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.

The extraordinary life of whale carcasses in the deep ocean

By Joan Manel Alfaro Lucas

Translated by: Lídia Paes Leme

Edited by: Katy Shoemaker

This story starts in 1987, when, during an oceanographic expedition lead by Dr. Craig Smith (University of Hawaii), the research robot Alvin found a whale carcass on the ocean floor in Santa Catalina Bay, California, 1240 meters deep (Smith et al., 1989). This discovery reinforced an idea that had been suggested before, that even though whale deaths are common in coastal zones, many die in spots far away from beaches and sink down to the depths of the ocean.

The deep ocean covers 63% of the planet's surface and is considered the biggest biome on Earth. It is unique and extreme due to its low temperatures, high pressure, and darkness (light doesn't penetrate more than 200 meters below surface, where the deep ocean starts). The absence of light makes organic matter production via photosynthesis impossible. Because of this, the deep ocean ecosystem is limited in food sources and depends almost exclusively on the sinking of organic matter produced in the surface waters. In the vast, cold, dark deserts of the deep ocean known as the abyssal plains, the few organisms that survive there filter water and sediments to take in the little organic matter that sinks down from the surface.

So now what about that Californian whale that Dr. Smith found? The carcass was completely missing meat, and other indicators suggested the whale carcass had been there for several years. However, the skeleton and the sediment around it were bursting with life! There were worms, snails, gastropods, dense mats of bacteria, and bivalves such as clams and mussels. The carcass was a real oasis of life in the deep desert of the bay. The scientists began to understand that, for an environment so poor in nutrients, the arrival of a whale carcass is an extraordinary event.

Whales are the largest animals that inhabit Earth. The blue whale can be 30 meters (~100 feet) long and weigh 120 kilotons and is the largest animal that has ever existed on our planet. To the desert depths of the ocean floor, their carcasses are the biggest source of organic matter that arrives from the surface. One carcass from a 40-kiloton whale is the equivalent of 2000 years worth of organic matter falling down at once!

Image 1 – Whale carcass on the deep ocean floor of Santa Catalina Bay, California, densely colonized by chemosynthetic bacterial mats. Photo by Craig R. Smith, University of Hawaii, USA.

Some of the organisms found for the first time on the carcass by Dr. Smith became much more interesting when identified. For example, some bivalve species found there are known to have symbiotic relationships with chemosynthetic bacteria. Those mussels feed on the matter produced by the bacteria, a process similar to what shallow water corals have with photosynthetic organisms. As it turns out, the dense bacterial mats found on the carcass were of that kind of bacteria.

Similar to vegetables in the terrestrial environment, these chemosythetic bacteria form the base of the food chain in the deep ocean. Chemosynthetic communities feed on organic compounds, some of which can be abundant on the sea floor. This is the case in hydrothermal vents, which form in parts of the floor where volcanic activity is elevated and hydrocarbons flow from underground reservoirs (post about hydrothermal vents here). The bivalve species associated with the whale carcass were discovered for the first time at cold hydrothermal vents! These similarities suggested that the whale carcass acts as a trampoline for the common habitants of different chemosynthetic communities to disperse, as they are usually separated by distances larger than can be reached by larval dispersion (Smith et al., 1989).

This discovery, other than being revolutionary for the ecology of chemosynthetic communities, led several groups of scientists to research more about these ecosystems. Rather than looking for a carcass on the vast ocean floor (a real needle in a haystack situation), scientists started to sink dead whale carcasses with weights. They were able to sink them in a determined spot where they could sample whenever needed. After these experiments, scientists began to understand that not only chemosynthetic communities developed in the carcasses, but also there were extremely diverse and abundant communities that explored the carcasses in amazing ways… for almost a century!

Image 2 – Hagfish feeding on a whale carcass during the ecological state of the mobile necrophagous organisms in Santa Catalina Bay, California, USA. Photo by Craig R Smith, University of Hawaii, USA

The whale carcasses develop mostly three ecological successive states, meaning three communities can be distinguished throughout time (Smith et al., 2015). The first stage starts with the arrival of the carcass in the bottom and includes the mobile necrophagous organisms. Hundreds of animals, like hagfish, drill the meat while sharks bite big chunks off. These communities, similar to vultures in a savanna, remove several dozen kilograms by day and can consume all the meat in up to two years, depending on the size of the carcass.

Image 3 – Crabs, snails, and anemones colonizing the skeleton during the enrichment and opportunist stage in a whale carcass in Monterey Canyon, California, USA. Photo by the Monterey Bay Aquarium Research Institute. USA.

The second stage involves the enrichment of opportunists and can also last up to two years. During this period, high densities of worms, crustaceans, and other invertebrates colonize the sediment around the skeleton that was exposed after the flesh was consumed. These invertebrates feed directly on the left over fat and meat left behind by the necrophagous organisms, as well as the bones, which are rich in protein and fat.

The last stage, the one Dr. Smith's whale was in when he found it, is the sulphophilic stage. Some microorganisms are able to penetrate the dense bone structure and access the big quantities of fat remaining in the interior of the bones. These organisms use the sulfur dissolved in water to digest the fat, creating inorganic compounds as secondary products. Similar process can also occur in the surrounding sediment, which was impacted by the organic matter of the carcass. This creates enough of a flux to develop a community based on chemosynthesis. This is the longest stage, lasting up to 80 years.

The discoveries around whale carcasses don't stop there. Since 1987, when Dr. Smith studied the first deep ocean carcass, 129 new species have been discovered, many of them only found in those communities. The most surprising one was discovered in 2002, when Osedax, a new kind of worm, was discovered in Monterey Canyon, California, at 2891 meters deep (Rousse et al., 2004). The species in this genre are sessile and don't have a mouth nor anus, nor any kind of digestive system, yet they feed on whale bones!

Osedax have a structure called a root, which helps to answer the multiple mysteries surrounding these organisms. This structure, with globular ramifications, fixes the organism to the bones and has pumps that acidify the bone matter. The “soup” produced in this process is sent up through the root into internal structures, where endosymbiotic bacteria are responsible for digestion. These worms are capable of completely decaying a whole juvenile skeleton (containing less calcified bone or fat then adults) in one decade. Impressive, no? Just wait…

All of these structures and endosymbionts only apply to female Osedax. The males are microscopic dwarves that live inside of the females, as simple sperm reservoirs. The Osedax larvae that are found on a skeleton develop as female, but if they find other females, they can get absorbed and develop as pedomorphic males, meaning they only develop sexually and not fully morphologically, retaining larval characteristics. Each female can absorb hundreds of males, which is believed to be a successful reproductive strategy.

Image 4 – Whale bone densely colonized by Osedax in Monterey Canyon, California, USA (left) and Osedax japonicus specimen with a yellow-colored root. Photos by Monterey Bay Aquarium Research Institute, USA, and Norio Miyamoto, from Japan Agency form Marine-Earth Science and Technology, respectively.

Organisms like Osedax show that whale carcasses are not only an oasis of life in the deep ocean, but also showcase uniquely evolved and specialized life forms. However, are the carcasses sustaining similar communities in all of the ocean basins? Or, like in hydrothermal vents, does each basin sustain communities with different evolutionary histories? This kind of question is still very hard to answer because practically all of the natural and placed carcasses have been studied in the Northern Pacific.

Only in 2010 was a natural carcass discovered on the seafloor near Antarctica, and, more recently in 2013, in the Southwest Atlantic off of the Brazilian coast. The latter is currently being studied by Brazilian and Japanese researchers, and is the topic of my Master's project at the University of São Paulo. This represents the first whale sink community to be studied in all of the deep Atlantic. The results of the research are beginning to emerge, reinforcing some previous hypotheses and explaining even more about the functioning of various ecological processes.

Many questions are still to be answered, and many more will be generated in the future. These extraordinary communities, not known 30 years ago, are a bottomless source of surprises!

References, links and videos:

Smith, C.R., Kukert, H., Wheatcroft, R.A, Jumars, P.A., Deming, J.W. (1989) Vent fauna on whale remais. Nature, 341. Pp 27-28.

Rouse, G.W., Goffredi, S.K., Vrijenhoek, R.C. (2004) Osedax: Bone-Eating Marine Worms with Dwarf Males. Science, 305.Pp 668-671.

Smith, C.R., Glover, A.G., Treude, T., Higgs, N.D., Amon, D.J. (2015) Whale-Fall Ecosystems: Recent Insights into Ecology, Paleoecology, and Evolution. Annual Review of Marine Science, 7. Pp 571-596.

About Joan Manel Alfaro Lucas:

A biologist from the Universitat Autonoma de Barcelona, Barcelona, I did a one year internship at the Federal University of Minas Gerais, which allowed me, among other things, to get to know Brazil and learn Portuguese. I'm passionate about the ecology of deep ocean communities, especially chemosynthetic ones. I did a Masters at the Oceanographic Institute of the University of São Paulo, where I had the opportunity to study the first whale carcass discovered in the deep Atlantic ocean. Other than that, I have experience in oceanographic cruises, sailed 2800 nautical miles across the southwest Atlantic, sampling, sorting and identifying benthic invertebrates, stable isotope analysis, and using the R language in ecological research.

Seagrass: canaries of the sea

By Juliana Imenis, Juliana Nascimento, Larissa de Araujo, Natalia Pirani, Otto Muller and Paula Keshia

In the early 20th century, coal miners frequently carried caged canaries to work. The little birds saved many miners' lives because their sudden death or sickness indicated a possible gas leak. An alarm would sound and the mine would be evacuated.

We could say the canaries were bioindicators, or organisms that indicate a possible environmental problem through their behavior or health status. Today, we no longer have a need to sacrifice the canaries because we have electronic indicators that can tell us about possible mine disasters.

Like the canary, some organisms are extremely sensitive to pollution and habitat alterations; their populations tend to diminish or even vanish quickly after environmental modifications take place. Other organisms may be very tolerant to poor environmental conditions and can sometimes have a population boom in areas where the conditions would be inadequate to the majority of other species. One of these bioindicators is the marine phanerogam, also known as marine seagrass.

Image by Joana Ho

This particular group of plants grow on the sea floor, have elongated straight leaves, and subterraneous stalks, called rhizomes. Seagrass may live completely immersed in water, and they are found in coastal waters of nearly every continent. Despite being known as “seagrass”, this group is closer to the lily and ginger families than grass (Figure 1). They are an important part of the diet of manatees and sea turtles, and they are used as habitat by many other sea animals (Figure 2), including commercially important fish and crustaceans. Although difficult to quantify, seagrasses have a large aggregated commercial value, estimated to be up to 2 million dollars a year. They also play an important role in sequestering carbon into their biomass and sediment, thus decreasing the carbon dioxide (CO2) concentrations in the atmosphere. This helps promote nutrient recycling, coastal protection, and improve overall water quality.

Figure 1 – Morphology and occurrence in the natural environment of genera Halophila. Despite being known as “seagrass,” this group is closer to the lily and ginger families than grass. Adapted from Sarah Lardizabal schematics. http://www.reefkeeping.com/issues/2006-04/sl/

Figure 2 – Many animals visit the seagrass fields searching for food. http://portuguese.alertdiver.com/Manguezais-e-Angiospermas-Marinhas

In Brazil, despite controversial information and the necessity of more genetic studies to differentiate the species correctly, there are so far, five known species of seagrass (Figure 3): Halodule wrightii Ascherson; Halodule emarginata Hartog; Halophila baillonii Ascherson; Halophila decipiens Ostenfeld and Rupia maritima Linnaeus. Seagrass are considered to be great environmental quality indicators, because they are very sensitive to light and nutrient availability variations.

Global climate change has many impacts on the marine environment, including the rise of global average sea surface temperatures, variations in pH (ocean acidification), and alterations of ocean currents. These are some of the rapid changes in marine environment that have been seen by researchers, and their consequences are still little known. There are many factors involved in the interactions between environmental variables and biological communities, making overall consequences hard to forecast (Figure 4).

Figure 3 – Identification of seagrass species can be controversial, but nowadays it is defined that there are five species along the Brazilian coast. Marques & Creed 2008.

Figure 4 – Many studies have been developed in this rich environment, but more research is needed if their importance and probable environmental changes are to be considered. http://portuguese.alertdiver.com/Manguezais-e-Angiospermas-Marinhas

Seagrass need specific environmental conditions, like low turbidity and high incidence of light. They are suffering local reduction and in some places completely vanishing, indicating that the anthropegenic environmental changes are happening fast, not giving the organisms enough time to respond to the new conditions. The capacity of ecosystems to respond to impact and return/maintain their original conditions is called resilience.

Although the degree and type of impact on seagrass may vary with geography, some hypothesis were generated by the Benthic Habitat Monitoring Network (ReBentos) about how climate change may affect them: (1) the increased concentration of nutrients, given the increased quantity of rain, may cause changes in the community composition, favoring the occurrence of opportunistic species, which can be damaging for the local species; (2) changes in sea surface temperature can affect tropical species, favoring the extension and displacement of their occurrence limits towards higher latitudes; (3) extreme events, like floods and storms, may cause reduction or disappearance of seagrass in a quick and abrupt way; (4) the increased quantity of continental matter in estuaries may affect the abundance and composition of the communities, due to the increased turbidity and salinity changes. On the other hand, the reduction of rain and/or increased penetration of seawater into continental waters could increase or alter the estuarine seagrass' area of occupation; and finally (5) days or week-long heat waves, derived from external events, may reduce or extinguish fields in shallow areas.

As an example of evidences that support these hypothesis, we can mention a study published by the Journal of Experimental Marine Biology and Ecology by Ricardo Coutinho and Ulrich Seeliger, that, in 1984, observed that the species R. maritima, although tolerant with eutrophicated conditions, was shadowed by epiphytes and macroalgae that grew due to an excess of nutrients in the water. Those organisms tangle in this seagrass species, causing reduction on its photosynthetic rates and increasing their drag, facilitating their detachment when subjected to waves and currents. Another example is the study published in the Marine Ecology by Frederick T. Short and collaborators, that in 2006 observed the reduction of H. hrightii through the movement of sediment, caused by stronger and more frequent storms, which buried the fields of seagrass.

Therefore, as mentioned by other authors, we can consider seagrass as the canaries of the sea, important in diagnosing the environment's health in response to global climate change. Certainly, the loss of these ecosystems will bring not only economic loss, but also the loss of biodiversity, a factor that is much more valuable and difficult to measure.

To know more:

COPERTINO, M.S.; CREED, J.C.; MAGALHÃES, K.M.; BARROS, K.V.S.; LANARI, M.O.; ARÉVALO, P.R.; HORTA, P.A. (2015). Monitoramento dos fundos vegetados submersos (pradarias submersas). IN: TURRA, A.; DENADAI, M. R.. Protocolos de campo para o monitoramento de habitats bentônicos costeiros - ReBentos, cap. 2, p. 17-47. São Paulo: Instituto Oceanográfico da Universidade de São Paulo. Disponível em: <http://www.producao.usp.br/handle/BDPI/48874>. Acesso em: 04 nov. 2015.

MARQUES, L. V.; CREED, J. C.(2008). Biologia e ecologia das fanerógamas marinhas do Brasil. Oecologia Brasiliensis, v. 12, n. 2, p. 315 - 331.

MCKENZIE, L.(2008). Seagrass Educators Handbook. Cairns: Seagrass Watch-HQ. Disponível em: <http://www.seagrasswatch.org/Info_centre/education/Seagrass_Educators_Handbook.pdf>. Acesso em: 30 out. 2015.

MCKENZIE, L (2009). Coastal Canaries. Seagrass Watch, v.39, p. 2-4. Disponível em: <http://www.seagrasswatch.org/seagrass.html>. Acesso em: 03 nov. 2015.

About the authors:

Juliana Imenis Barradas, CCNH-UFABC, PhD student in the postgraduate program in Evolution and Diversity, biologist, Master in Zoology (UFPB). juliana.imenis@ufabc.edu.br, http://lattes.cnpq.br/4843331968538355

Larissa de Araujo Kawabe, CCNH-UFABC, master graduate student of in the postgraduate program in Evolution and Diversity, biologist. http://lattes.cnpq.br/7133427266626274

Juliana Nascimento Silva, CECS-UFABC, undergrad in Environmental and Urban Engineering (UFABC) http://lattes.cnpq.br/5975285955317582

Paula Keshia Rosa Silva, CCNH-UFABC, mestranda em Evolução e Diversidade (UFABC), http://lattes.cnpq.br/9557245804556650

Natalia Pirani Ghilardi-Lopes, CCNH-UFABC, professora adjunta, bióloga, doutora em Botânica (USP), http://lattes.cnpq.br/8457066927181345

Otto Müller Patrão de Oliveira, CCNH-UFABC, professor adjunto, biólogo, doutor em Zoologia (USP), http://lattes.cnpq.br/7304237172635774