developed are difficult to test.

An important question when discussing the origin of life is how these biomolecules clustered together to form the first living cells capable of carrying genetic information and reproducing themselves. This is also a question that still challenges science, but many researchers are exploring new ideas that may explain the great leap from an essentially chemical world to a biological one.

Genetic information flux. Font

One of the first steps of this great leap is to understand how a nucleic acid molecule has the essential role of storing information that can be transmitted to subsequent generations. One of the most accepted hypotheses for the origin of genetic information is that of the RNA world, which suggests that RNA arose before the DNA molecule. However, in living organisms today, the flow of genetic information begins with DNA. Why then, would the first cells or proto-cells have RNA as the main source of genetic information?

DNA in today's cells require a complex machinery of proteins to be replicated. These proteins, in turn, require a DNA molecule that carries the information for later translation. Thus, the dichotomy of which originated first, DNA or protein, makes this question virtually unsolvable.

RNA world hypothesis. Font

For this reason, many scientists suggest that RNA was the first informational molecule to emerge, as it contains two essential properties for the maintenance of a primitive cell: a ribozyme activity, which makes it capable of catalyzing its own replication, and a catalytic activity capable of synthesizing some proteins. We still do not understand how mutations in the RNA molecule gave rise to DNA or how DNA was subsequently selected as the main source of genetic information of the cells.

Another important step for the formation of the first living cells is the emergence of compartmentalization. All cells have a plasma membrane composed essentially of phospholipids that guarantees the protection of the cytoplasmic content. Compartmentalization stores the molecules inside the membrane, facilitating chemical interactions. In addition, the selective permeability of the plasmatic membrane makes the chemical concentration inside of the cell different from the concentration of the surrounding environment, a characteristic fundamental for many cellular processes.

Lipid compartments are spontaneously formed due to their amphipathic nature - just mix a little oil into a glass with water and soap and watch. On primitive Earth, the compartments likely formed around biomolecules and some constituents that eventually gave rise to the first forms of metabolism and cellular functioning.


You can access Part I here!