AP Biology class blog for discussing current research in Biology

Tag: Marine Biology

Scientist Spotlight: Ernest E. Just

As Black History month comes to an end, it is extremely important that we continue to take moments to celebrate the accomplishments of the Black Community, as well as recognize and learn about Black STEM leaders who made impactful discoveries and innovations in science, technology, engineering, and mathematics. In this blog post, I will be spotlighting Dr. Ernest Everett Just.

Dr. Ernest E. Just was a renowned zoologist (with a focus in cytology) who received worldwide recognition for his work and discoveries in his respective field. Born in 1883, in Charleston, South Carolina, he lost his father at the age of four. Supported by his mother, Ernest was able to leave his home and pursue superior education in the north at the age of 17. Ernest earned a scholarship to the Kimball Union Academy in New Hampshire, where he would be the only Black student. He would then go on to attend Dartmouth and be the only student to graduate magna cum laude. Ernest majored in biology and minored in history. 

After graduating, Ernest went to teach at Howard University at the university’s Zoology department. In 1909, he began research at the Marine Biological Laboratory in Woods Hole, Massachusetts, where he would focus on studying marine eggs. Ernest soon realized that earning a Ph.D. would be a key to future success as a researcher, thus he began a self-study program at the University of Chicago. Again, Ernest would graduate magna cum laude. 

After the University of Chicago, Ernest was able to publish two very influential books about his research: Basic Methods for Experiments on Eggs of Marine Mammals and Biology of the Cell SurfaceThese books “reflected Just’s holistic view of eggs and embryos: that is, eggs are to be taken seriously in their own right rather than seen simply as tools to manipulate in order to prove a theory.” For his research, Ernest conducted chemical-induced parthenogenesis on sea urchins and sand worms; while doing this, he also observed the creature’s normal fertilization with sperm cells. Parthenogenesis allows an egg to develop into an embryo without fertilization from a sperm cell. In our AP Biology class, we learned about meiosis which is necessary for the creation of gametes such as sperm and egg cells. These cells develop into sperm or ova. Then during fertilization, a sperm and ovum (egg cell) unite to form a new diploid organism.

From his research, Ernest was able to conclude that eggs contained a necessary mechanism for starting development. The egg’s cytoplasm was the key to the cell’s development, not just the nucleus. Ernest’s work and research were crucial. His research was both creative and logically rigorous. Essentially, while other researchers at the time focused on how genes were responsible for how different organs develop, Ernest demonstrated that one of the most important factors for development was just the egg’s environment. 

After reading a lot on Dr. Just, I am truly astonished. He was a gifted scholar and a talented researcher. Ernest was one of the first African Americans to get worldwide recognition for scientific discovery and is also considered one of the first Black marine biologists in American history. After reading about Ernest, I am inspired to learn more about other excellent Black scientists who have gone underappreciated.

Diving Into the Life of Rene Francolini

Rene Francolini identifies as a proud bisexual, cisgendered female (she/her), who specializes in computational biology. Computational Biology combines her two greatest passions: marine biology and computer science.

Francolini discovered her love for computer science and marine biology in highschool, but was then introduced to the combination of those two topics by one of her highschool teachers. The rest is history. Francolini furthered her education in science and got her undergraduate and accelerated master’s degree at Carnegie Mellon University for Computational Biology. When she came right out of college, she worked as an oyster farmer for a few years before working at the Woods Hole Oceanographic Institute (WHOI). During the last two years spent there. Francolini spent her time in the environmental toxicology lab, collecting Environmental DNA (eDNA) from deep parts of the ocean, and the molecular ecology lab taking part in a larger project known as the Ocean Twilight Zone Project.

The Ocean Twilight Zone Project focuses on gathering research from a part of the ocean called the mesopelagic zone. It’s often referred to as the twilight zone, and is home to the greatest amount of fish in the sea. Often the fish we will find on our dinner plates like tuna and swordfish are coming from there. The twilight zone also takes part in removing some of the carbon in the atmosphere, which regulates our climate. In today’s world, we need to be careful in protecting it because it benefits not only the fish, but us too. This research will help advance ocean science; it will also give government officials insight on this zone, so hopefully they will try their best to protect it.

Francolini is currently getting her Marine Science PhD, while also taking part in the Maine-eDNA project as a Graduate Research Assistant. She’s specifically working on the Gulf of Maine’s kelp forests, and “how we anticipate climate change to alter the landscape and biodiversity of these vital ecosystems” (500 queer scientists). This project combines fieldwork, collecting samples, as well as computational and molecular work. This project showcases how versatile Francolini is as a biologist.

Franciolini loves that being a scientist means that you can share your passion with others, which even leads some to discover a love and interest in STEM and the environment around us. She is proud to be a part of the openly LGBTQ+ minority in STEM, as representation in this field encourages more young scientists that will be coming from our generation to outwardly be who they are without fear of not being accepted and/or respected.

Blue Whales: The Giants of the Real World

For the past twenty years, Jeremy Goldbogen and collaborators have been trying to figure out why blue whales were the biggest animal to ever live. The journey helped them find multiple different explanations as to why the blue whale is so unique and why it’s size is almost entirely based on two factors: their choice of prey and the coincidence of their evolution with the global increase of “upwelling of nutrient-rich water from the depths of the ocean.”

How does a Blue Whale’s diet affect its size?

Baleen Whales were able to evolve from filter-feeding on plankton to successfully lung-feeding on entire schools of fish and krill. This was a huge part of the whale’s evolution because of the ocean upwelling, which provided ample amounts of new prey for these whales.

What is specialization and how did it affect the evolution of Whales, particularly Blue Whales? 

During the ocean upwelling, not all types of swarming prey were the same. As a result, predators began to become a specialist in hunting certain groups. For example, some rorquals specialized in schooling fish, while others focused on plankton. Of all the present-day rorquals, the blue whale is the most specialized. They only eat Krill with very few exceptions. Specializing in Krill is far from easy. There is only a high concentration of Krill in certain regions of the world, therefore Blue Whales need to be extremely mobile. Because of this, they have sleek bodies and hydrodynamic flippers. Krill are also not easy to catch so Blue Whales sacrifice some mobility for a more hunting range. This means a bigger mouth which comes with a bigger body. The whale’s diet depends on being big but the energy needed to maintain this big body also balances out.

The Blue Whale: Stuck between the Old and the New

The Blue Whale is in an interesting predicament when it comes to their evolution and growth. They are stuck in their circle of specialization but their food web is deteriorating across the ocean and that is where they are also stuck. As I said before, being that big takes a lot of energy. These whales needed to eat as much as possible and when we pollute the ocean that hinders their ability to do so. I believe that it is extremely important for us to do what we can as humans in order to help these creatures because right now we are living during a truly unique time: we are on the earth at the same time as giants. I believe that it is our responsibility to save them for as long as we can.




Climate Change Affecting Marine Life

In 2016 Luisa Marcelino, research assistant professor of civil and environmental engineering at Northwestern Engineering, and Vadim Backman, Ph.D. Professor of Biomedical Engineering studied biomass of coral reefs. In doing so, their research team developed a quantitative coral bleaching response index. This database took historical statistics pertaining to mass of coral and compared it to an index of later development. By measuring the difference in the two groups of statistics, the team was able to draw conclusions on what specific species and locations were susceptible to bleaching – a phenomenon where coral expel’s its life prolonging algae. As of now, marine biologist do not have a clear response to why does thermal stress affect coral’s ability to sustain itself.


On October second of 2019 a team of researchers from the McCormick school of Engineering published a paper expanding on Marcelino and Backman’s previous work. It validates the current technology used for imaging coral since the technology was initially invented to examine carcinogenic cells in human tissue. The paper, titled “Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring,” starts by introducing the fact that the methods by which coral and Symbiodinium (life-prolonging algae within the coral) interact with one another are still unknown. It continues to state how ISOCT is a non-invasive, yet effective way to quantify living tissue in coral reefs along with their structures.

ISOCT measures the sub-micron spatial mass density distribution which helps develop estimates of the spatial directionality of light scattering (i.e. the coefficient and chemical concentration in coral). This technology, through the same methods, can characterize chlorophyll a concentration in skeletal structures of coral as well. By being able to compartmentalize different types of coral and measuring their individual success rates, researchers can then find correlational data and conclude which species and locations are in need of biomedical support against thermal stress. Characterizing their differences is a crucial part because it will also help scientists hypothesize and eventually discover in what way Symbiodinium and coral interact.






In the same way that biologists are not currently knowledgable about the relationship between the algae coral secretes under sub-optimal environmental conditions and the coral reef itself, they are also not certain about the ways in which escalated temperatures affect the physiology of coral. Once both of these occurrences are studied further it is believed that newly gathered information could give rise to new ways to protect coral reefs as well as new ways to harness solar energy.

New Hope For Coral Reefs

Coral reefs hold immense value for both human and marine life. As the most diverse of all ecosystems, coral reefs support one quarter of all ocean species. Coral reefs also affect human industry through providing tourist jobs, shoreline protection, food, and medicine. However, human activity has severely damaged and destroyed coral reefs directly through destructive fishing, overfishing, and pollution, as well as indirectly through warming oceans and invasive species.








In a relatively new study published in Restoration Ecology, researchers “documented a large coral reef rehabilitation in [Bahasa,] Indonesia aiming to restore ecosystem functions by increasing live coral cover on a reef severely damaged by blast fishing and coral mining.” Previously, most reef recovery programs were focused on setting up fisheries and MPAs in an effort to reduce the impact of overfishing, so this project was relatively novel in its strategy to restore damaged reefs on a large scale. The researchers, led by Susan L. Williams, set up “small, modular, open structures to stabilize rubble and support transplanted coral fragments” (also known as “spiders”).

These structures proved extremely successful as “live coral cover on the structures increased from less than 10% initially to greater than 60%” over the course of the study. Additionally, the project was relatively inexpensive; the 11,000 structures covering 7,000 m2 cost only $174,000 USD. This project is extremely exciting because it demonstrates that large scale efforts to rehabilitate coral reefs are achievable even where reefs have been severely damaged.

Don’t be Amoral… Help Rehabilitate the Coral!

The Rehabilitation of Coral Reefs with “Spiders”

Coral reefs have recently been decimated worldwide. While there have been countless efforts to rehabilitate damaged coral reefs, very few have been successful, up until now.

According to a study “led by the University of California, Davis, in partnership with Mars Symbioscience,” there is a new, relatively inexpensive technique that utilizes “spiders” – hexagonal, “three-and-a-half square ft. structures made from rust-protected reinforcing steel rods” – to facilitate the renewal of coral reefs. In order to test the effectiveness of this technique, researchers traveled to Indonesia’s Coral Triangle, a region possessing the greatest coral diversity in the world. As expansive as it is, the region is a skeleton of its former self. There, the researchers fixed 11,000 “spiders” onto 5 acres of reef, starting in 2013. The transformation of the reef was astonishing. Apparently, “Live coral cover on the structures increased from less than 10 percent to more than 60 percent.” Furthermore, while coral bleaching devastated entire reefs in various locations worldwide between 2014-2016, it had minimal effects (less than 5 percent) on the rehabilitated reefs. As Frank Mars, the vice president of Mars Sustainable Solutions, stated, healthy coral reef ecosystems are not only essential to the environment and the well-being of all people, but also provide economical opportunities, by providing a “foundation for many local fisheries, as well as jobs for tourism.”

diving underwater biology seaweed blue colorful coral coral reef invertebrate clown fish reef nemo turquoise algae creature beautiful exotic anemone meeresbewohner organism sea anemone marine biology coral reef fish marine invertebrates pomacentridae freshwater aquarium

“The image is released free of copyrights under Creative Commons CC0.”                                                       Taken by an “unknown lens”

While this news is very promising for the future, more still should be done. Human activities, such as illegal fishing and pollution, have to be better controlled, and their negative impact mitigated as much as possible. Also, more people have to be educated about the enormous adverse impact of their actions on the ocean environment. “In the meantime, the ‘spider’ technique and restoration projects offer a way to rehabilitate large swaths of coral reefs and the communities that depend on them, giving the reefs a chance to adapt or acclimate to worsening ocean conditions.”

Feature Image: Taken by Jan-Mallander


Effect of ocean acidification: Coral growth rate on Great Barrier Reef plummets in 30-year comparison


A new marine biological study conducted in Australia shows a correlation between rising ocean acidification levels and declining coral growth rates in the Great Barrier Reef. Scientists Ken Caldeira and Jacob Silverman carried out research testing growth rates from samples of current coral on the reef and records from the 1970’s. The findings were astounding. According to the comparison, coral growth rates have declined by almost 40% since the 1970’s and the scientists believe they have an explanation.

Coral produce their exoskeleton by utilizing aragonite, a naturally occurring calcium carbonate (CaCO3). This process is called calcification. However, when acid levels in the water become too high, the environment for producing healthy coral becomes compromised. Since the beginning of the Industrial Revolution about one third of all CO2 released into the atmosphere has made its way into the oceans. This lowers the Ph, causing the water to become more acidic, and creates an environment ill suited for coral growth. The scientists speculate that this acidification of the water is whats leading to decreased growth rates in not only coral, but also many other species of marine life.

Coral plays a vital role in underwater ecosystems, providing food sources and shelter for nearly 25 percent of all marine life. Some reefs admired and studied by scientists today began growing nearly 50 million years ago. There is no question that coral’s role is vital in the fabric of the ocean. However, recent studies similar to the research done by Caldeira and Silverman are prompting scientists to worry deeply about the future of our oceans. When quoted on the status of reefs today, Caldeira stated, “Coral reefs are getting hammered. Ocean acidification, global warming, coastal pollution, and overfishing are all damaging coral reefs. Coral reefs have been around for millions of years, but are likely to become a thing of the past unless we start running our economy as if the sea and sky matters to us very soon.”

Photo credit: Wikipedia Public Domain Images:


Links for further reading:




Colorless Coral?

Screen shot 2013-09-24 at 9.51.23 PM on flickr

When one usually thinks of a coral reef they think of bright vibrant colors… this may not be the case anymore. A recent study has found that climate change may be depleting coral of its color. In a process called “bleaching” the color is removed from the coral when the symbiotic algae that provide nutrients to the coral either lose their  photosynthetic pigmentation and their ability to perform photosynthesis or disappear entirely from the coral’s tissue.

While this strange and disturbing phenomenon has been receiving a lot of attention, there is very little concrete knowledge about the exact molecular process that causes the bleaching. Many hypothesized that the bleaching is a result chloroplast damage due to heat stress, which results in the production of toxic, highly reactive oxygen molecules during photosynthesis, they are linking the origin of the heat stress back to climate change.

To test this theory a team of researchers from Carnegie led by Arthur Grossman and accompanied by a few other scientist from Stanford conducted a study that resulted in the surprising discovery that the bleaching occurs when the algae is not performing photosynthesis, while it is surprising the team also concluded that it could be beneficial to aid in the fight against coral decline. “This is surprising since it means that toxic oxygen molecules formed in heat-damaged chloroplasts during photosynthetic reactions during the light are likely not the major culprits that cause bleaching.” (

While their initially theory was incorrect, this research has now motivated further study into the  molecular functions of coral as well as further efforts toward coral preservation.

Odd Little Species Survives Without Sex

Of the two million know species on Earth, only about two thousand reproduce entirely asexually. Scientists think this is because organisms that reproduce without sex – which provides healthy genes from one parent that act as a template to repair mutated genes, leading to “theoretically healthier offspring” – are unable to mitigate the deleterious effects of gene mutation, which leads to their extinction. The bdelloid, a tiny, all-female, sea creature with a name that means “leechlike” for the way it moves, however, has survived for tens of millions of years without sex. In fact, they have diversified into more than four hundred species.

Researchers at the Marine Biology Laboratory in Woods Hole, MA wanted to find out why the bdelloid had avoided extinction, so they zapped some of the creatures with gamma radiation, which breaks up DNA. Oddly, the bdelloids did not succumb to the exposure even as the scientists pushed the radiation levels far past what would naturally occur on earth. When the mystified biologists examined the bdelloids’ DNA, they discovered that an early mutation had copied the entire genome, giving each organism four copies as opposed to the common two, which allowed it to repair severely damaged DNA. This mutation turned out to be beneficial for the aquatic creatures because it allows them to survive desiccation, a danger for bdelloids because of their transient underwater habitats.

More recently, scientists at the University of Cambridge published a paper in the journal PLoS Genetics recounting their discovery that about ten percent of the bdelloid’s genome is composed of alien DNA amassed through the consumption of bacteria, fungi, and algae. These foreign genes become active when a bdelloid dries out, and are thought to be partly responsible for the creature’s incredible ability to survive dehydration. Those same genes might also be behind “powerful antioxidants that protect bdelloids from the by-products of drying out”.

Evolutionary biologists are hopeful that a better grasp of the mechanisms that allow bdelloids to survive will lead to much greater discoveries such as how sex evolved. Matthew Meselson, a geneticist at Harvard University, said in an interview with LifeScience that “being able to understand how animal cells can be so resistant to radiation may be of some interest in understanding how [cancer, aging, and inflammation, of which DNA damage and repair are factors] might be inhibited in human cells.” Further experimentation could uncover new treatments that prolong life or fight cancer.

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